NOAA TECHNICAL MEMORANDUM NOS NCCOS 202

October 2016

NOAA NCCOS Center for Coastal Monitoring and Assessment

An Integrated Environmental Assessment of the St. 

Thomas East End Reserves (STEER)

NOAA National Centers for Coastal Ocean Science

Center for Coastal Monitoring and Assessment

Anthony S. Pait

S. Ian Hartwell

Laurie J. Bauer

Dennis A. Apeti

Andrew L. Mason

.
ACKNOWLEDGEMENTS

The authors wish to acknowledge the support from NOAA’s Coral Reef Conservation Program (CRCP) for this project. 

We would also like to thank Jean-Pierre Oriol, Director of the Division of Coastal Zone Management, Department of 

Planning and Natural Resources (DPNR), Roy Pemberton (Director), DPNR Division of Fish and Wildlife, Anita Nibbs of 

DPNR Division of Environmental Protection, Tyler Smith, Sandra Romano, Renata Platenberg, Kevin Brown, and Stanley 

Lateski of the University of the Virgin Islands (UVI), and Rob Ferguson and Marlon Hibbert of NOAA’s CRCP for help 

with the planning, logistics, and fi eld work for this project, along with interpretation of results and for providing useful 

comments and editorial assistance. Erik Davenport, Larry Clafl in, Matthew Poti, and Matthew Kendall from NOAA’s 

National Centers for Coastal Ocean Science (NCCOS), Center for Coastal Monitoring and Assessment, provided valuable 

input into the statistical analysis of the data. We would also like to thank Sybille Sorrentino of Virgin Island Ecotours for 

graciously providing a base of operations for our fi eld work. We would like to acknowledge the help provided by Alexandra Holecek, Stephen Hale, John Barimo, and Jeanne Brown, formerly of the DPNR Division of Coastal Zone Management, Division of Fish and Wildlife, UVI, and The Nature Conservancy, respectively. Finally, we would like to thank 

Captains Bobby Vante, Kevin McCartney and Larry Aubain for their skill and patience in getting us safely to and from our 

sampling sites within the St. Thomas East End Reserves.

Government contract labor was provided by CSS-Dynamac, Fairfax, VA.

Mention of trade names or commercial products does not constitute endorsement or recommendation for their 

use by the United States Government.

Cover photograph courtesy of Amy Uhrin, NCCOS/CCFHR

Citation for the entire document:

Pait, A.S., S.I. Hartwell, L.J. Bauer, D.A. Apeti, and A.L. Mason. 2016. An Integrated Environmental Assessment of the 

St. Thomas East End Reserves (STEER). NOAA Technical Memorandum NOS NCCOS 202. Silver Spring, MD. 219 pp.

Example citation for an individual chapter

Pait, A.S., S.I. Hartwell, A.L. Mason, R.A. Warner, C.F.G. Jeffrey, A.M. Hoffman, D.A. Apeti, F.R. Galdo Jr, and S.J. 

Pittman. 2016. Chapter 4: An assessment of chemical contaminants, toxicity and benthic infauna in sediments

from the St. Thomas East End Reserves (STEER). pp 75-117. In: Pait, A.S., S.I. Hartwell, L.J. Bauer, D.A. Apeti, and 

A.L. Mason. 2016. An Integrated Environmental Assessment of the St. Thomas East End Reserves (STEER). NOAA 

Technical Memorandum NOS NCCOS 202. Silver Spring, MD. 219 pp.
An Integrated Environmental Assessment of the St. Thomas 

East End Reserves (STEER)

United States Department 

of Commerce

Penny Pritzker

Secretary 

National Oceanic and Atmospheric 

Administration

Kathryn Sullivan

Under Secretary

National Ocean 

Service

Russell Callender

Assistant Administrator

Prepared by the

National Oceanic and Atmospheric Administration

 National Ocean Service (NOS)

National Centers for Coastal Ocean Science (NCCOS)

Center for Coastal Monitoring and Assessment (CCMA)

1305 East/West Highway (SSMC-4, N/SCI-1)

Silver Spring, MD 20910

USA

October 2016

Editors

Anthony S. Pait

S. Ian Hartwell

Laurie J. Bauer

Dennis A. Apeti

Andrew L. Mason

p. i

About this Document

This report represents the culmination of three years of research by NOAA’s National Centers for Coastal Ocean Science (NCCOS), Center for Coastal Monitoring and Assessment (CCMA) and local partners, in the St. Thomas East 

End Reserves (STEER) in the U.S. Virgin Islands (USVI). 

The purpose of this work was to provide local resource 

managers with a spatially comprehensive characterization 

of stressors including chemical contaminants, nutrients, 

and sedimentation along with their effects, and a biological 

survey of the entire STEER. 

The work was requested by local resource managers, 

and the data and information generated from this project 

establishes a baseline of conditions within the STEER, and 

identifi es challenges to be addressed in order to protect and 

conserve the valuable natural resources within the STEER.

Funding for this project was provided by NOAA’s Coral 

Reef Conservation Program (CRCP). The efforts discussed 

here were led by NCCOS with signifi cant participation 

from partners, including CRCP, the USVI Department 

of Planning and Natural Resources (DPNR) Divisions of 

Coastal Zone Management, Fish and Wildlife, and Environmental Protection, along with the University of the Virgin 

Islands, and The Nature Conservancy. NCCOS has been 

proactive in collaborating with other NOAA line offi ces 

as well as federal, state and nongovernmental organization partners to maximize cost-sharing efforts and reach its 

goals. Their efforts and extramural funding has made it possible to complete assessments that would have otherwise 

been unobtainable through federal funding alone.

For more information on this work and other CCMA and 

NCCOS projects, please see:

http://coastalscience.noaa.gov/projects/detail?key=19

https://coastalscience.noaa.gov/about/centers/ccma

http://coastalscience.noaa.gov/

Direct questions or comments to:

Mark Monaco, PhD, Director

Center for Coastal Monitoring and Assessment 

NOAA National Centers for Coastal Ocean Science

Telephone: 240.533.0327

E-mail: Mark.Monaco@noaa.gov
p. ii
p. iii

Executive Summary

The St. Thomas East End Reserves, or STEER, is a collection of Marine Reserves and Wildlife Sanctuaries 

(MRWS) located on the southeastern end of the island of 

St. Thomas, U.S. Virgin Islands. With an area of approximately 9.6 km2

, the STEER contains extensive mangroves 

and seagrass beds, along with coral reefs, lagoons and cays. 

Within the surrounding watershed are numerous marinas 

and hotels/resorts, a landfi ll serving both St. Thomas and 

St. John, an EPA Superfund site, residential areas with 

individual sewage treatment systems, and in the nearshore 

environment live-aboard and derelict boats, all of which 

can be sources of pollution to the STEER.

Discussions with environmental managers from the USVI 

Department of Planning and Natural Resources (DPNR)

at a meeting in 2009 highlighted the STEER as a priority 

area. It was noted during these discussions that the input of 

pollutants to the STEER, many from land-based sources of 

pollution (LBSP) were thought to be impacting the health 

of the natural resources living there. DPNR managers also 

noted there were signifi cant data and information gaps, 

particularly in terms of the chemical contaminants present, 

their concentrations, effects, along with the overall health 

of the biological communities within the STEER. To 

address these needs, NOAA/NCCOS’ Center for Coastal 

Monitoring and Assessment (CCMA) worked with DPNR 

and other local partners to design a project that was subsequently funded by NOAA’s Coral Reef Conservation 

Program (CRCP), to develop an integrated chemical and 

biological characterization of the STEER. Partners in the 

project included the USVI DPNR Divisions of Coastal 

Zone Management, Fish and Wildlife, and Environmental 

Protection, along with the University of the Virgin Islands, 

and The Nature Conservancy. 

In 2011, sediment samples were collected throughout the 

STEER using a stratifi ed-random sampling design and 

subsequently analyzed for chemical contaminants, toxicity, 

and benthic infaunal community condition. This approach 

allowed for statistical comparisons between the strata 

established in the STEER. Beginning in 2012, the University of the Virgin Islands began monthly monitoring of 

nutrients, sedimentation and total suspended solids (TSS) at 

selected targeted sites. Also in 2012, the fi rst ever biological survey of the entire STEER was conducted by CCMA, 

NCCOS’ Center for Coastal Fisheries and Habitat Research 

(CCFHR) and The Nature Conservancy SCUBA divers. 

During that fi eld mission, samples of coral and conch were 

also collected at targeted sites, for analysis of chemical 

contaminants. 

Results from the analysis of sediments collected in 2011 

indicated elevated levels of certain contaminants in 

northern Benner Bay. A series of follow-up conversations with DPNR managers resulted in additional fi eld 

work, in which both surface and sediment core samples 

were collected and analyzed for chemical contaminants 

in 2013.

The results from the project in the STEER are contained 

in this report, which is organized into 10 chapters, representing the interrelated studies conducted with local 

partners. Chapter 1 provides background information 

on the project and an overview of the study area. Chapter 2 describes the benthic habitat mapping effort, which 

resulted in a revised high resolution map of the benthic 

environments in the STEER. Chapter 3 presents the results from the survey of fi sh communities and associated benthic habitats. Chapter 4 summarizes the fi rst-ever 

quantifi cation of sediment contaminants and sediment 

toxicity throughout the STEER. Chapter 5 presents the 

results of a follow-up effort in northern Benner Bay, 

to better characterize the distribution of contaminants 

in surface sediments, and through sediment coring, assess chemical contaminants in deeper, older sediments. 

Chapter 6 contains an assessment of water soluble 

contaminants at six sites in the STEER, including an 

upstream site in Turpentine Gut, using a series of passive water samplers. Chapter 7 summarizes the results 

of work to analyze coral, conch and fi sh samples for 

chemical contaminants. Chapter 8 presents a histologic 

examination of tissues from the coral Porites astreoides,

the same coral species analyzed for chemical contaminants. Chapter 9 summarizes the results of monitoring 

nutrients, sedimentation and total suspended sediments 

at six sites throughout the STEER for nearly two years. 

Finally, Chapter 10 provides a summary from the project along with a series of conclusions. Highlights from 

each chapter are summarized below.

Chapter 1. Introduction

• The STEER contains a variety of habitats and an 

abundance of natural resources.

• The western half of the STEER contains a greater 

amount of commercial, residential and industrial 

activities.

• The goals of the project were to quantify chemical 

contaminants and effects, and conduct a biological 

survey, establishing a baseline that can be used to 

assess change over time, as management actions are 

implemented to preserve and restore the STEER.
p. iv

Chapter 2. Benthic Habitat Mapping

• High resolution habitat maps were developed using a 

combination of semi-automated classifi cation methods. 

Habitats were interpreted from aerial photographs and 

LiDAR (Light Detection and Ranging) imagery. 

• One hundred ten distinct combinations of habitat 

classes describing the geology and biology of the seafl oor were identifi ed from the aerial photographs and 

LiDAR imagery.

• The overall map accuracies (corrected for proportional 

bias) were 93.0% for major structure, 75.1% for detailed structure, 86.2% for percent hardbottom, 86.5% 

for major cover and 74.5% for detailed cover and 

83.3% for live coral cover. 

• Unconsolidated sediments were dominant inside the 

STEER’s boundary, with sand colonized by seagrass 

being the most common habitat type.

• Live coral cover rarely exceeded 10% inside the 

STEER’s boundaries. However, habitat features with 

>10% live coral cover were located in the eastern 

portion of the study area, specifi cally west of Great 

St. James Island in the STEER, and south and west of 

Deck Point.

Chapter 3. Fish Communities and Associated Benthic 

Habitats

• A total of 80 sites were surveyed during a two-week 

fi eld mission in June 2012. 

• Hard coral cover averaged 5.2%, with the greatest coverage observed in the southern study area, particularly 

on the southwest reef tract near Long Point. Several of 

the survey sites with relatively high coral cover were 

located outside the STEER.

• Mustard hill coral (Porites astreoides) was the most 

abundant coral species, followed by boulder star coral 

(Orbicella annularis complex), lesser starlet coral 

(Siderastrea radians), symmetrical brain coral (Pseudodiploria strigosa), massive starlet coral (S. siderea), 

and fi nger coral (P. porites). 

• In general, both benthic and fi sh community metrics in 

the STEER were similar to other U.S. Caribbean monitoring locations sampled with the same methodology.

• Due to low visibility and concerns for diver health, no 

biological surveys could be conducted in the northern 

portions of Mangrove Lagoon and Benner Bay, which 

appear most impacted by LBSP. Previous studies 

have indicated that species richness and diversity are 

quite low in these areas, which would have impacted 

the overall benthic and fi sh community metrics for the 

STEER. 

• Surveys conducted in the southern portion of Mangrove Lagoon and adjacent coral reefs ranked high in 

regards to hard coral cover, fi sh species richness, total 

fi sh density and total fi sh biomass. Further research is 

needed to fully examine the current and potential nursery function of the entire lagoon. 

Chapter 4. Sediment Chemical Contaminants and Toxicity

• One hundred and eighty-fi ve chemical contaminants 

were analyzed in sediments, and a series of sediment 

toxicity bioassays were conducted along with a characterization of the benthic infaunal community, as part of 

the Sediment Quality Triad, to assess the presence and 

effects of chemical contaminant stressors within the 

STEER. 

• Higher levels of chemical contaminants were found in 

Mangrove Lagoon and Benner Bay in the western portion, than in the eastern part of the STEER. 

• Copper at one site in Benner Bay was above a NOAA 

guideline indicating that effects on benthic organisms 

were likely. 

• The banned antifoulant paint ingredient tributyltin or 

TBT, which had widespread use on boat hulls in the 

past, was found at the third highest concentration in the 

history of NOAA’s National Status and Trends (NS&T) 

Program. 

• The benthic infaunal communities in Mangrove Lagoon 

and Benner Bay appeared to be severely diminished. 

• Results of the bioassays indicated signifi cant sediment 

toxicity in Mangrove Lagoon and Benner Bay using 

multiple tests.

 Chapter 5. Butyltins and Metals in Sediment Cores

• The analysis of sediments in the STEER (Chapter 4) 

prompted a follow-up study in the marina area of northern Benner Bay. 

• Results indicated that surface and deeper sediments are 

highly contaminated with butyltin paint residues, copper, and other toxic metals. The concentration of total 

butyltins at a depth of 6-8 cm was 8,871 ng Sn/g (tributyltin or TBT was over 5,000 ng Sn/g) in a sample at 

depth; the NOAA National Status and Trends (NS&T) 

mean for butyltins in sediments is 8.9 ng/g. 

• The system is also receiving fresh inputs of TBT as evidenced by the percentage of undegraded TBT residues 

in some surface sediments; TBT has been banned for 

use on most vessels in the U.S. since 1989.

• If dredging to deepen the navigation channels or for 

remediation purposes occurs in the future in northern 

Benner Bay, a series of protocols would be needed to 

prevent resuspension of contaminated sediments into 

the water column, along with the proper disposal of 

dredged materials, so as not to impact marine or terrestrial environments. 
p. v

Chapter 6. Water Soluble Chemical Contaminants

• Passive water samplers (POCIS) were deployed in the 

STEER at fi ve locations in 2012 to detect the presence 

of water soluble contaminants.

• A total of 26 stormwater contaminants were detected at 

least once in the STEER. 

• From an earlier (2010) deployment in Turpentine Gut, 

31 stormwater contaminants were detected. 

• Ambient water concentrations could be estimated for 

a number of contaminants including the detergent/

surfactant metabolite 4-tert-octylphenol, phthalate 

ester plasticizers DEHP and DEP, bromoform, personal 

care products including menthol, indole, n,n-diethyltoluamide (DEET), along with the animal/plant sterol 

cholesterol, and the plant sterol beta-sitosterol. 

• The plasticizer DEHP appeared to be the only compound quantifi ed that exceeded a water quality guideline for the protection of aquatic organisms. 

Chapter 7. Contaminants in Coral, Conch and Fish

• Contaminant body burdens in coral (Porites astreoides), conch (Lobatus gigas) and fi sh (longspine 

squirrelfi sh, Holocentrus rufus, and the schoolmaster 

snapper, Lutjanus apodus) were quantifi ed at fi ve sites 

throughout the STEER. 

• Contaminants found in coral from the STEER were 

similar to the concentration ranges reported in corals 

from other reef areas in the U.S. Caribbean. 

• Conch from the STEER had lower contaminant body 

burdens relative to published data from south Florida 

and some other areas of the Caribbean. 

• The conch samples from the STEER had contaminant 

body burdens lower than available FDA action levels 

for molluscan shellfi sh consumption.

• PCBs in one fi sh exceeded an EPA screening value for 

recreational fi shers.

• A signifi cant correlation between higher concentrations 

of butyltins closer to shore existed for conch, despite 

relatively low overall concentrations as compared to 

previous results from the region.

Chapter 8. Histologic Analysis of Porites astreoides

• Examinations of the health of the scleractinian coral, 

Porites astreoides, were performed on samples collected at fi ve sites from the STEER. 

• Zooxanthellae were present in all samples and were in 

excellent condition microscopically. 

• Mangrove Lagoon had fewer colonies and developing 

gonads than other nearshore sites; the deepest offshore 

site in the STEER had the most larvae. 

• Some of the samples had single cell or segmental 

necrosis or apoptosis of the epidermis, gastrodermis, or 

calicodermis; colonies from Benner Bay were the most 

affected. 

• Due to the lack of a clear pattern in association of 

lesions with sites, the results do not support the hypothesis that exposure to land-based sources of pollution was affecting the corals, at least based only on the 

histopathological examinations. 

Chapter 9. Nutrients, Sedimentation and TSS

• As part of the project, the University of the Virgin Islands monitored nutrients, sedimentation, and total suspended solids (TSS) monthly at six sites in the STEER 

for nearly two years. 

• Concentrations of nutrients in the western part of 

the STEER and in nearshore areas were signifi cantly 

higher than at sites in the eastern portion of the STEER. 

• Using a set of nutrient threshold concentrations noted 

to sustain macroalgal blooms in Caribbean coral reefs, 

approximately 60% of the samples collected in the 

STEER were above the threshold for orthophosphate 

(HPO4

=

), while 55% of samples were above the dissolved inorganic nitrogen (DIN) threshold.

• Benner Bay had the highest sedimentation rate of any 

site in the STEER, including Mangrove Lagoon. 

• There was also an east/west and north/south gradient 

in sedimentation, indicative of higher sedimentation 

rates in the western, more urban areas surrounding the 

STEER, and in the more nearshore sites. 

• TSS also tended to be higher in the western and nearshore areas of the STEER.

Chapter 10. Summary and Conclusions

• The overall condition of the habitats and biological 

resources that could be surveyed within the St. Thomas 

East End Reserves appears similar to other coral reef 

areas in the U.S. Caribbean investigated by NOAA’s 

NCCOS. 

• The proximity of the Reserves to the Bovoni Landfi ll, 

marinas, and other commercial and industrial activities, combined with likely inputs from residential sewer 

systems are additional stressors on the STEER. 

• No biological surveys could be conducted in the northern portions of Mangrove Lagoon and Benner Bay, due 

to low visibility and concerns for diver health.

• The presence of chemical contaminants and other 

stressors (e.g., sedimentation and nutrients) in Mangrove Lagoon and Benner Bay are of particular concern 

as the mangroves serve as an important nursery area for 

a variety of vertebrate and invertebrate marine species. 

• Loss of suitable habitat further impacts the ability of 

the STEER to be a source of new recruits of marine 

resource species for St. Thomas and beyond. 
p. vi

Table of Contents

About this Document ......................................................................................................................................................i

Executive Summary ..................................................................................................................................................... iii

Chapter 1: Introduction ..................................................................................................................................................1

 Literature Cited .................................................................................................................................................5

Chapter 2: Benthic habitat mapping within the St. Thomas East End Reserves ...........................................................7

 2.1. Introduction ...................................................................................................................................................7

 2.2. History of benthic habitat mapping in STEER .............................................................................................7

 2.3. Habitat Mapping ...........................................................................................................................................8

 2.4. Results and Discussion ............................................................................................................................... 10

 Literature Cited ................................................................................................................................................... 15

Chapter 3: Characterization of fi sh communities and associated benthic habitats in the St. Thomas East 

End Reserves ................................................................................................................................................................ 17

 3.1. Introduction ................................................................................................................................................. 17

 3.2. Methods ...................................................................................................................................................... 17

 3.3. Results and Discussion ............................................................................................................................... 21

 3.4. Conclusions ................................................................................................................................................. 69

 Literature Cited ................................................................................................................................................... 71

Chapter 4: An assessment of chemical contaminants, toxicity and benthic infauna in sediments from the 

St. Thomas East End Reserves (STEER). .................................................................................................................... 75

 4.1. Introduction ................................................................................................................................................. 75 

 4.2. Methods ...................................................................................................................................................... 78

 4.3. Results and Discussion ............................................................................................................................... 85

 4.4. Conclusions ................................................................................................................................................111

 Literature Cited ..................................................................................................................................................113

Chapter 5: An assessment of tributyltin and metals in surface sediments and sediment cores from Benner 

Bay, St. Thomas East End Reserves ...........................................................................................................................119

 5.1. Introduction ................................................................................................................................................119

 5.2. Methods .....................................................................................................................................................120

 5.3. Results and Discussion ..............................................................................................................................122

 5.4. Conclusions ................................................................................................................................................129

 Literature Cited ..................................................................................................................................................130

Chapter 6: An assessment of chemical contaminants detected in passive water samplers deployed in the 

St. Thomas East End Reserves (STEER) ....................................................................................................................133

 6.1. Introduction ................................................................................................................................................133

 6.2. Methods .....................................................................................................................................................134

 6.3. Results and Discussion ..............................................................................................................................136

 6.4. Conclusions ................................................................................................................................................142

 Literature Cited ..................................................................................................................................................142
p. vii

Table of Contents (continued) 

Chapter 7: An assessment of contaminant body burdens in coral (Porites astreoides), conch (Lobatus gigas) 

and fi sh (Holocentrus rufus and Lutjanus apodus) from the St. Thomas East End Reserves (STEER).....................145

 7.1. Introduction ................................................................................................................................................145 

 7.2. Methods .....................................................................................................................................................145

 7.3. Results and Discussion ..............................................................................................................................149

 7.4. Conclusions ................................................................................................................................................166

 Literature Cited ..................................................................................................................................................167 

Chapter 8: Histological examination of coral tissue samples from St. Thomas East End Reserves (STEER), 

 USVI ..................................................................................................................................................................173

 8.1. Introduction ................................................................................................................................................173

 8.2. Methods .....................................................................................................................................................174

 8.3. Results and Discussion ..............................................................................................................................179

 8.4. Conclusions ................................................................................................................................................189

 Literature Cited ..................................................................................................................................................190

Chapter 9: An assessment of nutrients, sedimentation, and total suspended solids (TSS) in the 

St. Thomas East End Reserves (STEER). ...................................................................................................................193

 9.1. Introduction ................................................................................................................................................193

 9.2. Methods .....................................................................................................................................................193

 9.3. Results and Discussion ..............................................................................................................................196

 9.4. Conclusions ................................................................................................................................................213

 Literature Cited ..................................................................................................................................................214

Chapter 10: Summary and Conclusions ......................................................................................................................217 
p. viii

List of Tables

Table 2.1. The classifi cation scheme used to classify benthic habitats in the STEER in 2013 

(Costa et al. 2013) ..........................................................................................................................................................8

Table 2.2. Qualitative comparison of the 2001 and 2013 benthic habitat maps in the STEER using the modifi ed 

STEER boundary to include mangrove habitat in Mangrove Lagoon and Benner Bay .............................................. 14

Table 3.1. Abiotic and biotic variables measured in fi ve quadrats along fi sh transects ............................................... 19

Table 3.2. Number and type of fouling organisms on marine debris items found during 

STEER transects .......................................................................................................................................................... 33

Table 3.3. Top fi ve families in abundance and total biomass, shown as percent of total, 

by habitat strata ............................................................................................................................................................ 38

Table 3.4. Top fi ve species in abundance and total biomass, shown as percent of total, 

by habitat strata ............................................................................................................................................................ 38

Table 3.5. Pairwise Analysis of Similarities (ANOSIM) comparisons between habitat types based on 

fi sh species density and biomass data, and list of top fi ve species contributing to the dissimilarity 

from the SIMPER analysis ........................................................................................................................................... 39

Table 4.1. Compounds analyzed in sediments from the St. Thomas East End Reserves ............................................ 81

Table 4.2. Comparison of higher concentrations of individual PAHs at STEER sites with NOAA NS&T data ......... 87

Table 4.3. Comparison of higher concentrations (ng/g) of pesticides at STEER sites with NOAA NS&T data ........ 91

Table 4.4. Toxicity bioassay summary results from the STEER................................................................................ 102

Table 4.5. Average (n = 3) P450 bioassay response following 6 and 24 hour incubation with STEER 

sediment extracts ........................................................................................................................................................ 104

Table 4.6. Spearman Rank correlation coeffi cients (bold) and signifi cance level for community 

parameters and selected physical and chemical parameters, and toxicological results ............................................. 108

Table 4.7. Results of SIMPER analysis for Strata 1 and 2 ........................................................................................ 109

Table 4.8. Top 15 species in each stratum plus excluded sites .................................................................................. 109

Table 4.9. Average per-station abundance of selected taxonomic groups in Mangrove Lagoon and Benner 

Bay without stations 1-4P and 2-19P, stations 1-4P and 2-19P together, and the remaining 

strata in 3 (Nazareth Bay), 4 ( Cowpet/St. James Bay), and 5 (Great Bay) ................................................................111

Table 5.1. Concentrations of butyltins (ng Sn/g) and metals (μg/g) in surface sediments .........................................123

Table 5.2. Estimated ages of sections within sediment cores from the STEER .........................................................125

Table 6.1. Location and conditions during deployment of the POCIS canisters in February 2012 and 

May 2010 ....................................................................................................................................................................135

Table 6.2. Estimated water column concentrations of stormwater contaminant residues sampled by 

POCIS in the STEER and in Turpentine Gut ..............................................................................................................137

Table 6.3. Comparison of estimated concentrations of stormwater contaminants with available 

water quality criteria ...................................................................................................................................................141

Table 7.1. Chemical contaminants analyzed in STEER coral, conch and fi sh samples..............................................148

Table 7.2. Summary of means, standard error, and maximum values for organic chemical contaminants 

analyzed in STEER coral, conch and fi sh ...................................................................................................................150

Table 7.3. PAHs, TBT and total butyltins in coral tissues from NOAA Caribbean studies ........................................151

Table 7.4a. Summary statistics for contaminants (μg/g) in coral tissue, including comparison

with other studies ........................................................................................................................................................157

Table 7.4b. Summary statistics for contaminants (μg/g) in coral tissue, including comparison

with other studies ........................................................................................................................................................157

Table 7.5. Mean metal body burden (μg/g) in coral by stratum ..................................................................................158
p. ix

List of Tables (continued)

Table 7.6. Summary statistics for contaminants (μg/g) in conch tissue (n=10), including comparison with mean 

concentration values derived from study of conch contamination in South Florida (Glazer et al., 2008) 

and Johor Straits, Malaysia (Said et al., 2013) ...........................................................................................................158

Table 7.7. Mean metal body burden in conch collected from the fi ve strata in the STEER (μg/g) ............................159

Table 7.8. Trace and major element concentrations (μg/g) in fi sh from the STEER .................................................160

Table 7.9. Comparison of average elemental composition in fi sh tissues (μg/g) in STEER and Vieques.................160

Table 8.1. Characteristics and scoring of changes noted in cells and tissues using light microscopic 

examination of P. astreoides samples collected during this study ..............................................................................176

Table 8.2. Summary statistics for histopathological observations for each parameter for each stratum ....................187

Table 8.3. Summary of results of the histopathological examinations, means of Specifi c Condition 

Scores Sum and percent of colonies with selected condition at each site ..................................................................188

Table 9.1. Location of sites and mean water quality values from STEER sites .........................................................195

Table 9.2. Summary statistics for nutrients measured in the STEER .........................................................................197

Table 9.3. Comparison of STEER nutrient results with those from other U.S. Caribbean locations .........................198

Table 9.4. Comparison of TSS in the STEER with other locations in the USVI ........................................................212
p. x

List of Figures

Figure 1.1. Individual Marine Reserves that comprise the STEER .......................................................................................2

Figure 1.2. Primary watersheds adjacent to the STEER .........................................................................................................3

Figure 1.3. Marina area in Benner Bay .........................................................................................................................4

Figure 2.1. Spatial extent of benthic habitats in the STEER in the 2001 NOAA map (Kendall, 2001) ........................7

Figure 2.2. Aerial photos (left), LiDAR bathymetry (middle), and LiDAR refl ectivity (right) used to 

delineate and characterize the benthic habitats inside STEER (Costa et al. 2013) .......................................................9

Figure 2.3. Summary statistics describing the total amount of mapped area by geographic zone within the 

entire mapped area and for the portion within the STEER (adapted from Costa et al. 2013) ..................................... 10

Figure 2.4. Summary statistics describing the total amount of mapped area by percent hardbottom 

categories within the entire mapped area and for the portion within the STEER (adapted from Costa et al. 2013) ... 10

Figure 2.5. Summary statistics describing the total amount of mapped area by major and detailed 

geomorphological structure within the entire mapped area and for the portion within the STEER 

(adapted from Costa et al. 2013) .................................................................................................................................. 10

Figure 2.6. Summary statistics describing the total amount of mapped area by major and detailed biological 

cover categories within the entire mapped area and for the portion within the STEER .............................................. 10

(adapted from Costa et al. 2013).

Figure 2.7. Summary statistics describing the total amount of mapped area by percent live coral and dominant 

coral cover types within the entire mapped area and for the portion within the STEER (adapted from 

Costa et al. 2013) ......................................................................................................................................................... 11

Figure 2.8. Spatial extent of geographic zones in the STEER in the 2013 NOAA map (Costa et al. 2013) ............... 11

Figure 2.9. Spatial extent of major and detailed geomorphological structure types in the STEER in the 2013 

NOAA map (Costa et al. 2013) .................................................................................................................................... 12

Figure 2.10. Spatial extent of percent hardbottom categories in the STEER in the 2013 NOAA map

(Costa et al. 2013) ........................................................................................................................................................ 12

Figure 2.11. Spatial extent of major and detailed biological cover types in the STEER in the 2013 NOAA 

map (Costa et al. 2013) ................................................................................................................................................ 13

Figure 2.12. Spatial extent of percent live coral and dominant coral cover types in the STEER in the 2013 

NOAA map (Costa et al. 2013) .................................................................................................................................... 13

Figure 3.1. Benthic habitat strata and site locations of the June 2012 survey of benthic habitat composition, 

fi sh communities, invertebrates, and marine debris .....................................................................................................17

Figure 3.2. a) Diver collecting data on benthic habitat, b) diver collecting data on fi sh composition, and 

c) schematic representation of the placement of the 1m2

 quadrat along a 25 m transect tape during fi sh and 

benthic community surveys .........................................................................................................................................18

Figure 3.3. Mean (±SE) percent cover of abiotic substrate by bottom type ................................................................22

Figure 3.4. Mean (±SE) percent cover of major cover groups by bottom type ...........................................................22

Figure 3.5. Mean rugosity (hardbottom sites only) ......................................................................................................23

Figure 3.6. Mangrove prop roots colonized with algae and benthic fauna ..................................................................23

Figure 3.7. Percent live cover of hard corals ...............................................................................................................24

Figure 3.8. Hard coral species richness .......................................................................................................................24

Figure 3.9. a) Mean (±SE) percent cover of hard corals by species at hardbottom sites (N=44) ................................25

Figure 3.10. Percent cover of coral species listed as threatened under the Endangered Species Act (ESA) 

or proposed for future listing .......................................................................................................................................26

Figure 3.11. Percent gorgonian cover. .........................................................................................................................27

Figure 3.12. Percent sponge cover ...............................................................................................................................28

Figure 3.13. Percent macroalgae cover. .......................................................................................................................29

Figure 3.14. Percent turf algae cover ...........................................................................................................................29

Figure 3.15. Percent fi lamentous algae and cyanobacteria (FA & CB) cover .............................................................30

Figure 3.16. Percent seagrass cover .............................................................................................................................30

Figure 3.17. Percent cover of seagrass by species on unconsolidated sediments ........................................................31
p. xi

List of Figures (continued)

Figure 3.18. Density of longspined sea urchin (Diadema antillarum) ........................................................................31

Figure 3.19. Density of mature and immature queen conch (Lobatus gigas) ..............................................................32

Figure 3.20. Density of total observed marine debris ..................................................................................................32

Figure 3.21. Mean (±SE) fi sh species a) Shannon diversity, b) richness, c) density, and d) biomass by 

habitat type ..................................................................................................................................................................34

Figure 3.22. Fish species richness ................................................................................................................................34

Figure 3.23. Fish species diversity ...............................................................................................................................35

Figure 3.24. Total fi sh density ......................................................................................................................................35

Figure 3.25. Total fi sh biomass ....................................................................................................................................36

Figure 3.26. Proportional a) abundance and b) biomass of trophic groups across habitat types .................................36

Figure 3.27. Piscivore biomass. ...................................................................................................................................37

Figure 3.28. Non-metric multidimensional (nMDS) scaling ordination based on between site similarity 

composition using species a) density and b) biomass data ..........................................................................................39

Figure 3.29. Grouper (Family Serranidae) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ...........................................................................................40

Figure 3.30. Red hind (Epinephelus guttatus) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ...........................................................................................42

Figure 3.31. Graysby (Cephalopholis cruentata) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ...........................................................................................43

Figure 3.32. Snapper (Family Lutjanidae a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ...........................................................................................44

Figure 3.33. Gray snapper (Lutjanus griseus) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ...........................................................................................45

Figure 3.34. Schoolmaster (Lutjanus apodus) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 46

Figure 3.35. Yellowtail snapper (Ocyurus chrysurus) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 47

Figure 3.36. Mahogany snapper (Lutjanus mahogoni) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 48

Figure 3.37. Grunt (Family Haemulidae) a) spatial distribution, b) mean density (±SE) by habitat, c) mean 

biomass (±SE) by habitat, and d) size frequency ......................................................................................................... 49

Figure 3.38. French grunt (Haemulon fl avolineatum) a) spatial distribution, b) mean density (±SE) by 

habitat, c) mean biomass (±SE) by habitat, and d) size frequency .............................................................................. 50

Figure 3.39. Bluestriped grunt (Haemulon sciurus) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 52

Figure 3.40. Tomtate (Haemulon aurolineatum) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 53

Figure 3.41. Surgeonfi sh (Family Acanthuridae) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 54

Figure 3.42. Ocean surgeonfi sh (Acanthurus bahianus) a) spatial distribution, b) mean density (±SE) 

by habitat, c) mean biomass (±SE) by habitat, and d) size frequency ......................................................................... 55

Figure 3.43. Blue tang (Acanthurus coeruleus) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 56

Figure 3.44. Parrotfi sh (Family Scaridae) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 57

Figure 3.45. Redband parrotfi sh (Sparisoma aurofrenatum) a) spatial distribution, b) mean density (±SE) 

by habitat, c) mean biomass (±SE) by habitat, and d) size frequency ......................................................................... 58

Figure 3.46. Stoplight parrotfi sh (Sparisoma viride) a) spatial distribution, b) mean density (±SE) by 

habitat, c) mean biomass (±SE) by habitat, and d) size frequency .............................................................................. 59

Figure 3.47. Striped parrotfi sh (Scarus iseri) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 61
p. xii

List of Figures (continued)

Figure 3.48. Princess parrotfi sh (Scarus taeniopterus) a) spatial distribution, b) mean density (±SE) 

by habitat, c) mean biomass (±SE) by habitat, and d) size frequency ......................................................................... 62

Figure 3.49. Wrasse (Family Labridae) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 63

Figure 3.50. Goatfi sh (Family Mullidae) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 64

Figure 3.51. Damselfi sh (Family Pomacentridae) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 65

Figure 3.52. Queen triggerfi sh (Balistes vetula) a) spatial distribution, b) mean density (±SE) by habitat, 

c) mean biomass (±SE) by habitat, and d) size frequency ........................................................................................... 66

Figure 3.53. Comparison of benthic cover groups between STEER and other locations within NOAA’s 

Caribbean Coral Reef Ecosystem Monitoring Program .............................................................................................. 67

Figure 3.54. Comparison of community metrics between STEER and other locations within NOAA’s 

Caribbean Coral Reef Ecosystem Monitoring Program .............................................................................................. 68

Figure 4.1. Strata and sediment sites sampled in the St. Thomas East End Reserves (STEER) in June 2011 ............ 79

Figure 4.2. Combined cluster analysis overlays of species clusters and site clusters .................................................. 83

Figure 4.3. Hypothetical representation of the distribution of physicochemical habitat parameters, contaminant 

concentrations, and other site-specifi c data used to characterize site and species clusters .......................................... 84

Figure 4.4. Percent fi nes (percent silt plus percent clay fractions) in sediments from the STEER ............................. 85

Figure 4.5 Total polycyclic aromatic hydrocarbons (PAHs) detected in sediments from the St. Thomas East 

End Reserves ................................................................................................................................................................ 87

Figure 4.6. Total extractable hydrocarbons (TEH) detected in sediments from the St. Thomas 

East End Reserves ........................................................................................................................................................ 88

Figure 4.7. Straight chain and branched hydrocarbons (aliphatics) in sediments from the St.

Thomas East End Reserves .......................................................................................................................................... 89

Figure 4.8 Total PCBs detected in sediments from the St. Thomas East End Reserves .............................................. 90

Figure 4.9. Total DDT detected in sediments from the St. Thomas East End Reserves .............................................. 91

Figure 4.10. Tributyltin detected in sediments from the St. Thomas East End Reserves ............................................ 93

Figure 4.11. Tributyltin detected in sediments from southwest Puerto Rico and Vieques, Puerto Rico ..................... 94

Figure 4.12. Tributyltin detected in sediments from three sites in the STEER ........................................................... 94

Figure 4.13. Cadmium detected in sediments from the St. Thomas East End Reserves ............................................. 95

Figure 4.14. Chromium detected in sediments from the St. Thomas East End Reserves ............................................ 96

Figure 4.15. Copper detected in sediments from the St. Thomas East End Reserves ................................................. 98

Figure 4.16. Lead detected in sediments from the St. Thomas East End Reserves ..................................................... 99

Figure 4.17. Zinc detected in sediments from the St. Thomas East End Reserves .................................................... 100

Figure 4.18. Clostridium perfringens detected in sediments from the St. Thomas East End Reserves..................... 101

Figure 4.19. Amphipod mortality vs % sand and gravel in St. Thomas STEER sediments ...................................... 103

Figure 4.20. Amphipod mortality versus % total organic carbon in the STEER sediments ...................................... 103

Figure 4.21. P450 response vs PAH concentrations (a), P450 response in terms of B[a]P eq for the subset of

samples that exceeded the TCDD standard response (b) ........................................................................................... 104

Figure 4.22. P450 response (normalized to standard 10nM TCDD) following 6 and 24 hour exposures to extracts

from St. Thomas STEER sediment samples .............................................................................................................. 105

Figure 4.23. Distribution of bioassays showing responses that were signifi cantly different than controls or 

greater than a standard threshold (P450) in St. Thomas STEER sediments .............................................................. 106

Figure 4.24. Plot of total abundance of each taxa used in the analyses ..................................................................... 106

Figure 4.25. Total animal abundance at each station in the STEER .......................................................................... 107

Figure 4.26. Total number of species (taxa) and calculated diversity at each station in the STEER ........................ 107

Figure 4.27. Results of the SIMPER analysis for Strata 1-2 ..................................................................................... 110

Figure 4.28. Results of the SIMPER analysis for Strata 3-5 ..................................................................................... 110

Figure 4.29. Relationship between number of species and species diversity and the ERMq .................................... 111
p. xiii

Figure 4.30. Relationship between number of species and species diversity and percent fi nes ................................ 112

Figure 4.31. Relationship between mean ERMq and percent fi nes ........................................................................... 112

Figure 5.1 Sampling sites for surface and sediment core samples in Benner Bay within the STEER ..................... 120

Figure 5.2. Photograph of core BB2 showing shell hash in the lower part of the core, grading 

to fi ne mud up the core in more recent sediments ..................................................................................................... 122

Figure 5.3. Plots of 210Pb and 137Cs activities with depth for core 16P ..................................................................... 123

Figure 5.4. Plots of 210Pb and 137Cs activities with depth for core BB1 ..................................................................... 124

Figure 5.5. Plots of 210Pb and 137Cs activities with depth for core B3 ........................................................................ 124

Figure 5.6. Plots of 210Pb and 137Cs activities with depth for core BB2 .................................................................... 124

Figure 5.7. Percentage of fi ne grained sediment and gravel sized material (shell hash) down the 

length of the cores ...................................................................................................................................................... 126

Figure 5.8. Percentage of fi ne grained sediment and gravel sized material (shell hash) as a function of time. ...... 126

Figure 5.9. Concentration (ng/g) of total butyltins as a function of time ................................................................. 127

Figure 5.10. Changes in major element concentrations over time at station B3 ...................................................... 127 

Figure 5.11. Percent tributyltin as a proportion of the total butyltins as a function of time and core depth. ........... 127

Figure 5.12. Calcium detected in sediments collected in the STEER ...................................................................... 128

Figure 5.13. Concentration of copper in surface sediments in northern Benner Bay ............................................... 129

Figure 5.14. Copper concentrations as a function of time ......................................................................................... 129 

Figure 6.1. Example of a POCIS disk ........................................................................................................................ 133

Figure 6.2. A disassembled POCIS deployment canister with the POCIS disks ....................................................... 134

Figure 6.3. Locations of passive water samplers (POCIS) in the STEER ................................................................. 134

Figure 6.4. POCIS deployment canister (arrow) among the sediment traps at a site in the STEER ......................... 135

Figure 6.5. Number of stormwater contaminants with estimated water column concentrations in 

the STEER and in Turpentine Gut ............................................................................................................................. 140

Figure 7.1. Coral, conch and fi sh sites collected in 2012 in the St. Thomas East End Reserves (STEER) ............... 146

Figure 7.2. Total PAHs detected in the coral Porites astreoides ................................................................................ 150

Figure 7.3. Total PAHs detected in the conch Lobatus gigas .................................................................................... 151

Figure 7.4. Total PCBs detected in fi sh in the STEER ............................................................................................. 152

Figure 7.5. Total butyltins detected in the coral Porites astreoides ........................................................................... 154

Figure 7.6. Total butyltins detected in the conch Lobatus gigas ................................................................................ 154

Figure 7.7. Tributyltin detected in the coral Porites astreoides ................................................................................. 155

Figure 7.8. Tributyltin detected in the conch Lobatus gigas ...................................................................................... 155

Figure 7.9 Distribution of tributyltin (TBT), dibutyltin (DBT), and monobutyltin (MBT) from 

fi sh sampled in the STEER ........................................................................................................................................ 156

Figure 7.10. Concentrations (mean ±SE) of metals detected in the coral Porites astreoides .................................... 157

Figure 7.11. Concentrations (mean ±SE) of metals detected in the conch Lobatus gigas ......................................... 159

Figure 7.12. Concentrations (mean ±SE) of metals detected in the coral Porites astreoides .................................... 161

Figure 7.13. Concentrations (mean ±SE) of metals detected in the conch Lobatus gigas ........................................ 163

Figure 7.14. Scatter plot showing relationship between manganese and lead in coral .............................................. 164

Figure 8.1. Map of the St. Thomas East End Reserves showing site locations (in red circles) where the 

samples for histopathological examination were collected in June 2012 .................................................................. 173

Figure 8.2. Examples of fi xed coral samples as photographed in the GMU Histology Laboratory .......................... 174

Figure 8.3. Examples of surface body wall and gastrodermis ruptures and lysing ................................................... 180

Figure 8.4. Melanin-like granular amoebocytes (brown cells) infi ltrating between cells of the epidermis 

and gastrodermis of tentacles (arrow), rated severe (= 5) .......................................................................................... 180

Figure 8.5. Examples of apoptosis in the epidermis (at arrows) ................................................................................ 181

Figure 8.6. Examples of calicodermis condition ....................................................................................................... 182

List of Figures (continued)
p. xiv

Figure 8.7. Examples of bacterial aggregates in mesoglea of tentacles (a and b), 25x; calicodermis 

reaction to suspect fungal hyphae (c), 40x; endolithic algae or fungi where skeleton was removed 

along basal gastrovascular canals (d), 10x ................................................................................................................. 183

Figure 8.8. Examples of apicomplexan parasites of P. astreoides ............................................................................. 184

Figure 8.9. Examples of apparent destruction of the basal body wall of most aboral gastrovascular 

canals in the tissue layer of the perforate coral, P. astreoides .................................................................................... 185

Figure 8.10. Examples of other unknowns present in the STEER samples ............................................................... 185

Figure 8.11. Examples of reproductive structures present in the STEER samples .................................................... 186

Figure 8.12. Example of black particles trapped in mucus secretions (arrows), 40x ................................................ 188

Figure 8.13. Comparison of means of Specifi c Condition Scores Sum with standard deviations 

among the fi ve sites .................................................................................................................................................... 189

Figure 9.1. Sampling sites for nutrients, sedimentation, and TSS along with the STEER boundary ........................ 194

Figure 9.2. Mean and max concentrations of ammonium (NH4

+

) detected in water samples from the STEER ....... 199

Figure 9.3. Mean and max concentrations of nitrate (NO3

-

) and nitrite (NO2

-

) detected in 

water samples from the STEER ................................................................................................................................. 200

Figure 9.4. Mean and max concentrations of urea detected in water samples from the STEER ............................... 201

Figure 9.5. Mean and max concentrations of dissolved inorganic nitrogen (DIN) detected in water 

samples from the STEER ........................................................................................................................................... 202

Figure 9.6. Mean and max concentrations of total nitrogen (TN) detected in water samples from the STEER ....... 203

Figure 9.7. Mean and max concentrations of orthophosphate (HPO4

=

) detected in water samples 

from the STEER ......................................................................................................................................................... 204

Figure 9.8 Mean and max concentrations of total phosphorus (TP) detected in water samples 

from the STEER ......................................................................................................................................................... 205

Figure 9.9. Nitrate and nitrite concentrations versus rainfall in Benner Bay during the study period ...................... 206

Figure 9.10. Percent exceedances of DIN threshold by site in the STEER ............................................................... 206

Figure 9.11. Herbivore biomass in the STEER .......................................................................................................... 207 

Figure 9.12. Bulk deposition of sediment in traps placed in the STEER .................................................................. 207

Figure 9.13. Excavation activity on Little St. James Island, a possible source of terrigenous sediments 

found in the sediment traps at this site ....................................................................................................................... 208

Figure 9.14. Average accumulation rates at the sediment trap sites in the STEER ................................................... 208

Figure 9.15. Bulk deposition in Benner Bay sediment traps plotted against rainfall ................................................ 209

Figure 9.16. Percent and rates of deposition for terrigenous, carbonate and organic materials in the 

sediment traps in the STEER over time for Mangrove Lagoon (a, d), Benner Bay (b, e), 

and Little St. James (c, f) ........................................................................................................................................... 210

Figure 9.17. Plots of mean sediment deposition (a), rainfall (b) and wave height at Station 41052 (c) ................... 211

Figure 9.18. Total suspended solids (TSS) means (±SE) at sampling sites in the STEER ........................................ 212

 

List of Figures (continued)
p. xv
p. xvi
Chapter 1: Introduction

1

STEER Integrated Environmental Assessment Report

This report contains the results of a chemical and biological 

characterization of the St. Thomas East End Reserves, or 

STEER in St. Thomas, USVI. This integrated ecological 

assessment represents the fi ndings from a three-year project 

carried out by NOAA’s National Centers for Coastal Ocean 

Science (NCCOS) and local partners, to assess chemical stressors and impacts, and to characterize the marine 

biological communities throughout the STEER. This 

report combines the results from fi ve interim reports, along 

with data from two other assessments that were part of the 

project, into a fi nal integrated assessment. The reader will 

be referred to these other publications on occasion, for additional information. 

The St. Thomas 

East End Reserves, 

or STEER, is a 

collection of Marine Reserves and 

Wildlife Sanctuaries 

(MRWSs) located on 

the southeastern end 

of the island of St. 

Thomas, U.S. Virgin 

Islands (Figure 1.1). 

Within the STEER, 

there are extensive 

mangroves and 

seagrass beds, along 

with coral reefs, 

lagoons and cays. 

The value of the 

natural resources in 

the Reserves has long been recognized. In 1979, the area 

was identifi ed by NOAA’s National Marine Sanctuaries 

Program as a “marine area of national signifi cance, deserving of marine sanctuary designation” (NOAA, 1981). The 

same year, the Mangrove Lagoon/Benner Bay area was 

designated by the USVI government as an Area of Particular Concern, or APC, due to the abundance of important but 

threatened natural resources, and the desire to preserve and, 

as needed, restore these areas.

The STEER is made up of four MRWSs, including Inner 

Mangrove Lagoon, Cas Cay/Mangrove Lagoon, St James, 

and Compass Point Salt Pond Marine Reserves and Wildlife Sanctuaries (Figure 1.1). The STEER comprises an 

area of approximately 9.6 km2

, with 34 km of coastline 

(STEER, 2011). Boundaries for the STEER include the 

Mangrove Lagoon/Benner Bay MRWS with Long Point 

as the western border (Figure 1.1). The St. James MRWS 

forms the eastern boundary of the STEER, which includes 

the waters surrounding Great St. James and the north shore 

of Little St. James Island. To the north, the boundary of 

the STEER runs along the coastline, from Cabrita Point 

westward to Benner Bay. At Benner Bay, the boundary follows a line offshore from Coculus Rock along Roto Cay to 

the northeastern entrance of Mangrove Lagoon; the marina 

areas within Benner Bay are outside of the STEER. 

With mangroves, seagrass beds, lagoons, salt ponds, coral 

reefs and a number of cays, the STEER contains a multitude of natural habitats and resources. The STEER is 

thought to be one of 

the most valuable 

nursery areas remaining in St. Thomas, 

with many species 

of fi sh and shellfi sh 

spending some portion 

of their lives in the 

protected areas around 

the mangroves and in 

the extensive seagrass 

beds (STEER, 2011). 

Fishing is not allowed 

in most parts of the 

STEER, and where it 

is allowed (e.g., for 

baitfi sh), a permit is 

required. 

The abundance of 

natural resources has contributed to the STEER being a 

popular destination for recreational activities ranging from 

swimming, camping, snorkeling and SCUBA, to boating 

and ecotourism. 

The largest remaining mangrove system in St. Thomas 

occurs along the shores of Mangrove Lagoon/Benner Bay 

(IRF 1993; STEER, 2011). Mangrove species include 

the red mangrove (Rhizophora mangle), black mangrove 

(Avicennia germinans), and white mangrove (Laguncularia 

racemosa). Mangroves offer many ecological benefi ts. 

They serve as natural buffers against shore erosion, fl oods 

and hurricane waves. Mangroves also provide protection 

for juvenile fi sh and other organisms around the roots, 

and generate detrital material that enters the food chain, 

becoming a food resource for a number of marine organisms (DPNR-DFW, 2005). Sampling with fi sh traps along 

View into the St. Thomas East End Reserves (STEER).

CHAPTER 1: INTRODUCTION
Chapter 1: Introduction

2

STEER Integrated Environmental Assessment Report

the mangrove fringe in Benner Bay/Mangrove Lagoon has 

yielded as many as 40 fi sh species (Boulon, 1992; Colletti, 

2011). 

There are extensive areas of seagrass in Benner and Jersey 

Bays. Although seagrasses were also abundant throughout Mangrove Lagoon in the 1970s, macroalgae presently 

dominates the benthos (Colletti, 2011). Seagrasses in Mangrove Lagoon appear to be limited to the middle portion of 

the lagoon, near the mangroves on the eastern edge. In the 

rest of the STEER, turtle grass (Thalassia testudinum) and 

manatee grass (Syringodium fi liforme) are two of the major 

seagrass species found in the STEER (DPNR-DFW, 2005). 

Seagrasses provide habitat for many organisms, including 

juvenile fi sh. Seagrasses are also an important food source 

for parrotfi sh, surgeonfi sh, and pinfi sh, along with turtles, 

birds, and sea urchins. Conch feed off the epiphytes on the 

seagrass leaves (DPNR-DFW, 2005). Finally, seagrasses 

in the Caribbean as in other areas, help to improve water 

clarity and light penetration, by trapping fi ne sediments and 

allowing the sediment particles to settle out of the water 

column. 

There are signifi cant coral reef areas in Jersey Bay and also 

south of Cas and Patricia Cays. Many species of coral can 

be found in the STEER, including the star coral complex 

(Orbicella annularis, O. faveolata and O. franksi), mustard 

hill coral (Porites astreoides), lesser and massive starlet 

corals (Siderastrea radians and S. siderea), fi nger coral 

(P. porites), symmetrical brain coral (Diploria strigosa), 

and great star coral Montastraea cavernosa (DPNR-DFW, 

2005). Also within the STEER are the threatened elkhorn 

(Acropora palmata) and staghorn (A. cervicornis) corals. 

The STEER is a relatively shallow system, supporting both 

patch and fringing reefs. The coral reefs provide habitat 

and food for many organisms. 

Not surprisingly, the habitats in the STEER are closely 

linked to one another. For example, a variety of fi sh and 

invertebrates move between the mangroves, seagrass beds 

and coral reefs, either during the course of their lives (e.g., 

juvenile fi sh living among the mangrove prop roots for protection, with adults moving out onto the reefs), or as part 

of a diurnal cycle (e.g., invertebrates and fi sh feeding in the 

seagrass beds at night and returning to the protection of the 

coral reefs during the day) (STEER, 2011). 

Degraded environmental quality in any one of these 

habitats affects the others. Poor water and sediment quality in mangrove areas can result in lower dissolved oxygen 

concentrations from an overabundance of nutrients and 

organic matter, reducing habitat quality for fi sh species and 

their prey. Elevated levels of suspended sediments in the 

water column can lead to a reduction in the amount of light 

Figure 1.1. Individual Marine Reserves that comprise the STEER. 

Marine Reserves

Cas Cay-Mangrove Lagoon Marine Reserve and Wildlfie Sanctuary

St. James Marine Reserve and Wildlfie Sanctuary

Compass Point Salt Pond

012 0.5

Kilometers  ̄

Mangrove 

Lagoon

Benner Bay

Patricia

Cay

Cas Cay

Roto 

Cay

Coculus Coculus 

Rock

Jersey Bay

St. James Bay

Christmas Christmas 

Cove

Nazareth 

Bay Cowpet 

Bay

Great Bay

Great St. Great St. 

James

Little St. Little St. 

James

Cow and Calf Rocks

Long

Point

Cabrita

Point

Bovoni 

Landfill Landfill

Sources: Esri, GEBCO,

NOAA, National Geographic,

St. Thomas St. John

7XUSHQWLQH

*XW

'HFN

3RLQW
Chapter 1: Introduction

3

STEER Integrated Environmental Assessment Report

reaching seagrasses and corals, which can result in reduced 

growth or even die-off. Sediments that settle out of the 

water column can also act to smother corals, or at the very 

least, result in the corals having to expend more energy to 

remove the sediment. Elevated nutrient levels can result 

in increased algal growth in the water column and, as with 

sediments, reduce the amount of light reaching corals or 

seagrasses. Excess nutrients also promote the growth 

of epiphytic algae that may smother coral and seagrass. 

Chemical contaminants can impact a variety of organisms 

and life stages. 

Two watersheds, Jersey Bay and Red Hook drain to the 

STEER (Figure 1.2). The largest is the Jersey Bay watershed which empties 

into Mangrove Lagoon/

Benner Bay and Jersey 

Bay. The Frenchman Bay 

watershed drains to the 

west of the STEER. The 

area of the STEER east of 

Deck Point (Figure 1.1) 

receives input from the 

Red Hook watershed. 

Approximately one-third 

of the population of St. 

Thomas resides within 

the Mangrove Lagoon/

Benner Bay APC (IRF, 

1993). The area is 

considered highly impacted and urbanized, 

with numerous point 

and non-point sources of 

pollution (DPNR 2003; Horsley Witten, 2013a,b). These 

sources include the unlined Bovoni Landfi ll (Figure 1.1), 

adjacent to Mangrove Lagoon, which serves all of St. 

Thomas and St. John, an EPA Superfund site (EPA, 2011), 

numerous marinas and boatyards (Figure 1.3), a number 

of resorts, various commercial/industrial activities, and a 

horse racetrack. In addition, it has been estimated (Horsley 

Witten, 2013b) that approximately 70% of the residential 

housing adjacent to Mangrove Lagoon and Benner Bay is 

on septic systems, many of which are failing (IRF, 1993). 

There is also a deteriorating sewer infrastructure for those 

connected to the public sewer system and at one time, a 

wastewater treatment plant emptied directly into Mangrove 

Lagoon (Grigg et al., 1971). Elevated levels of chemical 

contaminants have been documented in the STEER watershed (EPA, 2011). 

Turpentine Gut, which was channelized during construction of the nearby Clinton Phipps racetrack, drains approximately 60% of the watershed, and discharges of 

untreated stormwater and sewage overfl ows go directly into 

Mangrove Lagoon. Elevated sedimentation, nutrient and 

bacterial levels have been detected in the lagoon, particularly following storm events (STEER, 2011). The EPA 

Superfund site (Tutu Wellfi eld Superfund Site) was established in 1996 due to contamination of groundwater and 

wells in the area by chlorinated volatile organic compounds 

(CVOC) (EPA, 2011). Finally, sediments are delivered to 

the STEER through conveyances such as Turpentine Gut, 

or directly to the STEER as a result of runoff from the steep 

island slopes surrounding the northern part of Mangrove 

Lagoon and Benner 

Bay. All of these have 

the potential to contribute both point and 

nonpoint source pollution to the STEER. 

Due to the threats 

along with the ecological value of the 

wetlands and adjacent 

marine ecosystems, the 

Jersey Bay and Red 

Hook watersheds have 

been designated as 

“priority watersheds” 

in St. Thomas (Platenberg, 2006). In addition, a management 

plan (STEER, 2011) 

was developed through 

the collaboration of the Department of Planning and Natural Resources (DPNR), the University of the Virgin Islands 

(UVI), The Nature Conservancy (TNC), and community 

groups (e.g., Friends of Christmas Cove). The goal of the 

STEER Management Plan is to “restore and maintain a 

functional coastal ecosystem that promotes sustainable 

recreational opportunities and compatible commercial uses 

with community engagement through effective management” (STEER, 2011). 

At a NOAA Coral Reef Ecosystem Integrated Observing 

System (CREIOS) Meeting in San Juan, Puerto Rico in 

2009, NOAA scientists met with resource managers and 

local scientists from the U.S. Caribbean, including representatives from the USVI, to elicit priority information 

needs, and to highlight important issues of concern. At that 

Jersey Bay 

Watershed Red Hook 

Bay 

Watershed

STEER

Figure 1.2. Primary watersheds adjacent to the STEER. 

Frenchman

Bay 

Watershed
Chapter 1: Introduction

4

STEER Integrated Environmental Assessment Report

meeting, representatives from DPNR’s Divisions of Coastal 

Zone Management and Environmental Protection identifi ed 

the STEER as a priority area, and noted that there were signifi cant data and information gaps in terms of the chemical 

contaminants present, effects, and the overall health of the 

biological communities within the STEER. 

Representatives from DPNR stated that the extent of chemical contamination and biological effects in the STEER 

were unknown, but that data would be critical in helping to 

make informed decisions on coastal resource management. 

With these needs in mind, NOAA’s NCCOS, in partnership with the STEER Core Planning Group made up of 

scientists and managers from DPNR’s Divisions of Coastal 

Zone Management, Fish and Wildlife, and Environmental 

Protection, along with the University of the Virgin Islands, and The 

Nature Conservancy, proposed 

a multiyear project to NOAA’s 

Coral Reef Conservation Program 

(CRCP), to develop an integrated 

assessment of the chemical and 

biological conditions within the 

STEER.

Several other CRCP-funded 

projects in the STEER have been 

completed. In 2012, a survey 

of human uses was documented 

in a coastal use mapping project 

(Dillard and D’lorio, 2012). In 

another CRCP-funded project, the goal of which was to 

develop a watershed management plan for the STEER, 

information from the current project was incorporated into 

the management plan. Reducing impacts from the landfi ll, 

along with improving wastewater and storm water management, pollution prevention, and wetland restoration, were 

seen as key items for STEER watershed restoration (Kitchell, 2012).

NOAA’s CRCP also funded an effort to develop a new high 

resolution map describing the distribution, quantity and 

type of seafl oor habitats inside the STEER. This map was 

developed from LiDAR (Light Detection and Ranging) bathymetry and refl ectivity imagery collected by Fugro LADS 

Corporation. The new habitat map and related products are 

described in Chapter 2, and will be used to: update nautical 

charts in the area to; help fi ll critical information gaps about 

the seafl oor in a priority area identifi ed by NOAA’s CRCP; 

support fi sheries-related performance measures outlined in 

the USVI Jurisdictional Working Group Priority Settings 

document; and to support best management practices inside 

the STEER, related to permitting activities, restoration, 

fi sheries, climate change and scientifi c research.

The USVI Territorial Coral Reef Monitoring Program 

(TCRMP) has been surveying reefs around St. Thomas 

since 2001 but only has one permanent site within the 

STEER, at Coculus Rock in Benner Bay, and an additional site located just outside STEER near Little St. James 

(Smith et al., 2011). Benthic metrics have been surveyed 

annually since 2001, and an annual fi sh census was added 

at the Coculus Rock monitoring site in 2009. The TCRMP 

data is collected using frame grabs from digital video to 

estimate benthic cover to the species level. While the data 

produced by both of these studies are robust, a STEERwide assessment characterizing the fi sh and benthic communities across all habitat types 

has been lacking.

Other recent research in the 

STEER has focused on limited 

geographic areas. A recent oneyear study of fi sh communities 

was conducted in Benner Bay/

Mangrove Lagoon. Fish traps were 

used to compare fi sh diversity and 

abundance among three geographic strata within the lagoon (Murray 

2009; Colletti, 2011). This study 

also produced a benthic habitat 

map of the lagoon using broad 

categories (coral reef, mangrove, 

cyanobacteria, seagrass, macroalgae, and coral rubble) 

(Colletti, 2011). 

EPA’s Environmental Monitoring and Assessment Program 

(EMAP) collected sediment samples in 2004, at a number 

of locations around St. Thomas. Four of the sites were in 

the STEER; two sites were in Benner Bay, and one site 

each in Jersey Bay and Great Bay. Data from the EMAP 

work are highlighted in Chapter 4. 

The overall objectives of the project in the STEER involving NCCOS and partners were to: 1) quantify chemical 

contamination in sediments, coral and conch, fi sh and 

water; 2) assess the effects that these stressors may be having on organisms living within the sediments; 3) characterize the fi sh communities and associated benthic habitats 

in the STEER; and 4) establish baseline values that can be 

compared with conditions following changes in land use 

practices or implementation of management actions. 

In 2011, NCCOS scientists along with project partners 

collected sediments for chemical contaminant analysis, 

Figure 1.3. Marina area in Benner Bay. 
Chapter 1: Introduction

5

STEER Integrated Environmental Assessment Report

toxicity bioassays, and benthic infaunal analysis. In early 

2012, the University of the Virgin Islands began monthly 

sampling for nutrients, and monthly monitoring of total 

suspended solids (TSS, a CRCP performance measure), and 

sedimentation using sediment traps placed at six locations 

within the STEER as part of the project. Passive water 

samplers were also deployed in the same locations as the 

sediment traps. The passive water samplers were used to 

quantify the presence of wastewater contaminants in the 

water column. Activities in the second year also included a 

biological survey of the entire STEER, along with the collection of coral, conch and fi sh for chemical contaminant 

analysis. In the third year (2013), a followup investigation 

of contaminants in surface sediments and also in sediment 

cores was completed in northern Benner Bay. The quantifi cation of sediment contaminants, toxicity, and the benthic infaunal community, along with the biological survey 

conducted as part of this project, have provided data needed 

to optimize management of the STEER.

LITERATURE CITED

Boulon, R.H. 1992. Use of mangrove prop root habitats by 

fi sh in the northern U.S. Virgin Islands. Proceedings, Gulf 

and Caribbean Fishery Institute 41:189-204.

Colletti, C.M. 2011. The effect of seascape structure on the 

spatial distribution of juvenile fi sh within Benner Bay Mangrove Lagoon, St. Thomas, United States Virgin Islands 

(USVI). MS Thesis. Masters of Marine and Environmental 

Sciences. University of the Virgin Islands. 118pp.

Dillard, M., and M. D’lorio. 2012. St. Thomas East End 

Reserves (STEER) Coastal Use Mapping Project: Ocean 

Uses Map Book. 32pp. 

DPNR-DFW (Department of Planning and Natural Resources, Division of Fish and Wildlife). 2005. Marine 

Resources and Fisheries Strategic and Comprehensive Conservation Plan. Division of Fish and Wildlife, Department 

of Planning and Natural Resources, U.S. Virgin Islands. 

554pp. 

DPNR. 2003. Draft Dissolved Oxygen TMDLs for the 

Mangrove Lagoon and Benner Bay. Department of Planning and Natural Resources, Division of Environmental 

Protection, US Virgin Islands.

EPA (U.S. Environmental Protection Agency). 2011. 

Remediation system evaluation. Tutu Wellfi eld Superfund Site, St. Thomas, U.S. Virgin Islands. Offi ce of Solid 

Waste and Emergency Response (5102G). Final Report. 

EPA-542-R-11-008. 37pp.

Grigg, D.I., R.E. vanEepoel, and R.W. Brody. 1971. Water 

Pollution Report no. 10. Water Quality and Environmental 

Status of Benner Bay-Mangrove Lagoon St. Thomas. 42pp 

plus appendices. 

Horsley Witten Group, Inc. 2013a. St. Thomas East End 

Reserves Watershed Management Plan. Prepared for 

NOAA Reef Conservation Program, USVI Department of 

Planning and Natural Resources, and The Nature Conservancy. 51pp + Appendices.

Horsley Witten Group, Inc. 2013b. STEER Watershed 

Existing Conditions Report. Prepared for NOAA Reef 

Conservation Program, USVI Department of Planning and 

Natural Resources, and The Nature Conservancy. 71pp + 

Appendices. 

IRF (Island Resources Foundation). 1993. Mangrove 

Lagoon/Benner Bay Area of Particular Concern (APC) and 

Area for Preservation and Restoration (APR) Management 

Plan: A Comprehensive Analytic Study. Prepared by Island 

Resources Foundation, St. Thomas, Virgin Islands, for 

USVI DPNR/CZM Program. 32pp. 

Kitchell, A. 2012. STEER Watershed Management Plan: 

12/6/2012. Presentation made at Ivanna Eudora Kean High 

School, Red Hook, St. Thomas, USVI. 

Murray, J. 2009. Final Performance Report: Sportfi sh 

Monitoring, Enhancement and Restoration Program. Division of Fish and Wildlife, U.S. Virgin Islands Department 

of Planning and Natural Resources. 90 pp.

NOAA (National Oceanic and Atmospheric Administration). 1981. Proposed St. Thomas National Marine Sanctuary. Draft environmental impact statement. 59pp and 

appendices. 

Platenberg, R.J., 2006. Wetlands Conservation Plan for St. 

Thomas and St. John, U.S. Virgin Islands. Division of Fish 

and Wildlife, Department of Planning and Natural Resources, St. Thomas. 101 pp.

Smith, T.B., E. Kadison, L. Henderson, J. Gyory, M.E. 

Brandt, J.M. Calnan, M. Kammann, V. Wright, R.S. Nemeth, and P. Rothenberger. 2011. The United States Virgin 

Islands Territorial Reef Monitoring Program. Year 11 Annual Report. 243 pp.

STEER. 2011. St. Thomas East End Reserves Management Plan. Edited by J. Brown, A. Holecek, J. Murray, L. 

Noori, J.P. Oriol, J. Pierce, R. Platenberg, S. Romano, D. 

Russo, and C. Settar. 99pp.
Chapter 1: Introduction 6

STEER Integrated Environmental Assessment Report
p. 7 7Chapter 2: Benthic Habitat Mapping

STEER Integrated Environmental Assessment Report

CHAPTER 2: BENTHIC HABITAT MAPPING WITHIN THE ST. THOMAS EAST END RESERVES

Bryan Costa1,2, Laurie Bauer1,2, and Tim Battista1

1

NOAA/NOS/National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment (CCMA), 

1305 East/West Highway, Silver Spring, MD 20910

2

CSS-Dynamac Consolidated Safety Services, Fairfax, VA 22030, under CSS-Dynamac Contract #EA-133C-14-NC-1384

2.1 INTRODUCTION

Scientists and managers need a baseline understanding of 

the benthic communities and associated living marine resources to effectively manage the STEER (STEER, 2011). 

Benthic habitat maps are an integral component to this process, as they support effective ecosystem-based approaches 

to management. Habitat maps inform local managers 

about the existing distribution of resources and how they 

have changed over time. They also help managers locate 

and protect sensitive marine communities, and help guide 

monitoring efforts and prioritize subsequent management 

actions. The objectives of this chapter are to 1) provide 

a synopsis of benthic habitat mapping efforts conducted 

within STEER, and 2) provide summary statistics and a 

description of benthic habitats within the STEER.

2.2 HISTORY OF BENTHIC HABITAT MAPPING IN 

STEER

A benthic habitat map for the USVI and Puerto Rico 

was completed in 2001 by NOAA’s National Centers 

for Coastal Ocean Science (NCCOS), Center for Coastal 

Monitoring and Assessment CCMA) Biogeography Branch 

(Figure 2.1, Kendall et al., 2001). This map is based on 

1999 aerial photography, and has a minimum mapping unit 

of 1 acre (4,048 m2

). Major mapped categories include 

unconsolidated sediments, submerged vegetation, and coral 

reef/hardbottom. 

Detailed habitat types for reef/hardbottom include colonized bedrock, colonized pavement, colonized pavement 

with sand channels, linear reef, patch reef (aggregated), 

patch reef (individual), and scattered coral/rock in unconsolidated sediment (Kendall et al., 2001). Detailed habitat 

types within unconsolidated sediments include sand and 

mud. Submerged aquatic vegetation was divided into 

macroalgae and seagrass and mapped at various levels of 

patchiness. Other delineations include mangrove, land, and 

artifi cial structures.

2001 Benthic Habitat Map

Habitat Type

Linear Reef

Aggregated Patch Reefs

Bedrock (Colonized)

Bedrock (Uncolonized)

Individual Patch Reef

Pavement (Colonized)

Pavement (Uncolonized)

Pavement with Sand Channels (Colonized)

Pavement with Sand Channel (Uncolonized)

Reef Rubble

Spur and Groove Reef

Macroalgae

Mangrove

Seagrass

Mud

Sand

Scattered Coral/Rock in Unconsolidated Sediment

Artificial

Land

Unknown

STEER Boundary

0 1.5 3 0.75

Kilometers  ̄

Figure 2.1. Spatial extent of benthic habitats in the STEER in the 2001 NOAA map (Kendall, 2001).
p. 8 8 Chapter 2: Benthic Habitat Mapping

STEER Integrated Environmental Assessment Report

In 2011, the National Oceanic and Atmospheric Administration (NOAA) collected LiDAR (Light Detection and 

Ranging) imagery of the nearshore, marine areas (0-40 

meters deep) around St. John and north of St. Thomas in 

the U.S. Virgin Islands (USVI). LiDAR sensors use lasers 

to collect depth and topographic information about the seafl oor. This seafl oor imagery was collected with a number 

of applications in mind (USVI and NOAA CRCP, 2010), 

including hydrodynamic modeling, chemical contaminant 

and sediment dispersal modeling, water quality monitoring, 

nautical chart updates and benthic habitat mapping. NOAA’s Biogeography Branch used this imagery to develop 

benthic habitat maps for three locations identifi ed as high 

priorities by local resource managers (USVI and NOAA 

CRCP, 2010), which included the marine areas in and 

around the STEER as well as Coral Bay and Fish Bay in St. 

John (Costa et al., 2013). 

The new NOAA map (Costa et al., 2013) was different 

than the previous version (Kendall, 2001) in several ways, 

including the use of: 1) a revised, expanded classifi cation 

scheme, 2) a fi ner scale of delineation, and 3) a smaller 

minimum mapping unit (100 m2

). In addition, whereas 

only aerial photos were used to create the 2001 maps, the 

new mapping effort utilized both aerial photos and LiDAR 

imagery, which when integrated provides a wealth of additional information about the seafl oor. 

2.3 HABITAT MAPPING

Methods

This section provides a general overview of the most recent 

benthic habitat mapping effort within STEER (Costa et 

al., 2013). The habitat classifi cation scheme used to map 

shallow-water benthic habitats (<30 m) is summarized in 

Table 2.1. This scheme was adapted from a scheme previously developed by NOAA to map benthic habitats around 

St. John (Zitello et al., 2009; Costa et al., 2009), Buck 

Island Reef National Monument in St. Croix (Costa et al., 

2012) and Southwest Puerto Rico (Bauer et al., 2012). The 

habitat classifi cation scheme defi nes benthic habitats based 

on six attributes: 1) broad geographic zone; 2) geomorphological structure type; 3) percent hardbottom; 4) dominant 

biological cover; 5) amount of live coral cover (includes 

both hard and soft corals); and 6) dominant coral type (hard 

or soft coral). Every feature in the benthic habitat map was 

assigned a class from each level of the scheme (Table 2.1).

The following steps were used to map shallow-water habitats (Costa et al., 2013).

GEOGRAPHIC ZONE BIOLOGICAL COVER

Back Reef Coral Reef and Hardbottom (Hard) Major Cover

Bank/Shelf Aggregate Reef Algae

Bank/Shelf 

Escarpment Aggregated Patch Reefs Live Coral

Channel Individual Patch Reef Mangrove

Dredged Pavement No Cover

Fore Reef Pavement with Sand Channels Seagrass

Lagoon Reef Rubble Percent Hard Unclassified

Land Rhodoliths 0% ≤ 10% Unknown

Reef Crest Rhodoliths with Scattered Coral & Rock 10% ≤ 30% Percent Major Cover

Reef Flat Rock/Boulder 30% ≤ 50% 10% ≤ 50%

Salt Pond Spur & Groove 50% ≤ 70% 50% ≤ 90%

Shoreline Intertidal Unknown 70% ≤ 90% 90% ≤ 100%

Unconsolidated Sediment (Soft) 90% - 100% N/A

Mud N/A Unknown

Sand Unknown Percent Coral Cover

Sand with Scattered Coral & Rock 0% ≤ 10% Dominant Type

Unknown 10% ≤ 50% Hard Coral

Other Delineations 50% ≤ 90% Soft Coral

Artificial 90% - 100%

Land N/A

Unknown Unknown

GEOMORPHOLOGICAL STRUCTURE

Table 2.1. The classifi cation scheme used to classify benthic habitats in the STEER in 2013 (Costa et al., 2013). 
p. 9 9Chapter 2: Benthic Habitat Mapping

STEER Integrated Environmental Assessment Report

1. Imagery Acquisition

Aerial photographs and LiDAR imagery were collected in 

2012 and 2011 (respectively) covering the full geographic 

extent of project area (Figure 2.2). These images were used 

to generate the benthic habitat map for STEER.

2. Habitat Boundary Delineation 

A semi-automated approach (Costa et al., 2009; Costa et 

al., 2012; Costa and Battista, 2013) was used to delineate 

habitat features visible in the aerial photographs and LiDAR imagery. In areas without LiDAR, habitat boundaries 

that were visible in the normalized aerial photos and whose 

area was ≥100 m2

 were manually delineated (at a scale of 

1:1,000). In areas with LiDAR, features were identifi ed and 

extracted habitat features on the seafl oor using the ENVI 

Feature Extraction (Fx) toolbox. This remote sensing software uses edge detection algorithms to detect and delineate 

seafl oor features visible in a single image or in a suite of 

spatially coincident images. This software defi nes a feature 

as a region of interest with unique spatial, spectral (brightness and color), and/or textural characteristics that make it 

visually distinct from its surroundings. 

3. Ground Validation (GV) and Habitat Classifi cation 

Ground validation is the process of collecting underwater 

photos and/or videos at discrete locations. GV sites are selected to explore habitats which were unknown, or to verify 

that habitat types look the same (in the source imagery) 

across the entire mapped area. Underwater video cameras 

were used to explore select habitat features delineated in 

step 2, and this video was used to classify each polygon 

and inform the draft habitat map creation. Areas without LiDAR were attributed manually. For the areas with LiDAR, 

classifi ed habitat maps were developed using features 

extracted and characterized by ENVI Fx and Random Forests in R, respectively. The two maps (i.e., one generated 

manually and the other using Fx and Random Forests) were 

then merged together to produce a fi nal, seamless map.

4. Expert Review 

Local marine biologists, scientists, resource managers 

and community groups reviewed these draft maps online 

to qualitatively assess the thematic accuracy of each map 

based on their local ecological knowledge.

5. Accuracy Assessment (AA) 

Underwater videos were collected (using a random stratifi ed sampling plan) to independently and quantitatively 

evaluate the accuracy of the habitat maps. Thematic accuracy was characterized for major and detailed geomorphological structure, major and detailed biological cover, percent 

hard bottom, percent coral cover and dominant coral type 

classifi cations using error matrices. Error matrices quantify 

the number of locations correctly classifi ed for each habitat 

class. These numbers were also corrected for proportional 

bias by accounting for the geographic area occupied by different habitat classes.

6. Final Product Creation

Errors identifi ed during the expert review and accuracy 

assessment were corrected to produce fi nal habitat maps 

for the STEER. Digital map products (i.e., benthic habitat 

map, imagery, GV and AA data) are available on the web 

(http://coastalscience.noaa.gov/projects/detail?key=171) 

and through an interactive, web-based GIS application 

(http://maps.coastalscience.noaa.gov/biomapper/biomapper.html?id=STEER). More details on the classifi cation 

scheme and each of these steps can be found in Costa et al., 

(2013). 

St. Thomas St. Thomas

STEER Boundary

0 m

40 m

STEER Boundary

High

Low

1 11

STEER Boundary

Habitat Map Boundary

Aerial Photos (Natural Color) LiDAR Depth (m) LiDAR Reflectivity (unitless)

St. Thomas

Figure 2.2. Aerial photos (left), LiDAR bathymetry (middle), and LiDAR refl ectivity (right) used to delineate and characterize the 

benthic habitats inside STEER (Costa et al., 2013).
p. 10 10 Chapter 2: Benthic Habitat Mapping

STEER Integrated Environmental Assessment Report

2.4. RESULTS AND DISCUSSION

The overall map accuracies (corrected for proportional 

bias) for this habitat map were 93.0% for major structure, 

75.1% for detailed structure, 86.2% for percent hardbottom, 

86.5% for major cover and 74.5% for detailed cover (Costa 

et al., 2013). The live coral and dominant coral type classes 

had 83.3% and 88.2% accuracies, respectively. These numbers are similar to the other benthic habitat maps created by 

NCCOS’s Biogeography Branch (Zitello et al., 2009; Bauer 

Study Area (km2) STEER (km2)

0% - <10% 18.408 7.196

10% - <30% 0.236 0.153

30% - <50% 0.186 0.115

50% - <70% 0.751 0.306

70% - <90% 1.461 0.835

90% - 100% 3.680 1.387

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100% Percent of Mapped Area 

Hard bottom 

Figure 2.4. Summary statistics describing the total amount of 

mapped area by percent hardbottom categories within the entire 

mapped area and for the portion within the STEER (adapted 

from Costa et al., 2013).

Study Area (km2) STEER (km2)

Artificial 0.041 0.032

Aggregate Reef 1.072 0.596

Aggregated Patch Reefs 0.400 0.282

Individual Patch Reef 0.061 0.045

Pavement 3.137 0.738

Pavement with Sand Channels 0.353 0.285

Reef Rubble 0.050 0.049

Rock/Boulder 1.074 0.644

Spur and Groove 0.167 0.159

Rhodoliths 8.365 0.111

Rhodoliths with Scattered Coral 0.777

Mud 1.159 1.035

Sand 7.620 5.771

Sand with Scattered Coral and Rock 0.487 0.278

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

Percent of Mapped Area 

Geomorphological 

Structure 

Unconsolidated 

Sediment 

Coral Reef and 

Hardbottom 

6.35 18.41 

2.83 

Other 

Delineations 

7.20 

Figure 2.5. Summary statistics describing the total amount of 

mapped area by major and detailed geomorphological structure 

within the entire mapped area and for the portion within the 

STEER (adapted from Costa et al., 2013).

Study Area (km2) STEER (km2)

Algae 10% - <50% 1.945 0.745

Algae 50% - <90% 6.162 1.398

Algae 90% - 100% 9.352 1.970

Live Coral 10% - <50% 0.005 0.001

Live Coral 50% - <90% 0.023

Mangrove 10% - <50% 0.014 0.014

Mangrove 50% - <90% 0.031 0.030

Mangrove 90% - 100% 0.570 0.517

No Cover 90% - 100% 0.031 0.030

Seagrass 10% - <50% 0.570 0.517

Seagrass 50% - <90% 1.497 0.964

Seagrass 90% - 100% 0.957 0.745

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

Percent of Mapped Area 

Detailed Biological 

Cover 

17.46 5.12 

4.35 4.11 0.56 

0.03 0.62 

Figure 2.6. Summary statistics describing the total amount of 

mapped area by major and detailed biological cover categories 

within the entire mapped area and for the portion within the 

STEER (adapted from Costa et al., 2013).

Figure 2.3. Summary statistics describing the total amount of 

mapped area by geographic zone within the entire mapped area 

and for the portion within the STEER (adapted from Costa et al., 

2013).

Study Area (km2) STEER (km2)

Back Reef 0.004 0.004

Bank/Shelf 21.733 7.867

Channel 0.001 0.001

Fore Reef 1.209 0.565

Lagoon 0.771 0.771

Reef Crest 0.026 0.026

Reef Flat 0.020 0.020

Salt Pond 0.126 0.065

Shoreline Intertidal 0.843 0.676

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100% Percent of Mapped Area 

Geographic Zone 
p. 11 11Chapter 2: Benthic Habitat Mapping

STEER Integrated Environmental Assessment Report

et al., 2012; Costa et al., 2012). As a result, these digital 

map products can be used with confi dence by scientists and 

resource managers for a multitude of different applications. 

The STEER benthic habitat map extends to the south and 

west of the STEER boundary. Summary statistics are presented here for both the entire mapped area and for mapped 

areas only within the STEER (Figures 2.3-2.7). 

The majority of mapped area (87.9%) was on the Bank/

Shelf (Figures 2.3 and 2.8), which extends offshore from 

the shoreline or seaward edge of a coral reef to the edge of 

the continental shelf. This pattern was also true within the 

STEER, but Bank/Shelf accounted for a slightly smaller 

percentage (78.7%). Lagoon and Shoreline Intertidal accounted for slightly higher percentages within the STEER 

compared to the overall study area. Geomorphological 

structure types (Figures 2.5 and 2.9) and the amount of 

hardbottom (Figures 2.4 and 2.10) were patchy across the 

total mapped area. Unconsolidated Sediment dominated 

the seafl oor overall (74.3%) and within STEER’s boundary (71.8%). Rhodoliths (i.e., calcareous nodules approximately 6 cm in diameter), and Sand were the two most 

common types of unconsolidated sediment, comprising 

33.8% and 30.8% of the total mapped area, respectively. 

However, while Rhodoliths dominated the area outside of 

the STEER’s boundary, Sand made up the majority of the 

area inside the MPA. Mud habitats made up a small amount 

(4.7%) of the total mapped area, and were located mainly 

in Mangrove Lagoon. Coral Reef and Hardbottom habitats 

constituted 25.5% of the total mapped area with Pavement 

(i.e., fl at, low-relief or sloping solid carbonate rock with 

little or no fi ne-scale rugosity), being the most dominant 

Study Area (km2) STEER (km2)

0% - <10%, N/A 23.534 9.559

10% - <50%, Hard Coral 0.221 0.131

50% - <90%, Hard Coral 0.811

10% - <50%, Soft Coral 0.010 0.295

50% - <90%, Soft Coral 0.146 0.009

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

Percent of Mapped Area 

Live Coral Cover 

& Dominant Type 

Figure 2.7. Summary statistics describing the total amount of 

mapped area by percent live coral and dominant coral cover 

types within the entire mapped area and for the portion within 

the STEER (adapted from Costa et al., 2013). 

2013 Benthic Habitat Map

Geographic Zone

Back Reef

Bank/Shelf

Channel

Dredged

Fore Reef

Lagoon

Land

Reef Crest

Reef Flat

Salt Pond

Shoreline Intertidal

STEER Boundary

0 1.5 3 0.75

Kilometers  ̄

Figure 2.8. Spatial extent of geographic zones in the STEER in the 2013 NOAA map (Costa et al., 2013).
p. 12 12 Chapter 2: Benthic Habitat Mapping

STEER Integrated Environmental Assessment Report

2013 Benthic Habitat Map

Percent Hardbottom

0% - <10%

10% - <30%

30% - <50%

50% - <70%

70% - <90%

90% - 100%

N/A

Unknown

STEER Boundary

0 1.5 3 0.75

Kilometers  ̄

Figure 2.10. Spatial extent of percent hardbottom categories in the STEER in the 2013 NOAA map (Costa et al., 2013).

2013 Benthic Habitat Map

Detailed Geomorphological Structure

Aggregate Reef

Aggregated Patch Reefs

Individual Patch Reef

Pavement

Pavement with Sand Channels

Reef Rubble

Rock/Boulder

Spur and Groove

Mud

Rhodoliths

Rhodoliths with Scattered Coral and Rock

Sand

Sand with Scattered Coral and Rock

Artificial

Land

Unknown

STEER Boundary

0 1.5 3 0.75

Kilometers  ̄

Figure 2.9. Spatial extent of major and detailed geomorphological structure types in the STEER in the 2013 NOAA map (Costa et al., 

2013).
p. 13 13Chapter 2: Benthic Habitat Mapping

STEER Integrated Environmental Assessment Report

2013 Benthic Habitat Map

Biological Cover

Algae, Patchy

Algae, Patchy

Algae, Continuous

Live Coral, Patchy

Live Coral, Patchy

Mangrove, Patchy

Mangrove, Patchy

Mangrove, Continuous

No Cover, Continuous

Seagrass, Patchy

Seagrass, Patchy

Seagrass, Continuous

Unclassified, N/A

Unknown

STEER Boundary

0 1.5 3 0.75

Kilometers  ̄

Figure 2.11. Spatial extent of major and detailed biological cover types in the STEER in the 2013 NOAA map (Costa et al., 2013).

2013 Benthic Habitat Map

Live Coral Cover

0% - <10%, N/A

10% - <50%, Hard Coral

50% - <90%, Hard Coral

10% - <50%, Soft Coral

50% - <90%, Soft Coral

Unknown

STEER Boundary

0 1.5 3 0.75

Kilometers  ̄

Figure 2.12. Spatial extent of percent live coral and dominant coral cover types in the STEER in the 2013 NOAA map (Costa et al., 

2013).
p. 14 14 Chapter 2: Benthic Habitat Mapping

STEER Integrated Environmental Assessment Report

(12.7%) structure type overall. Roughly 44% of this hardbottom habitat was inside the STEER’s boundaries, located 

mainly southeast of Long Point, south of Deck Point and 

surrounding the nearshore waters of Cabritta Point. These 

areas were dominated by Pavement, Rock/Boulder and 

Aggregate Reef (i.e., continuous, high-relief coral formation that occurs in various shapes and lacks sand channels) 

structure types, covering 7.4%, 6.4% and 5.9% of the area 

inside the STEER’s boundary, respectively. However, some 

of the largest and most continuous hardbottom features 

were located just outside of the MPA boundaries around 

Little St. James and Dog Islands. These areas were mainly 

comprised of Pavement features, although Aggregate Reefs 

were also present along the shoreline of both islands.

Biological cover differed greatly inside versus outside of 

the STEER’s boundary (Figures 2.6 and 2.11). Rhodolith 

habitats were dominated by Algae (39.2%), the majority 

of which was continuous (21.0%) covering 90-100% of a 

polygon. This cover type included various types of turf, 

fl eshy, coralline or fi lamentous species, which were found 

primarily in Mangrove Lagoon and outside of the STEER’s 

boundary. Hardbottom habitats inside and outside the 

STEER’s boundary were also colonized primarily by algae. 

Sand habitats were dominated by continuous (90% - 100%) 

seagrass beds, comprising about 5.4% of the total mapped 

area and 21.4% of the mapped area inside the STEER’s 

boundary. Continuous (90% - 100%) and patchy (50% - 

<90%) mangrove habitats constituted only 1.4% of the total 

mapped area, and were located mainly inside the STEER’s 

boundary in Mangrove Lagoon. For live coral, the majority 

(95.2%) of mapped area was colonized by 0% - <10% hard 

and soft corals (Figures 2.7 and 2.12). Areas with >10% 

live coral cover were rare (4.8%).

The new 2013 NOAA benthic habitat map differed from the 

2001 version in several ways. First, only aerial photos and 

satellite imagery were used to map habitats on the seafl oor 

in 2001, whereas both aerial photos and LiDAR imagery 

were collected and used to characterize benthic habitats in 

the 2013 map. Second, the 2013 map characterized more 

area than the previous map. For instance, parts of Benner Bay and an area between Cabrita Point and Great St. 

James Island had previously been classifi ed as “Unknown” 

(Figure 2.1). Third, the new map characterized benthic 

habitats at a higher spatial and thematic resolution than the 

previous map. It did so because it used: 1) a new classifi cation scheme with more classes, 2) a fi ner scale to delineate 

the boundaries of habitats, and 3) a smaller minimum 

mapping unit. These changes were made because a smaller 

geographic area was mapped using better quality source 

imagery. These different classifi cation schemes, delineation 

scales and minimum mapping units prohibit a quantitative 

comparison between the 2001 and 2013 benthic habitat 

Table 2.2. Qualitative comparison of the 2001 and 2013 benthic habitat maps in the STEER, using the modifi ed STEER boundary to 

include mangrove habitat in Mangrove Lagoon and Benner Bay.

2001 (4,046 m2 MMU) 2013 (100 m2 MMU) 2001 2013

Coral Reef and Hardbottom Coral Reef and Hardbottom 3.20 2.80

Unconsolidated Sediment Unconsolidated Sediment 6.12 7.20

Linear Reef Aggregate Reef 0.22 0.60

Patch Reef (Aggregated) Aggregated Patch Reefs 0.01 0.28

- Artificial -- 0.03

Patch Reef (Individual) Individual Patch Reef 0.05 0.05

Mud Mud 0.22 1.04

Colonized/Uncolonized Pavement Pavement 0.85 0.74

Colonized/Uncolonized Pavement with Sand Channels Pavement with Sand Channels 0.70 0.29

Reef Rubble Reef Rubble 0.09 0.05

- Rhodoliths -- 0.11

Colonized/Uncolonized Bedrock Rock/Boulder 1.07 0.64

Sand Sand 0.38 5.77

Sand with Scattered Coral and Rock Sand with Scattered Coral and Rock 0.09 0.28

Spur and Groove Reef Spur and Groove 0.12 0.16

Algal Dominated (on softbottom) Algae 0.05 4.11

- Live Coral -- 0.00

Mangrove Mangrove 0.48 0.56

- No Cover -- 0.96

Seagrass Seagrass 5.10 4.35

Class Names Area (km2

)

Major 

Structure

Detailed 

Structure

Major 

Cover
p. 15 15Chapter 2: Benthic Habitat Mapping

STEER Integrated Environmental Assessment Report

maps because coral reef habitat polygons and attributes 

(e.g., polygon area) are sensitive to the resolution at which 

they are mapped (Kendall and Miller, 2008). 

However, a broader qualitative comparison was conducted 

to highlight differences between benthic habitats maps 

within STEER (Table 2.2). For geomorphological structure, 

slightly less Coral Reef and Hardbottom was delineated in 

the 2001 map. This decrease in coral reef and hardbottom 

habitat was most likely due to the coarser scale at which 

features were delineated and the large areas on the seafl oor 

that were left uncharacterized. For major biological cover, 

a substantial amount of more algae was delineated in the 

2013 map as compared to the 2001 maps. This increase is 

most likely due to more seafl oor area being characterized 

in 2013, as well as to the inclusion of macro, crustose, turf 

and fi lamentous algae in the Algae class in the 2013 map. 

The 2001 map only included macroalgae on softbottom 

and ignored the other algal classes. Interestingly, more area 

dominated by seagrass was delineated in the 2001 map, 

than in the 2013 map. While this is likely partly due to the 

coarser MMU, areas of Mangrove Lagoon and Benner Bay 

that were previously classifi ed as seagrass in 2001 (Figure 

2.1) were mapped as algae in the most recent effort (Figure 

2.6) and may denote changes in seagrass distributions.

The fi nal deliverables for the 2013 NOAA mapping effort, 

which include the benthic habitat map, ground validation 

and accuracy assessment data, and associated aerial imagery, are available to the public: 1) on the web (https://

coastalscience.noaa.gov/projects/detail?key=171), 2) 

through an interactive, web-based map application (http://

maps.coastalscience.noaa.gov/biomapper/biomapper.

html?id=STEER), and 3) by request through the University 

of the Virgin Islands, Center for Marine and Environmental Studies. Potential uses for the STEER benthic habitat 

map include updating the management plan of the STEER, 

evaluating different zoning options for multiple use areas, 

evaluating the effi cacy of future management actions, and 

mapping ecosystem services and estimating economic 

value of goods and services across the seascape. Looking 

forward, these map applications may help scientists and 

managers to better understand the benthic communities, 

and their relationship with particular species and groups of 

species within the STEER. A better understanding of these 

ecological relationships is key to forecasting how the distribution of these benthic communities and their associated 

animals may change in the future.

LITERATURE CITED

Bauer, L.J., K. Edwards, K.K.W. Roberson, M.S. Kendall, 

S. Tormey and T.A. Battista. 2012. Shallow-Water Benthic 

Habitats of Southwest Puerto Rico. NOAA Technical Memorandum NOAA NOS NCCOS 155. Silver Spring, MD.

Costa, B.M., L.J. Bauer, T.A. Battista, P.W. Mueller and 

M.E. Monaco. 2009. Moderate-Depth Benthic Habitats of 

St. John, U.S. Virgin Islands. NOAA Technical Memorandum NOS NCCOS 105. Silver Spring, MD. 57 pp. 

Costa, B.M., S. Tormey and T.A. Battista. 2012. Benthic 

Habitats of Buck Island Reef National Monument. NOAA 

Technical Memorandum NOS NCCOS 142. Prepared by 

the NCCOS Center for Coastal Monitoring and Assessment 

Biogeography Branch. Silver Spring, MD. 64 pp.

Costa, B.M. and T. A. Battista (2013). The semi-automated 

classifi cation of acoustic imagery for characterizing coral 

reef ecosystems. International Journal of Remote Sensing.

DOI:10.1080/01431161.2013.800661

Costa, B.M., M.S. Kendall, K. Edwards, G. Kagesten and 

T.A. Battista. 2013. Benthic Habitats of Fish Bay, Coral 

Bay and the St. Thomas East End Reserve. NOAA Technical Memorandum NOS NCCOS 175. Prepared by the 

NCCOS Center for Coastal Monitoring and Assessment 

Biogeography Branch. Silver Spring, MD. 68 pp.

Kendall, M.S., C.R. Kruer, K.R. Buja, J.D. Christensen, M. 

Finkbeiner, R.A. Warner and M.E. Monaco. 2001. Methods 

Used to Map the Benthic Habitats of Puerto Rico and the 

U.S. Virgin Islands. NOAA Technical Memorandum NOS 

NCCOS CCMA 152. Silver Spring, MD.

Kendall, M.S. and T. Miller. 2008. The Infl uence of Thematic and Spatial Resolution on Maps of a Coral Reef 

Ecosystem. Marine Geodesy 31: 75-102.

STEER. 2011. St. Thomas East End Reserves Management Plan. Edited by J. Brown, A. Holecek, J. Murray, L. 

Noori, J.P. Oriol, J. Pierce, R. Platenberg, S. Romano, D. 

Russo, and C. Settar. 99pp.

Zitello, A.G., L.J. Bauer, T.A. Battista, P.W. Mueller, M.S. 

Kendall and M.E. Monaco. 2009. Shallow-Water Benthic 

Habitats of St. John, U.S. Virgin Islands. NOAA Technical 

Memorandum NOS NCCOS 96. Silver Spring, MD. 53 pp.
p. 16 16 Chapter 2: Benthic Habitat Mapping

STEER Integrated Environmental Assessment Report
Chapter 3: Fish Communities and Associated Benthic Habitats

17

STEER Integrated Environmental Assessment Report

3.1 INTRODUCTION

The objective of this chapter is to expand on previous 

knowledge to provide a spatially-comprehensive characterization of fi sh and benthic communities within the 

STEER. This comprehensive assessment of the fi sh and 

benthic communities will be used: 1) as an inventory of the 

current resources, 2) as a baseline from which to monitor 

the success rate of any future management actions, and 3) 

to inform management decisions for the STEER, such as 

the locations for restoration actions. Lastly, we compared 

results from STEER with other locations in the U.S. Caribbean.

CHAPTER 3: CHARACTERIZATION OF FISH COMMUNITIES AND ASSOCIATED BENTHIC HABITATS 

IN THE ST. THOMAS EAST END RESERVES

Laurie Bauer1,2, Jenny Vander Pluym3

, Chris Jeffrey1,2, Chris Caldow1, Amy V. Uhrin3

1

NOAA/NOS/National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment (CCMA), 

1305 East/West Highway, Silver Spring, MD 20910

2

CSS-Dynamac Consolidated Safety Services, Fairfax, VA 22030, under CSS-Dynamac Contract #EA-133C-14-NC-1384

3

Center for Coastal Fisheries and Habitat Research, National Centers for Coastal Ocean Science, National Ocean Service, 

National Oceanic and Atmospheric Administration

3.2 METHODS

Site Selection

Field surveys were conducted in June 2012 to characterize 

the fi sh communities and associated habitats in the STEER 

marine ecosystem. Sites were randomly selected within 

strata to ensure coverage of the entire study region (Figure 

3.1). NOAA’s existing benthic habitat map (Kendall et al., 

2001) was used as the basis for site stratifi cation. Although 

a newly updated benthic map was being produced (Costa 

et al., 2013) it was not yet completed at the time of this 

study. The strata that were chosen for this study included 

hardbottom, unconsolidated sediments, and mangrove. The 

Hardbottom comprised bedrock, pavement (i.e., fl at, lowHabitat strata

Coral Reef and Hardbottom

Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

June 2012 survey sites 012 0.5

Kilometers  ̄

Figure 3.1. Benthic habitat strata and site locations of the June 2012 survey of benthic habitat composition, fi sh communities, 

invertebrates, and marine debris. The boundaries of the St. Thomas East End Reserves (STEER) are shown for reference. 
Chapter 3: Fish Communities and Associated Benthic Habitats

18

STEER Integrated Environmental Assessment Report

relief hardbottom), rubble, and coral reef, while the Unconsolidated Sediments stratum comprised submerged aquatic 

vegetation (i.e., seagrass and macroalgae), as well as uncolonized sand and mud. The Mangrove stratum comprised the 

seaward edge of mangrove habitat able to be surveyed with 

these visual underwater survey methods. In addition, two 

hardbottom areas outside of STEER that were of interest to 

STEER’s Core Planning Group were included as a separate 

stratum (9 sites total). One of the “outside STEER” sites 

south of Little St. James was not part of the random selection but a targeted location. The site was chosen with input 

from The Nature Conservancy (TNC) during extra time at 

the end of the mission, due to interest in potential effects of 

island development on the surrounding marine ecosystem. 

Due to water quality concerns and low visibility, portions 

of Mangrove Lagoon and Benner Bay were excluded from 

the study area (Figure 3.1). In order to effectively survey 

fi sh using underwater visual methods, it is necessary that 

divers have a minimum of 2 meters visibility. Randomly 

selected alternate sites were available for each stratum if 

low visibility prevented a primary site from being surveyed. Surveys for two primary sites (both located south of 

Benner Bay) could not be completed because they did not 

meet the visibility requirements. In addition, extra precautions were taken in the area where the inter-island ferries 

traverse through STEER; while the majority of surveys in 

this high traffi c area were successfully completed, it was 

necessary to abort one site due to safety concerns. Surveys 

were completed at alternates sites for all low visibility and 

high traffi c sites that were aborted.

Field Methods

The surveys of benthic habitats, fi sh communities, marine 

debris and macroinvertebrates were conducted within a 

25x4 m transect (100 m2

), along a random heading. Two 

divers performed the survey at each site (Figure 3.2a,b). 

One diver (fi sh diver) was responsible for visual counts and 

size estimation of fi sh species. The second diver (habitat 

diver) quantifi ed benthic habitat composition, macroinvertebrates and marine debris. These methods have been 

used to monitor St. John, USVI and other locations within 

Figure 3.2. a) Diver collecting data on benthic habitat, b) diver collecting data on fi sh composition, and c) schematic representation 

of the placement of the 1m2

 quadrat along a 25 m transect tape during fi sh and benthic community surveys.

a) b)

c)
Chapter 3: Fish Communities and Associated Benthic Habitats

19

STEER Integrated Environmental Assessment Report

NOAA’s Caribbean Coral Reef Ecosystem Monitoring 

Project (CCREMP) (Pittman et al., 2008; Pittman et al., 

2010; Friedlander et al., 2013). The standardized protocols 

allow for comparisons to be made between different areas. 

In addition, the protocols include measurement of numerous variables that can be used to monitor and evaluate 

changes following the reduction in the input of land-based 

sources of pollution to the marine environment.

Fish Census

Fish surveys were conducted along the 25x4 m transect 

(100 m2

) using a fi xed survey duration (15 minutes) regardless of habitat type or complexity. The number of individuals per species was recorded in 5 cm size class increments 

up to 35 cm using visual estimation of fork length. If the 

individual could not be identifi ed to species, they were 

identifi ed to the extent possible (i.e., genus or family). 

Individuals greater than 35 cm were recorded as an estimate of the actual fork length to the nearest centimeter. At 

mangrove sites, the survey was conducted along the edge of 

the mangrove canopy. The transect was laid out as close to 

the prop roots and as far into the mangroves as possible, up 

to 2 m, and then out to the edge of the mangrove overhang 

such that the total area surveyed was still 100 m2

.

Benthic habitat composition

The habitat diver fi rst assigned an overall bottom type 

(i.e., hardbottom, unconsolidated sediments, or mangrove) 

to each transect based on in situ observation. Data on the 

percent cover of abiotic and biotic composition at each 

survey site were recorded within fi ve 1 m2

 quadrats placed 

randomly along the 25x4 m transect so that one quadrat fell 

within every 5 m interval along the transect. The quadrat 

was placed at each randomly chosen meter mark and systematically alternated from side to side along the transect 

tape (Figure 3.2c). Several variables were measured to 

characterize benthic composition and structure (Table 

3.1). The quadrat was divided into 100 smaller 10x10 cm 

squares with string (1 small square = 1% cover) to help the 

diver with estimation of percent cover. Percent cover was 

determined by looking at the quadrat from above and visually estimating per cent cover in a two dimensional plane. 

Information was recorded for the following variables:

Abiotic cover - the percent cover (to the nearest 1%) of four 

abiotic substrate categories (hardbottom, sand, rubble, and 

fi ne sediments/silt) was estimated within each 1 m2

 quadrat. 

The maximum vertical relief of the hardbottom was also 

measured. 

Biotic cover - the percent cover (to the nearest 0.1%) of algae, seagrass, live corals, sponges, gorgonians (also known 

as “soft” corals), and other biota was estimated within each 

1 m2

 quadrat. Taxa were identifi ed to the following levels: 

stony coral (species), seagrass (species), algae (morphological group), sponge (morphological group), and gorgonians (morphological group) (Table 3.1). For stony and 

fi re corals, the percentage of bleached coral and diseased/

dead coral was estimated to the nearest 0.1 percent. In addition, the presence of Acropora palmata or A. cervicornis 

either within the transect area (100 m2

) or the vicinity of the 

sample site was also noted by the divers. 

Maximum canopy height - the maximum height of sponges, 

gorgonians, and soft algal groups was recorded to the nearest 1 cm in each quadrat. 

Number of individuals - the number of individual upright 

sponges, gorgonians, non-encrusting anemones, and nonencrusting hydroids was recorded in each quadrat. 

Benthic Variables

Measurements

Cover 

(%)

Height 

(cm)

Abundance 

(#)

Abiotic

Hardbottom X X

Sand X

Rubble X

Fine sediment/silt X

Rugosity

Water depth

Biotic

Corals (by species) X

Algae

Macroalgae X X

Turf Algae X

Crustose/coralline algae (CCA) X

Filamentous algae/cyanobacteria X X

Seagrass (by species) X X

Gorgonians

Sea rods, whips and plumes XX X

Sea fans XX X

Encrusting form X

Sponges

Barrel, tubes, rope, vase XX X

Encrusting form X

Other benthic macrofauna

Anemones and hydroids X X

Tunicates and zoanthids X

Mangroves

Prop roots X

Prop roots colonized by algae X

Prop roots colonized by sponges X

Prop roots colonized by other biota X

Table 3.1. Abiotic and biotic variables measured in fi ve quadrats 

along fi sh transects.
Chapter 3: Fish Communities and Associated Benthic Habitats

20

STEER Integrated Environmental Assessment Report

Rugosity – for hardbottom sites, rugosity was measured 

by placing a 6 m chain at two randomly selected positions, 

ensuring no overlap, along the 25 m belt transect. The 

chain was positioned along the centerline of the transect 

such that it followed the substrate’s relief. The straight-line 

horizontal distance covered by the chain was measured. An 

index of rugosity (R) was calculated as the ratio of contoured surface distance (d) to linear distance (L = 6m) using 

R=1−d/L. Rugosity is unitless and can range from zero (no 

relief) to one.

Mangrove habitat data – For surveys conducted in mangrove habitat, all of the habitat variables were collected 

along with additional data, including: number of prop roots, 

number of prop roots colonized by algae, number of prop 

roots colonized by sponges and number of prop roots colonized by other biota (tunicates, anemones, zooanthids, etc).

Macroinvertebrate counts - The habitat diver counted the 

abundance of spiny lobsters (Panulirus argus), long-spined 

urchins (Diadema antillarum), and the abundance and 

sexual maturity of queen conchs (Lobatus gigas) within the 

25x4 m transect at each site. The maturity of each conch 

was determined by the absence (immature) or presence 

(mature) of a fl ared lip.

Marine debris

The number and type of marine debris within the 25x4 m 

transect were recorded. Marine debris size and the area of 

habitat it affected were estimated. Any fl ora or fauna that 

were colonizing the debris item were noted. 

Data Analysis

Benthic Habitat

While many benthic variables were measured during the 

surveys, data analyses for this report focused primarily on describing differences among major habitat types 

and broad-scale spatial patterns in the percent cover of 

the sessile biotic components as described in Table 3.1. 

Quadrat measurements along each transect were averaged 

and cumulative coral species richness (the total number of 

species present was calculated for each site. Average site 

values were used to calculate means and standard errors 

of measured variables for each habitat strata (mangrove, 

unconsolidated sediments, hardbottom inside STEER, hardbottom outside STEER). In addition, data were plotted in 

a geographic information system (ArcGIS v10.1, ESRI) to 

examine broad spatial patterns in the benthic cover variables. 

Fish

Several fi sh metrics were summarized by stratum (mangrove, unconsolidated sediments, hardbottom inside 

STEER, hardbottom outside STEER). Strata-wide means 

and standard errors (SE) were estimated for biological 

community metrics (total density, total biomass, species 

richness, Shannon diversity, and density and biomass of 

trophic groups). Means and SE calculations were computed 

employing methods described by Cochran (1977) in the statistical analysis software, SAS v9.3 (Proc Survey means). 

Trophic groups surveyed included piscivores, herbivores, 

invertivores, and zooplanktivores and were defi ned for each 

species based on diet information from Randall (1967). It is 

important to note that these groups are not mutually exclusive because many fi sh species can be classifi ed into two or 

more of these groups based on diet. In those circumstances 

the trophic group was assigned based on the dominant 

diet component. Biomass was calculated using published 

length-weight relationships based on the allometric scaling 

law, 

W = aLb 

where L is length in centimeters and W is weight in grams, 

a is a condition factor related to body from, and b is the 

scaling exponent indicating either isometric or allometric 

growth. The midpoint of each size class was used for L 

values up to 35 cm, and the actual length was used for fi sh 

>35 cm. For fi sh in the 0-5 cm size class, 3 cm was used as 

the mid-point because we do not typically observe fi sh <1 

cm. Values for a and b by species were obtained from FishBase (Froese and Pauly, 2008). Biomass for species with no 

published length-weight relationships was calculated using 

terms for the closest congener with most similar morphology. 

Species diversity was calculated using the Shannon Index 

(H’), a measure that incorporates both richness and evenness (relative abundances):

H’ = Σpi(logpi)

where pi is the relative abundance of each species. H’ increases as both the richness and evenness of the community 

increase. Typical values for H’ range from 1.5 – 3.5 and 

rarely exceed 4.

Data were plotted in ArcGIS to examine broad spatial 

patterns in the fi sh metrics. In addition, select families 

and species of commercial and/or ecological interest were 

selected for further examination. For each species/family, a summary of the species distribution, size frequency, 

and mean density and biomass by habitat type and study 

area was calculated. Age class (juveniles/sub-adults and 

adult) was identifi ed based on mean length at maturity 

as identifi ed by FishBase (Froese and Pauly, 2008) and 
Chapter 3: Fish Communities and Associated Benthic Habitats

21

STEER Integrated Environmental Assessment Report

García-Cagide et al. (1994). Where length at maturity was 

unknown, 1/3 of maximum size was used as a proxy as in 

Pittman et al. (2008, 2010). Percent occurrence, mean density and biomass (per 100 m2

) and corresponding SE were 

calculated for each species across the sites within STEER. 

This information was used to create a summary table of all 

species observed in this characterization across the STEER 

sampling domain (Appendix 1 in Bauer et al., 2014), as 

well as the hardbottom sites outside STEER (Appendix 2 in 

Bauer et al., 2014). 

Differences and similarities in species composition were 

further examined using multivariate statistical techniques 

(Primer v.6, Clarke and Warwick, 2001). Density and 

biomass data were square-root transformed prior to analysis. Data were arranged in a species density/biomass by 

site data matrix, which was used to construct a triangular 

matrix of the percentage similarity in community composition between all pairs of sites using the Bray-Curtis 

Coeffi cient. The coeffi cient is a measure of how similar 

samples were to each other, ranging from 0% (complete 

dissimilarity) to 100% (complete similarity). Next, nonmetric multidimensional scaling (nMDS) was used to place 

samples in a two-dimensional confi guration such that the 

rank order of the distances between the samples agreed 

with the rank-order of the similarities from the Bray-Curtis 

matrix. Sites were coded by bottom type and management 

(Inside/Outside STEER) for examination of visual patterns 

of between site similarity. These factors were also used to 

test for signifi cant differences in similarity using Analysis 

of Similarities (ANOSIM), a multivariate, non-parametric 

version of ANOVA. Outputs of the ANOSIM test include 

an R statistic and p-value. R is a difference of average rank 

dissimilarities between and within groups, scaled so that R 

ranges between 0 (no differences) and 1 (perfect division), 

while the p-value gives the statistical signifi cance for a test 

of R = 0. Signifi cant differences in fi sh community structure were examined with the similarity percentages (SIMPER) routine to identify those species that contributed most 

to the observed dissimilarity.

To see how fi sh communities in STEER compare with 

other parts of the U.S. Caribbean, key fi sh community 

metrics (species richness, total biomass, and biomass of 

groupers, snappers, grunts, and parrotfi sh) were compared 

with other locations within NOAA’s Caribbean Coral Reef 

Ecosystem Monitoring Project (http://www8.nos.noaa.

gov/biogeo_public/query_main.aspx), including St. John 

(2011), Eastern St. Croix (2010), which includes the Buck 

Island Reef National Monument and East End Marine 

Park, and Southwest Puerto Rico, including La Parguera/

Guanica (2012). Mangrove strata comparisons could only 

be made with SW Puerto Rico. Sites on the mid-shelf reef 

in St. John were removed from the analysis to allow for a 

more equitable depth comparison with STEER. A ShapiroWilks test and visual examination of the data were used to 

assess normality, and as data were non-normally distributed, nonparametric Wilcoxon tests and the corresponding 

non-parametric Dunn’s multiple comparisons tests (Zar, 

1999) were used to test for differences among regions (JMP 

v11.0). Means and standard errors of these metrics were 

also plotted for visualization.

3.3 RESULTS AND DISCUSSION

A total of 80 sites were surveyed during the two-week 

fi eld mission: 26 on unconsolidated sediments, 10 along 

the mangrove fringes, 35 on hardbottom within STEER, 

and nine on hardbottom outside STEER boundaries. Two 

sites within the hardbottom stratum were identifi ed as soft 

bottom habitat by the survey divers and were subsequently 

grouped with the unconsolidated sediment surveys for 

analysis. Conversely, one site within the unconsolidated 

sediment stratum was classifi ed as hardbottom during the 

survey and subsequently included with the hardbottom 

surveys for analysis.

Benthic Habitat

Abiotic composition

Not surprisingly, hardbottom substrate dominated sites 

within the hardbottom strata with minor components of 

rubble and sand. No fi ne sediment was observed along 

transects conducted at these sites (Figure 3.3a). In contrast, soft bottom sites were primarily composed of sandy 

bottom with some fi ne sediment and rubble (Figure 3.3b). 

A school of snapper swim below an undercut mangrove stand 

near the false entrance to Mangrove Lagoon.
Chapter 3: Fish Communities and Associated Benthic Habitats

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The predominance of sand over fi ne sediments may be 

attributable to several factors including bottom currents, 

and the proximity of hardbottom habitats to the unconsolidated sediment survey locations. Portions of Benner Bay 

and Mangrove Lagoon that were excluded from the survey 

are bordered by vegetated coastline and dominated by fi ne 

sediment. Mangrove sites were characterized with fi ne 

sediments and sandy bottom (Figure 3.3c).

Biotic Composition Overview 

Turf algae dominated the biotic composition of hardbottom sites with a mean (±SE) percent cover of 51.8 ± 4.5% 

inside/41.9 ± 10.1% outside, followed by macroalgae (14.9 

± 2.8% inside/14.1 ± 5.3% outside), hard (scleractinian) 

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Hardbottom Rubble Sand Fine sediment

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b) Unconsolidated Sediments 

Figure 3.3. Mean (±SE) percent cover of abiotic substrate by 

bottom type: a) hardbottom inside (N=35) and outside (N=9) 

the STEER boundaries, b) softbottom (N=26), and c) mangrove 

(N=10).

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Figure 3.4. Mean (±SE) percent cover of major cover groups by 

bottom type: a) hardbottom sites inside (N=35) and outside (N=9) 

the STEER boundaries, b) softbottom (N=26), and c) mangrove 

(N=10). FA & CB = fi lamentous algae and cyanobacteria.
Chapter 3: Fish Communities and Associated Benthic Habitats

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corals (5.2 ± 0.8% inside/5.2 ± 1.8% outside), sponges (4.8 

± 1.8% inside/4.6 ± 1.1% outside), cyanobacteria & fi lamentous algae (2.1 ± 0.2% inside/1.8 ± 0.1% outside), and 

gorgonians (1.3 ± 0.5% inside/2.9 ± 1.3% outside, Figure 

3.4a). Other types of biotic cover were documented in small 

amounts: fi re coral (Millepora spp.) (0.6 ± 0.2% inside/0.3 

± 0.1% outside), zoanthids (0.07 ± 0.02% inside/0.1 ± 0.1% 

outside), seagrass (0.06 ± 0.05% inside/0 outside), and 

tunicates (0 inside/0.008 ± 0.008% outside). Bare, uncolonized substrate averaged 19.1 ± 3.7% inside/30.4 ± 11% 

outside. Rugosity ranged from 0.02 to 0.41 and averaged 

0.17 ± 0.04% inside/0.15 ± 0.04% outside (Figure 3.5). 

The second highest rugosity (0.37) was recorded at a site 

in the southwestern portion of the study area, outside the 

STEER boundaries. 

Unconsolidated sediment site assemblages were composed 

of mostly seagrass (31.4 ± 5.9%) and macroalgae (17.9 

± 5.1%, Figure 3.4b). Minor components of the benthic 

community include: turf algae (0.5 ± 0.4%), sponge (0.25 ± 

0.11%), cyanobacteria & fi lamentous algae (0.23 ± 0.23%), 

hard corals (0.04 ± 0.02%), tunicates (0.009 ± 0.007%), and 

zoanthids (0.007 ± 0.007%). Bare substrate averaged 49.6 

(± 5.9%) which is over twice the mean at hardbottom sites.

Substrate found at mangrove sites was mostly bare, unconsolidated sediment (77.71 ± 6.30 %). The benthic community at these sites was comprised of macroalgae (13.9 ± 

5.1%) and seagrass (8.4 ± 3.9%, Figure 3.4c). Other algae 

types (turf algae, cyanobacteria and fi lamentous algae) 

were largely absent from the benthic substrate in mangrove 

habitats. Number of prop roots per 1 m2

 ranged from 8-50 

roots /m2 and averaged 20 (±4.0) across all mangrove sites. 

Almost 100% of prop roots had algae growing on them 

(99.9%) with sponges and other invertebrates (tunicates, 

anemones, and zoanthids) occurring on 28% and 47.4% of 

the prop roots, respectively (Figure 3.6).

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Rugosity

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Figure 3.5. Mean rugosity (hardbottom sites only).

Figure 3.6. Mangrove prop roots colonized with algae and 

benthic fauna.
Chapter 3: Fish Communities and Associated Benthic Habitats

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Excluded from survey

Live Coral Cover (%)

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Figure 3.7. Percent live cover of hard corals.

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Excluded from survey

Coral species richness

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012 0.5

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Figure 3.8. Hard coral species richness.
Chapter 3: Fish Communities and Associated Benthic Habitats

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Hard Coral Composition

Live scleractinian coral cover ranged from 0% in mangrove 

and soft bottom habitats to 0.08-29% cover in hardbottom 

sites (Figure 3.7). The greatest coverage of hard corals was 

found on a reef tract that runs from Long Point to just east 

of Cas Cay, located in the southwest corner of the STEER. 

The STEER boundary passes through the middle of the reef 

tract so that only half of the ecosystem falls under any management plan. Three of the four sites with the highest coral 

cover (11-29%) are in this reef tract with two sites (16.8% 

and 11%) located outside the STEER boundary. The top 

six sites for coral cover (7.6-29%) are all in open water 

conditions in the southern region of the STEER and further 

from land features. Overall, coral cover was still low with 

an average of 5.2 ± 0.8% and 5.2 ± 1.8% on hardbottom 

habitats inside and outside STEER, respectively.

Hard coral species richness ranged from 0-14 at individual 

sites with an average of 7.2 ± 0.4 inside and 6.9 ± 1.2% 

outside (Figure 3.8). Unlike percent cover, species richness 

did not refl ect any small scale regional patterns, and it does 

not appear to correlate with percent cover. The fi ve sites 

with highest richness are evenly distributed throughout 

hardbottom habitats inside and outside of STEER: two are 

adjacent to consolidated reef on the shoreline, two are open 

water hardbottom, and one is outside the STEER boundaries on a large reef tract. 

A total of 26 hard coral species were documented, with 25 

of those species recorded at sites inside STEER. Porites astreoides (mustard hill coral) was the most abundant species, 

followed by Orbicella annularis complex (boulder star 

0

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2.5

3

Percent Cover

Inside

Outside

Figure 3.9. a) Mean (±SE) percent cover of hard corals by species at hardbottom sites (N=44). b) From left to right: common star coral, 

grooved brain coral, mustard hill coral, and pillar coral.

a)

b)
Chapter 3: Fish Communities and Associated Benthic Habitats

26

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coral), Siderastrea radians (lesser starlet coral), Diploria 

strigosa (symmetrical brain coral), Siderastrea siderea

(massive starlet coral), and P. porites (fi nger coral) (Figure 

3.9). Outside the STEER boundaries 19 species were recorded with the most abundant species being M. annularis

complex followed by P. astreoides, S. siderea, P. porites, 

and S. radians.

Acropora cervicornis (staghorn coral), a species listed as 

threatened under the Endangered Species Act (ESA), was 

documented at three sites dispersed around the STEER and 

Dendrogyra cylindrus (pillar coral), a species of concern 

listed as threatened under the ESA, was recorded at two 

locations, both of which are on hardbottom close to the 

shoreline (Figure 3.10). One of the sites with A. cervicornis is located just inside the reserve on the reef tract 

bisected by the STEER boundary. This specifi c reef tract is 

also home to three sites out of the top four with the greatest 

overall hard coral cover (Figure 3.7). 

The low coral cover observed in STEER refl ects the record 

declines of coral reefs in the USVI and the Caribbean as 

a whole (Wilkinson, 2000; Catanzaro et al., 2002; Jeffrey 

et al., 2005; Rogers et al., 2008). Rogers et al. (2008) 

reported that some reefs in the USVI had over 40% coral 

cover during the 1980s but was subsequently reduced 

to 25% cover by the 1990s, with hurricane damage and 

disease cited as the main causative factors. Additional 

stressors contributing to decline in coral cover include 

sediment input from increased development (MacDonald et 

al., 1997; Brooks et al., 2007), associated nutrient enrichment (Fabricius, 2005) and land-based sources of pollution 

(Warne et al., 2005). Additionally, climate change poses a 

broader regional threat to corals (Donner et al., 2007). The 

mass bleaching event in 2005 followed by a coral disease 

outbreak (Bruno et al., 2007) caused a 60% decline in coral 

cover in the USVI (Miller et al., 2009). 

The 2005 bleaching event was captured by multiple monitoring programs around the Caribbean. Each region in the 

USVI being monitored had low coral cover across reef 

types and years (Rothensberger et al., 2008), with each 

island’s reefs exhibiting the trend of decline (Rogers et al., 

2008). In St. Croix, weighted mean estimates of live coral 

decreased from 8.0% in February 2001 to 2.9% in October 

2006, similar to reefs in St. John which were 8.4% in 2001 

and declined to 4.5% by July of 2006 (Rogers et al., 2008). 

Friedlander et al. (2013) reported that coral cover has continued to decline in St. John to less than 3% regardless of 

protective status as of 2009. 

Figure 3.10. Percent cover of coral species listed as threatened under the Endangered Species Act (ESA) or proposed for future listing. The sizes of the pies are scaled by the total percent cover of the six species at that site.

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STEER boundary

Excluded from survey

Total ESA Species Cover (%)

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Acropora cervicornis

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Montastraea annularis complex

D All ESA species absent

012 0.5

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Chapter 3: Fish Communities and Associated Benthic Habitats

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STEER Integrated Environmental Assessment Report

The Territorial Coral Reef Monitoring Program (TCRMP), 

which began in 2001, uses digital video transects to estimate benthic cover of hardbottom habitats at 33 long-term 

monitoring sites in the USVI, including 16 locations around 

St. Thomas (Smith et al., 2011). This effort includes nearshore, midshelf, and outershelf reef systems in an effort to 

capture the diversity of reef types in the USVI. Mean live 

coral cover for all nearshore reefs in St. Thomas declined 

from 20.3% in 2002 to 9.3% in 2007 after the bleaching 

event and subsequent disease outbreak. This is the lowest 

average cover observed since the monitoring began in 2001 

(unpublished data, Smith pers. comm). Since 2007, percent 

coral cover has made a comeback across all nearshore sites 

with a mean of 14.4% in 2013 (T. Smith, UVI, unpublished 

data).

Coral cover in STEER falls in line with values from similar 

studies and surveys conducted in St. Croix and St. John 

(Pittman et al., 2008, Friedlander et al., 2013), but were 

much lower than the data reported by TCRMP. For 

example, the only TCRMP site within STEER, at Coculus 

Rock, is reported to have over twice the coral cover than 

two randomly selected sites in the current study that were 

located within 300 m of the TCRMP site and at similar 

depths (11.5% TCRMP, 3.88% & 4.6% this study). Differences of overall coral cover across sites were most likely 

attributable to sample size within STEER, the focus of this 

study in the shallow waters of STEER (35% of NOAA sites 

were <5m; 100% of TCRMP were >5m), differences in 

how sites were selected, and the distinct estimation methods. The higher overall values at TCRMP sites do call 

attention to other nearshore reefs around St. Thomas that 

should be considered for protection (Smith et al., 2011). 

This may also refl ect deeper reefs being less susceptible to 

bleaching (Sheppard, 2006; T. Smith, UVI, pers comm.) 

and subsequent disease outbreaks and therefore maintain 

higher coral cover overall.

Coral community structure inside and around STEER is 

similar to that of nearshore reefs around St. John (Friedlander et al., 2013), St. Croix (Pittman et al., 2008), and 

Puerto Rico (Bauer et al., 2013). Our study sites also 

refl ect the species composition documented by TCRMP in 

STEER and around St. Thomas (Smith et al., 2011). The 

majority of reefs in the USVI have become dominated by 

Montastraea, Porites, Siderastrea, and Diploria genera 

(Jeffrey et al., 2005; Herzlieb et al., 2005; Rogers et al., 

2008), particularly after the decades long decimation of 

acroporids due to white band disease, hurricanes (Rogers et al., 1982), and bleaching events (Miller et al., 2006; 

Rogers et al., 2008). ESA-listed species were infrequently 

observed in the 2012 fi eld survey. Elkhorn coral (Acropora 

palmata), was documented at three sites in STEER during 

this study and ranged from 0.2% to 2.6 coverage. StagD

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Gorgonian Cover (%)

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Figure 3.11. Percent gorgonian cover.
Chapter 3: Fish Communities and Associated Benthic Habitats

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STEER Integrated Environmental Assessment Report

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Figure 3.12. Percent sponge cover.

horn coral (A. cervicornis) was not recorded in any survey 

quadrats, but was observed at one shallow site east of Great 

St. James Island.

Gorgonian Composition

Gorgonian cover ranged from 0-18.4% and primarily occurred on hardbottom habitat (Figure 3.11). Sites with the 

highest percent cover (7.44-18.4%) are all exposed to open 

ocean conditions. Each of the high cover sites are located 

in different quadrants of STEER: one is on the Long Point 

reef tract in the southwest corner, one is located outside the 

southeast corner of STEER Oceanside of Little St. James, 

and the other is outside the northeast corner of STEER on 

the eastern shoreline of St. James. This pattern is not surprising as all three of these sites are exposed to high wave 

action characteristic of open ocean and prevailing on-shore 

wind patterns, conditions in which gorgonian communities 

tend to thrive. Average gorgonian cover on hardbottom inside STEER was relatively low (0.9 ± 0.3%) and consisted 

of sea plumes/rods/whips (0.49 ± 0.14%), sea fans (0.36 ± 

0.19%), and encrusting gorgonians (0.05 ± 0.02).

Sponge Composition

Sponge cover ranged from 0-64.6% and averaged 2.71 ± 

0.84% across all sites (Figure 3.12). There was no distinctive spatial pattern exhibited by sponge communities—

sites with greater than average coverage are distributed 

on hardbottom habitats throughout STEER and outside 

the reserve. Inside STEER, mean percent cover differed 

greatly between hardbottom (4.82 ± 1.8%) and unconsolidated sediments (0.25 ± 0.11%) habitats. Barrel/tube/vase 

(BTV) sponges accounted for the majority of percent cover 

overall (3.44 ± 1.48%), while encrusting sponge comprised 

a smaller portion of the sponge community (1.38 ± 0.36%). 

On the nine hardbottom sites surveyed outside STEER, 

mean percent cover was similar to inside: overall sponge 

(4.59 ± 1.1%), BTV sponges (2.72 ± 0.82%), and encrusting sponge (1.86 ± 0.43%).

Algae and Seagrass Composition 

Macroalgal cover ranged from 0-100% and was found 

throughout the STEER. Means were similar across bottom 

types: hardbottom (14.77 ± 2.44%), unconsolidated sediments (17.99 ± 5.14%), and mangrove sites (13.94 ± 5.1%, 

Figure 3.13). Percent cover across STEER averaged 15.71 

± 2.21%. The two sites with the highest cover (90-100%) 

were located in soft bottom habitat near the Mangrove Lagoon. Turf algae ranged widely across STEER (0-91.56%) 

with an overall average cover of 27.53 ± 3.57% but was 

seen almost exclusively on hardbottom habitats (49.78 ± 

4.11%, Figure 3.14). Cyanobacteria and fi lamentous algae 

(CB & FA) was documented at only 17 out of the 80 sites 
Chapter 3: Fish Communities and Associated Benthic Habitats

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STEER boundary

Excluded from survey

Macroalgae Cover (%)

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Figure 3.13. Percent macroalgae cover.

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Excluded from survey

Turf Algae Cover (%)

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0.1 - 10

10.1 - 25

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Figure 3.14. Percent turf algae cover.
Chapter 3: Fish Communities and Associated Benthic Habitats

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Excluded from survey

FA & CB Cover (%)

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Figure 3.15. Percent fi lamentous algae and cyanobacteria (FA & CB) cover.

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Seagrass Cover (%)

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Figure 3.16. Percent seagrass cover.
Chapter 3: Fish Communities and Associated Benthic Habitats

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STEER Integrated Environmental Assessment Report

surveyed with an overall average of 0.99 ± 0.77% found 

almost exclusively on hardbottom habitats (Figure 3.15).

Seagrass was observed on unconsolidated sediments and 

mangrove areas, as well as some sand gaps interspersed 

among hardbottom habitats. Percent cover varied from 

0-99% (Figure 3.16). The absence of seagrass at only four 

of the 26 soft sediment sites is more informative than the 

pattern of seagrass presence: two sites devoid of seagrass 

border Mangrove lagoon and the other two sites are located 

in a channel through mangrove habitat that is near the Bovoni landfi ll. All four sites are documented as having only 

macroalgal cover: the two near the lagoon with macroalgal 

cover of 90% and 100%, the other two near the landfi ll had 

32% and 46%. The majority of seagrass was recorded in 

unconsolidated sediment habitats: Syringodium fi liforme 

(18.14 ± 4.76%) and Thalassia testudinum (13.04 ± 3.98%) 

were the most common species recorded with a very small 

amount of Halodule wrightii (0.21 ± 0.12, Figure 3.17). 

All three species were found on unconsolidated sediments, 

Halodule and Thalassia were both seen in mangrove habitats, and a minor amount of Thalassia was documented at 

hardbottom habitats. 

Macroinvertebrates

A total of seven spiny lobsters (Panulirus argus) were 

observed at three sites during the 80 surveys. Five lobsters 

were documented in a mangrove fringe near Mangrove 

Lagoon, one lobster was spotted outside the STEER along 

the reef tract located in the southwest region of the STEER, 

and one lobster was seen on hardbottom near Little St. 

James in the southeast corner of the reserve. 

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Syringodium filiforme Thalassia testudinum Halodule wrightii

Percent Cover 

Figure 3.17. Percent cover of seagrass by species on unconsolidated 

sediments.

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Longspined Sea Urchin Density (100 m2)

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Figure 3.18. Density of longspined sea urchin (Diadema antillarum).
Chapter 3: Fish Communities and Associated Benthic Habitats

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Habitat strata

Coral Reef and Hardbottom

Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Conch density ( 100 m2)

Mature conch

D 0

1 - 5

6 - 7

 

Immature conch

D 0

1 - 5

6 - 10

11 - 25

26 - 99

012 0.5

Kilometers  ̄

Figure 3.19. Density of mature and immature queen conch (Lobatus gigas).

Figure 3.20. Density of total observed marine debris.

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Coral Reef and Hardbottom

Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Marine debris density ( 100 m2)

D 0

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012 0.5

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Chapter 3: Fish Communities and Associated Benthic Habitats

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Long-spined urchin (Diadema antillarum) was reported 

at 9 sites, all hardbottom substrates, ranging from 2 to an 

impressive 139 individuals (Figure 3.18). The top three 

sites for urchin abundance making up 86.5% of the urchins 

documented (16-139 / 100m2

) are all located on land adjacent sites in Cowpet Bay.

Immature queen conch (Lobatus gigas) were documented 

at 13 sites (7 unconsolidated sediments, 4 hardbottom, 2 

mangrove, Figure 3.19) throughout the STEER and at one 

site outside the boundaries. Abundance ranged from 1-99 

individuals and showed no distinct spatial pattern. Mature queen conch were observed in much lower numbers 

(0-7 individuals, Figure 3.19) at 11 sites (6 soft bottom, 3 

hardbottom, 2 mangrove) dispersed around and outside the 

reserve. Mature conch were observed primarily at sites 

where immature conch were also present. 

Marine Debris

Marine debris was detected at 16 sites in all three bottom 

types (Table 3.2). Debris items were found primarily close 

to shore or in the southern part of Benner Bay (Figure 

3.20). Types of gear varied from minor fi shing leader wire 

to general trash items such as bottles and plastic bags.

Fish

Community metrics

The fi sh community observed in the 2012 survey consisted 

of 36 taxonomic families and 125 species within STEER 

(Appendix 1 in Bauer et al., 2014). An additional two 

families, represented by six species, were observed at the 

sites located in adjacent hardbottom areas outside STEER. 

Fish species richness ranged from 1 to 39 species per site 

(100 m2

). Mean richness was highest on hardbottom, with 

similar levels inside and outside STEER, followed by 

mangrove (Figure 3.21b, Figure 3.22). The two surveys 

with 39 observed species were conducted on hardbottom 

near Cow and Calf Rocks and on reef outside STEER south 

of Patricia Cay, respectively. Shannon diversity, which is a 

product of richness and evenness, followed similar trends, 

with highest diversity on hardbottom and intermediate 

levels in mangrove (Figure 3.21a, Figure 3.23). Unconsolidated sediments were typifi ed by lower species richness 

and diversity. 

Mangrove sites exhibited the highest mean total fi sh density 

(Figure 3.21c, Figure 3.24), whereas mean levels of biomass were highest on hardbottom (Figure 3.21d, Figure 

3.25). At many mangrove locations, the high density levels 

were largely due to the presence of schooling silversides 

and herring (Families Atherinidae and Clupeidae) and small 

juvenile grunts (Family Haemulidae). The hardbottom site 

with the highest density, located in Great Bay, was dominated by small gobies. Locations with both high density 

and biomass included sites on hardbottom adjacent to Cow 

and Calf Rocks, a patch reef southwest of Great St. James 

Island, a mangrove site near the false entrance to Mangrove 

Lagoon, and on the reef complex south of Patricia Cay, 

outside the STEER boundary. The survey with the third 

greatest biomass, located on a nearshore reef in Nazareth 

Bay, was characterized by the presence of several largebodied parrotfi sh. Lowest density and biomass was typically observed on unconsolidated sediments, particularly at 

unvegetated sites. 

Biomass and abundance were unevenly distributed among 

trophic groups (Figure 3.26). On all habitats, invertivores 

(I, e.g., grunts, butterfl y fi shes) and herbivores (H; e.g., 

parrotfi sh, damselfi sh) were the most numerically abundant, 

while piscivores (P; e.g., snappers, groupers) constituted a 

smaller percentage. Planktivores (PL; e.g., herring) accounted for over 20% of the abundance in mangroves, but 

due to their small size only 1% of the biomass. Conversely, 

piscivores accounted for higher proportional biomass 

across all habitats, particularly on unconsolidated sediments 

where the trophic group accounted for three-quarters of the 

observed biomass, largely due to the presence of several 

jacks and occasional barracuda. 

Highest mean density and biomass of piscivores occurred 

in mangrove surveys, although biomass was more equitable 

across bottom types. Piscivores were most frequent in 

Mangrove Lagoon and adjacent reef south of Patricia and 

Cas Cay, east of Cow and Calf Rocks and in the central 

portion of Jersey Bay. They were notably absent from 

the western portion of Benner Bay and most hardbottom 

surveys east of Great St. James, including outside STEER 

boundaries (Figure 3.27). 

Debris type Total number Colonized by

Trap fl oat 1 Uncolonized

Fishing leader 1 Uncolonized

Wood 1 Sponge

Ladder 1 Macroalgae

Chain 1 Macroalgae

Glass bottle 5 Macroalgae, invertebrates

Paper 1 Macroalgae

Plastic bag 2 Uncolonized

Clothing 1 Sponge

Barrel 1 Uncolonized

Sunglasses 1 Uncolonized

Table 3.2. Number and type of fouling organisms on marine 

debris items found during STEER transects.
Chapter 3: Fish Communities and Associated Benthic Habitats

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STEER Integrated Environmental Assessment Report

0

0.5

1

1.5

2

2.5

3

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Shannon diversity (100 m2) a)

0

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10

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25

30

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Number of species (100 m2) b)

0

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200

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350

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Total density (100 m2) c)

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2000

3000

4000

5000

6000

7000

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Total biomass (g/100 m2)

d)

Figure 3.21. Mean (±SE) fi sh species a) Shannon diversity, b) richness, c) density, and d) biomass by habitat type.

Habitat strata

Coral Reef and Hardbottom

Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Species Richness

1 - 5

6 - 10

11 - 20

21 - 30

31 - 39

012 0.5

Kilometers  ̄

Figure 3.22. Fish species richness.
Chapter 3: Fish Communities and Associated Benthic Habitats

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STEER Integrated Environmental Assessment Report

Figure 3.24. Total fi sh density.

Figure 3.23. Fish species diversity.

Habitat strata

Coral Reef and Hardbottom

Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Shannon Diversity

0 - 1

1.1 - 1.5

1.6 - 2

2.1 - 2.5

2.6 - 3.1

012 0.5

Kilometers  ̄

Habitat strata

Coral Reef and Hardbottom

Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Total Density (100 m2)

1 - 50

51 - 100

101 - 200

201 - 500

501 - 685

012 0.5

Kilometers  ̄
Chapter 3: Fish Communities and Associated Benthic Habitats

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STEER Integrated Environmental Assessment Report

Family and species composition differed across bottom 

types (Table 3.3, Table 3.4). Fishes of the Family Labridae 

(wrasses) accounted for over a quarter of the total number 

of fi sh on hardbottom, followed by Scaridae (parrotfi sh), 

Pomacentridae (Damselfi sh), Gobiidae (gobies) and Acanthuridae (surgeonfi shes). The most abundant species were 

members of these families (Table 3.3), with labrid species 

comprising two of the top fi ve most abundant species on 

hardbottom both inside and outside STEER (Thalassoma 

bifasciatum and Halichoeres bivittatus/ garnoti). Scaridae 

accounted for the highest proportion of biomass on hardbottom within STEER at 21%, followed by Acanthuridae, 

Haemulidae (grunts), and Lutjanidae (snappers). Two surgeonfi sh species, ocean surgeonfi sh (Acanthurus bahianus) 

and blue tang (A. coeruleus), ranked fi rst and third in total 

biomass on hardbottom within STEER. Two snapper species, gray snapper (Lutjanus griseus) and yellowtail snapper (Ocyurus chrysurus), were also in the top fi ve. While 

density proportions were similar in hardbottom surveys 

outside STEER, proportional biomass differed slightly, 

with snappers comprising 26% of the observed biomass. 

Yellowtail snapper accounted for the most biomass on 

hardbottom outside STEER, with another snapper species, 

lane snapper (L. synagris), also within the top fi ve. The 

Family Serranidae (seabasses and groupers), comprised a 

small percent of the biomass on hardbottom both inside and 

Habitat strata

Coral Reef and Hardbottom

Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Total Biomass (g/100 m2

)

0.3 - 1000

1000.1 - 5000

5000.1 - 10000

10000.1 - 20000

20000.1 - 38326.3

012 0.5

Kilometers  ̄

Figure 3.25. Total fi sh biomass.

Figure 3.26. Proportional a) abundance and b) biomass 

of trophic groups across habitat types.

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Proportion

Invertivores

Planktivores

Piscivores

Herbivores

0

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Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Proportion

Invertivores

Planktivores

Piscivores

Herbivores
Chapter 3: Fish Communities and Associated Benthic Habitats

37

STEER Integrated Environmental Assessment Report

outside STEER (4.4% and 7.6%, respectively). Although 

the invasive lionfi sh, Pterois volitans, did not occur in any 

survey transects, one individual was anecdotally sighted 

near Christmas Cove. 

In the mangrove habitat, over 45% of the total density was 

comprised of small bodied fi shes of the families Atherinidae (Atherinomorus sp.) and Clupeidae (Jenkinsia sp.). 

The Family Haemulidae was the third most abundant, with 

juvenile unidentifi ed grunts (Haemulon sp.), bluestriped 

grunt (H. sciurus), French grunt (H. fl avolineatum) accounting for the remaining species within the top fi ve. In 

contrast, snappers, which were the fi fth most abundant 

family, accounted for over half of the biomass surveyed 

in mangroves, with gray snapper comprising nearly 40% 

of the total biomass. Another snapper species, schoolmaster (L. apodus), and two grunt species (H. sciurus and H. 

fl avolineatum), were in the top fi ve for biomass, as was the 

nurse shark Ginglymostoma cirratum.

On unconsolidated sediments, Labridae accounted for 

37.5% of the total density, but only 7% of the biomass. The 

two most abundant species were the labrids slippery dick 

(Halichoeres bivittatus) and rosy razorfi sh (Xyrichtys martinicensis). Larger bodied jacks (Family Carangidae) and 

barracuda (Family Sphyraenidae) accounted for 36.6% and 

28.6% of biomass on unconsolidated sediments, respectively. Species within these two families accounted for the 

top three in proportional biomass.

Six species that were not observed in surveys within 

STEER were documented at hardbottom sites outside 

STEER. These included the redspotted hawkfi sh (Amblycirrhitus pinos), trumpetfi sh (Aulostomus maculatus), 

glasseye snapper (Heteropriacanthus cruentatus), hogfi sh 

(Lachnolaimus maximus), yellowmouth grouper (Mycteroperca interstitialis), and longjaw squirrelfi sh (Neoniphon 

marianus).

The nMDS and ANOSIM analyses further indicate that 

fi sh assemblages in STEER differ by bottom type. There 

was a clear separation of fi sh communities, based on fi sh 

density data, between hardbottom, unconsolidated sediment, and mangrove surveys (Figure 3.28a). Mangrove 

and hardbottom sites tended to be clustered within habitat 

type (Figure 3.28a), indicating a high degree of similarity 

in species composition among sites. In contrast, unconsolidated sediment sites tended to be more dispersed, indicating more dissimilarity among sites within this group. While 

sites within this bottom type were generally characterized 

Figure 3.27. Piscivore biomass.

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Habitat strata

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Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Piscivore biomass (g/100 m2)

D 0

0.1 - 1000

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2000.1 - 4000

4000.1 - 8554.1

012 0.5

Kilometers  ̄
Chapter 3: Fish Communities and Associated Benthic Habitats

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by low overall abundance, they often varied in their species composition. Within coral reef and hardbottom, there 

was not distinct separation of sites located inside versus 

outside the STEER. The results of the ANOSIM test also 

indicate that there was a statistically signifi cant difference 

in community composition among the three bottom types, 

and that the groups were well-separated (Global R= 0.757, 

p<0.001). Pairwise comparisons indicated high dissimilarity between hardbottom and unconsolidated sediments 

and between hardbottom and mangrove (Table 3.5). The 

top four species that contributed to dissimilarity between 

hardbottom and mangrove strata, as determined by the 

SIMPER analysis, included small herring (Jenkinsia sp.), 

fl agfi n mojara (Eucinostomus melanopterus), and schoolmaster (Lutjanus apodus), which were more common in 

mangroves, and bluehead wrasse (T. bifasciatum), and 

ocean surgeonfi sh (A. bahianus), which were more common on hardbottom. The top fi ve species contributing to the 

dissimilarity between hardbottom and unconsolidated sediments strata included wrasse, surgeonfi sh, parrotfi sh, and 

damselfi sh species that were all more abundant on hardbottom than unconsolidated sediments (Table 3.5). 

One of the hardbottom surveys outside STEER showed 

similarity with the surveys on unconsolidated sediments 

Hardbottom (Inside)

Family Density Family Biomass

Labridae 27.0% Scaridae 21.0%

Scaridae 15.8% Acanthuridae 18.3%

Pomacentridae 15.3% Haemulidae 18.0%

Gobiidae 13.8% Lutjanidae 17.7%

Acanthuridae 13.5% Serranidae 4.4%

Hardbottom (Outside)

Family Density Family Biomass

Labridae 27.8% Lutjanidae 26.1%

Scaridae 20.7% Scaridae 22.8%

Pomacentridae 15.9% Pomacanthidae 8.6%

Acanthuridae 9.5% Acanthuridae 8.3%

Gobiidae 9.1% Serranidae 7.6%

Mangrove

Family Density Family Biomass

Atherinidae 23.1% Lutjanidae 51.5%

Haemulidae 22.3% Haemulidae 21.7%

Clupeidae 21.2% Ginglymostomatidae 8.2%

Lutjanidae 13.1% Scaridae 4.4%

Gerreidae 8.2% Sphyraenidae 3.7%

Unconsolidated Sediments

Family Density Family Biomass

Labridae 37.5% Carangidae 36.8%

Scaridae 22.2% Sphyraenidae 28.6%

Gerreidae 10.3% Labridae 7.4%

Lutjanidae 7.8% Echeneidae 6.2%

Haemulidae 7.7% Scombridae 5.2%

Table 3.3. Top fi ve families in abundance and total biomass, shown 

as percent of total, by habitat strata.

Hardbottom (Inside)

Species Density Species Biomass

Thalassoma 

bifasciatum 15.9% Acanthurus bahianus 8.2%

Coryphopterus 

personatus/hyalinus 12.5% Haemulon fl avolineatum 7.6%

Acanthurus bahianus 7.9% Acanthurus 

coeruleus 6.0%

Halichoeres 

bivittatus 6.3% Lutjanus griseus 5.9%

Scarus iseri 5.7% Ocyurus chrysurus 5.2%

Hardbottom (Outside)

Species Density Species Biomass

Thalassoma 

bifasciatum 13.3% Ocyurus chrysurus 14.0%

Stegastes partitus 9.3% Sparisoma viride 11.7%

Halichoeres garnoti 6.9% Lutjanus synagris 9.2%

Coryphopterus 

personatus/hyalinus 6.8% Pomacanthus arcuatus 5.9%

Sparisoma 

aurofrenatum 6.5% Mulloidichthys martinicus 5.4%

Mangrove

Species Density Species Biomass

Atherinomorus 

species 23.1% Lutjanus griseus 39.3%

Jenkinsia species 21.2% Haemulon sciurus 13.6%

Haemulon species 8.0% Ginglymostoma 

cirratum 8.2%

Haemulon sciurus 7.1% Lutjanus apodus 7.5%

Haemulon 

fl avolineatum 6.8% Haemulon 

fl avolineatum 4.3%

Unconsolidated Sediments

Species Density Species Biomass

Xyrichtys 

martinicensis 18.1% Sphyraena 

barracuda 28.6%

Halichoeres 

bivittatus 16.2% Caranx crysos 24.1%

Gerres cinereus 7.5% Carangoides 

bartholomaei 10.2%

Sparisoma radians 6.7% Echeneis 

naucrates 6.2%

Ocyurus chrysurus 4.6% Scomberomorus 

regalis 5.2%

Table 3.4. Top fi ve species in abundance and total biomass, shown as percent of total, by habitat strata.
Chapter 3: Fish Communities and Associated Benthic Habitats

39

STEER Integrated Environmental Assessment Report

by its location on the nMDS plot. This site, located east of 

Great St. James Island, was characterized by rubble habitat 

and low overall abundance. The R statistic for the pair of 

mangrove and unconsolidated sediments was lower indicating while the two groups were still clearly different, there 

was some overlap in species composition. The top species 

contributing to the dissimilarity between the two strata 

were all more abundant on mangrove and included small 

herring (Jenkinsia sp.), schoolmaster (L. apodus), gray 

snapper (L. grisius), bluestriped grunt (H. sciurus), and 

fl agfi n mojarra (E. melanopterus). Using species biomass 

resulted in a similar MDS confi guration (Figure 3.28b) and 

ANOSIM results as for species density, albeit with a slightly lower Global R (R = 0.661, p<0.001). Pairwise comparisons showed hardbottom and unconsolidated sediments 

were well separated (Table 3.5). The results of the SIMPER 

analysis indicated that the top species contributing to the 

dissimilarity between these two strata included yellowtail 

snapper and two species of surgeonfi sh and parrotfi sh. The 

R value for the hardbottom-mangrove pairwise comparison was slightly lower than with the abundance data (R = 

0.662) indicating a slightly higher degree of similarity but 

still overall clearly different in terms of species biomass 

assemblage. Similar to the ANOSIM analysis using density 

data, mangrove and unconsolidated sediments showed less 

separation than the other paired habitats.

Figure 3.28. Non-metric multidimensional (nMDS) scaling 

ordination based on between site similarity composition using 

species a) density and b) biomass data. Sites are color-coded by 

habitat type and study area.

Resemblance: S17 Bray Curtis similarity

Transform: Square root

Habitat Strata

Hardbottom (STEER)

Unconsolidated Sediments

Hardbottom (Outside)

Mangrove

2D Stress: 0.14

2D Stress: 0.15

Resemblance: S17 Bray Curtis similarity

Transform: Square root

Habitat Strata

Hardbottom (STEER)

Unconsolidated Sediments

Hardbottom (Outside)

Mangrove

a) 

b) 

Species Density Species Biomass

Group R p-value Top species

(% contribution to dissimilarity) R p-value Top species(% contribution to dissimilarity)

Hardbottom, 

Mangrove 0.894 0.001

Jenkinsia sp. (6.02%)

0.662 0.001

Lutjanus griseus (9.96%)

Thalassoma bifasciatum (5.44%) Haemulon sciurus (5.89%)

Eucinostomus melanopterus

(4.15%) Lutjanus apodus (5.18%)

Acanthurus bahianus (3.92%) Acanthurus bahianus (5.03%)

Lutjanus apodus (3.92%) Acanthurus coeruleus (3.88%)

Hardbottom, 

Unconsolidated 

Sediments

0.772 0.001

Thalassoma bifasciatum (8.42%)

0.724 0.001

Acanthurus bahianus (8.07%)

Acanthurus bahianus (5.88%) Acanthurus coeruleus (5.73%)

Halichoeres bivittatus (4.51%) Sparisoma aurofrenatum (4.88%)

Sparisoma aurofrenatum (4.25%) Ocyurus chrysurus (3.86%)

Stegastes partitus (4.17%) Sparisoma viride (3.46%)

Unconsolidated 

Sediments, 

Mangrove

0.382 0.001

Jenkinsia sp. (9.55%)

0.327 0.001

Lutjanus griseus (16.93%)

Lutjanus apodus (7.61%) Haemulon sciurus (10.06%)

Eucinostomus melanopterus 

(7.45%) Lutjanus apodus (9.81%)

Haemulon sciurus (6.57%) Sphyraena barracuda (6.80%)

Lutjanus griseus (6.25%) Haemulon sp. (4.99%)

Table 3.5. Pairwise Analysis of Similarities (ANOSIM) comparisons between habitat types based on fi sh species density and biomass data, and list of top fi ve species contributing to the dissimilarity from the SIMPER analysis. Species are listed in decreasing order of percent contribution to the average dissimilarity. The R statistic ranges between 0 and 1 and represents whether pairs of habitats are 

well separated (closer to 1) or barely separable (closer to 0). Species are listed in decreasing order of percent contribution to the average dissimilarity.
Chapter 3: Fish Communities and Associated Benthic Habitats

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STEER Integrated Environmental Assessment Report

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Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Total Grouper Density (100 m2)

D 0

1 - 2

3 - 4

5 - 6

7 - 8

012 0.5

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a)

0

0.5

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Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Density (100 m2)

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50

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Hardbottom

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Hardbottom

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Sediments

Biomass (g/100 m2)

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15

20

25

30

0-5 5-10 10-15 15-20 20-25 25-30 30-35 >35

Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

b) c) 

d) 

Figure 3.29. Grouper (Family Serranidae) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, 

and d) size frequency.
Chapter 3: Fish Communities and Associated Benthic Habitats

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Select Families and Species

Groupers (Serranidae)

Groupers (Cephalopholis and Epinephelus spp.), rarely 

seen, were primarily small in size, and were exclusively 

associated with hardbottom (Figure 3.29). Most grouper individuals belonged to two species: graysby (Cephalopholis 

cruentata), and red hind (Epinephelus guttatus). Notably, 

only one coney (Cephalopholis fulva), typically a common 

grouper species in the Caribbean, was observed. Species in 

the larger-bodied genus Mycteroperca were largely absent 

from the survey, with the exception of one yellowmouth 

grouper (Mycteroperca interstitialis) documented at a site 

outside STEER on the reef complex south of Patricia Cay. 

Red hind was the most abundant grouper species observed 

in the study, occurring in 13% of surveys within STEER. 

The species was also sighted in three surveys outside of 

STEER, east of Great St. James Island and south of Patricia Cay/Mangrove Lagoon (Figure 3.30). The species 

was found exclusively on hardbottom, including patch 

reefs, nearshore rocky areas, and high aggregate reef. The 

site with the highest density was a patch reef southwest of 

Great St. James Island. The majority of observed individuals were small adults, although two 40 cm fi sh were also 

seen (Figure 3.30d).

Graysby showed a similar distribution pattern and habitat 

affi liation as red hind. The species occurred in 11% of transects within STEER and in two surveys outside STEER. 

Mean density was higher, but more variable, on hardbottom outside STEER compared to inside, primarily due to 

the presence of six individuals at one site (Figure 3.31). 

The majority of individuals were small adults 15-30 cm in 

length (Figure 3.31d). 

Snappers (Lutjanidae)

Snappers were detected across the shelf in all investigated 

habitats but were most abundant in mangroves (Figure 

3.32). However, as described below, distribution varied by 

species and lifestage. The lowest mean density and biomass 

was observed over unconsolidated sediments. A total of 

seven Lutjanid species were documented, with schoolmaster (Lutjanus apodus), yellowtail (Ocyurus chrysurus), and 

gray snappers (L. griseus) accounting for the majority of 

observations. The remaining species, mahogany (L. mahogoni), lane (L. synagris), dog (L. jocu) and mutton (L. 

analis) were less frequently sighted (Appendix 1 in Bauer 

et al., 2014). Lutjanidae size frequency was skewed toward 

smaller size classes (Figure 3.32d).

Gray snapper were observed in 23% of survey transects 

within STEER and were almost exclusively associated 

with mangrove fringes and cays (Figure 3.33). However, 

the second highest observed density, and second highest 

biomass, was observed on a patch reef in St. James Bay. 

The site with the highest density and biomass was located 

near the false entrance to Mangrove Lagoon. About 70% 

of observed individuals were juveniles/subadults, while the 

remaining were mostly small adults (Figure 3.33d). Two 

individuals >35 cm were observed in Mangrove Lagoon.

Schoolmaster were observed at 24% of sites within STEER 

and also at two additional reef sites outside the reserve. 

Similar to gray snapper, the species was most abundant in 

nearshore mangrove fringes and cays (Figure 3.34). A few 

individuals were observed on hardbottom habitat across the 

study area, while none were observed on unconsolidated 

sediments. The majority of schoolmaster (>90%) were 

juveniles/subadults (Figure 3.34d). All of the adult-sized 

individuals, about 9% of the total, were located on hardbottom.

Yellowtail snapper was the most frequently sighted Lutjanid species, occurring in over 50% of survey transects 

within STEER. Mean density of yellowtail snapper was 

similar in both mangrove and hardbottom habitats, with 

lower levels on unconsolidated sediments (Figure 3.35). 

The sites with the highest abundance and biomass were 

mostly located in the western half of the study area, and 

were less frequently sighted in the east (Figure 3.35). Highest biomass levels were observed on reefs south and east of 

Patricia and Cas Cays. The majority (~70%) of individuals 

were juveniles/subadults, particularly those associated with 

unconsolidated sediments and mangrove (Figure 3.35d). 

The majority of observed adults were located on hardbottom, leading to higher mean biomass compared to the other 

bottom types. Smaller sized adults were most common, 

with no individuals >35 cm length observed.

Mahogany snapper were not commonly observed, occurring at 7% of sites within STEER, but notably larger densities were present in survey transects at Cow and Calf Rocks 

(20 /100 m2

) and a nearby patch reef (10 /100 m2) (Figure 

3.36). This species was absent from unconsolidated sediments and from hardbottom surveys outside the reserve 

boundary. Adult-sized individuals were only observed on 

hardbottom.

Grunts (Haemulidae)

Fishes in the grunt family were present in all habitat types. 

Mangrove habitat had the highest mean density, while 

hardbottom and unconsolidated sediment habitats exhibited similar density levels (Figure 3.37). Mean biomass 

was highly variable on hardbottom habitat due to a large 

concentration of biomass near Cow and Calf Rocks (>23 
Chapter 3: Fish Communities and Associated Benthic Habitats

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Figure 3.30. Red hind (Epinephelus guttatus) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

a)
Chapter 3: Fish Communities and Associated Benthic Habitats

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Figure 3.31. Graysby (Cephalopholis cruentata) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Chapter 3: Fish Communities and Associated Benthic Habitats

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Figure 3.32. Snapper (Family Lutjanidae a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, 

and d) size frequency.

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Figure 3.33. Gray snapper (Lutjanus griseus) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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STEER Integrated Environmental Assessment Report

a)

Figure 3.34. Schoolmaster (Lutjanus apodus) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Chapter 3: Fish Communities and Associated Benthic Habitats

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Figure 3.35. Yellowtail snapper (Ocyurus chrysurus) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency. 

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d) 
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Figure 3.36. Mahogany snapper (Lutjanus mahogoni) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Figure 3.37. Grunt (Family Haemulidae) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, 

and d) size frequency.

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Figure 3.38. French grunt (Haemulon fl avolineatum) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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kg/100 m2). The family was represented by nine species 

(Appendix 1 in Bauer et al., 2014). French grunt (Haemulon fl avolineatum), bluestriped grunt (H. sciurus), white 

grunt (H. plumierri), and tomtates (H. aurolineatum) were 

most frequently sighted and had the highest mean abundance and biomass of the grunt species. Porkfi sh (Anisotremus virginicus), black margate (A. surinamensis), and the 

remaining species were observed less frequently (Appendix 

1 in Bauer et al., 2014). Over one-third of observed grunts 

in mangrove habitat were small juveniles that could not be 

identifi ed to the species level. These juveniles were also 

associated with unconsolidated sediments.

French grunt were present within 35% of survey transects 

in STEER, as well as two hardbottom sites outside the 

STEER boundary. The species was commonly observed 

on mangrove hardbottom habitats across the study area but 

absent from surveys on unconsolidated sediments (Figure 3.38). While mean density was highest in mangroves, 

variability was also relatively high and the majority of 

individuals were small juveniles. In contrast, a larger range 

of sizes were present on hardbottom habitat, although subadults and small adults were most common. 

Bluestriped grunt were sighted in 21% of surveys within 

STEER and one site outside the STEER boundary. The species was most abundant in mangrove habitat, with densities 

up to 50 / 100m2

 (Figure 3.39). Mean biomass was highest on hardbottom but varied across space; when present, 

the species generally occurred as singular individuals or 

occasional larger aggregations. While all size classes were 

present in mangroves, juveniles/sub-adults were most common (Figure 3.39d). Hardbottom was typically inhabited by 

the larger size classes. 

Tomtate were found across all habitats but was less frequently sighted than the previously described grunt species, 

occurring in only 8% of survey transects within STEER. 

However the species was observed in densities >10 /100m2

at a few locations, including Cow and Calf Rocks and a soft 

sediment site outside Cowpet Bay (Figure 3.40). Approximately 60% of observed individuals were juveniles/subadults, with the remaining being in the size class just above 

the average size at maturity (Figure 3.40d).

Surgeonfi sh (Acanthuridae)

Acanthurids (surgeonfi sh) were present in all three bottom 

types and across all depths throughout the STEER, but the 

family was most abundant in hardbottom habitats (Figure 

3.41). Fewer sightings were observed in Benner Bay and 

Mangrove Lagoon, with the exception of the survey near 

the false entrance. Ocean surgeonfi sh (Acanthurus bahianus) and blue tang (A. coeruleus) were the most frequently 

observed species in both study areas, while doctorfi sh (A. 

chirirgus) was relatively less common (Appendix 1 in 

Bauer et al., 2014).

Ocean surgeonfi sh were observed at multiple sites spanning 

the shelf and bottom types, including nearshore and lagoon 

areas (Figure 3.42). The species was present in over half of 

transects within STEER and all but two of the hardbottom 

sites outside STEER. A cluster of particularly high density 

sites were located on spur and groove and pavement with 

sand channels habitat in Jersey Bay. Mean density and biomass were higher on hardbottom inside STEER compared 

to outside the reserve. Size frequencies tended towards the 

smaller size classes, with >40% of observed individuals 

under 5 cm in length (Figure 3.42d).

Blue tang were documented in 42% of survey transects 

within STEER, primarily on hardbottom. The species 

was only present at one mangrove location and was absent 

from unconsolidated sediment surveys (Figure 3.43). Blue 

tang were also documented at the majority of hardbottom 

sites outside the reserve boundary, although mean density 

and biomass were lower compared to inside STEER. The 

species occurred across most hardbottom types but the two 

locations with highest observed densities were located on 

shallow nearshore rock/boulder habitat in Great Bay. Similar to ocean surgeonfi sh, smaller size classes were most 

frequent and all observed individuals were <20 cm (Figure 

3.43d).

Parrotfi sh (Scaridae)

Parrotfi shes (Family Scaridae) were a common component 

of the STEER fi sh community. The family was represented 

by 11 species (Appendix 1 in Bauer et al., 2014). The species with the highest site frequency, density and biomass 

were striped parrotfi sh (Scarus iseri), redband parrotfi sh 

(Sparisoma aurofrenatum), princess parrotfi sh (Sc. taeniopterus), and stoplight parrotfi sh (Sp. viride). Most largerbodied species were absent from the study areas, however 

rainbow parrotfi sh (Sc. guacamaia) occurred in one survey 

transect in Nazareth Bay. The site was also characterized 

by the largest observed parrotfi sh biomass in STEER and 

by the presence of several adult-sized yellowtail parrotfi sh 

(Sp. Rubripinne). A spawning aggregation of yellowtail 

parrotfi sh has previously been noted at nearby Coculus 

Rock (Smith et al., 2011). Overall, highest levels of density and biomass were generally observed on hardbottom 

habitat, with intermediate and lowest levels in mangroves 

and unconsolidated sediments, respectively (Figure 3.44). 

Species composition varied across bottom types. All eleven 

species were observed on hardbottom, while mangrove was 
Chapter 3: Fish Communities and Associated Benthic Habitats

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a)

Figure 3.39. Bluestriped grunt (Haemulon sciurus) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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a)

Figure 3.40. Tomtate (Haemulon aurolineatum) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Mangrove Unconsolidated

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Juveniles/subadults

b) c) 

d) 
Chapter 3: Fish Communities and Associated Benthic Habitats

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a)

Figure 3.41. Surgeonfi sh (Family Acanthuridae) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Land

STEER boundary

Excluded from survey

Total Surgeonfish Density (100 m2)

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26 - 50

51 - 67

012 0.5

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Mangrove Unconsolidated

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Frequency (%)

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b) c) 

d) 
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STEER boundary

Excluded from survey

Ocean Surgeonfish Density (100 m2)

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21 - 36

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Hardbottom

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Biomass (g/100 m2)

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Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

Juveniles/subadults

b) c) 

d) 

a)

Figure 3.42. Ocean surgeonfi sh (Acanthurus bahianus) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.
Chapter 3: Fish Communities and Associated Benthic Habitats

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Habitat strata

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Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Blue Tang Density (100 m2)

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11 - 20

21 - 39

012 0.5

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Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

Juveniles/subadults

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100

150

200

250

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350

400

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Biomass (g/100 m2)

b) c) 

d) 

a)

Figure 3.43. Blue tang (Acanthurus coeruleus) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.
Chapter 3: Fish Communities and Associated Benthic Habitats

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Habitat strata

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Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Total Parrotfish Density (100 m2)

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51 - 94

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(Outside)

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Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

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600

800

1000

1200

1400

1600

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Biomass (g/100 m2)

b) c) 

d) 

a)

Figure 3.44. Parrotfi sh (Family Scaridae) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.
Chapter 3: Fish Communities and Associated Benthic Habitats

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Habitat strata

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Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Redband Parrotfish Density (100 m2)

D 0

1 - 5

6 - 10

11 - 20

21 - 26

012 0.5

Kilometers  ̄

a)

Figure 3.45. Redband parrotfi sh (Sparisoma aurofrenatum) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Hardbottom

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Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Density (100 m2)

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Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Biomass (g/100 m2)

0

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30

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0-5 5-10 10-15 15-20 20-25 25-30 30-35 >35

Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

Juveniles/subadults

b) c) 

d) 
Chapter 3: Fish Communities and Associated Benthic Habitats

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Figure 3.46. Stoplight parrotfi sh (Sparisoma viride) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Habitat strata

Coral Reef and Hardbottom

Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Stoplight Parrotfish Density (100 m2)

D 0

1 - 5

6 - 10

11 - 20

21 - 28

012 0.5

Kilometers  ̄

0

1

2

3

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5

6

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Density (100 m2)

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100

200

300

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500

600

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Biomass (g/100 m2)

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20

30

40

50

60

0-5 5-10 10-15 15-20 20-25 25-30 30-35 >35

Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

Juveniles/subadults

b) c) 

d) 

a)
Chapter 3: Fish Communities and Associated Benthic Habitats

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only occupied by striped, redband, stoplight, and bucktooth 

parrotfi shes. Unconsolidated sediments were also typifi ed 

by juveniles of the aforementioned species, as well as the 

smaller bodied bluelip parrotfi sh (Cryptotomus roseus). 

Redband parrotfi sh were sighted in 54% of survey transects 

within STEER. Mean density was similar on hardbottom inside and outside STEER, with slightly higher mean 

biomass inside STEER (Figure 3.45). The species was 

common across all hardbottom types, including nearshore 

rock/boulder, patch reefs, and pavement. Lower densities 

were typically observed over unconsolidated sediments and 

mangrove, with the notable exception of mangrove sites 

near the false entrance to Mangrove Lagoon and Cas Cay. 

The size distribution was skewed towards the smaller size 

classes (0-10 cm TL) while ~20% of the observed individuals were above the mean size at maturity (Figure 3.45d). 

Stoplight parrotfi sh were observed in all three habitats with 

STEER but exhibited highest abundance and biomass on 

hardbottom (Figure 3.46). The species was present across 

all hardbottom types but sites with higher values occurred 

on nearshore rocky habitat in Cowpet and Great Bays and 

a patch reef in St. James Bay. Biomass at hardbottom sites 

outside STEER exhibited a relatively higher degree of variability due to the presence of a few larger sized individuals 

at one location. Over 50% of the observed individuals were 

in the smallest size class (0-5 cm), while 15% were small 

adults (Figure 3.46d). 

Striped parrotfi sh were present in 59% of survey transects 

within STEER and were common on both hardbottom and 

in mangroves (Figure 3.47). The site with the highest observed density, located in Cowpet Bay, was also characterized by the highest density of the spotlight parrotfi sh. The 

species was less frequently sighted in the eastern portion 

of the study area and was absent at several of the surveys 

east of Great St. James Island. Small juveniles were dominant, particularly in mangroves and on soft sediments, and 

overall only 5% of observed individuals were larger than 

the mean size at maturity(Figure 3.47d).

Princess parrotfi sh occurred in 23% of survey transects 

within STEER and in over half of the hardbottom surveys 

outside the reserve. Highest mean density and biomass 

occurred on hardbottom, while the species was absent from 

surveys in mangrove (Figure 3.48). The densest aggregation occurred on hardbottom in Great Bay, while the location with the second highest observed density was on unconsolidated sediments near the false entrance to Mangrove 

Lagoon. The overwhelming majority (95%) of observed 

individuals were juveniles/subadults (Figure 3.48d).

Other species

Wrasses (Labridae)

Fishes of the Family Labridae were ubiquitous members of 

the STEER fi sh community, occurring in 85% of all surveys 

within STEER and all but one hardbottom survey. Wrasses 

were present in all habitats and across the geographic area, 

but with fewer sighting frequencies in Mangrove Lagoon 

(Figure 3.49). Mean density and biomass were highest on 

hardbottom. The family was represented by 12 species 

(Appendix 1 in Bauer et al., 2014), with some variation by 

habitat. Bluehead (Thalassoma bifasciatum), slippery dick 

(Halichoeres bivittatus), yellowhead wrasse (H. garnoti), 

and clown wrasse (H. maculipinna) the most frequently 

encountered species on hardbottom, while razorfi sh species, particularly rosey razorfi sh (Xyrichtys martinicensis), 

were more frequent on unconsolidated sediments. Hogfi sh 

(Lachnolaimus maximus) was absent from surveys within 

STEER but one individual was sighted within a transect on 

the reef complex south of the reserve boundary. The size 

distribution skewed towards the smaller size classes (Figure 

3.49d) because small-bodied Labrid species were most 

abundant.

Goatfi shes (Mullidae)

Goatfi sh were present in 20% of survey transects within 

STEER, in addition to several of the hardbottom surveys 

outside STEER. The family was represented by two species, spotted goatfi sh (Pseudupeneus maculatus) and yellow 

goatfi sh (Mulloidichthys martinicus). Yellow goatfi sh was 

observed exclusively on hardbottom while spotted goatfi sh 

was documented within a couple of unconsolidated sediment surveys. Goatfi shes were typically observed in low 

densities (1-5/ 100 m2

) but one larger cluster (27/ 100 m2) 

was recorded on an area of pavement with sand channels in 

Jersey Bay (Figure 3.50). 

Damselfi shes (Pomacentridae)

Damselfi shes were present across all bottom types, occurring in 62% of surveys within STEER and all but one 

hardbottom site outside the reserve. Highest densities and 

biomass were observed on hardbottom, with intermediate 

levels in mangrove habitat and low frequency of occurrence 

on unconsolidated sediments (Figure 3.51). Damselfi sh 

were prevalent across hardbottom types but highest densities were observed at sites in the southern portion of the 

study area, including surveys near Cow and Calf Rocks, 

southeast of Great St. James Island, and outside the STEER 

boundary south of Patricia Cay. The family was represented by 10 species (Appendix 1 in Bauer et al., 2014). 

Frequently observed species included the bicolor damselfi sh (Stegastes partitus), cocoa damselfi sh (S. variabilis), 

longfi n damselfi sh (S. diencaeus), and beaugregory (S. 

leucostictus).
Chapter 3: Fish Communities and Associated Benthic Habitats

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Figure 3.47. Striped parrotfi sh (Scarus iseri) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Habitat strata

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Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Striped Parrotfish Density (100 m2)

D 0

1 - 10

11 - 20

21 - 40

41 - 58

012 0.5

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Hardbottom

(Inside)

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(Outside)

Mangrove Unconsolidated

Sediments

Density (100 m2)

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Hardbottom

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Biomass (g/100 m2)

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0-5 5-10 10-15 15-20 20-25 25-30 30-35 >35

Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

Juveniles/subadults

b) c) 

d) 

a)
Chapter 3: Fish Communities and Associated Benthic Habitats

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Figure 3.48. Princess parrotfi sh (Scarus taeniopterus) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Princess Parrotfish Density (100 m2)

D 0

1 - 5

6 - 10

11 - 20

21 - 61

012 0.5

Kilometers  ̄

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Hardbottom

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Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Density (100 m2)

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Hardbottom

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Hardbottom

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Mangrove Unconsolidated

Sediments

Biomass (g/100 m2)

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0-5 5-10 10-15 15-20 20-25 25-30 30-35 >35

Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

Juveniles/subadults

b) c) 

d) 

a)
Chapter 3: Fish Communities and Associated Benthic Habitats

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Figure 3.49. Wrasse (Family Labridae) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and 

d) size frequency.

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Habitat strata

Coral Reef and Hardbottom

Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Total Wrasse Density (100 m2)

D 0

1 - 10

11 - 25

26 - 50

51 - 129

012 0.5

Kilometers  ̄

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60

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Density (100 m2)

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Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

0

50

100

150

200

250

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Biomass (g/100 m2)

b) c) 

d) 

a)
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Figure 3.50. Goatfi sh (Family Mullidae) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

a)

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Habitat strata

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Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Total Goatfish Density (100 m2)

D 0

1 - 5

6 - 10

11 - 25

26 - 27

012 0.5

Kilometers  ̄

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Hardbottom

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Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Density (100 m2)

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Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

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Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Biomass (g/100 m2)

b) c) 

d) 
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Figure 3.51. Damselfi sh (Family Pomacentridae) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Habitat strata

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Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Total Damselfish Density (100 m2)

D 0

1 - 10

11 - 25

26 - 50

51 - 117

012 0.5

Kilometers  ̄

0

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Hardbottom

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(Outside)

Mangrove Unconsolidated

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Density (100 m2)

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Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

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100

150

200

250

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Biomass (g/100 m2)

b) c) 

d) 
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Figure 3.52. Queen triggerfi sh (Balistes vetula) a) spatial distribution, b) mean density (±SE) by habitat, c) mean biomass (±SE) by habitat, and d) size frequency.

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Habitat strata

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Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Queen Triggerfish Density (100 m2)

D 0

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012 0.5

Kilometers  ̄

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10

20

30

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50

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0-5 5-10 10-15 15-20 20-25 25-30 30-35 >35

Frequency (%)

Size class (cm)

Hardbottom Mangrove Unconsolidated Sediments

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0.02

0.04

0.06

0.08

0.1

0.12

0.14

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0.2

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Density (100 m2)

0

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100

150

200

250

Hardbottom

(Inside)

Hardbottom

(Outside)

Mangrove Unconsolidated

Sediments

Biomass (g/100 m2)

Juveniles/subadults

b) c) 

d) 

a)
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Triggerfi sh (Balistidae)

Queen triggerfi sh (Balistes vetula, Family Balistidae) was 

uncommonly encountered in the survey, occurring at only 

three sites within STEER and none outside (Figure 3.52). 

The species was observed exclusively on hardbottom in the 

central and southeastern areas of STEER and in densities 

of 1-2/ 100m2

. Three of the four observed individuals were 

adult-sized (Figure 3.52d).

Comparison with Other U.S. Caribbean Monitoring Locations

The benthic community found on hardbottom sites in 

STEER are similar to those described by long term monitoring programs using the same methods as this study in 

St. Croix, around Buck Island Reserve National Monument 

and the northeastern St. Croix shore including the East End 

Marine Park from 2001-2006 (Pittman et al., 2008), and 

around the island of St. John from 2001-2009 (Friedlander 

et al., 2013). Overall community structure was similar: 

hardbottom habitats in all three locations were dominated 

by turf and macroalgae with low overall coral cover (5.6 ± 

0.5% in St. Croix; 4.8 ± 0.5% St. John) (Figure 3.53). However, turf algae cover averaged 49.7% (± 4.11) in STEER 

compared to only 33% in St. John (Friedlander et al., 2013) 

and 36% (± 1.6) in St. Croix (Pittman et al., 2008). Due to 

the ephemeral nature of turf algae, percent cover values can 

be infl uenced by seasonal and interannual variation.

Unconsolidated sediments habitats in all three study regions were dominated by seagrass with STEER hosting the 

highest percent cover (31.4 ± 5.9% STEER; St. John 22.2 

± 1.6%; St. Croix 19.84 ± 2.9%). St. John and STEER data 

show similar macroalgal cover (17.9 ±5.1% STEER; 16.2 ± 

1.2% St. John). The unconsolidated sediments sites of St. 

Croix had much less macroalgae (6.92 ± 1.1%). Seagrass 

beds of all three studies were composed of mostly Syringodium fi liforme and Thalassia testudinum in which smaller 

amounts of sponges, gorgonians, living corals and other 

benthic invertebrates were also documented. Syringodium

was the dominant seagrass species found at STEER sites as 

opposed to Thalassia which was the greatest component in 

beds around St. Croix and St. John.

Nonparametric Wilcoxon tests and the corresponding nonparametric Dunn’s multiple comparisons tests (Zar, 1999) 

were used to test differences among regions (JMP v11.0). 

On hardbottom habitat, fi sh species richness in STEER was 

similar to St. John and was signifi cantly greater compared 

to St. Croix (p=0.001) and Southwest Puerto Rico (SWPR) 

(p<0.001) (Figure 3.54). Total biomass on hardbottom in 

SWPR was signifi cantly lower than in St. Croix and St. 

Figure 3.53. Comparison of benthic cover groups between 

STEER and other locations within NOAA’s Caribbean Coral Reef 

Ecosystem Monitoring Program. Estimated mean (±SE) percent 

cover on a) hardbottom, b) unconsolidated sediments, and c) 

mangrove.

0

10

20

30

40

50

60

Hard Corals Gorgonians Sponge Turf Algae Macroalage

Percent cover

a) Hardbottom

St. Croix St. John STEER SW Puerto Rico

0

5

10

15

20

25

30

35

40

Macroalage Seagrass

Percent cover

b) Unconsolidated Sediments

St. Croix St. John STEER SW Puerto Rico

0

5

10

15

20

25

Macroalage Seagrass

Percent cover

c) Mangrove

STEER SW Puerto Rico
Chapter 3: Fish Communities and Associated Benthic Habitats

68

STEER Integrated Environmental Assessment Report

John, but STEER did not differ signifi cantly from any of 

the other study areas (i.e., p>0.05). At the family level, 

biomass levels were not consistent across regions. Grouper 

biomass did not vary signifi cantly among regions, while 

grunt biomass was signifi cantly greater on hardbottom 

in STEER compared to St. Croix (p=0.009 and p=0.002, 

respectively). Similarly, snapper biomass was signifi cantly 

lower in St. Croix compared to STEER, SWPR, and St. 

John (p<0.01 for all comparisons). Parrotfi sh biomass was 

similar between all four regions with no signifi cant differences detected.

On unconsolidated sediments, total fi sh biomass was signifi cantly lower in STEER and St. John compared to NE St. 

Croix, due primarily to the occurrence of several southern 

stingrays in St. Croix in 2010. Grouper biomass did not 

vary signifi cantly among regions. While grunt biomass was 

signifi cantly greater in SWPR compared to St. Croix and 

St. John, no pairwise comparisons with STEER were signifFigure 3.54. Comparison of community metrics between STEER and other locations within NOAA’s Caribbean Coral Reef Ecosystem 

Monitoring Program. Estimated mean (±SE) a) species richness, b) total biomass, c) grouper biomass, d) grunt biomass, e) snapper 

biomass, and f) parrotfi sh biomass.

0

5

10

15

20

25

30

Hardbottom Mangrove Unconsolidaed

Sediments

Number of species (100 m2)

a) Species richness

STEER

St. John

E St. Croix

SW Puerto Rico

0

2000

4000

6000

8000

10000

12000

Hardbottom Mangrove Unconsolidaed

Sediments

Biomass (g/100 m2)

b) Total Biomass

STEER

St. John

E St. Croix

SW Puerto Rico

0

50

100

150

200

250

300

350

Hardbottom Mangrove Unconsolidaed

Sediments

Biomass (g/100 m2)

c) Grouper Biomass

STEER

St. John

E St. Croix

SW Puerto Rico

0

200

400

600

800

1000

1200

1400

1600

1800

Hardbottom Mangrove Unconsolidaed

Sediments

Biomass (g/100 m2)

d) Grunt Biomass

STEER

St. John

E St. Croix

SW Puerto Rico

0

500

1000

1500

2000

2500

3000

Hardbottom Mangrove Unconsolidaed

Sediments

Biomass (g/100 m2)

e) Snapper Biomass

STEER

St. John

E St. Croix

SW Puerto Rico

0

200

400

600

800

1000

1200

1400

1600

Hardbottom Mangrove Unconsolidaed

Sediments

Biomass (g/100 m2)

f) Parrotfish Biomass

STEER

St. John

E St. Croix

SW Puerto Rico
Chapter 3: Fish Communities and Associated Benthic Habitats

69

STEER Integrated Environmental Assessment Report

icant. Snapper and parrotfi sh biomass were similar across 

all study areas with no statistical differences detected. 

Mangroves in STEER had similar fi sh community metrics 

compared to SWPR. Although mean total biomass was 

larger in STEER than SWPR, there was high variance 

among STEER sites and results of the non-parametric tests 

indicated no signifi cant difference between locations. Species richness and biomass of the other groups also did not 

vary signifi cantly between STEER and SWPR.

Despite differences in fi shing regulations, fi sh community 

metrics in STEER were similar to other U.S. Caribbean 

monitoring locations sampled with the same methodology. 

With a few exceptions for baitfi shing and hook and line 

with permit, STEER is primarily a no-take reserve. Portions 

of the St. John (Virgin Islands National Park, Virgin Islands 

National Reef Monument) and St. Croix (Buck Island National Reef Monument, East End Marine Park) study areas 

are also no-take, while the SWPR study area is open to 

fi shing. In addition, the maximum depth in STEER is much 

shallower than the other locations. On hardbottom habitat, 

STEER differed only from SWPR (higher species richness) 

and St. Croix (higher grunt and snapper biomass). The difference from St. Croix may be partially due to differences 

in habitat as eastern St. Croix lacks the extensive mangroves that in STEER appear to serve as important nursery 

areas for juvenile fi shes in these families. No metrics were 

signifi cantly different between STEER and nearby St. 

John. Although this study focused on broad community 

metrics for this assessment, more in-depth analysis could 

be conducted to look for differences at the species level, 

or to examine how factors such as fi shing pressure and 

other anthropogenic factors, depth, and habitat complexity 

affect community composition across the USVI and Puerto 

Rico. For instance, although fi shing is greatly restricted 

in STEER, poaching may still occur (Dillard and D’lorio, 

2012). At the same time, fewer snapper are generally taken 

on the south shore of St. Thomas and St. John due to concerns about ciguatera poisoning (Smith et al., 2011). 

3.4. CONCLUSIONS

This study provides a baseline characterization of the fi sh 

and benthic communities of STEER necessary to implement and assess effectiveness of the comprehensive management plan (STEER, 2011) and potential watershed 

restoration activities (Horsley Witten, 2013a). STEER 

includes an interconnected mosaic of marine habitats, 

including the largest remaining mangrove system in St. 

Thomas (IRF, 1993), extensive beds of submerged aquatic 

vegetation, and coral reef communities. The establishment 

of STEER enables this complex area to be managed as 

one comprehensive unit rather than the existing individual 

reserves (STEER, 2011).

 

In general, both benthic and fi sh community metrics in the 

STEER were similar to other U.S. Caribbean monitoring 

locations sampled with the same methodology. The low 

coral cover observed in the STEER refl ects the signifi cant 

decline in corals seen throughout the Caribbean, likely due 

to a number of factors including disease and hurricane damage. Surveys conducted in the southern portion of Mangrove Lagoon and adjacent coral reefs, however, ranked 

higher in regards to hard coral cover, fi sh species richness, 

total fi sh density and total fi sh biomass. Further research is 

needed to fully examine the current and potential nursery 

function of the entire lagoon. 

The STEER encompasses a unique seascape in the USVI 

while possibly being one of the most impacted due to the 

high population density in the watershed. In addition to 

changes in the coral reefs as previously noted, historical 

studies also indicate changes in the mangrove and seagrass communities. Grigg et al. (1971) noted an increase 

in shoreline development and boating activity and associated poor water quality in Benner Bay. The authors also 

expressed concern about increasing anthropogenic stress 

on Mangrove Lagoon and Benner Bay, where turbidity and 

other water quality parameters varied with fl uctuations in 

storm runoff and tidal cycles. In addition to the increasing 

development and maritime activities, at that time, a sewage treatment plant also discharged effl uent directly into 

the inner Mangrove Lagoon, which receives little fl ushing 

(Grigg et al., 1971). The outfall continued to be operational 

until wastewater was diverted to the new Mangrove Lagoon 

Wastewater Treatment Plant (MLWTP) in 2003, which disGray Angelfi sh (Pomacanthus arcuatus) in STEER. charges into the ocean off Long Point (DPNR, 2003). There 
Chapter 3: Fish Communities and Associated Benthic Habitats

70

STEER Integrated Environmental Assessment Report

have been notable changes in the seascape of the Mangrove 

Lagoon complex over time. Whereas seagrass covered 

much of the seafl oor in the lagoon in the 1970s, macroalgae 

presently dominates the benthos (Colletti, 2011). 

In a recent assessment of chemical contaminants in sediments within STEER, higher levels of chemical contaminants were found in Mangrove Lagoon and Benner Bay, 

as well as signifi cant sediment toxicity (Pait et al., 2013). 

The areas where highest contaminant levels were observed 

were not sampled in this survey due to low visibility and 

water quality concerns for diver health. However, previous research indicated that the fi sh community in the inner 

Mangrove Lagoon differs from the middle and outer portions that were included in this study. In a recent trapping 

study, researchers from DPNR and UVI found signifi cant 

differences in species diversity, species composition, and 

abundance of fi shes between the degraded inner lagoon 

section and the middle/outer lagoon sections (Murray, 

2009; Colletti, 2011). In particular, Colletti (2011) found 

that mangrove fringes in close proximity to dense seagrass/

macroalgal beds and coral reefs in the southern areas had 

signifi cantly higher species richness and abundance of 

juvenile fi sh than the inner bay, which was characterized 

by high cyanobacterial cover. Similar trends of lower fi sh 

species richness and density in the inner lagoon in comparison to middle/outer sections were found in a previous 

trapping study conducted from 1986-1988 (Boulon, 1992). 

Overall, Colletti (2011) found similar patterns in juvenile 

fi sh abundance in comparison to Boulon (1992), but fewer 

species were observed in comparison to the earlier study. 

The differences in fi sh community between the different 

sections of the lagoon may be infl uenced by additional 

factors, including contaminated water/sediments and low 

dissolved oxygen. Murray (2009) observed that occasionally fi sh caught in the inner lagoon were dead when traps 

were retrieved after begin deployed for one day, and it 

was presumed that these fi sh died of suffocation due to 

the extremely low dissolved oxygen present. Insuffi cient 

food could also be a factor for species that are primarily 

benthic feeders (e.g., grunts) as Pait et al. (2013) observed 

diminished infaunal community in this area. The outer 

portion of the lagoon experiences more fl ushing from the 

false entrance to Mangrove Lagoon between Patricia and 

Bovoni Cays. Shoals have built up at the mouths of additional inlets (DPNR, 2003). Overall, the DPNR/UVI work 

and the current assessment demonstrate the importance of 

Mangrove Lagoon and Benner Bay as nursery habitat for 

snappers, grunts, parrotfi sh, and other species. 

Protected status and water quality improvement are two 

approaches that may help improve coral, mangrove and 

seagrass ecosystem health, but cannot mitigate the effects 

of the greatest global threat to coral reefs: high thermal 

stress (Hughes et al., 2003; Bruno et al., 2007; Baker et 

al., 2008). Sustained high water temperatures in the summer often lead to bleaching events that can be followed 

by disease outbreaks due to the compromised health of 

bleached corals (Miller et al., 2009). Contributing to the 

disease outbreaks are warmer winter temperatures that may 

reduce the mortality rates of coral pathogens and increase 

the amount of coral disease (Bruno et al., 2007). Adopting 

a seascape-wide coral reef management approach includes 

protecting mesophotic and mid-shelf reefs, which are not 

as susceptible to bleaching or disease and could serve as 

“reef refuges” to maintain healthy stocks of some benthic 

and fi sh communities. These stocks would then in turn 

provide source populations for nearshore systems like 

STEER (Smith et al., 2001). As part of this assessment, we 

also surveyed several locations just outside of the STEER 

boundaries that were of interest to managers. While the 

area to the east of STEER primarily consisted of pavement/

rubble, sites on the reef complex south of Patricia Cay/

Mangrove Lagoon ranked high in terms of coral cover and 

fi sh biomass. Although the shoreward portion of this reef 

complex is already included within STEER, this area could 

also be considered for inclusion in the reserve due to its 

ecological importance.

This study provides just one spatially comprehensive 

snapshot of the current conditions within STEER, so it is 

important that fi sh and benthic communities within the 

reserves continue to be monitored over time to meet management objectives (STEER, 2011). In addition to yearly 

monitoring of TCRMP permanent sites, the coral reef and 

hardbottom habitats in St. Thomas and STEER will continElkhorn coral (Acropora palmata) and other species colonize a 

coral reef in STEER.
Chapter 3: Fish Communities and Associated Benthic Habitats

71

STEER Integrated Environmental Assessment Report

ue to be surveyed every two years through NOAA’s National Coral Reef Monitoring Program (NCRMP). At each 

survey location, fi sh belt transects, as used in this study, 

will be conducted, while line point intersect (LPI) and 

coral demographics transects will be used to characterize 

the benthic communities (NOAA, 2013 a,b). Mangroves, 

seagrasses, and other soft sediments will not be included 

in the NCRMP monitoring; however these habitats provide 

critical ecosystem services, including nutrient cycling, carbon sequestration, shoreline stabilization, nursery habitat 

for fi sh, and protection from wind/waves. Hence, further 

research and monitoring in these areas are warranted. Due 

to the limitations in conducting visual surveys in much of 

Mangrove Lagoon and Benner Bay, a repeat of the trapping 

study (Murray, 2009; Colletti, 2011) or alternative methods 

could be explored to cover areas that cannot be surveyed by 

visual census. In addition, periodic re-mapping of benthic 

habitats will capture large-scale changes in the reserve and 

the habitats that support benthic invertebrate and fi sh communities. 

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seascapes. PLOS ONE 6(5): e20583.doi:10.1371/journal.

pone.0020583.

Pittman, S.J., B. Costa, C.F.G. Jeffrey, and C. Caldow. 

2011. Importance of seascape complexity for resilient fi sh 

habitat and sustainable fi sheries. Proceedings of the 63rd 

Gulf and Caribbean Fisheries Institute. 420-426. 

Platenberg, R.J., 2006. Wetlands Conservation Plan for St. 

Thomas and St. John, U.S. Virgin Islands. Division of Fish 

and Wildlife, Department of Planning and Natural Resources, St. Thomas. 101 pp.

Rogers, C.S., J. Miller, E. Muller, P. Edmunds, R.S. Nemeth, J. Beets, A. Friedlander, T.B. Smith, R. Boulon, 

C.F.G. Jeffrey, C. Menza, C. Caldow, N. Idrisi, B. Kojis, M. 

Monaco, A. Spitzack, E. Gladfelter, J. Ogden, Z. HillisStarr, I. Lundgren, W.B. Schill, I. Kuffner, L.L. Richardson, 

B. Devine, and J. Voss. 2008. Ecology of Coral Reefs in 

the U.S. Virgin Islands. pp. 303-374. In: B. Riegl and R.E. 
Chapter 3: Fish Communities and Associated Benthic Habitats

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STEER Integrated Environmental Assessment Report

Dodge (eds.). Coral Reefs of the USA. Coral Reefs of the 

World, Volume 1. Springer. 806 pp.

Rothenberger, P., J. Blondeau, C. Cox, S. Curtis, W.S. Fisher, V. garrison, Z. Hillis-Starr, C.F.G. Jeffrey, E. Kadison, I. 

Lundgren, W.J. Miller, E. Muller, R. Nemeth, S. Paterson, 

C. Rogers, T. Smith, A. Spitzack, M. Taylor, W. Toller, J. 

Wright, D. Wusinich-Mendez and J. Waddell. 2008. The 

State of Coral Reef Ecosystems of the U.S. Virgin Islands. 

pp. 29-73 In: J.E. Waddell and A.M. Clarke (eds.), The 

State of Coral Reef Ecosystems of the United States and 

Pacifi c Freely Associated States. 2008. NOAA Technical 

Memorandum NOS NCCOS 73. NOAA/NCCOS Center 

for Coastal Monitoring and Assessment's Biogeography 

Team. Silver Spring, MD. 569 pp.

Sheppard, C.R.C. 2006. Longer term impacts of climate 

change. In: Cote, I., and J. Reynolds. (Eds.), Coral Reef 

Conservation. Cambridge University Press, Cambridge, pp. 

264-290.

Smith, T.B., R.S. Nemeth, J. Blondeau, J.M. Calnan, E. 

Kadison, and S. Herzlieb. 2008. Assessing coral reef health 

across onshore to offshore stress gradients in the U.S. Virgin Islands. Marine Pollution Bulletin 56: 1983-1991.

Smith, T.B., E. Kadison, L. Henderson, J. Gyory, M.E. 

Brandt, J.M. Calnan, M. Kammann, V. Wright, R.S. Nemeth, and P. Rothenberger. 2011. The United States Virgin 

Islands Territorial Reef Monitoring Program. Year 11 Annual Report. 243 pp.

STEER. 2011. St. Thomas East End Reserves Management 

Plan. Edited by J. Brown, A. Holecek, J. Murray, L. Noori, 

J.P. Oriol, J. Pierce, R. Platenberg, S. Romano, D. Russo, 

and C. Settar. 99pp.

Warne, A.G., R.M.T. Webb, and M.C. Larsen. 2005. Water, 

Sediment, and Nutrient Discharge Characteristics of Rivers in Puerto Rico, and their Potential Infl uence on Coral 

Reefs: U.S. Geological Survey Scientifi c Investigations 

Report 2005-5206, 58 pp.

Wilkinson, C.R. (ed.). 2000. Status of the Coral Reefs of 

the World: 2000. Global Coral Reef Monitoring Network, 

Australian Institute of Marine Science, Queensland.

Zar, J.H. 1999. Biostatistical Analysis. Prentice Hall, New 

Jersey. 663pp. 
Chapter 4: Chemical Contaminants and Toxicity

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4.1 INTRODUCTION

This chapter covers the results of the chemical contaminant 

analysis in sediments, sediment bioassays, and benthic infaunal analysis in the STEER. In this phase of the project, 

185 chemical contaminants, including a number of organic 

(e.g., hydrocarbons and pesticides) and inorganic (e.g., 

metals) compounds, were analyzed in sediments from 24 

sites in the STEER. Sediment toxicity was characterized 

using a series of bioassays including amphipod mortality, 

sea urchin fertilization impairment, and the cytochrome 

P450 Human Reporter Gene System (HRGS), along with a 

characterization of the benthic infaunal community. 

The assessment of contaminants throughout the STEER 

was one of the assessment priorities voiced by environmental managers in the STEER, 

during initial discussions on 

the proposed project. Because 

of the presence of a number of 

potential sources of pollution 

including the Bovoni Landfi ll, 

marinas and boatyards, commercial/industrial operations, 

an EPA Superfund site, and 

residential areas served primarily by septic systems, it was 

thought that chemical contaminants and associated toxicity 

on resident biota might be an issue impacting the health 

and productivity of the STEER, including fi sheries nursery 

areas. Additional background information along with data 

(e.g., appendices) from this part of the project can be found 

in Pait et al. (2013), and online at: http://coastalscience.

noaa.gov/projects/detail?key=19. 

Sediment Quality Triad

Chemical contaminant analysis in sediments, along with 

sediment bioassays and benthic infaunal analysis make up 

what is referred to as the Sediment Quality Triad (SQT). 

The SQT has been developed to assess the presence and 

impacts of chemical contaminants in benthic habitats 

(Chapman et al., 1987). Additional information on each of 

these three components follows.

Overview of the Chemical Contaminants

The quantifi cation of chemical contaminants in sediments 

provides the opportunity for understanding what chemical stressors are present, their concentrations, how these 

concentrations compare to established sediment quality 

guidelines, along with providing input to the other two 

components of the triad. Each of the contaminant classes 

analyzed for this project are 

discussed below. 

Polycyclic Aromatic Hydrocarbons. Also referred to as PAHs, 

polycyclic aromatic hydrocarbons are associated with the use 

and combustion of fossil fuels 

(e.g., oil and gas) and other 

organic materials (e.g., wood 

and trash). Natural sources 

of PAHs include forest fi res, 

and the decay of vegetation. 

The PAHs analyzed are two to 

six ring aromatic compounds. 

A number of PAHs bioaccumulate in aquatic and terrestrial organisms, are toxic, and some including benzo[a]

pyrene, benz[a]anthracene, chrysene, benzo[b]fl uoranthene, benzo[k]fl uoranthene, dibenzo[a,h]anthracene, and 

indeno[1,2,3-c,d]pyrene, are likely carcinogens (USDHHS, 

1995). 

Aliphatic Hydrocarbons. In addition to the PAHs, another 

group of hydrocarbons, the aliphatics were analyzed in the 

sediments. Aliphatic hydrocarbons are characterized by 

straight chain or branched nonaromatic structures. Alia

d

P

b

p

b

a

(

o

a

o

a

T

The Bovoni Landfi ll on the western end of the STEER receives solid waste s

from both St. Thomas and St. John. 

CHAPTER 4: AN ASSESSMENT OF CHEMICAL CONTAMINANTS, TOXICITY AND BENTHIC INFAUNA 

IN SEDIMENTS FROM THE ST. THOMAS EAST END RESERVES (STEER)

Anthony S. Pait1, S. Ian Hartwell1, Andrew L. Mason1, Robert A. Warner1, Christopher F. G. Jeffrey1,2, Anne M. Hoffman3

, Dennis A. Apeti1, Francis R. Galdo Jr.4, and Simon J. Pittman1,5

1

NOAA/NOS/National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment (CCMA),

1305 East/West Highway, Silver Spring, MD 20910

2

CSS-Dynamac Consolidated Safety Services, Fairfax, VA 22030, under CSS-Dynamac Contract #EA-133C-14-

NC-1384

3

The Nature Conservancy, St. Thomas, USVI 

4

The University of the Virgin Islands, St. Thomas, USVI

5

The Marine Institute, Plymouth University, United Kingdom
Chapter 4: Chemical Contaminants and Toxicity

76

STEER Integrated Environmental Assessment Report

phatic hydrocarbons are often associated with uncombusted 

fuels such gasoline, diesel or oil. 

Polychlorinated Biphenyls. Commonly referred to as 

PCBs, polychlorinated biphenyls are synthetic compounds 

that have been used in numerous applications ranging from 

electrical transformers and capacitors, to hydraulic and heat 

transfer fl uids, to pesticides and in paints. Approximately 

60 percent of PCBs manufactured in the U.S. were used in 

electrical applications (EPA, 1997). PCBs have a biphenyl 

ring structure (two benzene rings with a carbon to carbon 

bond) and a varying number of chlorine atoms. There are 

209 PCB congeners. 

PCBs were manufactured in the U.S. between 1929 and 

1977. In the United States, all PCBs were produced by a 

single manufacturer, and the commercial products were 

referred to as Aroclors. Aroclors are mixtures of PCB congeners. The manufacture of PCBs in the U.S. was banned 

in 1979 due to their toxicity. Because PCBs bioaccumulate 

and degradation in the environment proceeds only slowly, 

they are now ubiquitous contaminants. Exposure to PCBs 

in fi sh has been linked to reduced growth, reproductive 

impairment and vertebral abnormalities (EPA, 1997). 

Organochlorine Pesticides. Beginning in the 1950s and 

continuing in to the early 1970s, a series of chlorine 

containing hydrocarbon insecticides were used to control 

mosquitoes and agricultural pests. One of the best known 

of the organochlorine pesticides was the insecticide DDT 

(dichlorodiphenyltrichloroethane). 

The use of many of the organochlorine pesticides, including DDT, was banned due to their environmental persistence, potential to bioaccumulate, and in particular chronic 

effects on nontarget organisms. Organochlorine pesticides 

are typically neurotoxins, and DDT along with PCBs have 

also been shown to interfere with the endocrine system 

(Rogen and Chen, 2005). DDT and its metabolite DDE, 

for example, were specifi cally linked to eggshell thinning 

in birds, particularly raptors, but also in pelicans (Lincer, 

1975). A number of organochlorine pesticides are toxic to 

nontarget aquatic life as well, including crayfi sh, shrimp 

and some species of fi sh. While DDT was banned by the 

EPA for most uses in the U.S. in 1972, it is still effectively 

used in some developing countries, particularly the inside 

of living areas, to help control mosquitos that can transmit 

malaria. 

Most uses of the organochlorine insecticide chlordane were 

banned in 1978, and all uses were banned by 1988. A primary non-agricultural use of chlordane was in the treatment 

of wooden structures to prevent damage by termites. 

Because of their persistence and heavy use in the past, 

residues of organochlorine pesticides can be found as well 

in the environment, including in biota. The persistence of 

these compounds and toxicity to nontarget organisms continues to be an environmental concern.

Butyltins. This compound class has a range of uses, from 

biocides to catalysts to glass coatings. In the 1950s, tributyltin, or TBT, was fi rst shown to have biocidal properties (Evans, 1970; Bennett, 1996). In the late 1960s, TBT 

was incorporated into an antifoulant paint system, quickly 

becoming one of the most effective paints ever used on 

boat hulls (Birchenough et al., 2002). TBT was incorporated into a polymer paint system that released the biocide 

at a constant and minimal rate, to control fouling organisms 

such as barnacles, mussels, weeds, and algae (Bennett, 

1996). 

TBT was linked to endocrine disruption, specifi cally an imposex (females developing male characteristics) condition 

in marine gastropods, and in other mollusks (e.g., oysters), 

abnormal shell development, and poor weight gain (Batley, 

1996). Beginning in 1989, the use of TBT as an antifouling agent was banned in the U.S. on non-aluminum vessels 

smaller than 25 meters in length (Gibbs and Bryan, 1996). 

In a survey of TBT in the USVI, Strand et al. (2009) found 

evidence of elevated levels of TBT and its degradation 

products in gastropod species, as well as imposex organisms at several locations, including the harbor in Charlotte 

Amalie Bay, St. Thomas. 

In the aquatic environment, TBT is degraded by microorganisms and sunlight (Bennett, 1996). The transformation 

involves sequential debutylization resulting in dibutyltin, 

monobutyltin, and fi nally inorganic tin (Batley, 1996). 

Major and Trace Elements. All the major and trace elements occur naturally to some extent in the environment. 

Aluminum, iron, and silicon are major elements in the 

Earth’s crust. As their name implies, trace elements occur 

at lower concentrations in crustal material, however, mining and manufacturing processes along with the use and 

disposal of products containing trace elements can lead to 

elevated concentrations in the environment. Some trace 

and major elements are essential micronutrients, however, a 

number of trace elements are toxic at low concentrations. 

Cadmium is used in a number of applications, including 

nickel-cadmium (Ni-Cd) batteries, paint pigments and in 

electroplating (Ellor and Stemniski, 2007). Cadmium has 

been shown to impair development and reproduction in 

several invertebrate species, and osmoregulation in herring 

larvae (USDHHS, 1999; Eisler, 1985). Mercury is volatile 
Chapter 4: Chemical Contaminants and Toxicity

77

STEER Integrated Environmental Assessment Report

and can enter the atmosphere through processes including 

mining, manufacturing, combustion of coal and volcanic 

eruptions (Eisler, 1987). Mercury is currently used in compact and other fl uorescent light bulbs, electrical switches 

and relays, thermostats and in some dental amalgams. Effects of mercury on copepods include reduced growth and 

rates of reproduction (Eisler, 1987). 

Chromium is used in stainless steel production, chromium 

plating, and as a pigment, and has been shown to reduce 

survival and fecundity in the cladoceran Daphnia magna, 

and reduced growth in fi ngerling chinook salmon (Oncorhynchus tshawytscha) (Eisler, 1986). 

Copper has many applications including use in wire, electronic circuits, antifouling paints for 

boat hulls, copper plumbing, industrial catalysts, and in a number of 

alloys (e.g., brass). Copper sulfate 

is used in agriculture and as an antialgal agent, although it is probably 

unlikely copper sulfate is used to 

any great extent in St. Thomas, as 

there appears to be little agriculture 

in the watershed. While an essential biological element, elevated 

levels of copper can impact aquatic 

organisms, including the functioning of gills along with reproduction 

and development (Eisler, 1998). 

Most of the current uses of lead appear to be in lead-acid 

batteries, although other uses include oxides in glass and 

ceramics. In the past, lead was used in paints and also 

in gasoline, however, these uses have ended due to environmental and human health concerns. Nickel has many 

applications in both industrial and consumer products. Approximately 65% of the nickel in the U.S. is used to make 

stainless steel. Other uses include its incorporation into 

a series of alloys, in rechargeable batteries (Ni-Cd), catalysts, coins, plating, and in foundry products. Corrosionresistant zinc plating of steel (hot-dip galvanization) is an 

important application, accounting for roughly 50% of zinc 

use. In the marine industry, zinc anodes are used to protect vital engine and boat parts (e.g., propellers, struts and 

rudders, along with outboard and inboard engines), and is 

a component in some antifoulant paint formulations. Zinc 

is also used in batteries, and in alloys such as brass. Lead, 

nickel and zinc have all been shown to impact fertilization 

success in corals, some effects being observed in the parts 

per billion range (Reichelt-Brushett and Harrison, 1999; 

Reichelt-Brushett and Harrison, 2005). If not included 

in this document, results from the analysis of additional 

trace and major elements, can be found in Pait et al (2013), 

and online at: http://coastalscience.noaa.gov/projects/

detail?key=19. 

Bacterial Indicator. Although not a chemical contaminant, 

the bacterium Clostridium perfringens has been used as an 

indicator of fecal pollution and was analyzed in the sediment samples from the STEER. This bacterium occurs in 

the intestines of humans and in some domestic and feral 

animals, and is a common cause of food poisoning.

Sediment Toxicity Tests

NOAA’s NCCOS, National Status and Trends (NS&T)

Bioeffects Program routinely uses a suite of tests to assess sediment toxicity through 

different modes of contaminant 

exposure (bulk sediment, sediment porewater, and chemical 

extracts of contaminants from 

sediment) to a variety of species 

(invertebrates, vertebrate cells 

and bacteria) and different assessment end-points (i.e., mortality, 

impaired reproduction, physiological stress, and enzymatic 

response). Since the test results 

are not necessarily axiomatic and 

biological effects of contaminants 

occur at different levels of biological organization, i.e., from cells to 

ecosystems, results from a suite of toxicity tests are used in 

the “weight of evidence” context to infer the incidence and 

severity of environmental toxicity (Chapman, 1996). The 

toxicity bioassays used in this project included amphipod 

(Ampelisca abdita) mortality, sea urchin (Arbacia punctulata) fertilization impairment, and cytochrome P450 Human 

Reporter Gene System (HRGS).

Benthic Infaunal Analysis. Mixtures of synthetic organic 

compounds (e.g., PCBs and DDT), metals, PAHs, excess 

nutrients, and various inorganic chemicals are released 

into the ocean from municipal and industrial point sources, 

atmospheric deposition, stormwater runoff, spills, and 

groundwater. These anthropogenic contaminants may accumulate in the sediment in coastal bays, estuaries, and 

nearshore coastal zones. 

Two of the most infl uential parameters in the distribution 

of benthic communities are salinity and sediment grain 

size. Environmental concentrations of organic enrichment 

and toxicants are often confounded in space and time with 

Marina area in Benner Bay. 
Chapter 4: Chemical Contaminants and Toxicity

78

STEER Integrated Environmental Assessment Report

gradients of salinity and grain size, making their separate 

and combined biological effects diffi cult to detect, especially at the levels of population and community. However, 

understanding toxic hazard due to sediment contamination 

by means of community assessment is valuable. Biological 

systems integrate the complexity of natural habitat stressors 

and ambient pollutant mixtures, through physical contact 

with sediments, ingestion of sediment, and the bioaccumulation of contaminants via food webs, along with the 

synergetic effects of exposure to multiple toxic chemicals. 

Many examples exist in which marine benthic communities’ response to contaminant and physical stressors have 

been documented (Hartwell and Clafl in, 2005; Hartwell and 

Hameedi, 2007; Hartwell et al., 2009; Oliver et al., 2011; 

Wlodarska-Kowalczuk et al., 2005). Impacts of contamination on marine benthos have 

shown that total biomass, relative 

proportion of deposit feeders, and 

abundance of species with ‘opportunistic’ life histories (e.g., high fecundity, short generation time, and 

rapid dispersal) increase with increasing organic enrichment. Some 

opportunistic taxonomic groups 

are known to be tolerant of chemical toxicants. Others are capable 

of thriving in physically disturbed 

habitats (e.g., high sedimentation, 

dredging operations, etc), but not 

necessarily in contaminated areas. 

In areas impacted by excessive sedimentation from terrestrial runoff, dominant organisms tend toward surface 

suspension feeding modes and high reproductive potential 

regardless of taxonomic relationship, whereas away from 

the sedimentation stress, feeding modes shift to species that 

are deep deposit feeders along with the emergence of fi lter 

feeders. Experimental manipulation of habitats have shown 

that polychaete worms, in specifi c taxonomic lines, with 

opportunistic life history strategies respond positively to 

organic enrichment (Fleeger et al., 2003). Infaunal arthropods respond negatively to toxicants and organic enrichment. The response of specifi c arthropod and echinoderm 

species to organic and toxic contamination is mediated by 

life history and feeding mode characteristics. Finally, the 

benthic community will respond to management actions 

that affect physical and chemical stressors in vastly shorter 

time frames than will coral reefs.

4.2 METHODS

The sampling strategy for sediments was developed in 

meetings with the STEER Core Planning Group. A stratifi ed random sampling design was selected, which is a 

standard benthic assessment technique. The STEER was 

fi rst subdivided into fi ve strata based on habitat and geography (e.g., hard bottom areas, seagrass beds, mangroves, etc) 

(Figure 4.1). Five sampling points on soft bottom sediments were then randomly selected using ArcGIS®. Both 

primary and alternate sites were identifi ed throughout the 

STEER. Alternate sites were sampled in the event that a 

primary site was unsuitable due to hard bottom, obstructions, etc. 

The stratifi ed random sampling design was used in order to 

characterize the spatial distribution of chemical contaminants, toxicity and the benthic infaunal community (organisms living within the sediment) throughout the STEER. 

Using this design, the extent and concentration of chemical 

contaminants and bioeffects can be 

compared between strata. The 2011 

collection of sediment samples in the 

STEER occurred 14 - 17 June. The 

samples were collected under DPNR 

Permit STX-032-11. 

All sediment sites were located using 

a GPS programmed with the site coordinates. Most of the sediment samples 

were collected from the charter vessel 

Bright Star, however, Mangrove Lagoon was too shallow for this vessel. 

To enable the collection of samples 

in that stratum, personnel from the DPNR Division of Fish 

and Wildlife brought in a shallow draft motor boat to help 

NOAA personnel collect the sediment samples in Mangrove Lagoon. 

In addition to the work in 2011, preliminary fi eld work took 

place in the STEER in May 2010. From that effort, a total 

of 13 sediment samples were taken, and enough funding 

was available at the time to analyze four of the samples collected. The results of the analysis of these samples is also 

included in this report. However, as the four samples were 

collected from targeted sites and were not selected randomly, they could not be included in the statistical comparisons 

between strata, nor were they included in the calculation of 

the mean (average) concentration of sediment contaminants 

in the STEER. 

Sampling Protocols

A PONAR grab (see inset) was deployed to collect the 

samples using a pulley and davit, and retrieved by hand. 

Rocks and bits of seagrass were removed. If a particular 

grab did not result in 200-300 g of sediment, a second grab 

was made and composited with material from the fi rst. If 

The PONAR grab used to take sediment samples in the 

STEER. 
Chapter 4: Chemical Contaminants and Toxicity

79

STEER Integrated Environmental Assessment ReportFigure 4.1. Strata and sediment sites sampled in the St. Th omas East End Reserves (STEER) in June 2011. 
Chapter 4: Chemical Contaminants and Toxicity

80

STEER Integrated Environmental Assessment Report

enough sediment had not been collected after three deployments of the grab, the site was abandoned and the boat 

moved on to an alternate site. 

A series of protocols (Apeti et al., 2012a) were used to 

avoid contamination of the sediment samples by equipment 

and cross contamination between samples and sites. All 

equipment was rinsed with acetone and then distilled water 

just prior to use at a site. Personnel handling the samples 

also wore disposable nitrile gloves. The top 3 cm of sediment were collected from the grab using a stainless steel 

sediment scoop. This top layer of sediment is referred to 

as surfi cial sediment, and is typically indicative of recent 

deposition. 

Sediments were placed into two certifi ed clean (I-Chem®) 

250 ml labeled jars, one for organic chemical analysis, the 

other for major and trace element analysis, capped and then 

placed on ice in a cooler. Sediments for grain size analysis 

were placed in a WhirlPack® bag, sealed and placed on ice 

in a cooler. At the end of each day, sediment samples for 

contaminant analysis were placed in a freezer. The WhirlPack® bags for the grain size analysis were placed in a 

refrigerator rather than frozen, to avoid altering the grain 

size structure of the sediment.

A series of water parameters (dissolved oxygen, temperature, salinity, and conductivity) were also measured at each 

site, using a YSI® salinity/conductivity/temperature meter. 

The instrument probe was submerged to a depth of approximately 0.5 meter for the surface measurement, and within a 

meter of the sediment for the bottom measurement. Secchi 

depth was also measured at each site. 

 

The sediment samples collected were analyzed for a suite 

of 185 organic (e.g., hydrocarbons and pesticides) and 

inorganic (e.g., metals) contaminants by TDI-Brooks 

International, using protocols from the NS&T Program. 

The list of chemical contaminants analyzed in the sediments is shown in Table 4.1. The 59 polycyclic aromatic 

hydrocarbons (PAHs) were analyzed using gas chromatography/mass spectrometry in the selected ion monitoring 

mode. The 37 aliphatic hydrocarbons were analyzed by 

gas chromatography/fl ame ionization detection. The 31 

organochlorine pesticides and 38 polychlorinated biphenyls 

(PCBs) were analyzed using gas chromatography/electron 

capture detection. The four butyltins were analyzed using gas chromatography/fl ame photometric detection after 

derivatization. A subset of the sediment samples were 

subsequently reanalyzed using gas chromatography/mass 

spectrometry for confi rmation of the TBT concentrations 

detected at certain sites from the initial analysis. Seventeen 

major and trace elements were analyzed. The major and 

trace elements were analyzed using inductively coupled 

plasma mass spectrometry and atomic-fl uorescence spectroscopy. Detailed descriptions of the NS&T protocols, 

including quality assurance/quality control (QA/QC) used 

in the analysis of the organic contaminants, can be found 

in Kimbrough et al. (2006); for inorganic analyses, Kimbrough and Lauenstein (2006). 

Statistical Analysis for Chemical Contaminants

The sediment contaminant data were analyzed using JMP®

statistical software. A Shapiro-Wilk test was fi rst run on 

individual parameters to see if the data were normally distributed. When data were normally distributed, an Analysis of Variance (ANOVA) was run followed by pairwise 

(Tukey HSD) comparisons. If the data were not normally 

distributed and a log10 transformation was not effective, 

Spearman’s nonparametric multivariate correlation was 

used. Some of the data were also subsequently ranked, followed by a Kruskal-Wallis test and pairwise comparisons. 

The statistical analyses were used, for example, to compare 

differences in contaminant levels between strata. 

NOAA numerical sediment quality guidelines (SQG) 

developed by Long and Morgan (1990) and Long et al. 

(1995), known as ERM (Effects Range-Median), and ERL 

(Effects Range-Low), express statistically derived levels 

of contamination, above which toxic effects would be 

expected with at least a 50% frequency (ERM), and below 

which effects were rarely (<10 %) expected (ERL). The 

ratio of the ERM value to the sediment concentration for 

each chemical is called the ERM quotient or ERMq (Long 

et al., 1998). The quotient expresses how close measured 

concentrations are to the ERM level on a zero to one scale. 

A quotient of one or greater means the concentrations are 

at or above the ERM. This also normalizes the ERMs for 

different chemicals to a common scale. The mean ERMq of 

all the contaminants averaged together expresses a measure 

of contamination across the entire spectrum of measured 

contaminants. Field research suggests that a mean ERMq 

value of 0.1 is a threshold where degraded communities 

begin to be seen, as observed in the southeast U.S. (Hyland 

et al., 1999). The mean quotient of the ERMs and observed 

contaminant concentrations were calculated on a site by site 

basis. 

Sediment Toxicity Bioassays

The protocols for the bioassays were based on standard 

methods, as outlined by the U.S. EPA (1999, 2002a) and 

ASTM (2008). Sediment samples for the bioassays were 

collected into three containers. Samples for the amphipod 

toxicity tests (bulk sediment) were collected in 1 liter (L) 
Chapter 4: Chemical Contaminants and Toxicity

81

STEER Integrated Environmental Assessment Report

Table 4.1. Compounds analyzed in sediments from the St. Thomas East End Reserves.

PAHs - Low MW PAHs - High MW Aliphatics O rganochlorine Pesticides PCBs Major and Trace ElementsNaphthalene Fluoranthene n-C9 Aldrin PCB8/5 Aluminum (Al)1-Methylnaphthalene Pyrene n-C10 Dieldrin PCB18 Antimony (Sb)2-Methylnaphthalene C1-Fluoranthenes/Pyrenes n-C11 Endrin PCB28 Arsenic (As)2,6-Dimethylnaphthalene C2-Fluoranthenes/Pyrenes n-C12 Heptachlor PCB29 Cadmium (Cd)1,6,7-Trimethylnaphthalene C3-Fluoranthenes/Pyrenes n-C13 Heptachlor-Epoxide PCB31 Chromium (Cr)C1-Naphthalenes Naphthobenzothiophene i-C15 Oxychlordane PCB44 Copper (Cu)C2-Naphthalenes C1-Naphthobenzothiophenes n-C14 Alpha-Chlordane PCB45 Iron (Fe)C3-Naphthalenes C2-Naphthobenzothiophenes i-C16 Gamma-Chlordane PCB49 Lead (Pb)C4-Naphthalenes C3-Naphthobenzothiophenes n-C15 Trans-Nonachlor PCB52 Manganese (Mn)Benzothiophene Benz[a]anthracene n-C16 Cis-Nonachlor PCB56/60 Mercury (Hg)C1-Benzothiophenes Chrysene i-C18 Alpha-HCH PCB66 Nickel (Ni)C2-Benzothiophenes C1-Chrysenes n-C17 Beta-HCH PCB70 Selenium (Se)C3-Benzothiophenes C2-Chrysenes Pristane Delta-HCH PCB74/61 Silicon (Si)Biphenyl C3-Chrysenes n-C18 Gamma-HCH PCB87/115 Silver (Ag)Acenaphthylene C4-Chrysenes Phytane DDMU PCB95 Tin (Sn)Acenaphthene Benzo[b]fluoranthene n-C19 2,4'-DDD PCB99 Zinc (Zn)Dibenzofuran Benzo[k]fluoranthene n-C20 4,4'-DDD PCB101/90Fluorene Benzo[e]pyrene n-C21 2,4'-DDE PCB105C1-Fluorenes Benzo[a]pyrene n-C22 4,4'-DDE PCB110/77C2-Fluorenes Perylene n-C23 2,4'-DDT PCB118C3-Fluorenes Indeno[1,2,3-c,d]pyrene n-C24 4,4'-DDT PCB128Carbazole Dibenzo[a,h]anthracene n-C25 1,2,3,4-Tetrachlorobenzene PCB138/160Anthracene C1-Dibenzo[a,h]anthracenes n-C26 1,2,4,5-Tetrachlorobenzene PCB146Phenanthrene C2-Dibenzo[a,h]anthracenes n-C27 Hexachlorobenzene PCB149/1231-Methylphenanthrene C3-Dibenzo[a,h]anthracenes n-C28 Pentachloroanisole PCB151C1-Phenanthrene/Anthracenes Benzo[g,h,i]perylene n-C29 Pentachlorobenzene PCB153/132C2-Phenanthrene/Anthracenes n-C30 Endosulfan II PCB156/171/202C3-Phenanthrene/Anthracenes n-C31 Endosulfan I PCB158C4-Phenanthrene/Anthracenes n-C32 Endosulfan Sulfate PCB170/190Dibenzothiophene n-C33 Mirex PCB174C1-Dibenzothiophenes n-C34 Chlorpyrifos PCB180C2-Dibenzothiophenes n-C35 PCB183C3-Dibenzothiophenes n-C36 Butyltins PCB187

n-C37 Monobutyltin PCB194n-C38 Dibutyltin PCB195/208n-C39 Tributyltin PCB201/157/173n-C40 Tetrabutyltin PCB206

PCB209

Abbreviations: MW, molecular weight; PAH, polycyclic aromatic hydrocarbons; HCH, hexachlorocyclohexane; DDMU, 1-chloro-2,2- (p-chlorophenyl)ethylene,

 DDT, dichlorodiphenyltrichloroethane; DDD, dichlorodiphenyldichloroethane; DDE, dichlorodiphenyldichloroethylene; PCB, polychlorinated biphenyl
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jars; for the sea urchin fertilization tests (porewater extraction), a 3.79 liter (one gallon) sample of sediment was 

collected; and for the P450 test, a sample of sediment was 

taken out of the 250 ml organics jar and extracted. 

Amphipod Toxicity Test

The whole sediment toxicity bioassay test is commonly 

used in North America for assessing sediment quality, 

in part because the test integrates the effects of complex 

contaminant mixtures in relatively unaltered sediment, and 

also because amphipods are fairly common and an ecologically important species in coastal waters. The organisms 

are standard test species with known ranges of sensitivity 

and their presence or absence in a particular habitat is not 

relevant because they are tested under standardized conditions. Results of increased mortality, signifi cantly different 

from controls, is considered an indicator of marginal toxicity. Results that are signifi cantly different from controls 

and greater than 20% mortality is indicative of highly toxic 

conditions (Thursby et al., 1997). 

Sea Urchin Fertilization Test

The sea urchin (A. punctulata) fertilization toxicity test 

(also known as the sperm cell test) involves exposing sea 

urchin sperm to sediment pore water (interstitial water), 

followed by the addition of eggs. This test is used extensively in assessments of ambient water quality, toxicity of 

industrial and municipal effl uents, and sediment toxicity in 

coastal waters. It combines the features of testing sediment 

pore waters (the phase of sediments in which dissolved 

toxicants may be bioavailable) and exposures of gametes 

which often are more sensitive than adult organisms. Increased fertilization failure which is signifi cantly different 

from controls is considered symptomatic of marginal toxicity. Results that are signifi cantly different from controls and 

greater than 20% below control fertilization is indicative of 

highly toxic conditions (Carr and Bidenbach, 1999). 

P450 Test

The Human Reporter Gene System (HRGS) P450 test 

was used to determine the presence of toxic organic compounds in the sediments. Cytochrome P450s are a family 

of membrane-bound enzymes that metabolize a diverse 

number of compounds, including natural substrates, drugs, 

hormones, and many toxic compounds. They are present 

in a wide variety of animals, plants and other organisms. 

P450 is shorthand for Pigment and 450 is the wavelength 

at which they most strongly absorb light. In this case, the 

HRGS reporter gene is a DNA sequence in a human cancer 

cell line that has been genetically engineered to include a 

gene (the reporter gene) from the fi refl y that produces luciferase, the chemical that produces light in the insect when 

presented with the proper substrate. The gene is spliced into 

the region of the DNA strand that is activated to produce 

P450 enzymes when the cell is exposed to chemicals that 

stimulate metabolic activity. The more stimulated the cell 

is to metabolize a foreign compound, the more the reporter 

gene produces luciferase, which can be measured by increased light output. 

Different compounds stimulate P450 production to differing degrees, which can be calibrated. PCBs and PAHs 

stimulate certain Cytochrome P450 enzymes (e.g., CYP1A), but each individual compound exhibits its own level 

of stimulation. Heavy metals do not stimulate P450 at all. 

Under appropriate test conditions, induction of CYP1A is 

evidence that the cells have been exposed to one or more 

xenobiotic organic compounds, including dioxins, furans, 

planar PCBs, and several PAHs. When run in parallel with 

a serial dilution of standard PAH toxicant benzo[a]pyrene 

(BaP), or TCDD (dioxin), test results can be expressed in 

terms of standard toxicant equivalents based on the relative 

reporter gene response. Samples that exhibited a response 

greater than 50% of a standard 10 nM TCDD threshold 

control were again tested against a B[a]P serial dilution to 

calculate responses normalized to the B[a]P EC50 (effective concentration for 50% of the test cells) or the B[a]P 

equivalents (B[a]P eq). 

Anderson et al. (1999a) calculated the mean and 95% confi dence interval of HRGS values from 527 sampling points 

in the NOAA biological effects database to be 22.7 ±10.1 

(CI=12.6-32.8) mg B[a]P Eq/kg. Hence, values less than 

12.6, forming the tail of the distribution in the direction of 

low induction (or impact) could be interpreted as a minimal 

(background) level. This is consistent with data from pristine sites in Alaska and California where HRGS values did 

not exceed 10.4 mg B[a]P Eq/kg (Anderson et al., 1999b; 

Fairey et al., 1996). Fairey et al. (1996) also demonstrated 

that HRGS values above 60 mg B[a]P Eq/kg were highly 

correlated with degraded benthic communities in San Diego and Mission Bays, and with PAH concentrations above 

the 9,600 μg/kg Probable Effects Level (PEL) guideline 

(MacDonald, 1993), which are similar to the ERLs. Based 

on these data, HRGS values greater than 10 and 60 mg B[a]

P Eq/kg were considered to represent marginal and highly 

contaminated thresholds, respectively.

Differences in the ability of the P450 enzyme system to 

metabolize chlorinated and non-chlorinated compounds 

allows for differentiation between these classes of compounds in environmental samples. Since most PAHs are 

metabolized, they exhibit a maximum response in 6 hours, 

at which point the response begins to fade. Chlorinated 
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hydrocarbons (dioxins, furans, and certain 

PCBs), on the other hand, are not degraded 

and continue to induce CYP1A, resulting 

in increasing responses after 24 hours following exposure. 

Benthic Infaunal Analysis

A benthic community sample was taken 

with the PONAR grab sampler, in addition 

to the samples for chemical analysis and 

toxicity testing. The entire contents of an 

acceptable grab (at least 5 cm deep) was 

sieved on site through a 0.5 mm mesh. In 

coarse sediments, nested sieves of 1.0 mm 

and 0.5 mm were sometimes necessary to 

reduce clogging of the screens and damage to the organisms. All organisms were 

retained in plastic containers and preserved 

in buffered 10% formalin containing Rose 

Bengal stain and sodium borate buffer. 

The following data and information were 

recorded at each site: stratum, site, alternate (if applicable), date, water depth, time, 

latitude, longitude, and depth of sediment 

in the grab. Also included was a written 

description of each sampling site including digital color photographs of the site, a 

physical description of sediment characteristics (texture, color, odor, benthos, sheen) 

and photographs of the undisturbed sediment. 

In the laboratory, all animals were carefully 

segregated into major groups (e.g., worms, 

clams, shrimp and crabs). They were then 

identifi ed to species unless the specimen 

was a juvenile or damaged. At a minimum, 

10% of all samples were re-sorted and 

re-counted on a regular basis. Also, 10% 

of samples were randomly selected and reidentifi ed. The minimum acceptable sorting 

and taxonomic effi ciency was 95%. A 

voucher collection composed of representative individuals of each species encountered in the project 

was accumulated and retained. 

The benthic communities were characterized by abundance 

(number of animals), number of species, and diversity. 

Abundance was calculated as the total number of individuals per grab; species richness as the total number of species 

represented at a given site; and diversity was calculated 

with the Shannon-Weiner Index (Shannon and Weaver, 

1949), using the following formula: 

 S

 H’ = -∑ pi

 (ln pi)

 i=1

where, S = is the number of species in the sample,

i is the ith species in the sample, and 

Figure 4.2. Combined cluster analysis overlays of species clusters and site clusters. 

The top fi gure illustrates the dominant species communities found in different site 

clusters. The lower fi gure illustrates how different species assemblages distribute 

themselves between different habitats.
Chapter 4: Chemical Contaminants and Toxicity

84

STEER Integrated Environmental Assessment Report

pi is the number of individuals of the ith species divided by 

the total number of individuals in the sample.

Nonparametric Spearman rank correlation coeffi cients were 

calculated for all parameters to assess relationships between 

the physical, chemical, toxicological and biological variables. Multivariate cluster analysis was employed to group 

site and species data. The objective was to produce a coherent pattern of association between sites and species (Figure 

4.2). Cluster analysis is a two-step process including: 1) 

creation of a resemblance data matrix from the raw data, 

and 2) clustering the resemblance coeffi cients in the matrix. 

The input resemblance (similarity or dissimilarity) matrix 

can be created by a number of methods. Input data may or 

may not be standardized or transformed depending on the 

requirements of the method (e.g., Bray Curtis). Based on 

previous research (Hartwell and Clafl in, 2005), the Jaccard 

method (Goodall, 1973) was used to generate the similarity matrix. The Jaccard method is a binary method based 

only on presence/absence data, and thus ignores abundance 

values. 

Cluster analyses were calculated from the matrices using the Unweighted Pair-Group Method Using Arithmetic 

Averages (UPGMA) procedure which clusters coeffi cients 

based on arithmetic mean distance calculations (Sneath 

and Sokal, 1973). To optimize the cluster analysis results, 

several manipulations of the input data were performed to 

remove confounding effects and bias:

1- Epibenthic species, such as sea anemones and tunicates, were eliminated from the data set as they are not 

truly infauna.

2- ‘Artifi cial species’ (resulting from failure to identify some specimens all the way down to species) were 

identifi ed as a data bias. For example, if specimens of 

two to three species were identifi ed in genus A, and other 

specimens were identifi ed only to genus A, this tends to 

artifi cially increase species richness and diversity of the 

sample when in fact that diversity is an artifact of imperfect taxonomic identifi cation. In some instances, specimens were only identifi able to family, order or class. To 

address this problem, specimens not identifi ed to species 

level were eliminated, unless they were identifi ed to a 

taxonomic level below which no other specimens in the 

collection belonged. That is, even though they were not 

identifi ed to species, they were the only representative 

Figure 4.3. Hypothetical representation of the distribution of physicochemical habitat parameters, contaminant concentrations, and 

other site-specifi c data used to characterize site and species clusters. 
Chapter 4: Chemical Contaminants and Toxicity

85

STEER Integrated Environmental Assessment Report

of that taxonomic line and did represent a non-redundant 

taxon. In other cases, where a specimen was identifi ed to 

genus and there was only one species identifi ed in that 

genus, they were combined at the genus level.

3- Rare and unique species were defi ned as those species 

that were found at no more than two sites. Although they 

do contribute to the overall assessment of biodiversity, 

they were eliminated from the cluster analysis data set. 

Because of their limited distribution, by defi nition, they 

do not provide information on the impact of contaminant 

or other stressor gradients in the environment because 

they do not occur across a gradient.

After the data set had been fi nalized, a nodal analysis 

routine was applied to the data (Lambert and Williams, 

1962). This consisted of combining independent cluster 

analyses in a graphical array. The fi rst analysis clustered 

sites using species occurrence data. The second calculation 

clustered species together into groups. The intersection of 

site clusters on the abscissa and species clusters on the ordinate axis yields a pattern of species associations with site 

clusters, termed nodes (Figure 4.2). The site and species 

clusters were also characterized by physicochemical habitat 

parameters, contaminant concentrations, and other sitespecifi c data. Plotting the tabulated values in parallel to 

the cluster output (Figure 

4.3), allows an empirical 

evaluation of similarities 

in habitat characteristics within and between 

species and site clusters 

(i.e., what they do or do 

not have in common) 

to guide interpretation 

of subsequent statistical contrasts. For each 

species, the parameters 

were normalized to their 

abundance at each site. 

Once the nodes were 

defi ned, the species 

data within each node 

were further assessed 

with methods developed 

by Clark and Warwick 

(2001) to assess the 

relative importance of a 

species in characterizing 

a set of sites in a quantitative way, called a Similarity Index. Average similarity for a species is the contribution of the species to the Bray-Curtis similarity within a site 

group (node). This value indicates how typical the species 

is for the group of sites and ranges from 0 to 100%.

4.3. RESULTS AND DISCUSSION 

Field Data

The collection of 25 sediment samples was planned for 

the June 2011 sampling mission. Twenty-nine sites were 

visited, however, at fi ve sites the fi eld team was unsuccessful in collecting sediments, resulting in sediment samples 

from 24 sites. 

The average water depth at the sites sampled was 7.2 meters (m). As might be expected, the shallower sites were 

in Mangrove Lagoon. The shallowest water depth was 0.6 

m at Site 1-5P in Mangrove Lagoon. The average salinity 

encountered on the surface of the sites was 33.2‰, the average bottom salinity 33.7‰, indicating fairly well mixed 

waters. The highest salinity encountered during the mission 

was 34.6‰, a bottom salinity reading taken at Site 5-61P; 

the lowest salinity encountered (28.3‰) was in Mangrove 

Lagoon on the surface at Site 1-1P. Additional information 

on fi eld data from this phase of the STEER project by site 

can be found in the appendices in Pait et al. (2013). The 

average water surface temperature at the sites in the STEER 

Figure 4.4. Percent fi nes (percent silt plus percent clay fractions) in sediments from the STEER. 
Chapter 4: Chemical Contaminants and Toxicity

86

STEER Integrated Environmental Assessment Report

was 30.1°C, the average bottom temperature was 29.5°C. 

A Kruskal-Wallis test run on the ranked data indicated that 

salinity (p < 0.0001) and temperature (p<0.0001) varied 

signifi cantly by stratum, with lower salinities and higher 

temperatures being found in Strata 1 and 2. 

Total Organic Carbon and Grain Size

The average percent total organic carbon (TOC) in the 

sediments collected was 2.49%, and ranged from a low of 

0.44% to a high of 5.44%. A Kruskal-Wallis test run on the 

ranked TOC values indicated no differences in percent TOC 

in the STEER by stratum (p = 0.0645). 

Chemical contaminants, particularly organic (carboncontaining) contaminants, tend to accumulate in sediments 

with higher TOC values. Chemical contaminants also tend 

to accumulate in sediments that have a higher proportion 

of the smaller grain sizes (i.e., silt and clay). Smaller grain 

size sediments have more surface area per unit volume 

available for the adsorption of contaminants, and are typically found in depositional habitats. In addition, metals are 

attracted to sediments with higher clay content due to the 

charge structure on the surface of the clay particles. 

For this report, the percent silt and percent clay fractions 

are combined and referred to as percent fi nes (sum of the 

percent silt and percent clay sediment fractions). Figure 

4.4 shows the percent fi nes in the sediments sampled in the 

STEER; the average content was 22.3 ±4.03%. It can be 

seen that areas in Mangrove Lagoon and to a certain extent 

in Benner Bay, had a higher proportion of percent fi nes in 

the sediments. However, the major sediment size class in 

the STEER was sand (68 ±4.35%). 

Chemical Contaminants

The results from the analysis of chemical contaminants in 

the sediments are discussed below. Additional information, 

including results from individual sites can be found in the 

appendices section in Pait et al (2013).

Polycyclic Aromatic Hydrocarbons

Total PAHs as used in this report refers to the sum of the 59 

PAH compounds and compound classes (e.g., anthracene, 

C1-napthalenes) analyzed in the STEER sediment samples. 

It can be seen in Figure 4.5 that there were a number of 

higher PAH concentrations, mainly in Mangrove Lagoon 

and Benner Bay, compared to the other strata and sites further offshore. As will be seen, the pattern of higher concentrations of chemical contaminants in the Mangrove Lagoon 

and northern Benner Bay areas was repeated for a number 

of the other contaminant classes analyzed.

The mean concentration of total PAHs in the sediment from 

the STEER was 142 ±58 ng/g. The units ng/g (nanogram/

gram) are also referred to as parts per billion (ppb). The 

median total PAH concentration was 6.02 ng/g. The highest total PAH concentration was at site 1-3P, with 1,131 

ng/g. In Mangrove Lagoon, the mean concentration of total 

PAHs in the sediments was 425 ±214 ng/g, with the standard error indicating a wide range in the concentrations in 

this stratum (Stratum 1). The lowest concentration of total 

PAHs was found in Stratum 4, at site 4-49P (0.93 ng/g) 

near St. James Island. From the preliminary sampling for 

this project in 2010, the highest concentration of total PAHs 

was found at the ML-10 site in Mangrove Lagoon, at 951 

ng/g. 

Variation of Total PAHs Across Strata. A Kruskal-Wallis 

test run on the ranked data indicated a signifi cant difference 

in total PAHs by stratum (p = 0.0210). A Tukey’s HSD 

(Highly Signifi cant Difference) analysis indicated that only 

Stratum 1 and Stratum 4 were signifi cantly different, due in 

part to the large standard errors in total PAHs within each 

stratum. Note that the targeted samples collected in 2010 

were not included in the statistical analysis by stratum. 

Comparison with Other Data. EPA’s Environmental Monitoring and Assessment Program (EMAP) was developed to 

monitor and assess the status and trends of national ecological resources (EPA, 2000). In 2004, sediment samples were 

collected and analyzed by EMAP at a number of locations 

around St. Thomas. Four of those sites were in the STEER; 

two sites were in Benner Bay, and one site each in Jersey 

Bay and Great Bay. The four EMAP sites are also included 

in Figure 4.1. A suite of 23 PAHs were analyzed in the 

sediments at each site. The detection limit for each PAH 

analyzed by EMAP was 10 ng/g. None of the sediments 

sampled within the STEER boundaries by EPA’s EMAP 

had a detectable level of the PAHs analyzed. 

Recent chemical contaminant studies have also been 

conducted in Puerto Rico and can be used to compare with 

the results found in the STEER. In Vieques, Puerto Rico, 

the mean concentration of total PAHs was 52.3 ±8.7 ng/g, 

somewhat below total PAHs found in the STEER sediments 

(Pait et al., 2010). In southwest Puerto Rico, Pait et al. 

(2008) reported a mean total PAH concentration in the sediments of 80.6 ±25.5 ng/g, also lower than the mean found 

in the STEER. 

Because of the national-level contaminant monitoring carried out by NOAA’s NS&T Program, data from the STEER 

can be compared with data from the rest of the Nation’s 

coastal waters. For this report, data from the STEER 

sediments are compared with the most recent (2006/2007) 

nationwide analysis of sediments from the NS&T Program. 

The most recent NS&T nationwide sediment analysis data 
Chapter 4: Chemical Contaminants and Toxicity

87

STEER Integrated Environmental Assessment Report

Figure 4.5 Total polycyclic aromatic hydrocarbons (PAHs) detected in sediments from the St. Thomas 

East End Reserves.

were used, as the number 

of compounds in some 

of the chemical contaminant classes (e.g., 

total PAHs, total PCBs 

and total DDT) that 

NS&T analyzes, have 

increased over time, and 

the 2006/2007 NS&T 

sediment data contains 

the most comparable list 

of analytes. 

The NS&T 2006/2007 

median (NS&T median) 

for total PAHs is 395 

ng/g. Three sites, two of 

which were in Mangrove 

Lagoon (1-3P, 1-2P, and 

3-32P), were above the 

NS&T median for total 

PAHs. None of the sites 

sampled in the STEER 

approached the NS&T 

2006/2007 85th percentile of 2,883 ng/g. The 

median (i.e., the “middle 

value”) and 85th percentile values (elevated contaminant concentrations), are used 

to show how the results from the STEER sediments compare with NOAA’s national results.

NOAA Sediment Quality Guidelines for Total PAHs. As 

noted earlier, the NS&T Program developed effects-based, 

numeric guidelines to estimate the toxicological relevance 

of certain sediment chemical contaminants (Long et al., 

1998). These guidelines, the Effects Range-Low (ERL) 

and the Effects Range-Median (ERM) defi ne sediment 

contaminant concentration ranges that are rarely (<ERL), 

occasionally (ERL to ERM) or frequently (>ERM) associated with toxic effects in aquatic biota (NOAA, 1998). 

The ERL and ERM values for total PAHs are also shown 

in Figure 4.5. As can be seen, total PAHs in the sediments 

were below the ERM and ERL as well. 

NOAA’s NS&T Program has also developed ERL and 

ERM guidelines for a number of individual PAHs, which 

are shown in Table 4.2. None of the sediments collected 

in the STEER exceeded the ERL, ERM or the NS&T 85th 

percentile for any of the individual PAHs listed. However, from the 2011 stratifi ed random sampling, Sites 1-2P, 

1-3P and 3-32 exceeded the NS&T median for a number 

Table 4.2. Comparison of higher concentrations of individual PAHs at STEER sites with NOAA NS&T data.

Sites NS&T Statistics and Guidelines

Compound 1-2P 1-3P 3-32P BB-1 BB-2 ML-10 Median 85th Percentile ERL ERM

Acenaphthylene 2.2 3.4 0.2 2.8 4.0 2.4 2.1 15.1 44 640

Anthracene 3.2 5.6 1.3 7.4 9.2 5.7 3.4 38.7 85.3 1,100

Napthalene 7.3 9.2 0.9 5.4 6.4 7.3 3.7 27.6 160 2,100

Benzo-a-pyrene 20.3 35.0 35.1 9.6 17.5 15.6 14.7 127 430 1,600

Dibenzo(a,h)anthracene 3.4 6.4 8.2 7.4 6.9 11.6 5.0 23.8 63.4 260

All concentrations are in ng/g.
Chapter 4: Chemical Contaminants and Toxicity

88

STEER Integrated Environmental Assessment Report

of the individual 

PAHs listed (Table 

4.2). From the 2010 

targeted sampling, 

BB-1, BB-2 and ML10 also exceeded the 

median for a number 

of the listed PAHs. 

As will be seen 

later, results from the 

P450 test indicated 

a response to PAHs 

in Mangrove Lagoon 

and northern Benner 

Bay. 

The ratios of phenanthrene-to-anthracene 

(P/A) and fl uoranthene-to-pyrene 

(F/P) have been used 

as a screening tool 

to assess the relative contributions of 

pyrogenic (combustion-related) versus 

petrogenic (uncombusted) sources of 

PAHs (Budzinski 

et al., 1997). Higher levels of uncombusted PAHs would 

be more indicative of the presence of spilled fuels, such 

as gasoline or oil. P/A ratios less than 10 are more indicative of pyrogenic sources; F/P ratios greater than 1 are also 

thought to be associated with pyrogenic sources. Most of 

the sites in the STEER had P/A ratios of less than 10, and 

the F/P ratio close to or above 1, indicating the pyrogenic 

nature of the PAHs present in the sediments. At 1-3P in 

Mangrove Lagoon, which had the highest total PAH level 

in the samples analyzed from the STEER, the P/A ratio was 

3.24, indicating pyrogenic sources, however the F/P ratio 

was 0.70, indicating that petrogenic sources may also have 

contributed to the mix of PAHs found in the sediments at 

this site. 

Effects of Sediment Grain Size and TOC. As noted earlier, 

the adsorption of organic contaminants onto sediments is 

strongly infl uenced by grain size (Hassett et al., 1980). The 

smaller grain sizes of the silts and clays have proportionally higher surface areas available for the adsorption of 

chemical contaminants and tend to have more TOC than 

coarse grained sediment. To assess this relationship for the 

samples collected in the STEER, a nonparametric correlation analysis (Spearman’s) was run between percent fi nes 

(sum of percent silt and percent clay) and the concentration 

of total PAHs found in the sediment samples. There was 

a highly signifi cant (p < 0.0001) and positive correlation 

between the percent fi nes and the concentration of total 

PAHs. There was also a signifi cant negative correlation (p 

<0.0001) between the concentration of PAHs and the sand 

fraction of the sediments, indicating that as the percent sand 

concentration increased in sediments, the amount of total 

PAHs present was correspondingly lower. 

Typically, a positive relationship also exists between sediment total organic carbon (TOC) and chemical contaminants in freshwater, estuarine and coastal waters (Shine 

and Wallace, 2000; Hassett et al., 1980). Because of this, 

organic contaminant concentrations are often normalized 

to the organic carbon content of sediments. However, a 

nonparametric correlation between TOC and total PAHs for 

the STEER samples was not signifi cant (Spearman Rho = 

-0.1779, p = 0.4057).

 

Total Extractable Hydrocarbons

The results of the analysis of total extractable hydrocarbons, or TEH, is shown in Figure 4.6. TEH is not only 

composed of PAHs, such as those occurring from the combustion of fuels, but also of straight and branched aliphatics 

Figure 4.6. Total extractable hydrocarbons (TEH) detected in sediments from the St. Thomas East End 

Reserves.
Chapter 4: Chemical Contaminants and Toxicity

89

STEER Integrated Environmental Assessment Report

(nonaromatic hydrocarbons) 

found in uncombusted fuels, 

in oil, and from natural sources (e.g., decaying vegetation). 

TEH provides a more complete assessment of the total 

mass of hydrocarbons present 

in a sediment sample. 

It can be seen from Figure 4.6 

that the relative concentration of TEH in the STEER 

mirrors total PAHs (Figure 

4.5). It should be noted, 

however, that the units for 

total PAHs are in ng/g (ppb), 

while TEH is in μg/g (ppm 

or parts per million). TEH in 

the sediments at a number of 

locations in the STEER were 

approximately an order of 

magnitude higher than total 

PAHs. The mean TEH concentration in the STEER was 

167 μg/g. The highest TEH concentration (1,104 μg/g) was 

found in Mangrove Lagoon at 1-3P. 

Variation of TEH Across Strata. An ANOVA run on the 

log10 transformed data indicated that TEH varied by stratum (p = 0.0018), and a Tukey-Kramer HSD test indicated 

that Stratum 1 was signifi cantly different (higher) than 

Strata 3, 4 and 5. 

Sediment Quality Guidelines and TEH. There are no 

NOAA sediment quality guidelines for TEH. Boehm et al. 

(2008) carried out a regression analysis between total PAHs 

and TEH, and calculated a TEH “ERL” of 2,600 μg/g, and 

a TEH “ERM” of 9,760 μg/g. Using these values as rough 

TEH sediment quality guidelines, none of the TEH concentrations found in the STEER exceeded the lower threshold 

estimated by Boehm et al. (2008). 

Effects of Sediment Grain Size and TOC. A nonparametric 

correlation run between TEH and percent fi nes indicated a 

signifi cant positive correlation (Spearman Rho = 0.5852, 

p = 0.0027), however, there was no signifi cant correlation 

between TEH and TOC (Spearman Rho = -0.0030, p = 

0.9887). 

Aliphatics. Straight chain and branched aliphatics, also a 

subset of TEH, are indicative of uncombusted fuels or oil, 

were analyzed in the sediment samples (Figure 4.7). There 

were a number of aliphatics in the C-19 (molecules containing 19 carbons), and the C-23 to C-31 range, with spikes 

at C-19 and C-27, particularly at Site 3-32P but also at Site 

5-70A. The aliphatics present appear to be in the range of 

diesel fuel and lubricating oils (Libes, 1992), and could 

indicate some type of discharge in the past or perhaps low 

level, chronic (longer term) inputs at this site. 

Polychlorinated Biphenyls

Total PCBs detected in the sediments are shown in Figure 

4.8. Total PCBs as included in this report represents the 

sum of the 38 congeners analyzed for the project (Table 

4.1). 

The mean concentration of total PCBs found in the STEER 

was 1.00 ±0.32 ng/g; the median was 0.37 ng/g. The highest concentration of total PCBs from the stratifi ed random 

sampling was 7.2 ng/g; from the targeted 2010 sampling, 

the highest concentration was 65.9 ng/g at BB-2 (Figure 

4.8). Eighteen, or 75%, of the sites sampled in the STEER, 

however, had a total PCBs concentration of less than 1 

ng/g. 

Variation of Total PCBs Across Strata. The variation of 

total PCBs by stratum was assessed using an ANOVA, run 

on the log10 normalized concentration values. The results 

indicated no signifi cant variation (p = 0.0573) in total PCBs 

across the fi ve strata established in the STEER.

Comparison with Other Data. EPA’s EMAP sampled and 

analyzed sediments in the STEER from four locations in 

2004 (Figure 4.1). A total of 21 congeners were analyzed 

in the sediment samples taken. No PCB congeners were 

detected in the four samples analyzed; the detection limit 

for each congener was 0.05 ng/g.

Figure 4.7. Straight chain and branched hydrocarbons (aliphatics) in sediments from the St. 

Thomas East End Reserves.

0.00

0.20

0.40

0.60

0.80

1.00

1.20

1.40

1.60

1.80

2.00

Aliphatic Chain Length 

ug aliphatics/dry g 

Site 3-32P

Site 5-70A
Chapter 4: Chemical Contaminants and Toxicity

90

STEER Integrated Environmental Assessment Report

In a project conducted 

by NCCOS in Jobos 

Bay, the mean total 

PCBs concentration 

found in the sediments 

was 2.09 ±0.50 ng/g 

(Pait et al., 2012). In 

Vieques, that value 

was 2.86 ±0.14 ng/g 

(Pait et al., 2010), both 

of which are higher 

than the STEER. In 

southwest Puerto Rico, 

the mean total PCBs 

concentration in sediments was 12.1 ±2.26 

ng/g not including two 

very high total PCBs 

concentrations (1,022 

ng/g and 2,710 ng/g) 

within Guanica Bay 

Pait et al., 2008). If 

the two sites in Guanica Bay are included, 

the mean for total 

PCBs in the southwest 

Puerto Rico study area 

was 74.7 ±47.9 ng/g 

(Pait et al., 2008). 

Four of the fi ve sites from the stratifi ed random sampling 

(in Mangrove Lagoon and northern Benner Bay) had a total 

PCBs concentration above the NS&T median of 2.2 ng/g. 

All four of the 2010 targeted sample were above the NS&T 

median. BB-2 (65.9 ng/g) from the targeted sampling was 

above the NS&T 85th percentile (23.7 ng/g) for total PCBs. 

NOAA Sediment Quality Guidelines for Total PCBs. The 

concentration of total PCBs at Site BB-2 (65.9 ng/g) from 

the 2010 targeted sampling was higher than the PCB 

ERL (Figure 4.8). At 21.8 ng/g, ML-10 was just below 

the ERL. Levels below the ERL indicate that effects on 

benthic infauna are not as likely. Concentrations above the 

ERL but below the ERM indicate that more sensitive species or life stages may be impacted. 

Effects of Grain Size and TOC. A nonparametric analysis of the data revealed a signifi cant positive correlation 

between total PCBs and the fi nes fractions of the sediment 

(Spearman Rho = 0.5452, p = 0.0059). No signifi cant correlation existed between total PCBs and gravel, and there 

was a signifi cant negative correlation (Spearman Rho = 

-0.4648, p = 0.014) between sand and total PCBs. 

An analysis of total PCBs and TOC revealed no signifi cant 

correlation (Spearman Rho = 0.0322, p = 0.8813), similar 

to what was observed for PAHs. For both PAHs and PCBs 

in the STEER, sediment concentrations appeared to be 

infl uenced more by sediment particle size than sediment 

TOC. 

DDT and Other Organochlorine Pesticides

Figure 4.9 contains the results of the analyses of total 

DDT in sediment samples from the STEER. Total DDT 

as defi ned in this report is the sum of the parent isomers 

(4,4’-DDT and 2,4’-DDT), along with degradation products 

DDE, DDD and DDMU. The mean concentration of total 

DDT in the sediments in the STEER was 0.047 ±0.025 

ng/g; the median was 0.002 ng/g. As with a number of 

the other chemical contaminants, higher concentrations of 

total DDT were found in the Benner Bay and Mangrove 

Lagoon areas. The highest total DDT concentration from 

the stratifi ed random samples collected in 2011 was 0.609 

ng/g at 2-20P (Table 4.3). The highest concentration of 

total DDT from the 2010 targeted sampling was 3.61 ng/g 

at BB-2 (Figure 4.9) in northern Benner Bay. The second 

highest concentration was also in Benner Bay (1.31 ng/g) at 

BB-1. Currently, there does not appear to be much agriculFigure 4.8 Total PCBs detected in sediments from the St. Thomas East End Reserves.
Chapter 4: Chemical Contaminants and Toxicity

91

STEER Integrated Environmental Assessment Report

ture on the island of St. 

Thomas, although in the 

past DDT could have 

been used on crops such 

as sugarcane, fruits and 

vegetables, along with 

use to control mosquitoes. 

Variation of Total 

DDT Across Strata. 

Although there were 

some elevated levels 

of DDT in Benner Bay 

and Mangrove Lagoon 

(Table 4.3), an ANOVA 

run on log10 normalized data indicated no 

signifi cant variation (p 

= 0.2575) in total DDT 

concentration across 

the fi ve strata in the 

STEER. In addition, 

the degradation products DDD and DDE 

appeared to make up 

much of the total DDT 

present, indicating that 

the parent compound had degraded over time. 

Comparison with Other Data. EPA’s EMAP analyzed DDT 

along with a number of DDT degradation products from 

four sites in the STEER. The only DDT-related compound 

detected was the degradation product 4,4’-DDD, at a 

concentration of 0.26 ng/g at one site. In southwest Puerto 

Rico, Pait et al. (2008) detected a mean total DDT concentration of 2.10 ±1.26 ng/g, higher than in the STEER. 

In Jobos Bay, the mean total DDT concentration was 0.54 

±0.10 ng/g. In Vieques, the mean concentration of total 

DDT in the sediments was substantially higher, 23.6 ±16.5 

ng/g, due in part to elevated concentrations (78 ng/g to 

1,274 ng/g total DDT) at four sediment sampling sites (Pait 

et al., 2010). 

The concentration of total 

DDT in the 

STEER exceeded the NS&T 

median value 

of 0.395 ng/g 

at four sites, 

three of those from the 2010 targeted sampling (Table 4.3). 

The concentration of total DDT at BB-2 was just above the 

NS&T 85th percentile of 3.49 ng/g.

NOAA Sediment Quality Guidelines for Total DDT. The 

concentration of total DDT at BB-2 (3.61 ng/g) from the 

2010 targeted sampling was also above the ERL (1.58 

ng/g). However, none of the sites sampled in the STEER 

had a concentration above the DDT ERM.

Effects of Sediment Grain Size and TOC. A nonparametric analysis of the data revealed no signifi cant correlation 

between total DDT and percent fi nes (Spearman Rho = 

0.2993, p = 0.1554), or total DDT and percent TOC (SpearFigure 4.9. Total DDT detected in sediments from the St. Thomas East End Reserves.

Sites NS&T Statistics and Guidelines

Compound 1-5P 2-16P 2-20P BB-1 BB-2 ML-10 Median 85th Percentile ERL ERM

Total DDT 0.10 0.082 0.609 1.31 3.61 0.86 0.395 3.49 1.58 46.1

Chlordane 0.07 0.18 0.02 0.22 0.2 0.85 0.195 0.975 0.5 6

Total Endosulfan 0.0 0.0 0.142 0.0 1.13 0.63 0.0 0.253 N/A N/A

Chlorpyrifos 0.0 0.253 0.0 1.33 0.13 0.62 0.01 0.328 N/A N/A

N/A, not available

Table 4.3. Comparison of higher concentrations (ng/g) of pesticides at STEER sites with NOAA NS&T data.
Chapter 4: Chemical Contaminants and Toxicity

92

STEER Integrated Environmental Assessment Report

man Rho = -0.0060, p = 0.9776), however, it should be 

noted that 13 of the 24 stratifi ed random samples had no 

detectable level of total DDT. 

Additional Pesticides. A number of other pesticides were 

analyzed in the sediments from the STEER as part of this 

project. Most of the results were below detection limits. 

Selected results are shown in Table 4.3. The highest concentration of chlordane (alpha and gamma isomers) detected in STEER sediments was 0.85 ng/g at site ML-10 at 

the mouth of Turpentine Gut, 

which empties into Mangrove 

Lagoon. This concentration 

is above the NS&T median 

but below the NS&T 85th 

percentile for chlordane (Table 

4.3). NOAA has also established ERL and ERM values 

for chlordane. Chlordane was 

above the ERL only at ML10. None of the sites had a 

chlordane concentration above 

the ERM. 

The insecticides endosulfan 

and chlorpyrifos have had 

both agricultural and nonagricultural (e.g., homeowner) 

uses. Endosulfan, an organochlorine insecticide, is currently being phased out for all uses due to health risks to 

farmworkers and wildlife, and its persistence in the environment (EPA, 2010). Since there appears to be little commercial agriculture currently on St. Thomas, it is likely that 

endosulfan was used in the past, perhaps on vegetables and 

fruits in gardens, prior to being phased out for homeowner 

use. The highest concentration of total endosulfan (sum of 

endosulfan I and II and endosulfan sulfate) detected in the 

STEER (1.13 ng/g) was at BB-2 in Benner Bay, which is 

above the NS&T median and 85th percentile. There are no 

NOAA sediment quality guidelines for endosulfan. 

Although the organophosphate insecticide chlorpyrifos has 

had widespread use both domestically and in agriculture, 

virtually all homeowner uses have been eliminated (EPA, 

2002b). Chlorpyrifos can still be used on certain food 

crops, on golf courses, for wood treatment (nonstructural), 

and as an adult mosquitocide. The highest concentration 

of chlorpyrifos (1.33 ng/g) was in Benner Bay at BB-1. 

This concentration was above the NS&T median and also 

above the 85th percentile (Table 4.3). The concentration of 

chlorpyrifos at ML-10 was also above the NS&T median 

and 85th percentile. There are no NOAA sediment quality 

guidelines for chlorpyrifos. 

Tributyltin (TBT)

The results of the analysis of butyltins in STEER sediments 

are shown in Figure 4.10. Mono-, di-, tri-, and tetrabutyltins were analyzed in the sediments. Tetrabutyltin is 

an intermediate in the manufacture of TBT compounds. 

As noted earlier, TBT has had extensive use in the past 

as an antifoulant on boat hulls. In the environment, TBT 

degrades to dibutyltin, then monobutyltin, and fi nally to 

inorganic tin. Experiments have shown that the half-life of 

TBT, the amount of time needed to convert half of the TBT 

to dibutyltin in natural water 

samples, is on the order of 

days; degradation to monobutyltin takes approximately 

a month (Batley, 1996). Experiments with aerobic sediments have shown that the 

half-life of TBT is similar 

to that measured in solution. 

In deeper, anoxic sediments, 

however, the half life of TBT 

appears to be considerably 

longer, on the order of years 

(Batley, 1996) to decades 

(Mathiessen, 2013). 

The mean concentration of 

TBT in the sediments in the 

STEER was 1.85 ±1.30 ng Sn/g; the median was zero. The 

highest concentration of TBT detected in STEER sediments 

collected using the stratifi ed random sampling design was 

at site 2-20P in Benner Bay, with a concentration of 31 

ng/g. However, of the samples analyzed from 2010, BB-1 

and BB-2 had even higher TBT concentrations. The concentration of TBT at BB-1 was 77 ng/g; the TBT concentration at BB-2 was 248 ng/g. 

Variation of TBT Across Strata. Because the targeted 2010 

samples were collected nonrandomly, that data cannot be 

used to assess the variation of TBT in sediments across the 

STEER strata. An ANOVA run on the log10 transformed 

data for the 2011 samples collected using the stratifi ed random design did not indicate any signifi cant differences (p = 

0.4368) in the concentration of TBT between strata. 

Comparison with Other Data. The NS&T median concentration of TBT in sediments is 0.16 ng Sn/g. The NS&T 

85th percentile for TBT is 1.38 ng Sn/g, lower than the 

mean concentration of TBT found in STEER sediments. 

The highest concentration of TBT detected in the STEER 

(248 ng Sn/g) represents the third highest detection ever 

in sediments in NOAA’s NS&T Program (not just the 

2006/2007 nationwide sediment sampling). The only two 

s

d

b

a

p

m

h

t

I

h

a

l

(

(

Sampling of sediments in the STEER.
Chapter 4: Chemical Contaminants and Toxicity

93

STEER Integrated Environmental Assessment Report

higher TBT concentrations from 

NOAA’s NS&T 

Program were 

from the Elizabeth River in the 

southern Chesapeake Bay area, 

and Elliot Bay 

in Puget Sound. 

Pait et al. (2008) 

detected a mean 

TBT concentration of 0.01 

±0.01 ng Sn/g 

in southwest 

Puerto Rico. In 

Vieques, Puerto 

Rico, the mean 

concentration of 

TBT was 0.05 

±0.02 ng Sn/g 

and in Jobos 

Bay, the mean 

concentration 

was 0.56 ±0.28 

ng Sn/g. 

It should be 

noted, however, 

that 15 of the 24 sediment samples taken in the STEER had 

no detectable TBT at all. The higher concentrations of TBT 

tended to occur in the northern Benner Bay area. For the 

most part, this was also the case for the TBT degradation 

products dibutyltin and monobutyltin. 

Sediment Quality Guidelines and TBT. There are no established sediment quality guidelines for TBT, due in part 

to the complex chemistry of this compound, including its 

bioavailability largely being governed by partitioning into 

porewater (water in between sediment particles), which is 

in turn is governed by a number of parameters of the sediment at a site. 

One of the few attempts at establishing guidelines for TBT 

was reported by Weston (1996). In that document, lower 

and upper screening values were established for TBT, based 

on a sediment organic carbon content of 2%. The intent 

was to establish thresholds for cleanup actions at EPA Superfund sites in Puget Sound. The lower and upper values 

are not analogous to NOAA ERL or ERM values, but rather 

represent a range that was to be used to determine when 

additional testing (e.g., additional toxicity testing) at a site 

would be advisable. Using this approach, Weston (1996) 

recommended TBT values between 10 and 144 ng Sn/g as 

the lower and upper screening values, respectively, with the 

actual screening value selected being determined by an EPA 

site manager at a particular EPA Superfund site. If these 

two values are used as rough boundaries for determining 

when additional work (e.g., toxicity testing) would be recommended, it indicates there should be concern regarding 

the elevated TBT level at BB-2, especially as the concentration was above the higher screening value developed 

by Weston (1996). Sites BB-1 and 2-20P were above the 

lower screening value but below the upper screening value, 

but are also of concern. The results did not change even 

when the organic carbon content from each of these three 

sites was incorporated into the equations used in Weston 

(1996), including BB-2, which had an organic carbon 

content of roughly 2%. In the next chapter, results from 

follow-up sampling and analysis of surface sediments, and 

of sediment cores in northern Benner Bay are presented. 

Figure 4.10. Tributyltin detected in sediments from the St. Thomas East End Reserves. BB-1 and BB-2 represent targeted, nonrandomized samples taken in 2010.
Chapter 4: Chemical Contaminants and Toxicity

94

STEER Integrated Environmental Assessment Report

Butyltin Levels in the Sediments. A summary of the results 

for TBT and its metabolites in southwest Puerto Rico (Pait 

et al., 2007) and Vieques, Puerto Rico (Pait et al., 2010) is 

shown in Figure 4.11. From this fi gure, it can be seen that 

the majority of the butyltin present in the sediment samples 

taken from both southwest Puerto Rico and Vieques were 

primarily in the form of monobutyltin and dibutyltin, with 

only a small fraction of the total as the parent or undegraded TBT. This would be expected if TBT use had occurred 

primarily in the past. 

Figure 4.12 shows the same type of information for the 

three sites in the STEER that had the highest TBT concentrations. Not only are the absolute concentrations much 

higher, the ratios of TBT to monobutyltin and dibutyltin at 

these three sites are different from those shown in Figure 

4.11. The concentration of TBT at the three sites in the 

STEER was similar to, if not higher than, the concentration 

of monobutyltin and dibutyltin at these same sites. The 

higher concentrations of TBT relative to monobutyltin and 

dibutyltin, along with the overall higher concentration of 

TBT, may be indicative of recent TBT deposition. This may 

be a result of the mooring of boats and/or the cleaning and 

scraping of boat bottoms containing TBT-based paints, with 

subsequent input of these materials (e.g., paint chips or 

dust) through stormwater runoff into adjacent waters. 

The higher levels of TBT found could also be related to 

past deposition. As noted, the sediment samples analyzed 

as part of this project were surfi cial or surface sediments. 

For this part of the project, the top three cm (centimeters) 

Mean butyltins in sediments from southwest Puerto Rico.

% indicates percent of butyltin total

Mean butyltins in sediments from Vieques, Puerto Rico.

Figure 4.11. Tributyltin detected in sediments from southwest 

Puerto Rico and Vieques, Puerto Rico. Values represent means. 

Butyltins in sediments from 20P in the STEER (2011).

% indicates percent of butyltin total

Figure 4.12. Tributyltin detected in sediments from three sites 

in the STEER.

Butyltins in sediments from BB-1 in the STEER (2010).

Butyltins in sediments from BB-2 in the STEER (2010).
Chapter 4: Chemical Contaminants and Toxicity

95

STEER Integrated Environmental Assessment Report

of sediment were collected from the sediment grab. Given this, 

it is likely that the samples analyzed represent 

more recently deposited 

sediments. In order to 

confi rm this, additional 

studies were used to assess the sedimentation 

rate in this part of Benner Bay. As part of the 

monthly monitoring in 

the STEER conducted 

by UVI, six sediment 

traps were installed in 

the STEER, including sites in Mangrove 

Lagoon, Benner Bay, 

Rotto Cay, Cowpet Bay, 

and adjacent to Great 

St. James and Little St. 

James. As will be seen 

in Chapter 9, terrestrial inputs into Benner 

Bay and Mangrove 

Lagoon were higher 

than the other sites in 

the STEER. Regardless of whether the TBT found in the 

Benner Bay area is from past inputs, more recent inputs, or 

both, the elevated levels suggests the need for additional 

work to quantify the distribution of this contaminant in the 

sediments along with effects (toxicity), particularly in mollusks. As noted earlier, Strand et al. (2009) found evidence 

of elevated levels of TBT and its degradation products in 

several gastropod species, as well as imposex at several locations, including Charlotte Amalie Bay in St. Thomas. As 

part of the project in the STEER, samples of queen conch 

(Lobatus gigas) and coral (Porites astreoides) were analyzed for chemical contaminants, including butyltins, which 

are reported in Chapter 7. 

Follow-up sampling was conducted in 2013 in northern 

Benner Bay to assess TBT in sediment cores as well as 

additional surface samples, at the request of DPNR. The 

results of that work are reported in Chapter 5. This information is of particular importance if dredging operations 

(e.g., for deepening the navigation channels) in this part of 

Benner Bay were to occur in the future, as it could be used 

to help guide dredging operations to limit the transport and 

more importantly the impact of contaminated sediments. 

Effects of Sediment Grain Size and TOC. The correlation 

of TBT concentrations to grain size and TOC was examined for sediments sampled in the STEER. A nonparametric analysis of the data revealed a signifi cant correlation 

between TBT and percent fi nes (Spearman Rho = 0.5759, 

p = 0.0032). As noted earlier, smaller grain sizes (silt and 

clays) of sediments have more surface area available for 

the adsorption of contaminants. There was no correlation, 

however, found between TBT and percent TOC (Spearman 

Rho = 0.0430, p = 0.8419), similar to what was seen for a 

number of the other organic chemical contaminants analyzed for this project. 

Cadmium

The range of cadmium concentrations in the sediments 

sampled in the STEER can be seen in Figure 4.13. The 

mean concentration in the STEER sediments was 0.03 

±0.02 μg/g. Only three sediment samples from the stratifi ed random sampling had a detectable level of cadmium, 

including 1-1P and 1-3P in Mangrove Lagoon, and 2-16P in 

Benner Bay. The highest concentration of cadmium in the 

samples was 0.264 μg/g at site 1-3P. Of the four samples 

collected in 2010, the highest concentration was 0.371 μg/g 

at ML-2 in Mangrove Lagoon. At BB-2, no cadmium was 

detected. 

Figure 4.13. Cadmium detected in sediments from the St. Thomas East End Reserves.
Chapter 4: Chemical Contaminants and Toxicity

96

STEER Integrated Environmental Assessment Report

Variation of Cadmium Across Strata. 

Because of the low 

number of detections 

of cadmium in the 

STEER, no analysis 

by stratum was carried 

out. 

Comparison with 

Other Data. EPA’s 

EMAP analyzed 

cadmium in sediments 

from four locations 

in the STEER. The 

mean concentration 

of cadmium was 0.25 

μg/g, higher than the 

mean detected in the 

STEER in the current 

project. In southwest 

Puerto Rico, the mean 

cadmium concentration in sediments was 

0.01 μg/g, similar 

to that found in the 

STEER. In Vieques, 

the mean cadmium 

concentration in sediments was 0.13 μg/g (Pait et al., 

2010). In Jobos Bay, the mean cadmium concentration 

was 0.01 μg/g, similar to southwest Puerto Rico (Apeti et 

al., 2012b). The NS&T median for cadmium in sediments 

is 0.19 μg/g, the 85th percentile is 0.44 μg/g. All three sites 

in the STEER where cadmium was detected from the stratifi ed random sampling were at or above the NS&T median, 

but below the 85th percentile. Three of the four sites from 

the 2010 targeted sampling were also above the NS&T 

median, but all were below the 85th percentile. 

NOAA Sediment Quality Guidelines for Cadmium. Figure 

4.13 also contains the NOAA ERL and ERM. All cadmium levels detected in the STEER sediments, either from 

the stratifi ed random sampling or from the 2010 targeted 

sampling, were below the ERL. Sites 1-1P and 1-3P are 

both in Mangrove Lagoon, which is adjacent to the Bovoni 

Landfi ll, and could be one source of the cadmium found 

in the sediments. At this time, it is not known whether the 

cadmium detected is associated with runoff or subsurface 

fl ow from the landfi ll, or perhaps input from septic systems 

or runoff from residential areas. At one time, a wastewater 

treatment plant emptied directly into Mangrove Lagoon 

(Grigg et al., 1971). Additional work is needed to better 

assess the possible sources of cadmium to the area of Mangrove Lagoon and Benner Bay. 

Effects of Sediment Grain Size. Because of the low number of cadmium detections, an assessment of the effects of 

grain size and TOC was not carried out. 

Chromium

The concentrations of chromium detected in the sediments 

collected from the STEER are shown in Figure 4.14. Higher concentrations were detected in the Mangrove Lagoon 

and Benner Bay areas, a pattern similar to a number of the 

organic compound classes (e.g., PAHs, PCBs) analyzed for 

this project. 

The mean concentration of chromium in the STEER from 

the stratifi ed random sampling was 14.1 ±1.76 μg/g; the 

median was 11.4 μg/g. The highest concentration of chromium in the sediments analyzed from the stratifi ed random 

sampling was 35.7 μg/g at site 1-1P in Mangrove Lagoon. 

The second highest concentration, 32.3 μg/g, was also in 

Mangrove Lagoon at site 1-3P. The lowest level of chromium detected from the stratifi ed random sampling was at 

2-24A (4.91 μg/g). Figure 4.14 also contains the results 

of the targeted sampling in 2010. The highest chromium 

Figure 4.14. Chromium detected in sediments from the St. Thomas East End Reserves.
Chapter 4: Chemical Contaminants and Toxicity

97

STEER Integrated Environmental Assessment Report

concentration detected was 40.4 μg/g at BB-2, similar to 

the concentration of chromium at the sites in Mangrove 

Lagoon. 

Variation of Chromium Across Strata. An ANOVA carried 

out on the log10 transformed data indicated that chromium 

varied signifi cantly (p = 0.0090) by stratum. A subsequent 

pair wise comparison (Tukey HSD) indicated that Stratum 

1 was signifi cantly different (higher) from Strata 3, 4 and 

5, however, Stratum 2 (Benner Bay) was not signifi cantly 

different from Stratum 1. 

Comparison with Other Data. EPA’s EMAP analyzed four 

samples from the STEER in 2004. The mean concentration from these four samples was 3.06 μg/g, lower than the 

mean found in the current study in the STEER. The highest 

chromium concentration found in the STEER by EMAP 

was 4.8 μg/g. 

In southwest Puerto Rico, Pait et al. (2008) calculated a 

mean chromium concentration of 31.2 μg/g, higher than in 

the STEER. In Vieques, mean 

chromium levels in the sediment were somewhat higher 

as well, 22.5 μg/g (Pait et al., 

2010). In Jobos Bay, the mean 

chromium concentration was 

18.3 μg/g (Apeti et al., 2012b), 

similar to what was found in 

the STEER. The NS&T median 

for chromium in sediments is 

66 μg/g, higher than any of 

the chromium levels found in 

sediments in the STEER in this 

study.

As with cadmium, it is not 

known if the chromium detected in the Mangrove Lagoon 

area is associated with inputs from the landfi ll, from septic 

systems, runoff from residential areas, or perhaps a combination of these sources. Keller et al. (2014) noted elevated 

aqueous concentrations of chromium in groundwater 

sampled from wells installed in the Bovoni Landfi ll in the 

mangrove area on the western border of Mangrove Lagoon. 

They also found evidence that the mangroves and associated clay-rich sediments in that area may be holding back 

higher levels of metals such as chromium from entering 

Mangrove Lagoon, likely another benefi t that mangroves 

are providing in this area. 

NOAA Sediment Quality Guidelines for Chromium. The 

ERL and ERM for chromium are also included in Figure 

4.14. All STEER chromium values were below both of 

these NOAA guidelines. 

Effects of Sediment Grain Size. Using the log10 normalized data, chromium was found to be correlated with the 

percent fi nes (p = 0.0180). A nonparametric analysis 

showed this metal had a slightly higher correlation with 

percent clay (Spearman Rho = 0.5441, p = 0.0060) than the 

percent silt content (Spearman Rho = 0.4767, p = 0.0185). 

Copper

Results from the analysis of copper in the sediments from 

the STEER can be seen in Figure 4.15. The mean concentration of copper found in the sediments was 21 ±7.46 μg/g; 

the median was 3.75 μg/g. The highest copper concentration from the stratifi ed random sampling was 155 μg/g at 

site 2-20P, followed by 69.9 μg/g at site 1-1P in Mangrove 

Lagoon. From the targeted sampling in 2010, the lowest concentration was 60.6 μg/g at ML-10. At BB-1, the 

concentration of copper in the sediment was 145 μg/g. At 

BB-2, the copper concentration was quite high, 1,010 μg/g. 

Variation of Copper Across 

Strata. A Kruskal-Wallis 

test run on the ranked values 

from the stratifi ed random 

sampling indicated a signifi -

cant difference (p = 0.0001) 

in the concentration of 

copper across the strata. A 

Tukey-Kramer HSD analysis 

indicated that copper did not 

vary signifi cantly between 

Strata 1 and 2 (i.e., Mangrove 

Lagoon and Benner Bay), but 

was different from Strata 3, 

4, and 5. 

Comparison with Other Data. EPA’s EMAP collected and 

analyzed sediments from four sites within the STEER for 

copper in 2004. The mean concentration of copper in the 

sediments from the EMAP work was 3.9 μg/g, substantially 

less than the mean concentration found in the STEER in the 

current study. It is unclear why the means for the stratifi ed 

random sampling done in both studies were quite different, 

although it may be related to the greater number of samples 

taken in the current study, particularly in the Mangrove 

Lagoon area. As noted earlier, Mangrove Lagoon was not 

included in the EMAP work. 

In southwest Puerto Rico, Pait et al. (2008) detected a mean 

copper concentration of 5.21 μg/g, lower than the mean in 

S

t

f

s

c

i

c

T

i

v

S

L

Sediment sample in the PONAR grab from Stratum 1 (Mangrove Lagoon). 
Chapter 4: Chemical Contaminants and Toxicity

98

STEER Integrated Environmental Assessment Report

the STEER. In Vieques, the mean copper 

concentration was 25.9 

μg/g, and in Jobos Bay, 

Apeti et al. (2012b) 

found a mean copper 

concentration of 34.1 

μg/g, somewhat higher 

than the mean found in 

the STEER. 

The NS&T median for 

copper in sediments 

is 16 μg/g. From the 

stratifi ed random sampling in 2011, six sites 

(2-20P, 1-1P, 1-3P, 1-2P, 

2-16P, 1-5P), all either 

in Mangrove Lagoon or 

northern Benner Bay, 

had copper levels above 

the NS&T median. The 

NS&T 85th percentile 

for copper is 38.3 μg/g. 

Five of these sites had 

copper levels above 

the NS&T 85th percentile level. All four of the targeted samples were above 

the NS&T median and 85th percentile. Finally, the concentration in the sediment at BB-2, is one of the 10 highest 

concentrations of copper that has been detected in NOAA’s 

NS&T Program. 

NOAA Sediment Quality Guidelines for Copper. The ERL 

for copper is 34 μg/g (Figure 4.15); the ERM is 270 μg/g. 

From the stratifi ed random sites, six sites (2-20P, 1-1P, 

1-3P, 1-2P, 2-16P, 1-5P) exceeded the ERL, but none exceeded the ERM for copper, indicating that more sensitive 

life stages in these areas could, however, be experiencing 

effects related to the presence of copper. 

All four of the 2010 targeted sites (i.e., BB-1, BB-2, ML-2 

and ML-10) were above the NOAA ERL for copper. At 

Site BB-2 (1,010 μg/g), the level of copper substantially 

exceeded the copper ERM of 270 μg/g, indicating that effects from this trace element on biota inhabiting the sediments are likely. 

Copper in the Sediments in Northern Benner Bay and Mangrove Lagoon. The pattern of copper seen in the sediments 

in Mangrove Lagoon and Benner Bay, with higher concentrations in the northern part of Benner Bay, and somewhat 

lower concentrations in Mangrove Lagoon, suggests a possible gradient. The fl ow of water into and out of Mangrove 

Lagoon appears to have a number of driving forces, including a clockwise pattern through Cas Cay, a reversing tidal 

current, along with wind drift and runoff fl ow through both 

entrances (Tetra Tech, 2005). The three highest concentrations of copper were found at sites BB-1, 2-20P and BB-2, 

all in the northern part of Benner Bay. Given the variable 

direction of water currents in the area, a signifi cant source 

of the higher copper concentrations in the sediments could 

be from the northern part of Benner Bay. However, additional work would be needed to assess this possibility. 

Marinas and boat yards are a major commercial land use 

adjacent to the northern portion of Benner Bay. Copper 

has been used for years in antifoulant paint systems on 

boat hulls. Activities such as the mooring of vessels with 

hulls painted with copper-containing bottom paints, along 

with the cleaning, scraping and repainting of boat hulls, 

and subsequent runoff containing paint chips and dust, that 

might occur during a rainstorm, could lead to elevated concentrations of this metal in the environment. The elevated 

levels of TBT in the sediments in this same part of Benner 

Bay and lower levels of TBT in Mangrove Lagoon support the possibility that the copper found in the sediments 

in the northern part of Benner Bay are related to the use of 

Figure 4.15. Copper detected in sediments from the St. Thomas East End Reserves.
Chapter 4: Chemical Contaminants and Toxicity

99

STEER Integrated Environmental Assessment Report

both copper and TBT 

over the years in boatrelated activities. A 

nonparametric correlation analysis between 

copper and TBT in the 

STEER showed a very 

signifi cant positive correlation (Spearman Rho 

= 0.7078, p = 0.0001). 

As noted earlier, TBT 

has had signifi cant use 

as an antifoulant on 

boat hulls. For copper, 

however, inputs into 

Mangrove Lagoon from 

Turpentine Gut, runoff 

from residential areas, 

and inputs from the adjacent Bovoni Landfi ll 

could also be contributing sources. 

In any case, the concentration of copper at 

BB-2 is indicative of 

levels that are likely impacting benthic organisms in this area. The next chapter contains the results of 

additional monitoring in northern Benner Bay, including an 

analysis of metals in sediment cores. 

Effects of Sediment Grain Size. A nonparametric analysis 

revealed that copper was signifi cantly correlated with the 

percent fi nes (Spearman Rho = 0.7852, p < 0.0001) fraction 

of the sediments. 

Lead

The concentrations of the trace element lead detected in 

the STEER sediments are shown in Figure 4.16. The mean 

concentration was 5.87 ±1.90 μg/g; the median was 0.82 

μg/g. The highest concentration of lead in the sediments 

from the stratifi ed random sampling was 31 μg/g at 1-2P in 

Mangrove Lagoon. The lowest concentration detected was 

0.371 μg/g at 4-50P in Cowpet Bay. The highest concentration from the 2010 targeted sampling was 81.2 μg/g at 

BB-2 in Benner Bay (Figure 4.16). 

Variation of Lead Across Strata. A log10 transformation 

of the results failed to normalize the stratifi ed-random 

sampling data. The data were subsequently ranked, and a 

Kruskal-Wallis test on the ranked data showed a signifi cant 

(p <0.0001) difference in the concentration of lead across 

the STEER. A Tukey HSD test indicated that Stratum 

1 was signifi cantly higher than Strata 3, 4, and 5. The 

concentration of lead in Stratum 2 was not signifi cantly 

different from Stratum 1 or Stratum 3, but was signifi cantly 

higher than in Strata 4 and 5. 

Comparison with Other Data. The mean concentration of 

lead in the sediments in the STEER analyzed by EMAP 

was 1.02 μg/g, lower than the mean concentration found in 

the STEER in the current study. In southwest Puerto Rico, 

Pait et al. (2008) detected a mean lead concentration of 

1.93 μg/g, less than that found in the STEER. In Vieques, 

the mean lead concentration was 5.42 μg/g, close to that in 

the STEER. In Jobos Bay, the mean concentration of lead 

in the sediments sampled was 7 μg/g (Apeti et al., 2012b), 

also similar to the STEER. 

The NS&T median sediment concentration for lead is 22.3 

μg/g. Only two sites (1-2P and 1-3P) from the stratifi ed 

random sampling, both in Mangrove Lagoon, had lead 

levels above the NS&T median. The NS&T 85th percentile 

for lead is 39.1 μg/g. None of the sites in the STEER from 

the stratifi ed random sampling had a lead concentration 

in the sediments above this level. From the 2010 targeted 

Figure 4.16. Lead detected in sediments from the St. Thomas East End Reserves.
Chapter 4: Chemical Contaminants and Toxicity

100

STEER Integrated Environmental Assessment Report

sampling, three of the 

four sites were above 

the NS&T median, 

with one site (BB-2) 

above the NS&T 85th 

percentile. 

NOAA Sediment 

Quality Guidelines 

for Lead. The ERL for 

lead is 46.7 μg/g (Figure 4.16); the ERM 

is 216 μg/g. None of 

the randomly chosen 

sites had a concentration above the ERL. 

However, BB-2 (81.2 

μg/g) from the 2010 

targeted sampling had 

a concentration above 

the ERL, but still well 

below the ERM of 218 

μg/g. 

Effects of Sediment 

Grain Size. A nonparametric correlation 

analysis between lead 

and percent fi nes in the sediment indicated a signifi cant 

positive correlation (Spearman Rho = 0.7643, p < 0.0001). 

Zinc

The results of the analysis of zinc in the sediments collected in the STEER are shown in Figure 4.17. The mean zinc 

concentration in the sediments from the stratifi ed random 

sampling was 37.3 ±10.7 μg/g; the median was 11.1 μg/g. 

The highest concentration of zinc from these collections 

was found at site 1-2P, at 159 μg/g. The second highest 

zinc concentration from the stratifi ed random sampling was 

also in Mangrove Lagoon at site 1-3P, with a concentration 

of 154 μg/g.

From the 2010 targeted sampling, the highest zinc concentration detected was 392 μg/g in Benner Bay (BB-2), followed by 192 μg/g in BB-1, also in Benner Bay. As with 

a number of the other contaminants included in this report, 

higher concentrations were found in northern Benner Bay 

and in Mangrove Lagoon. 

Variation of Zinc Across Strata. A Kruskal-Wallis test 

on the ranked values from the stratifi ed random sampling 

indicated zinc varied signifi cantly (p = 0.0006) by stratum, 

and the Tukey-Kramer HSD test indicated that Strata 1 and 

2 were signifi cantly different (higher) from Stratum 5. 

Comparison with Other Data. The mean for the four 

samples that EPA’s EMAP collected outside of Mangrove 

Lagoon in the STEER was 5.8 μg/g, substantially below the 

mean for the STEER in the current project. If the samples 

from Mangrove Lagoon are left out, the mean for the 

STEER is 18.4, still higher than was found by EMAP. 

The concentration of zinc detected in the STEER can also 

be compared with work completed in southwest Puerto 

Rico. Pait et al. (2008) detected a mean zinc concentration 

of 8 μg/g, below the mean found in the STEER. In Vieques, Pait et al. (2010) calculated a mean zinc concentration of 34.4 μg/g, similar to what was found in the STEER. 

In Jobos Bay, Apeti et al. (2012b) found a mean zinc 

concentration of 54.7 μg/g, somewhat higher than what was 

found in the STEER. 

The NS&T median for zinc is 74 μg/g; the 85th percentile 

is 143 μg/g. From the stratifi ed random sampling, there 

were six sites above the NS&T median, and two sites (1-

2P and 1-3P) above the NS&T 85th percentile. From the 

2010 targeted sampling, three (BB-2, BB-1, and ML-2) of 

Figure 4.17. Zinc detected in sediments from the St. Thomas East End Reserves.
Chapter 4: Chemical Contaminants and Toxicity

101

STEER Integrated Environmental Assessment Report

the four sites analyzed 

were above the NS&T 

85th percentile. 

NOAA Sediment Quality Guidelines for Zinc. 

The ERL for zinc is 

150 μg/g. There were 

two sites (1-2P and 

1-3P) from the stratifi ed random sampling 

that exceeded the ERL. 

From the 2010 targeted 

sampling, three of the 

four sites (BB-2, BB-1, 

and ML-2) analyzed 

exceeded the ERL. The 

results of this analysis indicate that some 

of the more sensitive 

species or life stages 

in both Benner Bay 

and Mangrove Lagoon 

could begin to experience effects related to 

the elevated levels of 

zinc. In addition, any 

additive effects that 

may be present as a result of multiple contaminants (e.g., TBT and copper) from 

this area are unknown. While none of the sites exceeded 

the ERM, BB-2 (392 μg/g) from the 2010 targeted sampling was fairly close to the zinc ERM of 410 μg/g. 

Effects of Sediment Grain Size. The nonparametric Spearman’s analysis between zinc and the sediment percent fines 

indicated a significant positive correlation (Spearman Rho 

= 0.5678, p = 0.0038) between zinc and the smaller grain 

sizes of the sediments sampled in the STEER. The correlation between zinc and percent clay (Spearman Rho = 

0.7270, p < 0.0001) appeared somewhat higher than silt 

(Spearman Rho = 0.5235, p = 0.0038). 

Clostridium perfringens

Although not a chemical contaminant, this bacterium is 

often included in the analyses done by NOAA’s NS&T Program. This anaerobic, gram-positive staining rod-shaped 

bacterium frequently occurs in the intestines of humans, as 

well as in domestic and wild animals, and has been used as 

a human/animal waste indicator. The results of the analysis 

of sediments for C. perfringens are shown in Figure 4.18. 

Higher levels of C. perfringens were found primarily in 

Mangrove Lagoon, with lower concentrations in most other 

locations. 

To assess the presence of viable C. perfringens, sediment 

extracts are plated on growth medium and the number of 

colonies that develop are counted. The mean C. perfringens concentration in the sediments was 291 ±167 CFU/g 

(colony forming units per gram of dry sediment). The sediment sample from 1-2P contained 3,493 CFU. Site 1-3P 

had a C. perfringens count of 2,137 CFU/g. Both 1-2P 

and 1-3P are near the mouth of Turpentine Gut, as it enters 

Mangrove Lagoon, which may be indicative of input from 

septic systems, domestic animals such as dogs, and from a 

nearby horse race track. From the 2010 targeted sampling, 

the highest concentration of C. perfringens found was at 

ML-10, also at the mouth of Turpentine Gut (2,558 CFU/g).

Variation of C. perfringens Across Strata. A Kruskal-Wallis 

test run on the ranked C. perfringens data indicated a signifi cant difference (p < 0.0001) between strata. A Tukey 

HSD test indicated that Strata 1 and 2 were signifi cantly 

different (higher counts) from Strata 3, 4 and 5. 

An analysis of C. perfringens and grain size was also 

carried out. A strong (p = 0.0010) correlation was found 

Figure 4.18. Clostridium perfringens detected in sediments from the St. Thomas East End Reserves.
Chapter 4: Chemical Contaminants and Toxicity

102

STEER Integrated Environmental Assessment Report

between the log10 normalized C. 

perfringens data and percent fi nes. 

A nonparametric analysis indicated 

a signifi cant negative correlation 

between C. perfringens and percent 

sand (Spearman Rho = -0.6342, 

p = 0.0009), but no correlation 

between C. perfringens and percent 

gravel (Spearman Rho = 0.1907, p 

= 0.3722). 

 

Sediment Quality Guidelines and 

C. perfringens. No NOAA or 

other health guidelines exist for 

C. perfringens in sediments. C. 

perfringens is a common cause of 

foodborne illnesses. A more severe 

form of the disease can be fatal and 

results from ingesting large numbers of the active bacteria, typically 

from food. C. perfringens also has 

the capability of forming spores 

which can persist in soils and sediments. 

The high levels of C. perfringens

within Mangrove Lagoon indicate 

there is a need to reduce wastewater, stormwater and various sources 

of inputs for this pathogen, and 

other pathogenic microorganisms 

that may be present as well. Reducing the levels of bacterial contamination would not only benefi t 

ecological health, but human health 

as well.

Sediment Toxicity

The use of sediment toxicity bioassays, along with the 

benthic infaunal community analysis, provides important 

information on the impacts of the chemical contaminants 

present in STEER sediments. While the NOAA ERMs 

and ERLs provide an indication of the likelihood of effects 

from one chemical contaminant or chemical contaminant 

class, the bioassays (and the benthic community analysis) 

integrate the effects of all contaminants present along with 

other environmental parameters. For this project, the sediment toxicity bioassays included amphipod (Ampelisca 

abdita) mortality, sea urchin (Arbacia punctulata) fertilization impairment, and cytochrome P450 Human Reporter 

Gene System (HRGS) response tests. The bioassay results 

for all tests are summarized in Table 4.4. All values are 

control corrected. 

Amphipod Toxicity

Signifi cant amphipod mortality occurred throughout the 

STEER study area. The highest mortality values observed 

were in the eastern strata. This may be infl uenced by sediment grain size. The amphipod A. abdita normally live in 

silty sand habitats and may not thrive well in coarse sand 

(ASTM, 2008), however, this has not been tested rigorously. All the amphipod bioassays with mortality elevated 

above 20% were in sediments that were greater than 60% 

sand and gravel (Figure 4.19). Other parameters (e.g., 

higher TOC) may ameliorate this effect. Most of the highly 

toxic amphipod results were in coarse sand with very low 

TOC (Figure 4.20). 

Sea Urchin Fertilization

Half of the signifi cant sea urchin fertilization bioassays 

were in sediments from Mangrove Lagoon or the canal 

Table 4.4. Toxicity bioassay summary results from the STEER.

Site

Amphipod Mortality (%) Different from Control

Sig

Sea Urchin 

Fertilization Failure (%) Different 

from Control

Sig P450 

Response

BaP Eq. 

(ng/g)

1-1P 10.31 23.7 * 4.94 5.64

1-2P 14.43 * 14.5 * 13.79 12.98

1-3P 4.12 8.2 14.24 44.83

1-4P 7.22 6.3 9.86 0.12

1-5P 15.46 97.6 * 15.66 0.80

2-16P 12.37 * 40.4 * 11.12 8.33

2-19P 4.12 2.9 2.39

2-20P 8.25 0.0 13.35 1.78

2-24A 13.40 5.1 2.88

3-32P 10.31 15.5 * 15.64 8.58

3-33P 7.22 65.9 * 2.47

3-37A 10.31 9.2 3.36

3-38A 7.22 0.0 4.76 2.03

3-45A 47.42 * 0.0 2.49

4-46P 29.90 * 30.5 * 2.20

4-47P 21.65 * 13.8 2.75

4-48P 12.37 13.3 1.23

4-49P 10.31 18.2 * 2.73

4-50P 37.11 * 6.8 1.49

5-61P 9.28 0.0 1.45

5-62P 22.68 * 3.6 1.90

5-70A 53.61 * 0.2 5.57

5-71A 4.12 5.8 3.14 0.97

5-75A 28.87 * 13.6 2.15

* - statistically different from control 
Chapter 4: Chemical Contaminants and Toxicity

103

STEER Integrated Environmental Assessment Report

joining it to Benner Bay (Table 4.4). Jersey Bay and St. 

James Bay also showed signifi cant results in two locations. 

P450

Most of the signifi cant P450 responses were in the western 

strata, including all of the Mangrove Lagoon sites. Further 

testing of those samples that exceeded 50% of the 10 nM 

TCDD (tetrachlorodibenzodioxin) standard are also presented in Table 4.4 in terms of B[a]P eq. The P450 response 

in terms of B[a]P eq is strongly correlated with PAH concentrations (Figure 4.21). 

Results of the timed exposure (6 vs 24 hrs) to test for the 

relative contribution of labile versus persistent contaminants are shown in Table 4.5. In all cases, the 6 hr incubation showed a higher response than the 24 hr incubation 

(Figure 4.22). This indicates that the predominant chemical 

classes the cells were responding to were PAHs, as they are 

more easily degraded than the more recalcitrant PCBs. It is 

noteworthy that the level of response in Mangrove Lagoon 

and portions of Benner Bay and Cowpet Bay exhibit initial 

responses as high as the spiked sample and the positive 

control. 

Taken together, the bioassay results indicate a gradient of 

effect from west to east within the STEER (Figure 4.23). 

Toxic responses occurred in all strata, but the western 

portion of the study area exhibited signifi cant results from 

multiple bioassays. As noted above, several of the amphipod bioassay results may be an artifact of the coarse coralline sediment present in many of the eastern sites (Strata 4 

and 5). 

With the exception of TBT and copper, extremely high concentrations of individual chemical pollutants were not seen. 

However, the observed widespread toxicological responses 

indicate the interaction of a variety of factors, including 

multiple contaminants, physicochemical characteristics 

of the sediment, and likely chemical pollutants beyond 

the standard list of analytes that may vary from stratum to 

stratum. 

Benthic Community Analysis

A total of 10,926 organisms were enumerated, comprised 

of 434 taxa (species or higher taxonomic level). Following elimination of epibenthic species (dwelling on hard 

surfaces, not within the sediment) and ‘artifi cial’ species 

(see page 84), there were 333 taxa and 10,605 individuals 

for analysis. There were 168 rare and unique taxa. One 

hundred fi fty seven taxa were found at only one location. 

Annelids were the dominant taxa, accounting for 59.2% of 

all the organisms. Mollusks and arthropods accounted for 

19.2 and 15.7%, respectively. Less than 1% of the animals 

were echinoderms. In the STEER, abundance was dominated by two dozen taxa that were found throughout most 

strata and a large number of taxa only represented by a few 

individuals (Figure 4.24). 

Abundance was more uniform on average than diversity or 

number of species, but some locations had extremely low 

abundance and some sites were extremely high (Figure 

4.25). Site 1-1P in Mangrove Lagoon only had 4 species 

and fi ve organisms in total. Site 2-16P had over 1,000 

organisms. 

Gradients of diversity and species richness were seen from 

low in the west to higher in the eastern strata (Figure 4.26). 

With two exceptions (Sites 1-4P and 2-19P), diversity was 

higher in the eastern strata than in Mangrove Lagoon and 

Benner Bay. These are refl ected in the calculated correlaFigure 4.19. Amphipod mortality vs % sand and gravel in 

St. Thomas STEER sediments. 

0

20

40

60

80

100

0 20 40 60 80 100

% Amphipod Mortality 

% Sand & Gravel 

Figure 4.20. Amphipod mortality versus % total organic carbon (%TOC) in the STEER sediments.

0

20

40

60

80

100

0123456

% Amphipod Mortality 

% TOC 
Chapter 4: Chemical Contaminants and Toxicity

104

STEER Integrated Environmental Assessment Report

tion coeffi cients. Number of species and diversity were 

negatively correlated with the ERMq, (Table 4.6). The 

ERMq is calculated by dividing the concentration of each 

contaminant analyzed in the sediment by its available ERM 

to produce a quotient. Number of species and diversity 

were positively correlated with stratum. There were no signifi cant correlations with amphipod mortality or sea urchin 

fertilization failure. The number of species and diversity 

were signifi cantly and negatively correlated with the PAH 

benzo[a]pyrene concentrations. A similar pattern was seen 

with respect to the percentage of fi nes in the sediments, and 

sand plus gravel showed the inverse. 

Nodal Analysis

The nodal analysis revealed two site groups and three 

species groups. The site groups divided cleanly between 

Stratum 1 and 2 (Mangrove Lagoon and Benner Bay) vs 3, 

4, and 5. There was almost no overlap in species makeup 

between the site groups. In Mangrove Lagoon and Benner 

Bay, there were 25 species, versus 109 species found in the 

other three strata. Species that were found in Mangrove Lagoon and Benner Bay were generally rarely found or were 

completely absent in the other three strata, and vice versa. 

The three species groups corresponded to the site groups. 

Mangrove Lagoon and Benner Bay have a different species 

assemblage than the other three strata, and were dominated 

by polychaete worm species that are neither widespread 

nor numerous in the rest of the STEER. Strata 3, 4 and 5 

shared a common assemblage of species. 

Table 4.5. Average (n = 3) P450 bioassay response following 6 

and 24 hour incubation with STEER sediment extracts. 

Site 6 Hour 

Response

24 Hour 

Response

1-1P 104.9 13.3

1-2P 113.3 24.7

1-3P 117.3 35.0

1-4P 78.5 10.4

1-5P 129.8 14.1

2-16P 89.7 22.6

2-19P 12.3 3.53

2-20P 113.4 29.0

2-24A 17.3 1.37

3-32P 134.4 41.0

3-33P 39.0 3.00

3-37A 21.6 9.24

3-38A 100.0 9.44

3-45A 39.8 5.22

4-46P 11.0 3.19

4-47P 16.1 3.28

4-48P 6.12 1.74

4-49P 15.9 1.86

4-50P 13.0 2.46

5-61P 11.9 0.30

5-62P 24.0 1.42

5-70A 42.0 3.84

5-71A 57.0 5.17

5-75A 30.6 3.26

clean 4.44 0.56

blank -1.39 0.10

spike 125.5 46.5

contam 123.2 55.9

Values are expressed as % of the 10nM TCDD standard 

response. QA/QC samples: blank = solvent blank; clean = 

uncontaminated site in the Chesapeake Bay; contam = contaminated site in Chesapeake Bay; spike = spiked solvent solution.

Figure 4.21. P450 response vs PAH concentrations (a), P450 

response in terms of B[a]P eq for the subset of samples that exceeded the TCDD standard response (b).

0

5

10

15

20

0 500 1000 1500

P450 response 

total PAH ug/g 

a

y = 0.0323x - 2.3609 

R2 = 0.8181 

0

10

20

30

40

50

0 500 1000 1500

BaP Eq 

total PAH ug/g 

b
Chapter 4: Chemical Contaminants and Toxicity

105

STEER Integrated Environmental Assessment Report

The third group of 26 species were found at sites 1-4P and 

2-19P (hereinafter referred to as excluded sites). These 

species were rarely found elsewhere in either Mangrove 

Lagoon and Benner Bay, or the other three strata. These 

two sites had a unique species assemblage, different from 

the other areas. Site 1-4P in the lower part of Mangrove 

Lagoon away from the infl uence of Turpentine Gut and the 

landfi ll, and 2-19P in central Benner Bay have sediment 

that is predominantly sand, unlike most of the other sites 

in those strata. These two locations shared a number of 

species found within Strata 1 and 2, but also another set of 

species that were much more diverse and included polychaetes, crustaceans, bivalves and snails. 

SIMPER Analysis

The difference in dominant species between strata is also 

illustrated in the results from the SIMPER analysis. Figure 

4.27 shows the similarity index values for Strata 1 and 2 

(Mangrove Lagoon and Benner Bay, respectively), and the 

values for the excluded sites (excluded from the Stratum 

1 and 2 lists), ranked from highest to lowest. Only a small 

number of species have high scores in Strata 1 and 2. That 

is, only a few are dominant. In contrast, none of the species in the two excluded sites have high scores. They are all 

equally important in defi ning the community makeup. The 

top 15 species in each group are listed in Table 4.7. Species 

highlighted in yellow were found in both Strata 1 and 2 (the 

colors are arbitrary). The strata have very similar dominant 

species makeup (there are many overlapping species that 

have high index values in both strata). Only two of the top 

species found in the excluded sites were present in both 

Strata 1 and 2. Thus, the species that are considered ‘typical’ in Strata 1 and 2 were generally not ‘typical’ in the two 

excluded sites (1-4P and 2-19P). The taxa highlighted in 

green were found in all fi ve strata. Tubifi cids are a family 

of oligochaete worms. Nemerteans, also called proboscis 

worms, constitute an entire phylum. Both are diffi cult to 

identify to species without highly specialized expertise. 

Thus, these taxa actually represent potentially hundreds of 

Figure 4.22. P450 response (normalized to standard 10nM TCDD) following 6 and 24 hour exposures to extracts from St. 

Thomas STEER sediment samples. (QA/QC samples; blank=solvent blank; clean=uncontaminated site in Chesapeake Bay; 

contam.=contaminated site in Chesapeake Bay; spiked solvent solution). 
Chapter 4: Chemical Contaminants and Toxicity

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STEER Integrated Environmental Assessment Report

Figure 4.24. Plot of total abundance of each taxa used in the analyses. Each triangle represents the total 

abundance of each individual taxa collected in the STEER. 

Figure 4.23. Distribution of bioassays showing responses that were signifi cantly different than controls or greater than a standard 

threshold (P450) in St. Thomas STEER sediments.
Chapter 4: Chemical Contaminants and Toxicity

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Figure 4.25. Total animal abundance at each station in the STEER.

Figure 4.26. Total number of species (taxa) and calculated diversity at each station in the STEER.
Chapter 4: Chemical Contaminants and Toxicity

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Parameter Statistics ERMq Stratum Amphipod 

Mortality

Fertilization 

Failure B[a]P %Silt and %Clay (Fines)

%Sand and 

%Gravel

Species Spearman Rho -0.65154 0.44292 0.12172 -0.25736 -0.64343 -0.62068 0.62068

Signifi cance 0.0006 0.0302 0.571 0.2247 0.0007 0.0012 0.0012

Abundance Spearman Rho 0.16565 0.04081 0.13534 -0.16166 -0.01359 0.01913 -0.01913

Signifi cance 0.4392 0.8498 0.5283 0.4505 0.9497 0.9293 0.9293

Diversity Spearman Rho -0.56542 0.47125 0.22625 -0.24324 -0.65588 -0.55937 0.55937

Signifi cance 0.004 0.0201 0.2877 0.2521 0.0005 0.0045 0.0045

Table 4.6. Spearman Rank correlation coeffi cients (bold) and signifi cance level for community parameters and selected physical and 

chemical parameters, and toxicological results. 

species and are not particularly informative. Syllis cornuta

is a polychaete worm with a worldwide distribution. Thus, 

outside of these cosmopolitan taxa, the excluded sites had 

very little in common with the species makeup of Strata 1 

and 2. 

Figure 4.28 shows the indices for the species found in 

Strata 3-5. The numbers of species in these strata are much 

higher than in Strata 1 and 2. All the scores are relatively 

low because of the much higher diversity than in Strata 1 

and 2, but the infl ection of the curves shows that the top 

15-20 species are the most important. Table 4.8 shows the 

top 15 species in each stratum, plus the excluded sites (1-4P 

and 2-19P) for comparison. Species names highlighted in 

blue were found in all three strata. Again, the taxa highlighted in green were cosmopolitan and are not informative. 

The species makeup of Strata 3, 4 and 5 is very similar. 

That is, the species highlighted in blue are typical in all 

three strata. The dominant species found in the excluded 

sites has almost no overlap with these strata. Thus there 

are three distinct species assemblages in the STEER. One 

in Mangrove Lagoon and Benner Bay, which are relatively 

depauperate. The two excluded sites that share some of the 

species found in Strata 1 or 2, but also another group of 

species not common anywhere else. The third assemblage 

is a much more diverse group, and occupies the bulk of the 

STEER area. 

Overall Patterns in the STEER Benthic Community

The average diversity and species richness is lower in 

Mangrove Lagoon and Benner Bay than the other strata, 

but abundance varies throughout the study area. Diversity 

and species richness are better indicators of stress than 

abundance, however. Extremely depressed abundance is indicative of highly stressed habitats, but marginally stressed 

areas may have as high or higher an abundance of organisms as healthy habitats, because those species that can 

thrive in stressed habitats may be released from competitive 

and predation pressure. Species in stressed environments 

also tend to have opportunistic and mobile life styles. 

The composition of species present in various locations is 

also an indicator of stressed habitats. Many authors consider amphipods and echinoderms to be relatively sensitive to 

contaminant stress (Long et al., 2001, Llanso et al., 2002). 

Similarly, several types of polychaetes, such as Spionids 

and Capitellids, and oligochaete tubifi cids, are considered 

to be tolerant of contamination and/or other stressful conditions, such as hypoxia (Lenihan and Micheli. 2001; Llanso 

et al., 2002). 

The community makeup of specifi c taxonomic groups in 

the different strata is shown in Table 4.9. Average total 

abundance of the large taxonomic groups was not informative. However, pollution tolerant species of annelids make 

up a much larger proportion of the organisms in Mangrove 

Lagoon and Benner Bay than in the two excluded sites or 

any other strata. The number of amphipods show the opposite pattern. 

Infl uence of Habitat Characteristics and Chemical Contamination on the Benthic Infaunal Community

Both species richness and diversity declined with ERMq 

(Figure 4.29, Table 4.6). Likewise, species richness and 

diversity declined with increasing percent fi nes (percent 

silt+clay) in the sediment (Figure 4.30). The relationship 

between contaminants and muddy sediment is clear (Figure 

4.31), but which is the causative factor for reduced species 

community condition cannot be determined from the data. 

Resident communities found in muddy areas are inherently 

different from the areas with coarser grained sediments. 

However, it is clear that the occurrence of signifi cant toxic-
Chapter 4: Chemical Contaminants and Toxicity

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STEER Integrated Environmental Assessment Report

Table 4.7. Results of SIMPER analysis for Strata 1 and 2. Taxa highlighted in green were cosmopolitan and were found in 

all strata. Taxa highlighted in yellow were found in strata 1 and 2. 

Stratum 1 Stratum 2 Excluded Sites

Index 

Value Species

Index 

Value Species

Index 

Value Species

23.8 Tubifi cidae (lpil) 15.3 Tubifi cidae (lpil) 6.11 Tubifi cidae (lpil)

13.07 Macoma brevifrons 14.83 Mediomastus (lpil) 5.32 Prionospio heterobranchia

6.23 Prionospio heterobranchia 14.01 Prionospio heterobranchia 4.65 Schistomeringos pectinata

5.98 Podarkeopsis levifuscina 11.95 Nemertea (lpil) 4.65 Branchiomma nigromaculata

5.56 Caecum pulchellum 11.64 Cirrophorus lyra 4.65 Maldanidae (lpil)

4.71 Exogone verugera 7.19 Podarkeopsis levifuscina 4.47 Podarkeopsis levifuscina

4.01 Nemertea (lpil) 3.68 Schistomeringos pectinata 4.47 Sabellidae (lpil)

3.99 Mediomastus (lpil) 3.66 Pseudopolydora (lpil) 4.27 Cumella (lpil)

3.94 Naineris setosa 3.08 Scoletoma verrilli 4.27 Leptochelia forresti

3.89 Pseudopolydora (lpil) 2.87 Syllis cornuta 4.27 Nemertea (lpil)

3.83 Caulleriella cf. alata 2.6 Aoridae (lpil) 4.27 Syllis cornuta

3.67 Podarke obscura 2.59 Capitella capitata 3.76 Chione cancellata

3.58 Sphaerosyllis piriferopsis 2.41 Exogone verugera 3.76 Mesanthura bivittata

1.89 Sabellidae (lpil) 2.18 Nereis acuminata 3.76 Cirratulidae (lpil)

1.81 Grandidierella bonnieroides 2.03 Schistomeringos rudolphi 3.76 Terebellidae (lpil)

Table 4.8. Top 15 species in each stratum plus excluded sites. Taxa highlighted in green were cosmopolitan and were found in all 

strata. Taxa highlighted in blue were found in strata 3, 4, and 5.

Stratum 3 Stratum 4 Stratum 5 Excluded Sites

Index 

Value Species

Index 

Value Species

Index 

Value Species

Index 

Value Species

5.01 Nemertea (lpil) 5.44 Nemertea (lpil) 6.83 Nemertea (lpil) 6.11 Tubifi cidae (lpil)

4.47 Galathowenia oculata 5.42 Exogone lourei 6.4 Lucinidae (lpil) 5.32 Prionospio heterobranchia

4.05 Exogone lourei 5.22 Tubifi cidae (lpil) 5.1 Tubifi cidae (lpil) 4.65 Schistomeringos pectinata

4.02 Prionospio (lpil) 4.82 Lucinidae (lpil) 4.97 Prionospio steenstrupi 4.65 Branchiomma nigromaculata

3.84 Armandia maculata 4.79 Heteropodarke formalis 4.94 Galathowenia oculata 4.65 Maldanidae (lpil)

3.69 Lucinidae (lpil) 4.52 Armandia maculata 4.82 Exogone rolani 4.47 Podarkeopsis levifuscina

3.59 Maldanidae (lpil) 3.21 Pionosyllis gesae 4.18 Cumella (lpil) 4.47 Sabellidae (lpil)

3.49 Ischyroceridae (lpil) 3.11 Pseudoleptochelia (lpil) 3.64 Aricidea taylori 4.27 Cumella (lpil)

3.4 Sipuncula (lpil) 2.96 Terebellidae (lpil) 3.62 Codakia (lpil) 4.27 Leptochelia forresti

2.48 Aspidosiphon (lpil) 2.89 Fabricinuda trilobata 3.47 Leptochelia (lpil) 4.27 Nemertea (lpil)

2.35 Fabricinuda trilobata 2.89 Caulleriella cf. alata 3.26 Xenanthura brevitelson 4.27 Syllis cornuta

2.34 Sphaerosyllis piriferopsis 2.87 Saltipedis (lpil) 3.13 Exogone lourei 3.76 Chione cancellata

2.33 Exogone dispar 2.85 Tellinidae (lpil) 3.1 Sipuncula (lpil) 3.76 Mesanthura bivittata

2.16 Ophiuroidea (lpil) 2.71 Protodorvillea kefersteini 2.81 Pitar simpsoni 3.76 Cirratulidae (lpil)

2.13 Ampharetidae (lpil) 2.68 Magelona sp. c 2.6 Armandia maculata 3.76 Terebellidae (lpil)
Chapter 4: Chemical Contaminants and Toxicity

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STEER Integrated Environmental Assessment Report

Figure 4.27. Results of the SIMPER analysis for Strata 1-2. Figure 4.28. Results of the SIMPER analysis for Strata 3-5.

0

1

2

3

4

5

6

7

Index Value

Species #

1_4P, 2_19P, Excluded Sites

0

2

4

6

8

10

12

14

16

18

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Index Value

Species #

Stratum 2

0

5

10

15

20

25

Index Value

Species #

Stratum 1

0

1

2

3

4

5

6

7

8

Index Value

Species #

Stratum 5

0

1

2

3

4

5

6

Index Value

Species #

Stratum 4

0

1

2

3

4

5

6

Index Value

Species #

Stratum 3
Chapter 4: Chemical Contaminants and Toxicity

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STEER Integrated Environmental Assessment Report

ity and the variety of 

signifi cant endpoints 

is highest in Mangrove 

Lagoon (Figure 4.23). 

Many of the signifi cant 

results from the amphipod bioassays are likely 

due to the coarse grain 

size of the sediments in 

the eastern strata. Consequently, amphipod 

mortality appears to be 

more widespread than 

the other toxicity endpoints. Abundance did 

not decline as sharply 

as species richness 

with increasing contamination, suggesting 

that pollution tolerant 

species are able to grow 

and reproduce in contaminated areas in the 

absence of competitors, predators, and/or indirect effects 

on the habitat. The weight of evidence between the toxicity, 

diversity, community makeup, and chemical contamination 

indicate pollution impacts in Benner Bay and, especially, in 

Mangrove Lagoon. 

4.4 CONCLUSIONS

The degradation of coral reef ecosystems worldwide has 

led to intensive efforts to understand and mitigate the 

stressors responsible for the declines of these ecosystems. 

The role of pollution is often cited as a major factor, but the 

degree to which pollution, and more specifi cally, chemical 

contaminants, impact coral reefs and associated habitats is 

largely unknown. Because of this, coral reef managers may 

be missing an important, and in some locations, a critical 

piece of information required to effectively manage and, 

where needed, initiate restoration efforts.

For this part of the project in the STEER, a stratifi ed 

random sampling design was utilized to characterize the 

distribution and concentrations of chemical contaminants, 

toxicity, and the benthic infaunal community on an areal 

basis. This allows for a quantitative analysis of habitat condition between strata. The Sediment Quality Triad, or SQT 

approach, which combines three types of analyses, was 

used to provide a means for more holistically assessing the 

presence and impacts of anthropogenic stressors. Sediment 

samples for the analysis of both organic contaminants (e.g., 

polycyclic aromatic hydrocarbons (PAHs), polychlorinated 

biphenyls (PCBs) and pesticides), and inorganic contaminants (trace elements such as chromium, nickel and copper) 

were collected during a mission in June 2011. In 2010, 

a preliminary targeted sampling exercise resulted in the 

analysis of four of the sediment samples collected. 

Elevated levels of chemical contaminants were primarily 

found in Mangrove Lagoon and in northern Benner Bay. 

There is a large landfi ll adjacent to Mangrove Lagoon, that 

likely contributes a variety of contaminants through runoff, 

groundwater seeps, and perhaps from atmospheric deposition (e.g., from tire/trash fi res). Mangrove Lagoon also 

Figure 4.29. Relationship between number of species and species diversity and the ERMq.

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

0

20

40

60

80

100

120

0 0.02 0.04 0.06 0.08 0.1 0.12 0.14

# Species

Diversity

Mean ERMq

Species

Diversity

Table 4.9. Average per-station abundance of selected taxonomic groups in Mangrove Lagoon and Benner Bay without stations 1-4P and 2-19P, stations 1-4P and 2-19P together, and the remaining strata in 3 

(Nazareth Bay), 4 (Cowpet/St. James Bay), and 5 (Great Bay). 

Organism Taxa Mangrove Lagoon 

and Benner Bay 

 Stations 1-4P 

and 2-19P Stratum 3 Stratum 4 Stratum 5

Annelids 331.1 298.0 298.2 147.6 246.4

Tubificidae 106.1 48.0 18.0 7.2 16.8

Capitellidae 28.1 6.5 6.0 2.8 7.6

Spionidae 77.4 28.0 27.2 8.4 38.4

Malacostraca 7.6 78.0 141.2 57.6 100.0

Amphipoda 5.3 43.0 39.8 23.2 14.8

Echinoderms 0.0 17.0 8.8 1.2 1.6

Molluscs 73.4 84.0 77.0 41.8 172.0

Bivalva 16.9 24.5 60.6 31.4 144.4

Gastropoda 56.6 58.0 12.6 8.0 26.0

Miscellaneous 13.9 38.5 24.6 7.6 53.2

Total 426.0 515.5 549.8 255.8 573.2
Chapter 4: Chemical Contaminants and Toxicity

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STEER Integrated Environmental Assessment Report

receives input from various commercial/industrial sources, 

as well as from adjacent residential/urbanized areas in the 

watershed via Turpentine Gut. Land use around northern 

Benner Bay appears dominated by marina-related activities, 

including the mooring, maintenance, and repair of boats, 

which is likely a source of chemical contaminants to the 

STEER.

Tributyltin, or TBT, was found at high levels at three sites 

in the northern Benner Bay area (two from the targeted 

2010 sampling). The level of TBT detected at one site in 

Benner Bay was the third highest quantifi ed in NOAA’s 

NS&T Program. The presence of high concentrations of 

TBT likely represents the results of past application of 

TBT, mooring of vessels that contain TBT, along with the 

cleaning and scraping of hulls that may have had TBT applied at some point. Unfortunately, there are no established 

guidelines for TBT in sediment. A site specifi c numerical 

upper guideline established for an EPA Superfund site in 

the state of Washington was exceeded in northern Benner 

Bay. The purpose of the guideline developed was to inform 

EPA site managers when additional testing (e.g., toxicity 

testing) would be recommended. 

Copper and zinc were elevated at several locations in 

Benner Bay and Mangrove Lagoon. The elevated copper level was above the NOAA ERM at one site from the 

2010 targeted sampling, indicating that impacts to benthic 

organisms and within the broader food web are likely. This 

also appears to be associated with marina activities, including the mooring of vessels, along with the cleaning, and 

scraping of the hulls and subsequent transport (i.e., through 

rainfall and subsequent runoff) of these materials 

into northern Benner Bay. The locations where the three 

highest copper concentrations were found was also the 

location of the three highest TBT concentrations. 

A number of other chemical contaminants analyzed for this 

project, including zinc, lead, copper, mercury, total PCBs, 

and total DDT, were above ERLs at one or more sites in the 

STEER, indicating that impacts may be occurring in some 

of the more sensitive species or life stages that may be present. Additive effects of these levels of contaminants on 

biota in the STEER are also possible. Clostridium perfringens, a pathogenic bacterium used as sewage indicator, was 

found at high levels in Mangrove Lagoon.

The elevated levels of chemical contaminants in the Mangrove Lagoon and northern Benner Bay areas were refl ected in the results of a number of the toxicity tests. Overall, 

the bioassays indicated a signifi cant gradient (high to low) 

of effects from west to east in the STEER. The widespread 

toxicological responses likely indicate the interaction of 

multiple chemicals, including those beyond the standard 

suite of NS&T analytes, along with other physicochemical 

characteristics which also vary between strata. 

Half of the signifi cant sea urchin fertilization failure bioassays in the STEER were in sediments from Mangrove Lagoon or the canal that joins it to Benner Bay. In addition, 

most of the signifi cant P450 responses were in the western 

strata in the STEER, including all of the Mangrove Lagoon 

sites. The predominant class of contaminants to which the 

cells were responding to appeared to be the PAHs or polycyclic aromatic hydrocarbons, which were elevated in this 

part of the STEER, as opposed to PCBs. 

The benthic infaunal analysis also correlated with the 

chemical contaminant and bioassay data, indicating gradients of diversity and species richness, with lower values 

in the western strata, especially in Mangrove Lagoon, and 

higher values towards the east. Similar to the results of the 

Figure 4.30. Relationship between number of species and species diversity and percent fi nes. 

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

0

20

40

60

80

100

120

0 20 40 60 80 100

# Species

Diversity

%Silt Clay

Species

Diversity

Figure 4.31. Relationship between mean ERMq and percent fi nes. 

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0.14

0 10 20 30 40 50 60 70

Mean ERMq

% Silt + Clay
Chapter 4: Chemical Contaminants and Toxicity

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Batley, G. 1996. Distribution and fate of tributyltin. In: S. 

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Bennett, R.F. 1996. Industrial manufacture and applications 

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Cambridge University Press. Cambridge, England. 301pp.

Birchenough, A.C., N. Barnes, S.M. Evans, H. Hinz,

I. Kronke, and C. Moss. 2002. A review and assessment 

of tributyltin contamination in the North Sea, based on 

surveys of butyltin tissue burdens and imposex/intersex in 

four species of neogastropods. Marine Pollution Bulletin 

44:534-543. 

Boehm, P.D., D.S. Page, J.S. Brown, J.M. Neff, J.R. Bragg, 

and R.M. Atlas. 2008. Distribution and weathering of 

crude oil residues on shorelines 18 years after the Exxon 

Valdez spill. Environmental Science and Technology 

42:9210–9216. 

Boulon, R.H. 1992. Use of mangrove prop root habitats by 

fi sh in the northern U.S. Virgin Islands. Proceedings, Gulf 

and Caribbean Fishery Institute 41:189-204

Budzinski, H., I. Jones, J. Bellocq, C. PiCrard, and P. Garrigues. 1997. Evaluation of sediment contamination by 

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Marine Chemistry 58:85-97. 

Carr, R.S. and J.M. Biedenbach. 1999. Use of power analysis to develop detectable signifi cance criteria for sea urchin 

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P450 analysis, the number of species and diversity were 

signifi cantly and negatively correlated with benzo[a]pyrene 

concentrations, indicating the likely impacts of this PAH 

and other chemicals present. 

Finally, the nodal analysis showed that the community 

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Bay were for the most part absent from the other strata and 

vice versa, likely due in part to natural and anthropogenic 

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The ecological health and condition of the interconnected 

mangroves, seagrass beds, and coral reefs within the 

STEER are a signifi cant management concern for many, 

including the USVI DPNR and NOAA’s CRCP. The proximity of the Reserves to the Bovoni Landfi ll, marinas, and 

other commercial and industrial activities, combined with 

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the bioeffects, establishes a baseline of conditions so that 

managers can understand not only the status, but also the 

challenges that exist to improve the ecological functioning 

of the STEER.

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Chapter 5: TBT and Metals in Sediment Cores

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CHAPTER 5: AN ASSESSMENT OF TRIBUTYLTIN AND METALS IN SURFACE SEDIMENTS AND SEDIMENT CORES FROM BENNER BAY, ST. THOMAS EAST END RESERVES

S. Ian Hartwell

1

, Dennis A. Apeti

1

, Andrew L. Mason

1

, and Anthony S. Pait

1

1

NOAA/NOS/National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment (CCMA), 

1305 East/West Highway, Silver Spring, MD 20910

5.1 INTRODUCTION

This chapter summarizes the results of a follow-up study in 

northern Benner Bay to assess the distribution of tributyltin 

(TBT), metals and metalloids in surface sediments and in 

sediment cores. Results from the initial characterization of 

sediment contaminants (Chapter 4) in the area of Benner 

Bay indicated unusually elevated concentrations of TBT 

in sediments in the Benner Bay region of the STEER. 

After reviewing these results, the USVI DPNR requested 

that NCCOS conduct a follow-up study to better assess 

the extent of contamination in surface sediments and to 

determine contaminant concentrations in 

the deeper underlying sediments in the 

area. In 2013 we conducted the follow-up 

study to determine the distribution of TBT 

and other heavy metal residues in the area 

in more detail, and also to take sediment 

cores at a number of locations to assess the 

record of TBT concentrations and metals 

over time. 

The antifouling properties of TBT 

compounds were discovered in the 1950s. 

For 40 years tributyltin (TBT) was used 

as a prime ingredient in antifouling 

paint applied to the hulls of boats and 

ocean going vessels. The function of 

the biocide in the antifouling paint is to 

prevent the settling of organisms on the 

hull and to poison the organisms that do.

By the mid-1960s it became the most 

popular antifouling paint worldwide. 

Although the paints were effective, the TBT slowly leaches 

out into the marine environment where it was highly toxic 

to a wide range of organisms. 

The formulation of TBT paints changed over time. Initially 

it worked by contact leaching to release the TBT to 

water. However, the release rate proved inconsistent and 

unpredictable, and as a result self-polishing co-polymer 

paints were developed. These paints used a polymer base 

through which the biocide discharge rate is regulated by 

reacting with water, and resulted in the TBT being slowly 

released in water. Once a surface covering was worn away, 

TBT release continued with the next layer. TBT-based 

paints were extremely effective and long lasting. 

Bottom paint improves ship performance and durability by 

reducing biofouling on the ship's hull (Bray and Langston, 

2006). This allowed increased ship speed and lower fuel 

consumption due to the lack of fouling organisms on 

the hull, and increased the time between scraping and 

repainting, all of which were economically advantageous. 

By the late 1970s, TBT paints were commonly used on 

commercial and recreational vessels. 

Negative aspects of TBT were 

suspected in the late 1960s when it 

was recognized that the release of 

organotin into aquatic environments 

was impacting non-target organisms. 

Toxic effects in some species occur 

at a concentration as low as one 

part per trillion (i.e., 1 nanogram 

per liter (ng/L)) of water (Bray 

and Langston, 2006). TBT is toxic 

to bacteria, algae, fungi, mollusks 

and crustaceans (Cruz et al., 2015). 

There are implications of effects 

on cetaceans and bioaccumulation 

of TBT in the human food chain. A 

galvanizing event occurred in the late 

1970s and early 1980s, when oyster 

crops in Arcachon Bay, France, 

failed. Subsequent research identifi ed 

that TBT had caused decreased spatfall, unnatural shell 

thickening and abnormal structure that weakened the shells (Bray and Langston, 2006). Similar observations were 

seen in United Kingdom oyster stocks. Away from hull 

cleaning operations, TBT sediment concentrations were 

higher in harbors with many small boats than in industrial 

harbors with commercial ships (Bryan and Gibbs 1991; 

Page et al, 1996). In 1982, France banned TBT use on 

recreational vessels less than 25 meters long. Subsequent 

work showed that TBT was an endocrine disruptor in 

marine gastropods causing masculinization (imposex) in 

females and widespread population decline. By the early 

NOAA scientists with sediment core from 

the STEER.
Chapter 5: TBT and Metals in Sediment Cores

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STEER Integrated Environmental Assessment Report

1990s, many nations had partial or complete bans on TBT. 

In 1999, the International Maritime Organization (IMO) 

a United Nations agency, came to agreement that TBT 

would be phased out between 2003 and 2008, with a total 

ban of organotin antifouling coatings by January 2008. 

The U.S. ratifi ed the agreement in 2012. However, while 

the agreement requires compliance from the developed 

nations, much of the developing world are not signatories. 

Also, TBT is still used as a slimicide in power plant cooling 

towers and other industrial heat exchange equipment, as a 

wood preservative, and as a molluscicide. It was reportedly 

still available in bottom paint as recently as 2014 in the 

Caribbean and Central America through U.S. outlets 

(Turner and Glegg, 2014). 

TBT is a persistent and bioaccumulative compound. The 

degradation pathways proceed from tributyltin to dibutyl-, 

to monobutyl-, and fi nally to elemental tin. The reported 

half-life in estuarine waters range from days to weeks 

(Omae, 2005). TBT is strongly sorbed to sediments 

particles, however, and the half-life of TBT in sediments 

is years, and in anaerobic sediments extends to decades 

(Matthiessen, 2013). Also, paint chips from boat hulls, for 

example as might occur during the scraping and repainting 

process, can ultimately be fl ushed into a water body, and 

serve as a reservoir for release to the sediment. Thus high 

concentrations may persist in older buried sediments where 

uncontrolled releases have occurred in the past. This 

material may or may not become bioavailable depending on 

local sediment deposition rates and subsequent disturbance 

(e.g., dredging).

5.2 METHODS

Sampling

Surface Sediments

Surfi cial sediment samples were collected at six locations 

in Benner Bay leading away from the main marina facility 

on two transects, one out the approach channel (S4-6) and 

one through an offshore boat anchoring area (S1-3) (Figure 

5.1). Sampling protocols were the same as those used in 

2010 and 2011 (Chapter 4). Water quality measurements 

and sediments were collected using standard NOAA 

National Status and Trends (NS&T) protocols (Apeti et 

al., 2012). A PONAR grab (see insert, next page) was 

Figure 5.1 Sampling sites for surface and sediment core samples in Benner Bay within the STEER.
Chapter 5: TBT and Metals in Sediment Cores

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STEER Integrated Environmental Assessment Report

deployed to collect the samples, and retrieved by hand. 

As with the collection of sediments for the assessment of 

contaminants throughout the STEER (see Chapter 4), the 

top 3 cm of sediment were collected from the grab using 

a stainless steel sediment scoop. Surface sediment was 

used for chemical analyses to assess current depositional 

conditions. 

Sediments were placed into certifi ed clean (I-Chem®) 

250 ml labeled jars, capped and then kept on ice in a 

cooler. Sediments for grain size analysis were placed in a 

WhirlPack® bag, sealed and then kept on ice in a cooler. 

At the end of each day, sediment samples for contaminant 

analysis were frozen. The WhirlPack® bags for the grain 

size analysis were placed in a refrigerator rather than 

frozen, to avoid altering the grain size structure. 

Sediment Cores

The sediment core samples were collected at four locations 

starting from the approach channel leading from Mangrove 

Lagoon to the southwest, and up into the head of Benner 

Bay in the heart of the area where the marina facilities are 

located (Figure 5.1). The 

BB2 and BB1 sites had 

been sampled for surface 

sediment in 2010. The B3 

site was roughly equidistant 

between them, and site 

16P was sampled in 2011 

for surface sediment. The 

boat was anchored at the 

bow and stern to minimize 

drift so the core could be 

deployed vertically. The 

corer was designed to 

collect undisturbed cores 

of the sediment and mudwater interface. The corer 

drove a 7 cm diameter 

polycarbonate tube into the 

sediment with a hand-held 

weight. A one-way check valve seated in the core head 

allowed water and sediment to move through the core 

barrel. During retrieval the check valve automatically seats, 

creating a partial vacuum which retains the sample in the 

core barrel. The core was returned to the dock where it was 

extruded in 2 cm sections by means of a plunger provided 

with the corer. Each section was placed into a certifi ed 

clean (I-Chem®) 250 ml labeled jar and homogenized. A 

sub-sample was removed for grain size analysis. Sediments 

for grain size analysis were placed in a WhirlPack® bag, 

sealed and then kept refrigerated. Sediment samples for 

metals and TBT analyses were frozen. An additional 

surface sediment sample was collected for TBT analysis 

with the PONAR grab at station BB2 as a check on 

potential gear bias.

Chemical Contaminants Analyzed

The sediments were analyzed for a suite of 16 major and 

trace elements, grain size analysis and for four butyltin 

compounds by TDI-Brooks International, using protocols 

established by the NS&T Program. The major and trace 

elements were analyzed using inductively coupled plasma 

mass spectrometry and atomicfl uorescence spectroscopy. 

Detailed descriptions of the NS&T protocols, including 

quality assurance/quality control (QA/QC) used in the 

analysis can be found in Kimbrough and Lauenstein 

(2006). The four butyltins were analyzed using gas 

chromatography/fl ame photometric detection after 

derivatization with hexyl-MgBr. 

Radiochemical Dating

The core sections were also analyzed for two isotopes 

in order to estimate the age of the sediments down the 

core length. In depositional environments, sediments are 

continually laid down and 

compacted by overlying 

sediment. In a continuous 

sequence, the age of the 

sediment can be estimated 

and the history of chemical 

contamination can be 

recreated. Depending on the 

rate of sediment deposition, 

changes in contaminant 

inputs will be obvious. 

Bioturbation by burrowing 

organisms will tend to mix 

the surface layers as they 

accumulate and may blur 

the history. Also, powerful 

storms, like hurricanes, may 

scour out whole sections, or, 

conversely bury layers with 

large deposits from runoff or resuspension. Also, human 

activities such as dredging and spoil disposal may cause 

breaks in the historical record. Activities on land that alter 

sediment delivery from runoff may increase or decrease the 

rate of sedimentation over time. 

The age of the sediment sections were estimated by 

measuring an isotope of lead (210Pb) and of cesium (137Cs). 

Briefl y, uranium-238 (238U) decays through a series of 

isotopes to radium-236 (226Ra). 226Ra has a half-life of 

16,000 yr, so the background supply is virtually constant. 

Radium eroded from rocks is deposited in sediments. 

Sample of surface sediment being taken from PONAR grab by 

NOAA scientists. 
Chapter 5: TBT and Metals in Sediment Cores

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STEER Integrated Environmental Assessment Report

Radium decays into radon-222 (222Ra) which has a halflife of only 3.8 days. Finally, radon decays to 210Pb with 

a moderate half-life of 22.3 yr., so a constant background 

level of 210Pb is present in rock and eroded sediments. 

Because radon is a gas, some of it escapes from the earth 

into the atmosphere to yield atmospheric 210Pb. This is 

washed out of the air by rain and is deposited into fresh 

sediments. Thus sediment deposits have two sources of 

210Pb, the background amount constantly derived from slow 

radium decay, and from atmospheric deposition. The older 

a layer of sediment is, the more of the atmospherically 

derived 210Pb will have decayed until only background 

levels remain. Therefore, looking at 210Pb levels down the 

length of a core you would expect to see concentrations 

decline in proportion to the sediment deposition rate, until 

only background levels are seen. 210Pb is used to determine 

the age of sediments and accumulation rate of sediments 

in water bodies. In a typical application, the average 

accumulation rate over a period of 100 - 200 years is 

obtained. From the accumulation rate, the age of sediment 

from a particular depth in the sediment column can be 

estimated. 

Cesium-137 (137Cs) measurements are used as a check on 

calculated age profi les by providing date “markers” rather 

than concentration slopes. 137Cs is derived from atomic 

bomb testing. The fi rst appearance of 137Cs in sediments 

marks the year 1954, which is the year when global 

concentrations generally achieved detectable levels. The 

other 137Cs marker is the concentration maximum in the 

year 1963, after which atmospheric testing ceased. 

Lead and cesium measurements were performed at 

the University of Maryland, Horn Point Environmental 

Laboratory. 210Pb measurements were carried out via 

analysis of its short-termer daughter product polonium-210 (

210Po), measured by alpha spectroscopy (Palinkas 

and Nittrouer, 2007). Briefl y, 1-2 g of dry, ground 

sediment samples were spiked with a known volume of 

polonium-209 (209Po), leaching 

fi rst in 15.8 N HNO

3

, then 

in 6 N HCl. 210Po and 209Po were then electroplated onto 

silver planchets and counted for 24 hours in a Canberra 

Alpha Analyst alpha spectrometer (Nittrouer et al., 

1979). Age models were fi t to the data, as appropriate, 

to determine sediment accumulation rates (Appleby and 

Oldfi eld, 1978; Carroll and Lerche, 2003; Hancock et al., 

2000). 137Cs measurements were performed using gamma 

spectroscopy. Dry, ground sediment from each sampling 

interval (~3-5 g) was sealed in 60-mL plastic jars. The 

gamma emissions from each sample was counted for 

approximately 24 hr with a calibrated Canberra germanium 

detector, using the 661 KeV photopeak of the gamma 

spectrum. Accumulation rates were calculated from both 

the depth of fi rst appearance and maximum activity.

Core depth varied and was limited by the depth of dense 

and/or shell hash layers (Figure 5.2) which was the depth of 

refusal for the corer. Cores from 16P, BB1, and B3 were 16, 

20 and 16 cm deep, respectively. Two cores were taken at 

BB2. The fi rst core was 28 cm deep, but the core above 18 

cm was disturbed by air bubbles during handling. A second 

core sample was taken which was only 14 cm deep so there 

is a break in the data. There was only enough material to do 

butyltins and the radiochemical analyses on the 18-20 cm 

section.

5.3 RESULTS AND DISCUSSION

Contaminants in Surface Sediments

Metals and butyltin concentrations in the surface samples 

and the top layer of the cores are shown in Table 5.1. The 

concentration of total butyltins (the sum of the butyltins 

analyzed) at BB2 was orders of magnitude above all other 

stations. There is a clear gradient of butyltins from BB2 out 

into Benner Bay and down the channel toward Mangrove 

Figure 5.2. Photograph of core BB2 showing shell hash in the 

lower part of the core, grading to fi ne mud up the core in more 

recent sediments. 
Chapter 5: TBT and Metals in Sediment Cores

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STEER Integrated Environmental Assessment Report

Figure 5.3. Plots of 210Pb and 137Cs activities with depth for core 16P.

Lagoon. There was good agreement between the top core 

section at BB2 and sample S7, indicating no gear bias. The 

concentration of Cu was also orders of magnitude higher at 

station BB2 than all other stations. Copper concentrations 

exceeded the ERM by 5X at BB2. Zinc also exceeded the 

ERM at BB2. Impacts to benthic organisms in this area are 

likely as a result of these concentrations.

Isotope Analysis of Cores

Plots of 210Pb and 137Cs activities with 

depth are shown for each core in 

Figures 5.3 - 5.6. Core 16P had the 

best profi le of all the cores, showing 

the characteristic shape of logarithmic 

210Pb decay with depth until the 

background activity (0.1 dpm/g) is 

reached (Figure 5.3). The accumulation 

rate calculated from the 210Pb data is 

0.073 cm/yr. For 137Cs, the depth of 

fi rst 

appearance (1954) is 6-8 cm; the depth 

of maximum activity (1963) is 4-6 cm. 

Calculated accumulation rates based 

on the 137Cs data are 0.10-0.14 cm/y 

and 0.08-0.12 cm/y, respectively. All 

of these rates are in rough agreement, 

given errors and assumptions inherent in both methods, and 

the profi les are very clear. The accumulation rates using 137Cs are slightly higher than from the 210Pb data, indicating 

somewhat younger sediment at depth. This becomes more 

obvious when the TBT data is plotted vs YBP (years before 

present). 

Site LatDD LongDD Monobutyltin Dibutyltin Tributyltin Total butyltin %Tributyltin Tetrabutyltin Ag As Cd Pb

16P 0-2 18.31690 -64.87339 6.61 10.43 66.4 83.5 79.6 0.31 0.00 11.0 0.16 15.7

B3 0-2 18.31849 -64.86831 13.3 11.2 12.4 36.9 33.6 0.20 0.00 10.0 0.09 17.4

BB1 0-2 18.31841 -64.87144 12.6 28.2 40.0 80.8 49.5 0.14 0.00 9.6 0.23 25.4

BB2 0-2 18.32103 -64.86668 940 700 1102 2,741 40.2 37.6 0.27 16.4 0.28 129

S1 18.31953 -64.86732 72.6 68.7 134 275.0 48.6 1.20 0.08 9.7 0.08 119

S2 18.31804 -64.86787 25.7 9.74 12.2 47.6 25.6 0.39 0.00 7.0 0.08 24.1

S3 18.31725 -64.86745 7.61 3.93 4.01 15.6 25.8 0.10 0.00 3.4 0.07 7.77

S4 18.31807 -64.86893 6.25 5.07 6.24 17.6 35.5 0.11 0.00 5.1 0.07 10.2

S5 18.31750 -64.86900 11.2 8.29 5.57 25.0 22.2 0.11 0.00 4.0 0.00 15.9

S6 18.31627 -64.86901 8.33 6.21 217 231.3 93.7 1.82 0.00 4.5 0.07 7.51

S7 18.32103 -64.86668 692 592 993 2,277 43.6 12.8

ERM 3.7 70 9.6 218

ERL 1 8.2 1.2 46.7

Site Sb Sn Al Cr Cu Fe Mn Ni Zn Si Se Hg

16P 0-2 0.46 1.99 38,600 16.8 92.9 23,200 176 5.28 118 140,000 0.746 0.061

B3 0-2 0.22 1.76 21,400 10.3 97.4 11,700 94.1 3.12 92.9 57,000 0.34 0.050

BB1 0-2 1.00 3.32 48,900 19.7 88.7 27,000 200 5.09 145 222,000 0.605 0.096

BB2 0-2 0.73 22.2 64,700 61.5 1,520 36,200 225 8.86 574 141,000 0.521 0.410

S1 1.49 5.25 29,500 18.9 373.0 17,100 115 4.4 206 62,600 0.24 0.126

S2 0.19 3.06 26,500 15.9 115.0 15,000 124 3.32 104 76,400 0.238 0.083

S3 0.10 0.82 7,660 2.5 51.7 4,760 38.9 2.59 47.5 22,700 0 0.030

S4 0.13 1.21 13,300 6.13 50.6 7,810 61.7 3.01 52.7 32,600 0.237 0.032

S5 0.12 1.2 12,400 5.13 54.8 6,840 55.3 2.57 49.4 29,800 0.151 0.033

S6 0.09 0.901 9,450 4.43 41.6 6,210 49.3 2.37 45.4 26,200 0.092 0.033

S7

ERM 370 270 51.6 410 0.71

ERL 81 34 20.9 150 0.15

Abbreviations: LatDD, latitude in decimal degrees; LongDD, longitude in decimal degrees; ERL, effects range low; ERM, effects range median 

Note - Sediment from site S7 was analyzed for butyltins, to check on potential gear bias (PONAR versus sediment corer) with BB-2. No trace or

major element analysis performed at S7.

Tables 5.1. Concentrations of butyltins (ng Sn/g) and metals (μg/g) in surface sediments.
Chapter 5: TBT and Metals in Sediment Cores

124

STEER Integrated Environmental Assessment Report

Figure 5.4 shows the profi le for 

core BB1. The accumulation 

rate calculated from the 210Pb 

data is 0.06 cm/y. The profi le is 

straightforward – 210Pb decays 

logarithmically with depth to a 

background level of 0.1 dpm/g. For 

137Cs, the depth of 

fi rst appearance 

(1954) is 6-8 cm, yielding an 

accumulation rate of 0.10-0.14 

cm/y. The depth of maximum 137Cs 

activity (1963) is 2-4 cm, yielding 

an accumulation rate of 0.04-0.08 

cm/y. There is good agreement 

between the 137Cs and 210Pb 

data. There is some evidence for 

increased accumulation rates over 

time, but increased depth resolution 

would be needed for further 

evaluation.

Figure 5.5 shows the profi le for 

core B3. The 210Pb data for this core 

are subject to interpretation. It does 

not appear that the core was long 

enough to reach the background 

210Pb level, so the background 

activity was assumed to be equal 

to that used for 16P and BB1 (0.1 

dpm/g). The background level 

within a small region should be 

the same. If a higher background 

activity is used, the accumulation 

rate will decrease – for example, 

using 0.5 dpm/g as the background 

level yields a rate of 0.085 cm/y. 

Also, there is some question as 

to whether all data points refl ect 

sedimentation, and thus should 

be used in the rate calculation, or 

whether the upper 4 data points 

refl ect mixing and should be 

neglected in the rate calculation. 

The accumulation rates are 0.32 

cm/y (all data) or 0.16 cm/y (only 

the lower 4 data points).

For 137Cs data, the depth of 

fi rst appearance (1954) is 8-10 

cm, yielding an accumulation rate of 0.14-0.17 cm/y. This 

is in agreement with the 21 Pb rate from the lower four 

points. There are two depths, above and below the 6-8 

cm interval, with identically high activities that could be 

considered the depth of maximum 137Cs activity (1963). 

The fi rst, at the top of the higher-activity layer, is 4-6 cm 

and yields an accumulation rate of 0.08-0.12 cm/y. One 

could also assume a typical profi le shape and assume that 

the sediment in the 6-8 cm interval has anomalously low 

activities. If 6-8 cm is used as the depth of maximum 

activity, the accumulation rate would be 0.12-0.16 cm/y. 

However, the anomaly in the 210Pb data occurs at the 6-8 

Figure 5.4. Plots of 210Pb and 137Cs activities with depth for core BB1.

Figure 5.5. Plots of 210Pb and 137Cs activities with depth for core B3.

Figure 5.6. Plots of 210Pb and 137Cs activities with depth for core BB2.
Chapter 5: TBT and Metals in Sediment Cores

125

STEER Integrated Environmental Assessment Report

cm depth interval, 

so it may be an 

event-related 

disturbance of 

the sediment 

layer is 

responsible. 

Figure 5.6 

shows the 

profi le for 

core BB2. The 

210Pb pro

fi le 

for this core is 

also subject to 

interpretation 

because of 

the break in 

the data set. 

Accumulation 

rates were 

calculated both using all points and the lower points. 

Accumulation rates are 0.35 cm/y for all data points and 

0.12 cm/y for only the lower points. A supported value of 

0.1 dpm/g was used, consistent with cores 16P and BB1, 

since the core does not appear to be long enough for 210Pb 

activities to have reached background activities. As noted 

previously, a higher background value would yield a lower 

accumulation rate. There is an anomaly at the 6-8 cm depth 

interval, which may be an event-related disturbance of the 

sediment layer similar to core B3. Station BB2 was in the 

heart of the marina facilities, adjacent to the boat ramp and 

travel lift. 

137Cs samples down to 12 cm were originally analyzed, 

with no detectable 137Cs. The reason for this is unclear; 

one potential explanation is that sediment properties differ 

between this core and the others. The remaining samples 

were counted with detections for the 20-22 cm and 22-24 

cm intervals. However, these detections occurred at the 659 

keV photopeak (part of gamma spectrum); the photopeak 

that represents Cs-137 is 662 keV. In practice, a deviation 

of ±~2 keV is accepted when evaluating gamma spectra, 

using information about sample and site to guide decisions. 

Thus, the 20-22 and 22-24 sections are considered 

borderline; they would likely be recorded as detectable 

137Cs, unless other evidence suggested otherwise. It is 

diffi cult to determine whether these detections represent the 

depth of fi rst appearance or maximum activity. Using the 

point as a fi rst occurrence (1954) yields an accumulation 

rate of 0.42 cm/yr. Using the point as a maximum (1963) 

occurrence yields an accumulation rate of 0.50 cm/yr.

The age of each layer of the cores as calculated by the 210Pb 

and 137Cs methods are shown in Table 5.2. The sections 

representing 1963 (upper) and 1954 (lower) are highlighted 

(shaded). These represent 50 and 59 years before 2013 

respectively. The ages determined by the 137Cs method 

appear to more closely refl ect years before present (YBP). 

Years at 16P, BB1 and BB2 are overestimated while B3 

is underestimated by the 210Pb method. It is unclear which 137Cs accumulation rate to use at BB2 so the most recent 

marker (1963) was used. 

Grain Size in the Sediment Cores

The characteristics of the sediment in the area have 

changed dramatically over the years. Figures 5.7 and 5.8 

show the proportion of fi ne grained (silt + clay) and gravelsized particles in the cores over time and down the length 

of the cores. All the cores show a much higher percentage 

of gravel-sized material at the bottom of the cores than 

the top. These particles, however, were not gravel but 

were in fact shell hash (Figure 5.2). The shift toward fi negrained material is most dramatic at BB2. Station BB2 is 

surrounded by bulkheads and sits beneath constant boat 

activity. It is next to the main marina ramp. While BB2 

was the deepest core, it covers the shortest time span due 

to the much higher accumulation rate (Table 5.2). Recall 

that there were anomalies in the cores from BB2 and B3 

and that the calculated accumulation rates in the lower half 

of the cores were much lower than in the top half. A much 

lower accumulation rate in the deeper, older, layers at BB2 

is logical as human activity has clearly and drastically 

altered the bottom sediment characteristics. Note also that 

Table 5.2. Estimated ages of sections within sediment cores from the STEER.

210Pb age 137Cs age 210Pb age 137Cs age 210Pb age 137Cs age 210Pb age 137Cs age 

1954

137Cs age 

1963

1 13.7 9.1 16.7 11.1 3.1 6.7 2.9 2.4 2.0

3 41.1 27.3 50.0 33.3 9.4 20.0 8.7 7.1 6.0

5 68.5 45.5 83.3 55.6 15.6 33.3 14.5 11.8 10.0

7 95.9 63.6 116.7 77.8 21.9 46.7 20.3 16.5 14.0

9 123.3 81.8 150.0 100.0 28.1 60.0 26.1 21.3 18.0

11 150.7 100.0 183.3 122.2 34.4 73.3 31.9 26.0 22.0

13 178.1 118.2 216.7 144.4 40.6 86.7 37.7 30.7 26.0

15 205.5 136.4 250.0 166.7 46.9 100.0

17 283.3 188.9

19 316.7 211.1 55.1 44.9 38.0

21 60.9 49.6 42.0

23 66.7 54.4 46.0

25 72.5 59.1 50.0

27 78.3 63.8 54.0

Rate cm/yr 0.07 0.11 0.06 0.09 0.32 0.15 0.35 0.42 0.50

Mean Core 

Depth cm

16P BB1 B3 BB2
Chapter 5: TBT and Metals in Sediment Cores

126

STEER Integrated Environmental Assessment Report

the most dramatic shifts have occurred in the last 50-75 

years. 

Reviews done in the 1980s to evaluate the potential 

outcomes of declaring the STEER a NOAA National 

Marine Sanctuary noted that Mangrove Lagoon and 

Benner Bay were dominated by turtle grass beds in the 

1960s, but in the 1970s the bottom was becoming mud, 

and was converting to a calcareous macroalgae-dominated 

benthic community (NOAA, 1981). Extensive shoreline 

development, increasing boating activity, pollution from 

terrestrial runoff and sewage discharges were all impacting 

Benner Bay water quality by the early 1970s (Grigg et al., 

1971). The watersheds immediately adjacent to Benner 

Bay that drain into it are the Nadir and Compass Pt. 

subwatersheds. More recent assessments describe the Nadir 

shoreline and watershed as being “a highly dense chain of 

marinas and commercial properties that transitions to single 

family residential area moving uphill”, and Compass Pt. 

includes “a residential area that extends from the top of 

the subwatershed down to Benner Bay; the main gut fl ows 

behind single family homes on the hillside, then under or 

on the road through the marina complex” (Horsley Witten, 

2013).

Butyltin Concentrations in the Sediment Cores

The concentrations of total butyltins are shown in Figure 

5.9. The peak concentrations occur at less than 50 years 

ago, which is consistent with historical use patterns. There 

are low concentrations of butyltins in sections 2-4 cm 

below 50 years ago which may refl ect the initial buildup 

of TBT contamination and/or an indication of how deep 

sediments are churned by storms and bioturbation. Butyltin 

concentrations are vastly higher at BB2 which also shows a 

peak in the past. The break in the data unfortunately occurs 

where the use of TBT was initiated so it is impossible to 

conclude if concentrations were even higher in the past, or 

if TBT use continued into more recent years. 

Concentrations have declined in recent years. Nevertheless, 

the observed concentrations at depth are vastly higher than 

anywhere else in Benner Bay or the rest of the STEER. 

Concentrations of this magnitude have only been observed 

in a few places (Page et al., 1996, 24-12,400 ng/g - Maine, 

USA; Shim et al. 2002, 33-19,780 ng/g – S. Korea; Diaz 

et al. 2002, 123-6,692 and 574-1,970 – NE and SE Spain; 

EVS, 1999, 8-6,200 - Seattle, USA). All of these studies 

were sampling in marinas and/or ship yards for the purpose 

of locating hot spots. Also, our data is reported as ng/g of 

tin (ng Sn/g), as opposed to TBT which has a 60% higher 

molecular weight than elemental tin. Of 1,506 data points 

in the NS&T data base with TBT sediment analyses, the 

05

10

15

20

25

30

0.0 20.0 40.0 60.0 80.0 100.0

Core Depth cm

% Fines

16P

BB1

B3

BB2

05

10

15

20

25

30

0.0 10.0 20.0 30.0 40.0 50.0 60.0

Core Depth cm

% Gravel

16P

BB1

B3

BB2

Figure 5.7. Percentage of fine grained sediment and gravel sized 

material (shell hash) down the length of the cores. 0

50

100

150

200

250

0.0 20.0 40.0 60.0 80.0 100.0

Years BP

% Fines

16P

BB1

B3

BB2

0

50

100

150

200

250

0.0 10.0 20.0 30.0 40.0 50.0 60.0

Years BP

% Gravel

16P

BB1

B3

BB2

Figure 5.8. Percentage of fine grained sediment and gravel sized material 

(shell hash) as a function of time. Years BP, years before present.
Chapter 5: TBT and Metals in Sediment Cores

127

STEER Integrated Environmental Assessment Report

median total butyltin value is 0.95 ng/g, the average is 8.9 

ng/g. The highest value is 990 ng/g from Elliott Bay, a 

Superfund site in Puget Sound sampled in 1989. 

There was relatively little butyltin in the B3 core. Neither is 

there evidence of historical changes over the years. Relative 

to the 137Cs date markers, the 210Pb analyses severely 

underestimated the age of the B3 sediments unlike the other 

cores (Table 5.2). There are obvious discontinuities in 

both the 137Cs and 210Pb records (Figure 5.4). Its location is 

in the middle of the channel, perhaps the natural channel, 0

50

100

150

200

250

0 100 200 300 400

Years BP

tot BT

16P

BB1

B3

0

20

40

60

80

100

0 2000 4000 6000 8000 10000

Years BP

tot BT

BB2

Figure 5.9. Concentration (ng/g) of total butyltins as a function of time. 

Figure 5.10. Changes in major element concentrations 

over time at station B3. 0

20

40

60

80

100

120

140

160

0 20000 40000 60000

Years BP

ug/g

Al

Fe

Si

05

10

15

20

25

30

0.0 20.0 40.0 60.0 80.0 100.0

Core Depth cm

% Tributyltin

16P

BB1

B3

BB2

Figure 5.11. Percent tributyltin as a proportion of the total butyltins as a 

function of time and core depth. 

leading into inner Benner Bay. What events or processes 

(e.g., storms, dredging, etc.) may have contributed to the 

history of deposition at this location is unknown. The 

concentrations of the major soil elements of aluminum, 

iron and silicon all show a major shift at B3 in the mid1940s (Figure 5.10), which coincides with the discontinuity 

in the 210Pb and 137Cs anomalies (Figure 5.4). Interestingly, 

the same is true for all the trace metals as well. Clearly, 

some event or change in circulation or terrestrial input 

occurred then. 

Another puzzling aspect is the percentage of tributyltin 

as a proportion of total butyltins in the sediment. While 

the concentration of butyltins is decreasing over time, the 

proportion of tributyltin is increasing at 16P, BB1 and B3 

up to the present, indicating continuing fresh inputs (Figure 

5.11). The peak concentrations at BB2 in the marina are 

only 4-10 cm deep. The proportion of tributyltin at those 

depths is 50-70%. Prop wash from boats and storm-driven 

tidal currents may be the source of fresh tributyltin at the 

outer stations. Unlike BB2, the proportions below 10 cm 

depth in the cores at 16P, BB1 and B3 are meaningless as 

the concentrations are essentially zero and they date back 

to before TBT existed. Station 16P was located behind a 

mangrove island in the middle of the waterway between 

Benner Bay and Mangrove Lagoon (Figure 5. 1). There 
Chapter 5: TBT and Metals in Sediment Cores

128

STEER Integrated Environmental Assessment Report

are moored boats, but no marina facilities in the immediate 

vicinity, so the TBT load there must be drifting in from 

other areas. The currents in the waterway are highly 

variable and dependent on tidal fl ux and wind driven 

currents. The last tropical storm to hit St. Thomas was 

Irene in 2011, which passed just south of the island with 

sustained gale force winds and heavy rain.

Gradients in Chemical Contamination

Chemical results from the top sections in the cores and 

the surface sediment grabs illustrate consistent gradients 

away from inner Benner Bay for almost all constituents. 

With three exceptions (Se, Sb, Si) the highest metals 

concentrations are all found at BB2. Metals concentrations 

were higher in 

general at the 

stations located 

closest to shore 

and declined 

further out into 

Benner Bay. 

Mercury was 

an order of 

magnitude higher 

at BB2 than all 

other stations 

except S1. 

Zinc exceeded 

the ERM. As 

noted above, 

the copper 

concentration 

was more than fi ve times the 

ERM. Arsenic, 

Pb, Hg, and 

Zn exceeded 

the ERLs at 

multiple stations. 

Aluminum, 

silicon, and 

iron are the 

most common 

elements in 

the earth’s crust. Decreasing gradients of these elements 

leading away from Benner Bay all indicate a greater 

contribution of land-based sediment material close to the 

shoreline, as opposed to marine sources. The pattern of 

calcium decreasing from offshore toward Benner Bay 

and Mangrove Lagoon locations in the 2011 data are 

consistent with this interpretation (Figure 5.12). All of 

these observations, plus the historical patterns revealed in 

the cores indicate a disturbed habitat that is heavily and 

increasingly impacted by land-based sediment input and 

chemical contamination from boating related activities. 

The gradient of butyltins in the surface from BB2 out 

into Benner Bay and down the channel toward Mangrove 

Lagoon clearly illustrate the impact of boating related 

activities (Table 5.1). Surface concentrations in the marina 

complex are one to two orders of magnitude higher than 

anywhere else. Butyltins at S1 leading out of the harbor 

were higher than at core B3 and those stations further out. 

Stations 2-5 were laid out on two transects leading away 

from core B3 on different routes. Concentrations drop off 

rapidly further out. The one exception was station S6 that 

had a total butyltins concentration of 231 μg/g. Station S6 

was taken on the edge of the channel leading out to open 

waters. The spike in concentration at that point, was almost 

as high as seen at S1. Notably, the percentage of tributyltin 

(relative to total butyltins) at that site was 93.7%, indicating 

fresh contamination. This strongly suggests a recent spill or 

perhaps grounding of a freshly painted vessel. It is unclear 

why butyltins are elevated at 16P and BB1, unless there are 

Figure 5.12. Calcium detected in sediments collected in the STEER.
Chapter 5: TBT and Metals in Sediment Cores

129

STEER Integrated Environmental Assessment Report

Figure 5.13. Concentration of copper in surface sediments in northern Benner Bay.

92.9 μg/g 

97.4 μg/g 

88.7 μg/g 

373 μg/g 

115 μg/g 

51.7 μg/g 

50.6 μg/g 

41.6 μg/g 

54.8 μg/g 

1,520 μg/g 

Figure 5.14. Copper concentrations as a function of time. 0

50

100

150

200

250

0 20 40 60 80 100 120

Years Before Present 

Cu ug/g 

16P

B3

BB1

0

10

20

30

40

50

60

0 500 1000 1500 2000

Years Before Present 

Cu ug/g 

BB2

other sources in the 

area as well. 

There is also a 

strong gradient 

of copper leading 

away from the 

marina complex 

(Figure 5.13, Table 

5.1). Copper-based 

bottom paints were 

used before the 

advent of TBT, and 

copper-based paints 

have replaced the 

TBT paints. Note 

also, that copper 

at Station S6 is 

not elevated, in 

contrast to TBT. 

The concentration 

of copper in the 

cores show a 

clear increase in 

concentrations over 

time at all locations 

(Figure 5.14), 

including at B3. Copper concentrations exceeded the ERL 

at all surface stations. 

5.4 CONCLUSIONS

The inner reaches of northern Benner Bay are degraded by 

marina operations, shoreline development and watershed 

changes. Sediment dynamics and sediment quality are, 

and have been for decades, heavily impacted. The benthic 

community was once a thriving ecosystem as evidenced 

by the remnants of shelled species, that, at the bottom of 

some cores exceeded the volume of sediment present. That 

community has vanished and was smothered by very fi ne 

sediment that accumulates at rates an order of magnitude 

above rates seen at other core locations in the STEER. 

The sediment is highly contaminated with butyltin paint 

residues, copper, and other toxic metals. The sediment 

is contaminated below the surface as well. Dredging 

new or deeper channels will spread these contaminants 

over a wide area. Dredging for remediation purposes is 

advisable, but will be expensive to do with methods that 

will properly prevent dredge spoil release to the water 

column. Otherwise, the benthic community will likely 

never recover, and environmental damage may expand if 

contaminants are diffused over a larger area. Matthiessen 

(2013) reported that benthic communities do not recover 
Chapter 5: TBT and Metals in Sediment Cores

130

STEER Integrated Environmental Assessment Report

from TBT contamination until the concentration of 

butyltins is reduced to 10-40 ng/g. The concentration of 

butyltins at a depth of 6-8 cm was 8,871 ng/g at Station 

BB2. The system may be receiving fresh inputs of TBT 

as evidenced by the percentage of tributyltin residues at 

station S6. The system is dynamic. Between sampling in 

2011 and 2013, the concentration of TBT had more than 

doubled at station BB2. Copper had increased by 50%. 

What event(s) may have caused such large changes in such 

a short time are unknown. Boat groundings, prop wash, and 

pile driving are all likely activities present at a marina that 

would stir up the bottom, and bring up contaminants from 

deeper in the sediment column. 

LITERATURE CITED

Apeti, D.A., S.I. Hartwell, W.E. Johnson, and G.G. 

Lauenstein, G.G., 2012. National Status and Trends 

Bioeffects Program: Field methods. NOAA National 

Centers for Coastal Ocean Science, Center for Coastal 

Monitoring and Assessment. NOAA NCCOS Technical 

Memorandum 135. Silver Spring, MD. 52pp.

Appleby, P.G. and F. Oldfi eld. 1978. The calculation 

of 210Pb dates assuming a constant rate of supply of 

unsupported 210Pb to the sediment. Catena 5, 8pp.

Bray, S. and W.J. Langston. 2006. Tributyltin Pollution 

on a Global scale. An Overview of Relevant and Recent 

Research: Impacts and Issues. Report to Dr. Simon 

Walmsley, WWF UK. BaSECO Consultants and the 

Marine Biological Association of the United Kingdom. 

48pp.

Bryan G.W. and P.E. Gibbs. 1991. Impact of low 

concentrations of tributyltin (TBT) on marine organisms: 

A review. In: Metal Ecotoxicology, Concepts and 

Applications. MC Newman, AW McIntosh (eds). Lewis 

Publishers, Chelsea, Mich. pp323-362. 

Carroll, J., and I. Lerche. 2003. Sedimentary Processes: 

Quantifi cation Using Radionuclides. Elsevier. 272pp.

Cruz, A., A.M. Anselmo, S. Suzuki, and S. Mendo. 2015. 

Tributyltin (TBT): a review on microbial resistance and 

degradation. Critical Reviews in Environmental Science 

and Technology, 45:970–1006. Dı́

az, S., M. Ábalos, & J.M. Bayona. 2002. 

Organotin contamination in sediments from the Western 

Mediterranean enclosures following 10 years of TBT 

regulation. Water Research 36(4):905-918.

EVS (1999). Tributyltin in Marine Sediments and the 

Bioaccumulation of Tributyltin: Combined Data Report. 

Report to Port of Seattle, Lockheed Martin Corporation, 

Todd Shipyards Corporation.

Hancock, G., D. N. Edgington, J. A. Robbins, J. N. 

Smith, G. Brunskill and J. Pfi tzner. 2002. Workshop 

on radiological techniques in sedimentation studies: 

methods and applications, In Environmental Changes and 

Radioactive Tracers, Proceedings of the South Pacifi c 

Environmental Radioactivity Association (SPERA). J. M. 

Fernandez and R. Fichez, Eds. IRD Editions, Paris. 532 pp.

Horsley Witten Group, Inc. 2013. St. Thomas East End 

Reserves Watershed Characterization Report. Prepared for: 

NOAA Coral Reef Conservation Program, VI Department 

of Planning and Natural Resources, The Nature Conservancy. 97 pp.

Grigg, D.I., R.E. vanEepoel, and R.W. Brody. 1971. Water 

Pollution Report No. 10. Water Quality and Environmental 

Status of Benner Bay-Mangrove Lagoon St. Thomas. 42pp 

plus appendices. 

Kimbrough, K. L., and G. G. Lauenstein (Editors). 2006. 

Major and Trace Element Analytical Methods of the 

National Status and Trends Program: 2000-2006. Silver 

Spring, MD. NOAA Technical Memorandum NOS NCCOS 

29. 19 pp.

Matthiessen, P. 2013. Detection, monitoring, and 

control of tributyltin – an almost complete success story. 

Environmental Toxicology and Chemistry, 32(3):487-489. 

Nittrouer, C.A., R.W. Sternberg, R. Carpenter, and J.T. 

Bennett. 1979. The use of Pb-210 geochronology as a 

sedimentological tool: Application to the Washington 

continental shelf. Marine Geology 31, 297-316.

NOAA (National Oceanic and Atmospheric Administration). 1981. Proposed St. Thomas National Marine Sanctuary. Draft Environmental Impact Statement. 59pp and 

appendices

Omae, I. 2014. Chemistry and fate of organotin antifouling 

biocides in the Environment. In: Antifouling Paint 

Biocides, L.K Konstantinou (ed). Chapter 2, p18-50. 

Springer Verlag, Berlin, Germany

Page, D.S., C.C. Ozbal, and M.E. Lanphear. 1996. 

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with shipyard activity. Environmental Pollution 91(2):237-

243. 

Palinkas, C.M., and C.A. Nittrouer. 2007. Modern sediment 

accumulation on the Po shelf, Adriatic Sea. Continental 

Shelf Research 27, 489-505.

Shim W.J., S.H. Hong, U.H. Yim, N.S. Kim, and J.R. 

Oh. 2002. Horizontal and vertical distribution of butyltin 

compounds in sediments from shipyards in Korea. Archives 

of Environmental Contamination and Toxicology, 43, 

277–283.

Turner, A, and G. Glegg. 2014. TBT-based antifouling 

paints remain on sale. Marine Pollution Bulletin. http://

dx.doi.org/10.1016/j.marpolbul.2014.08.041.
Chapter 5: TBT and Metals in Sediment Cores

132

STEER Integrated Environmental Assessment Report
133Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report

Many stormwater chemical contaminants, if present in 

the aquatic environment, are at very low concentrations, 

typically in the low parts per billion (ppb or μg/L) or even 

parts per trillion (ppt or ng/L) ranges. A classic approach 

for detecting compounds at very low concentrations in the 

aquatic environment has been to collect, fi lter and extract 

large volumes of water, to enable their detection by analytical 

instrumentation. The POCIS disk, 

however, can potentially sample 

tens to hundreds of liters of water 

during deployment, providing timeweighted concentration estimates of 

contaminants present in the water 

column (Alvarez et al., 2008). This 

technology also has an advantage 

over discrete water samples, as 

POCIS can sequester chemical 

contaminants that may be present 

in the water only episodically, such 

as during storm events or during a 

small discharge or spill (Alvarez et 

al., 2008). Typical deployments of 

the POCIS last approximately 30 

days. 

The USGS (Alvarez et al. (2004) has also developed 

methods to estimate the ambient water concentration for 

a number of stormwater contaminants sequestered by the 

POCIS, using individual sampling rate values (Rs

). The Rs

values are experimentally determined for each chemical, 

and incorporated into the following equation: 

 Cw = N 

 Rs

t

where 

Cw is the ambient water concentration of the chemical

N = the amount (e.g., ng) of chemical accumulated by the 

POCIS

CHAPTER 6: AN ASSESSMENT OF CHEMICAL CONTAMINANTS DETECTED IN PASSIVE WATER SAMPLERS DEPLOYED IN THE ST. THOMAS EAST END RESERVES (STEER)

Anthony S. Pait1

, S. Ian Hartwell1, Andrew L. Mason1, Francis R. Galdo Jr.2, Robert A. Warner1, Christopher F. G. Jeffrey1,3, Anne M. Hoffman4

, Dennis A. Apeti1, and Simon J. Pittman1,5

1

NOAA/NOS/National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment (CCMA),

1305 East/West Highway, Silver Spring, MD 20910

2

The University of the Virgin Islands, St. Thomas, USVI

3

CSS-Dynamac Consolidated Safety Services, Fairfax, VA 22030, under CSS-Dynamac Contract #EA-133C-14-NC-1384

4

The Nature Conservancy, St. Thomas, USVI

5

The Marine Institute, Plymouth University, United Kingdom

6.1. INTRODUCTION

Polar Organic Chemical Integrative Samplers or POCIS 

were developed by the U.S. Geological Survey (USGS) as 

a tool to detect water soluble contaminants in the environment. They were deployed in the STEER at fi ve locations 

in February 2012. 

The goal of using POCIS in the 

STEER was to assess the presence of 

and when possible, estimate ambient concentrations of water soluble 

contaminants. While the concentration and effects of chemical contaminants in sediments in the STEER were 

reported in earlier chapters, there are 

many chemical contaminants that 

don’t readily accumulate in sediments, 

but are toxic to biota (e.g., some current use pesticides). Determining the 

presence and estimating the concentration of water soluble chemicals, 

specifi cally stormwater contaminants, 

provides additional information on 

stressors present in the STEER. As 

noted earlier, the STEER watershed 

contains hotels/resorts, an active landfi ll, an EPA Superfund site, residential 

areas with individual sewage treatment systems, all of 

which can be sources of a variety of stormwater contaminants to the STEER.

The POCIS (Figure 6.1) is a disk consisting of a sorbent 

matrix (Waters Oasis® HLB) sandwiched between two 

membrane sheets (Alvarez et al., 2008). The porous 

membrane sheets allow water to fl ow through the sorbent, 

enabling the sorbent material to sequester (accumulate) the 

contaminants of interest. For deployment, the POCIS disks 

are assembled onto a frame and then placed in a deployment canister (Figure 6.2). 

Figure 6.1. Example of a POCIS disk. Image 

courtesy of the USGS.
134Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report

Rs is the sampling rate (L/d), i.e., liters of water cleared of 

analyte per day, and

t is the number of days of deployment for the POCIS. 

The number of days the 

POCIS is deployed is used in 

calculating estimated concentrations of the chemicals of 

interest, providing some fl exibility in the length of time the 

POCIS is deployed. Additional information on this technology can be found in Alvarez et 

al. (2004, 2008). 

6.2. METHODS

The POCIS deployment canisters containing the POCIS 

disks were shipped on ice to 

the University of the Virgin Islands in sealed solvent-rinsed 

metal cans. On arrival at UVI, 

the cans with the canisters 

were placed in a freezer until 

deployment. 

The POCIS deployment canisters were placed in the 

STEER on 16 February 2012 at fi ve locations (Figure 

6.3), by scientists from UVI, and DPNR’s Division of Fish 

and Wildlife. The fi ve sites where the POCIS were deployed were the same 

targeted (not randomly 

selected) sites used for 

the monthly sampling in 

the STEER for nutrients, 

TSS and sedimentation 

(see Chapter 9). At each 

of these sites, sediment 

traps were attached 

to rods secured in the 

sediments (Figure 6.4). 

The POCIS deployment 

canisters were tethered 

to these same rods, by 

UVI and DPNR SCUBA 

divers. 

A summary of conditions at each site at the 

time of POCIS canister 

deployment is provided in Table 6.1. The depth of the POCIS deployment canisters ranged from 1 meter at the site 

Figure 6.3. Locations of passive water samplers (POCIS) in the STEER.

Figure 6.2. A disassembled POCIS deployment canister with the 

POCIS disks. Image courtesy of the USGS. 
135Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report

in Benner Bay, to 12.2 meters at the site adjacent to Great 

St. James Island. Each POCIS deployment canister was set 

between 20 and 50 cm from the bottom. 

As part of the preliminary work for the project in 2010, a 

POCIS deployment canister was placed in Turpentine Gut, 

the only perennial stream 

in St. Thomas (Nemeth 

and Platenberg, 2007). 

Although Turpentine Gut 

(site TG) is not within the 

boundaries of the STEER, it 

drains directly to Mangrove 

Lagoon (Figure 6.3), and is 

not only a signifi cant source 

of freshwater to the STEER, 

but also of sediments 

(STEER, 2011), and likely 

other types of nonpoint 

source pollution including 

stormwater contaminants. 

The POCIS deployment 

canister in Turpentine 

Gut was suspended in the 

water column at a depth of 

approximately 1.5 meters 

(Table 6.1). As with the 2012 deployment, two POCIS 

stormwater disks were included in the deployment canister. 

NOAA and DPNR Division of Fish and Wildlife personnel 

placed the POCIS deployment canister approximately 20 

meters south of the unfi nished bridge adjacent to Bovoni 

Road, on the east bank of Turpentine Gut. 

Field blank canisters were used in both the 2012 and 2010 

deployments. The fi eld blank, a POCIS disk and frame, 

was exposed to the air during the time the POCIS canisters 

were being deployed, in order to assess the presence of 

airborne contaminants. 

During the 2012 deployment in the STEER, the fi eld blank 

was exposed to the air at each of the fi ve sites, and served 

as a cumulative fi eld blank. For the 2010 deployment 

in Turpentine Gut, 

one fi eld blank was 

used. After a POCIS 

deployment canister 

entered the water, the 

POCIS fi eld blank 

was placed back in 

its protective canister 

(solvent-rinsed metal 

container also used 

for shipping), sealed 

and then returned to 

UVI and placed in a 

freezer. 

The fi ve POCIS 

deployment canisters 

from the STEER 

were retrieved by 

UVI and DPNR 

Division of Fish and 

Wildlife scientists using SCUBA on 14 March 2012. During the time the POCIS deployment canisters were out of 

the water, the fi eld blank was again opened and exposed 

to the air. Once retrieved, the POCIS deployment canisters were returned to their protective canisters, and then 

placed in the freezer at UVI until they were shipped on ice 

along with the fi eld blank in its own protective canister to 

the USGS for analysis. Additional information on POCIS 

deployment techniques can be found in Alvarez (2010). 

Table 6.1. Location and conditions during deployment of the POCIS canisters in February 2012 and May 2010. 

Site Date Latitude Longitude Deployment 

Depth (m) Water Conditions

Great St. James (SJ) 2/16/2012 18.30302 -64.83671 12.2 Clear, calm

Cowpet Bay (CB) 2/16/2012 18.31487 -64.84267 5.5 Clear, calm

Rotto Cay (RC) 2/16/2012 18.31331 -64.86423 5.5 Clear, calm

Benner Bay (BB) 2/16/2012 18.3167 -64.8674 1 High turbidity

Mangrove Lagoon (ML) 2/16/2012 18.31385 -64.87988 1.3 High turbidity

Turpentine Gut (2010) (TG) 5/5/2010 18.32046 -64.87719 1.5 Moderate flow, high turbidity

Note - depth of POCIS canister in meters (m)

Figure 6.4. POCIS deployment canister (arrow) among the sediment traps 

at a site in the STEER.
136Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report

At the USGS laboratory, the POCIS disks were removed 

from the deployment canisters, and dichloromethane and 

methyl-tert-butyl ether were used to extract the stormwater contaminants accumulated by the POCIS, for analysis. 

The analysis of the extracts from the POCIS was carried 

out using gas chromatography/mass spectrometry in the 

selected ion monitoring mode, and results were reported 

as a quantity of each chemical per POCIS extract (i.e., ng/

ampoule). The sampling rate values (Rs

) mentioned earlier 

were then used to estimate ambient water concentrations of 

those compounds found to be above the Quantitation Level. 

The Quantitation Level is the minimum concentration of 

the stormwater contaminant in the POCIS extract needed to 

ensure confi dence in the reported values. Additional information on the analysis of the POCIS disks can be found in 

Alvarez et al. (2008). 

The 69 stormwater contaminants analyzed from the POCIS 

are listed in Table 6.2, and include a number of pesticides, 

detergent metabolites, animal and plant sterols, fl ame 

retardants, fecal indicators and ingredients in personal care 

products. They represent a suite of water soluble contaminants analyzed by USGS, and are primarily associated with 

urban and domestic human use. 

Pesticides include the herbicides atrazine, metolachlor and 

bromacil, and the insecticides chlorpyrifos, carbaryl, and 

diazinon. The metabolites of the surfactants/detergents 

included 4-octylphenol and para-nonylphenol, along with 

nonyl- and octylphenol polyethoxylates such as NPEO1 

(nonylphenol monoethoxylate) and OPEO2 (octylphenol 

diethoxylate). The environmentally ubiquitous phthalate 

ester plasticizers diethyl phthalate (DEP) and diethylhexyl 

phthalate or DEHP, are also sequestered by POCIS. 

A number of animal and plant-related compounds accumulated by the POCIS include the animal/plant sterol cholesterol, and the plant sterols beta-sitosterol and stigmastanol. 

Fecal indicators 3-beta-coprostanol and skatol are also 

sequestered by POCIS. 

6.3. RESULTS AND DISCUSSION

A total of 26 stormwater contaminants were detected at 

least once in the STEER, although the majority (65%) of 

detections for these 26 were below the Quantitation Level, 

the minimum concentration sequestered in the POCIS disk 

needed to estimate concentrations. In Turpentine Gut, 31 

stormwater contaminants were detected, a little over half 

(55%) of these 31 were below the Quantitation Level. 

Table 6.2 presents the estimated ambient water concentrations of the stormwater contaminants accumulated by the 

POCIS disks in the STEER and in Turpentine Gut. Additional information on the results, including the raw data 

can be found in Pait et al. (2013). The shading in Table 

6.2 indicates those stormwater contaminants in the POCIS 

that were high enough to estimate ambient water concentrations. The Reporting Limit represents the lower limit for 

estimating the ambient water concentration of a stormwater 

contaminant.

Estimated Concentrations of Stormwater Contaminants in 

the STEER in 2012

From the February 2012 deployment at the fi ve sites in the 

STEER, ambient water concentrations could be estimated 

for nine stormwater contaminants which are highlighted 

in Table 6.2. The highest estimated concentration for any 

of the compounds detected in the STEER was the animal/

plant sterol cholesterol at the Benner Bay site (1,100 ng/L), 

followed by Cowpet Bay (800 ng/L) and Rotto Cay (550 

ng/L). Cholesterol is an essential and natural component 

of cell membranes in animals, as well as an ingredient in 

some personal care products. Cholesterol is found to a 

lesser degree in some plant and fungal species, and has 

sometimes been used as a fecal indicator (Francy et al., 

2003).

Bargar et al. (2013) conducted a study on nearby St. John, 

in the Virgin Islands National Park and the Virgin Islands 

Coral Reef National Monument. Cholesterol concentrations detected by Bargar et al. (2013) ranged from 240 

ng/L at Round Bay, to 440 ng/L at Whistling Cay in the 

POCIS deployed, similar to the concentrations found in the 

STEER. Along the South Florida coast (Miami to Looe 

Key), concentrations ranged from below the detection limit 

to 2,896 ng/L (Singh et al., (2010). 

Another class of stormwater contaminant detected in the 

STEER by POCIS were two phthalate ester plasticizers, diethylhexyl phthalate (DEHP), and diethyl phthalate (DEP). 

The highest estimated concentration of DEHP detected in 

the STEER was 300 ng/L at Great St. James. Due to health 

concerns regarding DEHP, including evidence that DEHP 

is an endocrine disruptor (Gray et al., 2000) and a possible 

carcinogen (USDHHS, 2011), the use of DEHP has been 

reduced or eliminated for some applications. 

The highest estimated concentration of DEHP detected in 

St. John, USVI by Bargar et al. (2013) was 820 ng/L at 

Whistling Cay, somewhat higher than what was estimated 

at Great St. James. As noted earlier, the deployment of the 

POCIS in the STEER was made in February 2012, during 

the dry season. Lower rainfall levels would likely lead to 

less runoff, which in turn could result in lower concentra-
137Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report

Table 6.2. Estimated water column concentrations of stormwater contaminant residues sampled by POCIS in the STEER and in Turpentine Gut. 

Mangrove Lagoon Benner Bay Rotto Cay Cowpet Bay Great St. James Reporting Limit Turpentine Gut Reporting Limit

Compound Use ng/L ng/L ng/L ng/L ng/L ng/L ng/L ng/L

1,4-Dichlorobenzene Moth repellant, fumigant, deodorizer <RL <RL <RL <RL <RL 130 <RL 100

3,4-Dichlorophenyl isocyanate (m) Degradation product of diuron or linuron <RL <RL <RL <RL <RL 240 <RL 1903-Beta-coprostanol (m) Fecal indicator <RL <RL <RL <RL <RL 240 <RL 190

4-Cumylphenol (m) Detergent metabolite <RL <RL <RL <RL <RL 12 <RL 104-n-Octylphenol (m) Detergent metabolite <RL <RL <RL <RL <RL 5.2 <RL 4.24-Tert-octylphenol Detergent metabolite <RL <RL <RL <RL <RL 5.2 17 4.25-Methyl-1H-benzotriazole Anticorrosive used in antifreeze <RL <RL <RL <RL <RL 110 140 86Acetophenone Fragrance used in detergent and tobacco <RL <RL <RL <RL <RL 29 41 24

Anthraquinone (m) Used in the manufacture of dyes/textiles <RL <RL <RL <RL <RL 18 <RL 15

Atrazine Herbicide <RL <RL <RL <RL <RL 20 <RL 16Benzophenone Component of perfumes and soaps <RL <RL <RL <RL <RL 36 <RL 30

Beta-sitosterol (m) Plant sterol <RL <RL 620 <RL <RL 480 <RL 380BHA (m) Food additive, preservative <RL <RL <RL <RL <RL 73 <RL 61Bisphenol A (m) Manufacturing resin <RL <RL <RL <RL <RL 1.9 6.2 1.5Bromacil Herbicide <RL <RL <RL <RL <RL 72 <RL 60Bromoform Byproduct of water chlorination 230 84 230 160 160 49 <RL 41

Caffeine Stimulant <RL <RL <RL <RL <RL 19 <RL 16Camphor Fragrance in personal-care products <RL <RL <RL <RL <RL 35 45 29Carbaryl (m) Insecticide <RL <RL <RL <RL <RL 35 <RL 29Carbazole Used in the manufacture of dyes and lubricants <RL <RL <RL <RL <RL 8.1 <RL 6.7Chlorpyrifos Insecticide <RL <RL <RL <RL <RL 180 <RL 150Cholesterol (m) Plant/animal sterol <RL 1100 550 800 380 240 610 190Cotinine (m) Nicotine metabolite <RL <RL <RL <RL <RL 70 <RL 58Cumene Paint thinner <RL <RL <RL <RL <RL 16 <RL 13Diazinon Insecticide <RL <RL <RL <RL <RL 22 <RL 18Dichlorvos Insecticide (e.g., used in pet collars) <RL <RL <RL <RL <RL 110 <RL 94Diethyl phthalate Plasticizer 97 92 72 100 120 20 120 16Diethylhexyl phthalate Plasticizer 77 66 65 83 300 29 1100 24

d-Limonene Antimicrobial, fungicide, fragrance <RL <RL <RL <RL <RL 70 <RL 58Ethanol,2-butoxy-,phosphate Flame retardant <RL <RL <RL <RL <RL 170 220 140

Ethyl citrate Plasticizer <RL <RL <RL <RL <RL 4.5 <RL 3.7Galaxolide (HHCB) Synthetic fragrance <RL <RL <RL <RL <RL 5.4 18 4.4Contaminant residues sampled by POCIS in the STEER; concentrations above the Reporting Limit for a compound are indicated by shading. POCIS, polar organic chemical 

integrative sampler; ng/L, estimated water concentration reported; (m), indicates a highly variable compound; <RL, less than the reporting limit. 

February 2012 POCIS Deployment May 2010 POCIS Deployment
138Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report Table 6.2. Estimated water column concentrations of stormwater contaminant residues sampled by POCIS in the STEER and in Turpentine Gut (continued). Mangrove Lagoon Benner Bay Rotto Cay Cowpet Bay Great St. James Reporting Limit Turpentine Gut Reporting Limit Compound Use ng/L ng/L ng/L ng/L ng/L ng/L ng/L ng/L Indole Component of fragrances <RL 17 <RL <RL <RL 14 110 11 Isoborneol Natural insect repellent <RL <RL <RL <RL <RL 35 <RL 29 Isophorone Solvent <RL <RL <RL <RL <RL 4.5 <RL 3.6 Isoquinoline Flavor and fragrance ingredient <RL <RL <RL <RL <RL 14 <RL 12 Menthol Decongestant <RL 200 <RL <RL <RL 150 <RL 120 Metalaxyl Fungicide <RL <RL <RL <RL <RL 90 <RL 74 Methyl salicylate Liniment, flavoring agent <RL <RL <RL <RL <RL 30 <RL 25 Metolachlor Herbicide <RL <RL <RL <RL <RL 2.7 <RL 2.2 n,n-Diethyltoluamide (DEET) Mosquito repellent 7.6 <RL <RL <RL <RL 4.9 95 4.0 NPEO1-total (m) Detergent metabolite <RL <RL <RL <RL <RL 100 <RL 83 NPEO2-total (m) Detergent metabolite <RL <RL <RL <RL <RL 170 <RL 140 OPEO1 (m) Detergent metabolite <RL <RL <RL <RL <RL 17 <RL 13 OPEO2 (m) Detergent metabolite <RL <RL <RL <RL <RL 17 21 14

Para-cresol Wood preservative <RL <RL <RL <RL <RL 27 520 23Para-nonylphenol-total (m) Detergent metabolite <RL <RL <RL <RL <RL 76 <RL 63Phenol Disinfectant, manufacturing intermediate 150 250 <RL 29 <RL 25 35 20Prometon Herbicide <RL <RL <RL <RL <RL 10 <RL 9Skatol Present in feces and coal tar <RL <RL <RL <RL <RL 21 20 17Stigmastanol (m) Plant sterol <RL <RL <RL <RL <RL 240 <RL 190Tetrachloroethylene (m) Dry cleaning <RL <RL <RL <RL <RL 54 <RL 45Tonalide (AHTN) Synthetic fragrance <RL <RL <RL <RL <RL 5.2 <RL 4.3Tri(2-chloroethyl)phosphate Plasticizer, flame retardant <RL <RL <RL <RL <RL 15 <RL 13Tri(dichlorisopropyl)phosphate Flame retardant <RL <RL <RL <RL <RL 190 <RL 150Tributylphosphate Anti-foaming agent, fire retardant <RL <RL <RL <RL <RL 7.9 7.3 6.5

Triclosan Disinfectant, antimicrobial <RL <RL <RL <RL <RL 4.9 <RL 4.0Triphenyl phosphate Plasticizer, flame retardant <RL <RL <RL <RL <RL 47 <RL 39Contaminant residues sampled by POCIS in the STEER; concentrations above the Reporting Limit for a compound are indicated by shading. POCIS, polar organic chemical integrative sampler; ng/L, estimated water concentration reported; (m), indicates a highly variable compound; <RL, less than the reporting limit. 

February 2012 POCIS Deployment May 2010 POCIS Deployment
139Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report

The Bovoni Landfi ll in the western end of the STEER receives solid waste 

from both St. Thomas and St. John. 

tions of contaminants in the water column. The deployment of POCIS in St. John occurred in May, which Bargar 

et al. (2013) identifi ed as the beginning of the rainy season.

Alvarez et al. (2014) quantifi ed contaminants of emerging 

concern at 11 sites along the California coast including the 

Southern California Bight and San Francisco Bay. The 

mean estimated concentration of DEHP using POCIS was 

400 ng/L, and ranged from not detected to 1,100 ng/L. In 

a study to assess organic micropollutants in coastal waters 

from the northwestern Mediterranean Sea (Catalonia to Valenica, Spain), Sánchez-Avila et al. (2012) sampled coastal 

seawater from 22 sites. DEHP was detected in over 90 percent of the water samples collected. The mean concentration 

was 145 ng/L, the maximum 

detected in coastal seawaters 

was 617 ng/L (Sánchez-Avila et 

al., 2012). 

The highest estimated ambient 

water concentration of DEP 

from the STEER was 120 ng/L, 

at the Great St. James site. The 

mean concentration of DEP estimated by Alvarez et al. (2014) 

in California from the POCIS 

was 150 ng/L, similar to the 

highest estimated concentration 

in the STEER; the highest concentration estimated by Alvarez et al. (2014) was 600 ng/L. 

In the northwestern Mediterranean, the mean concentration 

of DEP detected in coastal seawaters was 253 ng/L with a 

maximum of 483 ng/L. DEP has also been identifi ed as a 

possible endocrine disruptor (Cólon et al., 2000). 

 

Phenol had an estimated ambient water concentration of 

250 ng/L at the Benner Bay site, and 150 ng/L in Mangrove 

Lagoon. Phenol is a common intermediate used in the 

production of many types of products including detergents 

and plastics, and is also used in oral antiseptics and as a 

disinfectant. Phenols can be released into the environment 

through wastewater treatment systems, from either the 

direct use of phenol or degradation of phenolic compounds, 

and also as leachate from landfi lls, as materials containing 

phenols degrade (Masoner and Mashburn, 2004). Phenol 

was also a low level contaminant in the POCIS fabrication 

and fi eld blanks. Phenol was not detected in the POCIS 

deployed by Bargar et al. (2013) in St. John. 

In the marine environment, the presence of bromoform is 

often the result of algal metabolism (Palmer and Reason, 

2009). In freshwater, bromoform can be an indicator of the 

effects of chlorination or ozonation of drinking water, or 

from the chlorination of treated wastewater. The highest estimated bromoform concentration from the POCIS 

deployed in the STEER was 230 ng/L in Mangrove Lagoon 

and Rotto Cay, followed by 160 ng/L in Cowpet Bay and 

Great St. James Bay. In St. John, Bargar et al. (2013) detected concentrations of bromoform ranging from 73 ng/L 

to 170 ng/L, similar to what was found in the STEER. In 

their work along the California coast, Alvarez et al. (2014), 

detected concentrations of bromoform ranging from 5 ng/L 

to 77 ng/L; bromoform was detected in all POCIS samples. 

A number of fragrance-related 

compounds were detected in 

the POCIS in the STEER as 

well. The concentration of 

indole at the Benner Bay site 

was estimated at 17 ng/L, just 

above the Reporting Limit of 

14 ng/L (Table 6.2). Indole 

was detected at two of the four 

sites in St. John, by Bargar 

et al. (2013) and the highest 

estimated concentration was 

17 ng/L, the same as the Benner Bay site in the STEER. A 

number of other fragrances, 

including acetophenone, benzophenone, d-limonene, and 

galaxolide (HHCB) were detected at most of the STEER 

sites, but the concentrations were below the Reporting 

Limit (Table 6.2). Acetophenone and galaxolide were also 

below the Reporting Limit at the sites sampled by POCIS 

in St. John (Bargar et al., 2013). 

Estimates of the concentration of two other personal care 

product ingredients, including menthol and n,n-diethyltoluamide (DEET) could be made for the STEER. There 

was only one detection of menthol, at an estimated ambient 

water concentration of 200 ng/L from the POCIS placed 

in Benner Bay. The menthol could be related to its use in 

cigarettes, however cotinine, a degradation product of nicotine, could not be quantifi ed in any of the POCIS deployed 

in the STEER or in Turpentine Gut. 

The highest estimated concentration of DEET in the 

STEER was 7.6 ng/L from the POCIS deployed in Mangrove Lagoon. DEET is an insect repellent and its use 

would not be surprising, given the likely need for protection against mosquitos and other insect pests in the area. In 

St. John, DEET was detected but was below the method detection limit (Bargar et al., 2013). On the California coast, 
140Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report

DEET was detected in 60 percent 

of the POCIS deployed, with an 

average concentration of 10 ng/L 

and a maximum concentration 

of 69 ng/L, lower than in the 

STEER (Alvarez et al., 2014). 

Along the South Florida coast, 

DEET ranged from not detected 

to 68 ng/L (Singh et al., 2010). 

The presence of beta-sitosterol 

typically results from the decay 

of plant materials from natural 

sources, and from the use and decay of paper products. The only 

occurrence for which an estimate 

of the ambient water concentration could be made in the STEER 

was at Rotto Cay with an estimated concentration of 620 ng/L, 

although beta-sitosterol was 

detected (but below the Reporting Limit) at all the other sites. 

Although Mangrove Lagoon receives inputs from the Bovoni Landfi ll through runoff, and inputs from surrounding 

residential/commercial areas and from Turpentine Gut, this 

did not seem to result in a greater number of stormwater 

contaminants in Mangrove Lagoon compared to the other 

POCIS sites in the STEER, as was expected. The sites 

in the STEER in Figure 6.5 are ordered in a west to east 

fashion. There did not appear to be an obvious pattern or 

gradient in the number of compounds in the STEER, moving west to east away from Turpentine Gut and Mangrove 

Lagoon. There were four compounds with estimated ambient water concentrations in Mangrove Lagoon, however, 

there were fi ve compounds each at Benner Bay, Rotto Cay 

and Cowpet Bay. Additional POCIS, perhaps offshore of 

these areas would provide more information, including the 

possibility of gradients. 

Estimated Concentrations of Stormwater Contaminants in 

Turpentine Gut (2010)

The deployment of the POCIS in Turpentine Gut was 

almost two years earlier than the POCIS deployed in the 

STEER. In addition, the deployment in Turpentine Gut and 

the STEER were done at somewhat different times of the 

year; mid-spring for Turpentine Gut, and mid to late winter 

for the POCIS deployment in the STEER. Nevertheless, 

the earlier POCIS deployment in Turpentine Gut provides 

a useful snapshot of stormwater contaminants present in St. 

Thomas’ only perennial stream during the deployment of 

the POCIS there.

As was noted earlier, ambient water concentrations could 

be estimated for a greater number of compounds in Turpentine Gut than in the STEER (Figure 6.5). Disregarding 

the temporal aspects of the deployment, these fi ndings are 

not surprising, as Turpentine Gut runs through the heart 

of the Jersey Bay watershed before it empties into Mangrove Lagoon, and likely receives input from a variety of 

sources. Land use in the watershed surrounding Jersey Bay 

is roughly 30% low- and mid-density urban development, 

with the remaining land use primarily forest and shrub 

(62%) (Cadmus, 2011).

Two compounds, the plasticizer DEHP (1,100 ng/L) and 

the insect repellent DEET (95 ng/L) could be quantifi ed 

in Turpentine Gut. Both DEHP and DEET are common 

stormwater/wastewater contaminants, and their appearance 

in Turpentine Gut is not surprising. The DEHP concentration in Turpentine Gut was similar to the maximum concentration found by Bargar et al. (2013) in St. John (820 ng/L), 

and was the same as the maximum found by Alvarez et al. 

(2014), along the California coast (1,100 ng/L). The estimated concentration of DEET found in Turpentine Gut was 

higher than the highest concentrations estimated by Alvarez 

et al. (2014) (69 ng/L) along the California coast, and by 

Singh et al. (2010) (68 ng/L) in South Florida. 

There were 10 compounds in the POCIS for which ambient 

water concentration estimates could be made from Turpentine Gut, that were either not found or were below Reporting Limits at the sites in the STEER. Two of these were the 

Figure 6.5. Number of stormwater contaminants with estimated water column concentrations in the STEER and in Turpentine Gut.
141Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report

detergent metabolites 4-tert-octylphenol and OPEO2. The 

estimated concentration of 4-tert-octylphenol in Turpentine Gut was 17 ng/L (Table 6.2). Bargar et al. (2013) did 

not detect 4-tert-octylphenol in the POCIS deployed in St. 

John. 

The estimated ambient water concentration of bisphenol-A 

or BPA in Turpentine Gut was 6.2 ng/L. Bisphenol-A was 

detected by Singh et al. (2010) at concentrations up to 190 

ng/L in South Florida. In coastal seawater, Sánchez-Avila 

et al. (2012) detected an average bisphenol-A concentration 

of 18 ng/L, ranging from 2.3 ng/L to 102 ng/L. BisphenolA has also been identifi ed as an endocrine disruptor in 

rainbow trout (Lindholst et al., 2000). 

There were three personal care product ingredients detected 

above the Reporting Limit in Turpentine Gut. Camphor (45 

ng/L) and galaxolide (18 ng/L) are fragrance ingredients. 

Acetophenone was also identifi ed in Turpentine Gut at an 

estimated ambient concentration of 41 ng/L. As noted earlier, acetophenone was detected in the STEER at all sites, 

but below the Reporting Limit. Along the California coast, 

galaxolide was present in 80 percent of the POCIS samples, 

with a mean concentration of 150 ng/L, and acetophenone 

was also present in 80 percent of the samples from POCIS, with a mean concentration of 11 ng/L (Alvarez et al., 

2014). 

The corrosion inhibitor, 5-methyl-1H-benzotriazole was 

detected at an estimated concentration of 140 ng/L in 

Turpentine Gut, and may be related to its use in antifreeze 

formulations for automobiles. Two fl ame retardants, 

ethanol,2-butoxy-,phosphate (220 ng/L), and tributylphosphate (7.3 ng/L) were only found in the Turpentine Gut POCIS. In addition to being a fl ame retardant, tributylphosphate has a number of other uses including as a defoamer in 

detergent solutions and in paints and adhesives. Alvarez et 

al. (2014), estimated a mean tributylphosphate concentration of 6.6 ng/L along the California coast, similar to the 

concentration estimated in Turpentine Gut. 

Para-cresol, used as a wood preservative, was detected in 

Turpentine Gut with an estimated water concentration of 

520 ng/L. As with a number of the other stormwater contaminants, para-cresol was detected in the POCIS from all 

sites in the STEER, but was below the Reporting Limit. 

The fecal marker 3-methyl-1(H)-indole, or skatol, was 

detected at an estimated ambient water concentration in 

Turpentine Gut of 20 ng/L, just above the Reporting Limit 

of 17 ng/L. A second fecal indicator, 3-beta-coprostanol 

was also detected in Turpentine Gut, however, at a level 

too low to estimate a water concentration. The presence 

of both these fecal indicators from Turpentine Gut would 

seem indicative of inputs from septic systems and from 

animals (e.g., dogs and horses). 

No cotinine or caffeine was detected in the POCIS deployed in Turpentine Gut or in the STEER, which was 

somewhat surprising given the density of the population 

in this part of St. Thomas, and likely presence of these 

compounds in tobacco products or in caffeinated beverages. Neither of these compounds were detected in POCIS 

deployed in St. John (Bargar et al., 2013). 

Comparison with Water Quality Criteria

Table 6.3 lists a number of water quality criteria developed 

by the U.S. Environmental Protection Agency (EPA) and 

others. Almost all the estimated water concentrations of 

the contaminants from both the STEER and Turpentine Gut 

(Table 6.2) were below, in most cases orders of magnitude 

below, the criteria listed in Table 6.3. The only exception 

was the plasticizer DEHP from Turpentine Gut. The estimated water concentration in Turpentine Gut (1.1 μg/L or 

1,100 ng/L) is above a lower chronic (longer-term exposure) criteria (0.3 μg/L) (Table 6.3). 

Finally, the compound tetrachloroethylene is also included 

in Table 6.3. Within the watershed that drains to Turpentine 

Gut and then to the STEER is the Tutu Wellfi eld Superfund Site. This EPA Superfund site was established due 

to contamination of groundwater and wells in the area by 

chlorinated volatile organic compounds (CVOC), including 

tetrachloroethylene. This compound was used extensively 

for dry cleaning by a textile plant located in the watershed, 

Table 6.3. Comparison of estimated concentrations of 

stormwater contaminants with available water quality 

criteria. 

Acute Chronic Acute Chronic

Bromoform − − 2,300 320

DEP 2,944 3.4 1,800 110

DEHP 400 360 400 0.3-16

Para-cresol − − <230 <13

Phenol 5,800 400 10,200 180-320

Tetrachloroethylene 10,200 450 830 45

DEP, diethyl phthalate; DEHP, diethylhexyl phthalate.

Marine and freshwater criteria represent water guidelines 

developed by the USEPA. Water Quality Criteria values

taken from NOAA Screening Quick Reference Tables 

(SQuiRTs; Buchman, 2008). 

Wastewater 

Contaminant

Water Quality Criteria

Marine (μg/L) Freshwater (μg/L)
142Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report

that operated from 1969 to 1982 (EPA, 2011). Contamination of the groundwater and commercial and private wells 

in the Tutu area resulted in EPA establishing the Superfund 

site and installing groundwater treatment systems to remove CVOCs, including tetrachloroethylene (EPA, 2011).

In Table 2, it can be seen that there were no estimated water 

concentrations for tetrachloroethylene in either Turpentine 

Gut or in Mangrove Lagoon. There was one detection of 

tetrachloroethylene from the POCIS deployed adjacent to 

Great St. James Island, however, the level was below the 

Quantitation Level, that would have allowed an ambient 

water concentration estimate to be made. The location of 

this POCIS adjacent to Great St. James (Figure 6.3), would 

make a connection to the Tutu Wellfi eld Superfund Site appear unlikely, due to the distance from the Superfund site, 

along with the lack of detections in the POCIS deployed in 

Turpentine Gut and Mangrove Lagoon, both of which are 

closer to the Superfund site. 

6.4. CONCLUSIONS

The deployment of fi ve POCIS in the STEER in February 

2012, and one in Turpentine Gut in May 2010 provides 

information on the presence of stormwater contaminants 

that might be missed if sediments alone were sampled. Although Turpentine Gut is not within the boundaries of the 

STEER, this perennial stream drains most of the Jersey Bay 

watershed and empties into the STEER through Mangrove 

Lagoon. The stormwater contaminants detected appear 

fairly representative of the low- and mid-density urban 

development in the watershed. 

The deployment and analysis of POCIS from the STEER 

and Turpentine Gut represents a snapshot of stormwater 

contaminants in these systems. The analysis resulted in 

the identifi cation of a number of stormwater contaminants, 

however, the majority at concentrations were below reporting limits established by the USGS for the compounds 

analyzed. Stormwater contaminants that could be quantifi ed at least once included phthalate ester plasticizers, wood 

preservatives, personal care product/fragrance ingredients, 

plant sterols and a fecal indicator. 

Signifi cantly, none of the nine pesticides, primarily agricultural use herbicides and insecticides, were detected in 

the POCIS. This would appear to refl ect the low level of 

agriculture in the watersheds surrounding the STEER and 

in St. Thomas in general. 

The most common contaminants identifi ed in the POCIS 

were the phthalate ester plasticizers DEP and DEHP. Both 

were present in the POCIS at all sites, and their concentrations were high enough to estimate ambient water concentrations. Both of these phthalates are ubiquitous environment contaminants. The estimated water concentration of 

DEHP in Turpentine Gut (1,100 ng/L) was above a chronic 

freshwater quality criteria, and was the only stormwater 

contaminant found to be above an available water quality 

criteria. 

The POCIS passive water samplers represent a fairly new 

technology used by NOAA’s National Centers for Coastal 

Ocean Science along with project partners. The use of 

POCIS provides the opportunity to assess the presence of 

water soluble chemical contaminants in coral reef environments. It would be useful to do additional deployments of 

POCIS in the STEER and perhaps in Turpentine Gut during 

different times of the year, to assess how the concentration 

of the stormwater contaminants might vary during the wet 

and dry seasons in St. Thomas. It would also be useful to 

target additional POCIS in Mangrove Lagoon and in northern Benner Bay, the areas that appear to be most impacted 

by LBSP. 

LITERATURE CITED

Alvarez, D.A., J.D. Petty, J.N. Huckins, T.L. Jones-Lepp, 

D.T. Getting, J.P. Goddard, and S.E. Manahan. 2004. 

Development of a passive, in situ, integrative sampler for 

hydrophilic organic contaminants in aquatic environments: 

Environmental Toxicology and Chemistry. 23:1,640–1,648.

Alvarez, D.A., W.L. Cranor, S.D. Perkins, V.L. Schroeder, 

S. Werner, E.T. Furlong, and J. Holmes. 2008. Investigation of Organic Chemicals Potentially Responsible for 

Mortality and Intersex in Fish of the North Fork of the 

Shenandoah River, Virginia, during spring of 2007: U.S. 

Geological Survey Open-File Report 2008–1093, 16 p.

Alvarez, D.A. 2010. Guidelines for the Use of the SemiPermeable Membrane Device (SPMD) and the Polar Organic 

Chemical Integrative Sampler (POCIS) in Environmental 

Monitoring Studies: U.S. Geological Survey, Techniques 

and Methods 1–D4, 28pp.

Alvarez, D.A., K.A. Maruya, N.G. Dodder, W. Lao, E.T. 

Furlong, and K.L. Smalling. (2014). Occurrence of contaminants of emerging concern along the California coast 

(2009–10) using passive sampling devices. Marine Pollution Bulletin. 81:2 347-354. 

Bargar, T.A., V.H. Garrison, D. Alvarez, and K. Echols. 

2013. Contaminants assessment in the coral reefs of Virgin 
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STEER Integrated Environmental Assessment Report

Islands National Park and Virgin Islands Coral Reef Monument. Marine Pollution Bulletin 70(1-2): 281-288. 

Cadmus Group, Inc. (Cadmus). 2011. Watershed Characterization and Planning for Pathogen Source Reduction 

in the U.S. Virgin Islands. Report prepared for the U.S. 

Environmental Protection Agency Region 2. Cadmus Task 

order 17. 95pp. 

Cólon, I., D. Caro, C. J. Bourdony, and O. Rosario. 2000. 

Identifi cation of phthalate esters in the serum of young 

Puerto Rican girls with premature breast development. 

Environmental Health Perspectives 108: 895–900. 

Francy, D.S., A. M. Gifford, and R. A. Darner. 2003. 

Escherichia coli at Ohio Bathing Beaches - Distribution, 

Sources, Wastewater Indicators, and Predictive Modeling. 

Water-Resources Investigations Report 02-4285. 47pp. 

Gray, L.E., J. Ostby, J. Fukrr, M. Price, D.N. Veeramachaneni, and L. Parks. 2000. Perinatal exposure to the 

phthalates DEHP, BBP, and DINP, but not DEP, DMP, or 

DOTP, alters sexual differentiation of the male rat. Toxicological Science 58(2): 350-365. 

Lindholst, C., K.L. Pedersen, and S.S. Pedersen. 2000 

Estrogenic response of bisphenol A in rainbow trout (Oncorhynchus mykiss). Aquatic Toxicology 48: 87-94. 

Masoner, J.R., and S. L. Mashburn. 2004. Water Quality 

and Possible Sources of Nitrate in the Cimarron Terrace 

Aquifer, Oklahoma, 2003. Scientifi c Investigations Report 

2004–5221. 60pp. 

Nemeth, D. and R. Platenberg. 2007. Diversity of Freshwater Fish and Crustaceans of St. Thomas: Watersheds and 

its Relationship to Water Quality as Affected by Residential and Commercial Development. WRRI Project 

2006VI73B. Division of Fish and Wildlife, Department of 

Planning and Natural Resources, St. Thomas. 28 pp. 

Pait, A.S., S.I. Hartwell, A.L. Mason, F.R. Galdo, Jr., R.A. 

Warner, C.F.G. Jeffrey, A.M. Hoffman, D.A. Apeti, and S.J.

Pittman. 2013. An Assessment of Chemical Contaminants 

Detected in Passive Water Samplers Deployed in the St. 

Thomas East End Reserves (STEER). NOAA Technical 

Memorandum NOS/NCCOS 157. Silver Spring, MD. 22 

pp.

Palmer, C. J., and C. J. Reason. 2009. Relationships of 

surface bromoform concentrations with mixed layer depth 

and salinity in the tropical oceans, Global Biogeochemical 

Cycles, 23, GB2014, doi:10.1029/2008GB003338

Sánchez-Avila, J., R. Tauler, and S. Lacorte. 2012. Organic micropollutants in coastal waters from NW Mediterranean Sea: sources distribution and potential risk. Environment International 46:50-62. 

Singh, S.P., A. Azua, A. Chaudhary, S. Khan, K.L. Willett, 

and P.R. Gardinali. 2010. Occurrence and distribution of 

steroids, hormones and selected pharmaceuticals in South 

Florida coastal environments. Ecotoxicology 19:338-350. 

St. Thomas East End Reserves (STEER). 2011. Management Plan. Edited by J. Brown, A. Holecek, J. Murray, L. 

Noori, J.P. Oriol, J. Pierce, R. Platenberg, S. Romano, D. 

Russo, and C. Settar. 99 pages.

USDHHS (U.S. Department of Human Health and Services). 2011. Report on Carcinogens. Twelfth Edition. U.S. 

Department of Health and Human Services Public Health 

Service National Toxicology Program. 499pp. 

EPA (United States Environmental Protection Agency). 

2011. Remediation System Evaluation (RSE) Tutu Wellfi eld Superfund Site St. Thomas, U.S. Virgin Islands. 

Offi ce of Solid Waste and Emergency Response. EPA542-R-11-008. 37pp. 
144Chapter 6: Water Soluble Chemical Contaminants

STEER Integrated Environmental Assessment Report
STEER Integrated Environmental Assessment Report

145Chapter 7: Contaminants in Coral, Conch and Fish

CHAPTER 7: AN ASSESSMENT OF CONTAMINANT BODY BURDENS IN CORAL (PORITES ASTREOIDES), CONCH (LOBATUS GIGAS) AND FISH (HOLOCENTRUS RUFUS AND LUTJANUS APODUS) 

FROM THE ST. THOMAS EAST END RESERVES (STEER)

Dennis A. Apeti1

, Andrew L. Mason1 , S. Ian Hartwell1, Anthony S. Pait1, Laurie J. Bauer1,2, Christopher F. G. Jeffrey1,2, 

Anne M. Hoffman3, Francis R. Galdo, Jr.4, and Simon J. Pittman1,5

1

NOAA/NOS/National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment (CCMA), 

1305 East/West Highway, Silver Spring, MD 20910

2

CSS-Dynamac Consolidated Safety Services, Fairfax, VA 22030, under CSS-Dynamac Contract #EA-133C-14-NC-1384

3

The Nature Conservancy, St. Thomas, USVI

4

The University of the Virgin Islands, St. Thomas, USVI

5

The Marine Institute, Plymouth University, United Kingdom

7.1 INTRODUCTION

Contaminant body burdens in coral, conch and fi sh 

were assessed for this part of the project in the STEER. 

Samples were collected from each of the fi ve previously 

identifi ed strata and analyzed for more than 150 chemical 

contaminants, including organic 

contaminants (e.g. polycyclic 

aromatic hydrocarbons, 

polychlorinated biphenyls and 

pesticides), along with trace (e.g. 

cadmium, copper, and mercury), 

and major (aluminum, iron and 

manganese) elements. Although 

the number of samples that could 

be collected for this project was 

low due to harvest limitations and 

funding, the information generated 

will benefi t management by 

providing additional information 

on contaminant body burdens 

for informed coastal resource 

management decisions, as well as 

providing data for the Reserveswide assessment of contaminant 

issues. 

7.2. METHODS

Sampling Methods

Samples of coral were collected 

under the Department of Planning

and Natural Resources (DPNR) 

permit STT-0023-12. Samples 

of coral, conch and fi sh were 

collected under DPNR permit STT-022-12. Collection 

of biota for this study followed the standard protocols 

established by the NOAA National Status and Trends 

(NS&T) Program (Apeti et al., 2012). Sampling was 

conducted in collaboration with USVI partners who also 

provided logistical and boat support for the fi eldwork.

Coral

Mustard hill coral, Porites astreoides, was chosen as it is 

abundant and has been used in a number of other NOAA 

NCCOS projects for body burden analyses. Coral tissue 

sampling locations for this 

study, with the exception of the 

coral collected in Mangrove 

Lagoon (Stratum 1), were 

chosen from a subset of preselected hard bottom (HB) 

locations where NCCOS 

Biogeography divers had 

determined that P. astreoides 

were present (Chapter 3). The 

hard bottom habitats were 

grouped into four separate 

strata (stratum 2 – 5), which 

in addition to the Mangrove 

Lagoon (ML) stratum, 

represented fi ve strata for 

sampling. A coral sample site 

was defi ned as a single dive 

area with a 50 meter radius 

where enough P. astreoides

colonies (“heads”) were 

available for sampling multiple 

heads. While in stratum 1, 

only one P. astreoides colony 

was found at site MLC01; 

within each of the HB strata 

two sample sites were selected 

(Figure 7.1). The coral sample 

collected at HBI24p, was considered part of Stratum 

2 because of the proximity of the site to the stratum 

boundary. 

The coral samples were collected by SCUBA divers using 

a hammer and a titanium coring punch. At each site, 

Image of the coral Porites astreoides in the southern portion of Mangrove Lagoon.
STEER Integrated Environmental Assessment Report

146Chapter 7: Contaminants in Coral, Conch and Fish

coral cores were collected from 5 different coral heads to 

constitute a site-composite. The titanium coring punch was 

driven into the coral colonies with a hammer, to extract 

cores of coral tissue approximately 1.5 cm in diameter and 

1-1.5 cm in depth. Coral cores were dislodged from the 

corer with a Tefl on stir stick. At each sampling site two 

sets of coral tissues were collected, one for contaminant 

analyses and the other for histopathology assessments. 

Care was taken to avoid removal of large amounts of 

unnecessary skeletal material, however, whatever skeletal

material was removed along with the tissue was analyzed

for this study. The cores of coral tissue were placed 

inside pre-labeled 250 ml IChem® jars and then capped 

underwater. The jars were brought to the surface, drained 

of water and placed on ice. The coral samples were then 

frozen at -15 oC until shipped overnight on ice to the 

analytical laboratory. At the laboratory, coral skeletal

material and tissue were cryogrinded using liquid nitrogen.

Conch

Queen conch (Lobatus gigas) were chosen for this study

because they are herbivorous gastropods that live in 

sand, seagrass beds and coral reefs, feeding on seagrass 

and various species of algae (Davis, 2005). It has been 

determined that through their feeding process, conch ingest 

considerable amounts of sediment particles (Brownell and 

Stevely, 1981), along with any contaminants that may be 

associated with the sediment. 

Conch specimens were collected at locations within the 

previously defi ned fi ve strata (Figure 7.1). Due to limited 

conch resources, only two specimens were collected per 

stratum. Collections of conch were made using SCUBA 

or snorkeling. Thus, from 10 separate locations (2 per 

stratum) (Figure 7.1) a total of 10 conch were collected by 

hand and placed in labeled 2 gallon ZiplockTM bags. 

Figure 7.1. Coral, conch and fi sh sites collected in 2012 in the St. Thomas East End Reserves (STEER).
STEER Integrated Environmental Assessment Report

147Chapter 7: Contaminants in Coral, Conch and Fish

The bags containing the specimens were placed in a cooler 

with ice, and at the end of the day, frozen at the University 

of the Virgin Islands. At the end of the fi eld mission, 

conch specimens were partially thawed, removed from 

their shells, weighed, and placed into labeled 1 liter Tefl on 

jars and refrozen. Once completely frozen, the samples 

were shipped on ice to TDI-Brooks, International. There, 

the soft tissues were homogenized prior to contaminant 

analysis. This resulted in the production of only one data 

point per stratum, and consequently limited statistical 

comparisons of contaminant concentrations in conch 

between strata. However, lateral (east-west) and nearshore 

versus off shore contrasts could be made. 

Fish

Fish were collected using nets and with hook and line. 

Spearfi shing was avoided to reduce the possibility of 

biasing sample results via loss of fl uids during and after 

collection, and possible introduction of additional metals 

into the tissues. Two species of fi sh were targeted for this 

study, the longspine squirrelfi sh (SQ) (Holocentrus rufus) 

and the schoolmaster snapper (SN) (Lutjanus apodus). Due 

to the diffi culty in collecting the targeted species, a total 

of only eight fi sh, representing four of each species, were 

collected from across the STEER (Figure 7.1). Squirrelfi sh 

were taken in strata 1-4. Snappers were taken in strata 2-5. 

Because of the limited spatial nature of the data, statistical 

comparisons of contaminant concentrations between the 

strata identifi ed during phase 1 of the study cannot be 

made, but lateral (east-west) contrasts can be made. All 

fi sh samples were stored at -15° C prior to shipment to the 

laboratory for analysis. At the laboratory the whole fi sh

was homogenized, including both edible and inedible

portions.

Water Quality Measurements

A series of water quality parameters (dissolved oxygen, 

temperature, and salinity) were also measured at each 

site using a YSI® salinity/conductivity/temperature 

meter. The instrument probe was submerged to a depth of 

approximately one meter. 

Analytical Methods

The list of chemical contaminants analyzed in the coral 

and conch tissues is shown in Table 7.1. This contaminant 

list constitutes the suite of compounds regularly quantifi ed 

nationwide as part of NOAA’s NS&T Program.

For over 20 years, the Mussel Watch and NS&T Programs 

have monitored the Nation’s estuarine and coastal waters 

for chemical contaminants in bivalve mollusk tissues and 

in sediments. Work to characterize chemical contaminants 

as part of the NCCOS Center for Coastal Monitoring 

and Assessment’s (CCMA) ecological characterizations 

in tropical waters, represents a fairly recent expansion 

of NS&T activities. The compounds analyzed included 

59 polycyclic aromatic hydrocarbons (PAHs), 31 

organochlorine pesticides, 38 polychlorinated biphenyls 

(PCBs), four butyltins, and 15 trace and major elements. 

Organic Contaminants

Coral, conch and fi sh tissues were subjected to the same 

procedures for the determination of organic contaminant 

concentrations. Whole tissues were analyzed for both fi sh

and conch, while coral tissues were analyzed along with

attached skeletal material. Aliquots of tissue samples were 

chemically dried using Hydromatix®. Tissue/Hydromatix 

mixtures were then extracted with 100% dichloromethane 

using accelerated solvent extraction (ASE). Detailed 

analytical protocols are provided in Kimbrough and 

Lauenstein (2006) for organic compounds. 

PAHs and their alkylated homologues (Table 7.1) were 

quantifi ed using gas chromatography mass spectrometry 

(GC/MS) in the selected ion monitoring mode (SIM). 

Concentrations of PCBs and chlorinated pesticides were 

determined by capillary gas chromatography with an 

electron capture detector (ECD). All results are reported in 

ng/g dry weight (dw). Analysis for butyltins was based on 

high resolution, capillary gas chromatography using fl ame 

photometric detection (GC/FPD), which quantitatively 

determined tributyltin (TBT), dibutyltin (DBT), and 

monobutyltin (MBT). The concentration of butyltins was 

expressed as the concentration of tin (ng Sn/g). 

Major and Trace Elements

The major and trace elements measured are presented in 

Table 7.1. Most of these elements are metals, however, 

antimony, arsenic and silicon are metalloids, and selenium 

is a nonmetal. Coral, conch, and fi sh were subjected to 

the same digestion and analytical methods (Kimbrough 

and Lauenstein, 2006). The whole animal was fi rst 

homogenized, freeze-dried to a constant weight, and acid 

digested in Tefl on bombs. For all metals except mercury, 

the tissue samples were prepared for inductively coupled 

plasma mass spectrometric (ICP-MS) analysis. For mercury 

quantifi cation, tissue homogenates were acid digested based 

on a modifi ed version of the Environmental Protection 

Agency (EPA) method 245.5 and measured using cold 

vapor atomic absorption spectroscopy.

Metals can exist in the environment in several forms 

(e.g., organic versus inorganic arsenic), but the analytical 

methods used by the NS&T does not distinguish between 
STEER Integrated Environmental Assessment Report

148Chapter 7: Contaminants in Coral, Conch and Fish

Table 7.1. Chemical contaminants analyzed in STEER coral, conch and fish samples.PAHs - Low MW PAHs - High MW Organochlorine Pesticides PCBs PCBs (continued) ButyltinsNaphthalene Fluoranthene Aldrin PCB8/5 PCB170/190 Monobutyltin

1-Methylnaphthalene Pyrene Dieldrin PCB18 PCB174 Dibutyltin2-Methylnaphthalene C1-Fluoranthenes/Pyrenes Endrin PCB28 PCB180 Tributyltin

2,6-Dimethylnaphthalene C2-Fluoranthenes/Pyrenes Heptachlor PCB29 PCB183 Tetrabutyltin1,6,7-Trimethylnaphthalene C3-Fluoranthenes/Pyrenes Heptachlor-Epoxide PCB31 PCB187C1-Naphthalenes Naphthobenzothiophene Oxychlordane PCB44 PCB194 Major and Trace ElementsC2-Naphthalenes C1-Naphthobenzothiophenes Alpha-Chlordane PCB45 PCB195/208C3-Naphthalenes C2-Naphthobenzothiophenes Gamma-Chlordane PCB49 PCB201/157/173 Aluminum (Al)

C4-Naphthalenes C3-Naphthobenzothiophenes Trans-Nonachlor PCB52 PCB206 Antimony (Sb)Benzothiophene Benz[a]anthracene Cis-Nonachlor PCB56/60 PCB209 Arsenic (As)C1-Benzothiophenes Chrysene Alpha-HCH PCB66 Cadmium (Cd)C2-Benzothiophenes C1-Chrysenes Beta-HCH PCB70 Chromium (Cr)C3-Benzothiophenes C2-Chrysenes Delta-HCH PCB74/61 Copper (Cu)Biphenyl C3-Chrysenes Gamma-HCH PCB87/115 Iron (Fe)Acenaphthylene C4-Chrysenes DDMU PCB95 Lead (Pb)Acenaphthene Benzo[b]fluoranthene 2,4'-DDD PCB99 Manganese (Mn)Dibenzofuran Benzo[k]fluoranthene 4,4'-DDD PCB101/90 Mercury (Hg)Fluorene Benzo[e]pyrene 2,4'-DDE PCB105 Nickel (Ni)C1-Fluorenes Benzo[a]pyrene 4,4'-DDE PCB110/77 Selenium (Se)C2-Fluorenes Perylene 2,4'-DDT PCB118 Silicon (Si)C3-Fluorenes Indeno[1,2,3-c,d]pyrene 4,4'-DDT PCB128 Silver (Ag)Carbazole Dibenzo[a,h]anthracene 1,2,3,4-Tetrachlorobenzene PCB138/160 Tin (Sn)Anthracene C1-Dibenzo[a,h]anthracenes 1,2,4,5-Tetrachlorobenzene PCB146 Zinc (Zn)

Phenanthrene C2-Dibenzo[a,h]anthracenes Hexachlorobenzene PCB149/1231-Methylphenanthrene C3-Dibenzo[a,h]anthracenes Pentachloroanisole PCB151C1-Phenanthrene/Anthracenes Benzo[g,h,i]perylene Pentachlorobenzene PCB153/132C2-Phenanthrene/Anthracenes Endosulfan II PCB156/171/202C3-Phenanthrene/Anthracenes Endosulfan I PCB158C4-Phenanthrene/Anthracenes Endosulfan SulfateDibenzothiophene MirexC1-Dibenzothiophenes ChlorpyrifosC2-DibenzothiophenesC3-DibenzothiophenesAbbreviations: MW, molecular weight; PAH, polycyclic aromatic hydrocarbons; HCH, hexachlorocyclohexane; DDMU, 1-chloro-2,2- (p-chlorophenyl)ethylene,

 DDT, dichlorodiphenyltrichloroethane; DDD, dichlorodiphenyldichloroethane; DDE, dichlorodiphenyldichloroethylene; PCB, polychlorinated biphenyl
STEER Integrated Environmental Assessment Report

149Chapter 7: Contaminants in Coral, Conch and Fish

these various forms. Instead, analytical results are reported 

as total metal concentration (aggregation of all species of a 

metal) in microgram per gram (μg/g) for dry tissue weight 

(dw).

Statistical Analyses

Concentration values for individual compounds that 

were lower than the method detection limits (MDL) 

were qualifi ed as undetected and assigned a value of 

zero. Concentration values of organic contaminants 

were presented as “total” concentration (e.g., PAHs), 

were derived as the arithmetic sum of all the individual 

congeners or homologues of the same group of compounds 

as listed in Table 7.1.

Primary statistical analyses were conducted using 

the JMP-5.1® system statistical package. The nonparametric Wilcoxon test was used for data comparisons, 

while relationships between variables (e.g. inter-metal 

correlations) were assessed using the Pearson correlation 

coeffi cient. A three-group classifi cation scheme based on 

ArcGIS Jenks grouping method was used to assess the 

spatial distribution of the contaminants. Signifi cance of 

statistical tests was reported at a probability level of 0.05.

A non-parametric Wilcoxon test showed that with the 

exception of percent tributyltin in total butyltins, there were 

no statistical differences between longspine squirrelfi sh and 

schoolmaster snapper for any contaminant for the limited 

number of samples collected in this study. As such we 

treat all fi sh as one population for calculating contaminant 

means and spatial analysis. 

To put the concentrations found in coral, conch and fi sh 

from the STEER into context, results were compared to 

previously published studies conducted in the Caribbean. 

Additionally, contaminant body burdens of toxic metals and 

organic compounds in conch and fi sh were compared to 

available FDA and EPA guidelines for chronic consumption 

limits. FDA reports concentrations on a wet weight basis. 

The average measured percent moisture content of the 

conch from the STEER was 76%. A factor of four was 

therefore used to convert wet weight concentrations to dry 

weight in order to compare to results from other non-NS&T 

studies. Since acceptable concentrations of metals in fi sh 

tissue are determined on a case-by-case (including factors 

like region, and subsistence vs. recreational fi shing) basis 

by the FDA, and because this study was not designed to 

measure the impacts of metals in fi sh tissues on human 

health, we used EPA’s Guidance for Assessing Chemical 

Contaminant Data for Use in Fish Advisories (EPA, 2000) 

as a guideline, where possible. 

7.3. RESULTS AND DISCUSSION

Comparisons between strata were conducted using 

nonparametric Kruskal-Wallis tests (α = 0.05). None of the

strata were signifi cantly different from any other for any 

contaminant in any matrix. To further explore spatial

patterns, the strata were pooled into two groups, Western 

(strata 1 and 2) and Eastern (strata 3, 4, and 5). With the

exception of mercury concentrations in fi sh tissues, there 

were no signifi cant differences between the pooled groups 

of Eastern and Western for any contaminant for fi sh, coral, 

or conch.

Field Data

Sampling for the coral and conch in the STEER occurred 

18-22 June 2012. The mean water depth at the coral sites 

was 5.1 ± 1.67 m; the mean surface water temperature was 

29.1 ± 0.34 oC. The average surface salinity was 35.9 ± 

0.07 ppt. The average surface water dissolved oxygen for 

coral sites was 3.96 ± 0.18 mg/L. 

The mean water depth for the sites where conch were 

sampled was 5.97 ± 1.19 m; the mean surface water 

temperature was 29 ± 0.21 oC. The average surface 

salinity was 36 ± 0.01 ppt. The average surface water 

dissolved oxygen for conch sites was 4.17 ± 0.21 mg/L. 

Sampling for fi sh in the STEER occurred between July and 

November of 2013. No water quality measurements were 

taken during fi sh collections.

Organic Contaminants

Polycyclic Aromatic Hydrocarbons

Also referred to as PAHs, polycyclic aromatic 

hydrocarbons are associated with the use and combustion 

of fossil fuels (e.g., oil and gas) and other organic materials 

(e.g., wood). Natural sources of PAHs include forest fi res 

and decaying plant material. 

A number of PAHs can bioaccumulate to toxic

concentrations in aquatic biota, and some PAHs including

benzo[a]pyrene, benz[a]anthracene, chrysene, benzo[b]

fl uoranthene, benzo[k]fl uoranthene, dibenzo[a,h]

anthracene, and indeno[1,2,3-c,d]pyrene have been 

linked to carcinogenicity in vertebrates (USDHHS 1995). 

Signifi cant relationships have also been established

between PAHs in sediment and prevalence of liver lesions

in English sole in Puget Sound, Washington (Malins et al.

1984). Very little research has been carried out to address

the effects of PAHs on coral or conch. Vertebrates can

metabolize PAHs, often into more harmful substances

(e.g. carcinogens); mollusks do not. Solbakken et al.

(1984) showed that both phenanthrene and naphthalene

accumulate to detectable levels in brain coral Diploria
STEER Integrated Environmental Assessment Report

150Chapter 7: Contaminants in Coral, Conch and Fish

Figure 7.2 Total PAHs detected in the coral Porites astreoides.

strigosa and green 

cactus coral Madracis 

decatis. While the

simple accumulation 

of a PAH is not an 

impact in and of itself, 

the accumulation of 

exogenous chemicals in 

living tissue increases 

the likelihood of 

adverse effects. The 

PAHs fl uoranthene and 

pyrene at μg/L level 

concentrations have

been shown to be toxic 

to coral, particularly 

in the presence of 

increased ultraviolet 

radiation, termed 

phototoxicity (Peachey 

and Crosby 1996; 

Guzman-Martinez et 

al., 2007). Peters et 

al. (1981) found that 

exposure to No. 2 fuel 

oil at concentrations as 

low as 70 μg/L in the 

rose coral (Manicina 

areolata) over a 12 week period resulted in substantial 

histologic changes in both the somatic and reproductive 

tissues, along with the loss of the zooxanthellae.

PAHs in Corals. The concentrations of total PAHs found 

in coral tissues are presented in Figure 7.2. The mean 

concentration of total PAHs in the tissues of P. astreoides

(22.0 ± 8.6 ng/g) (Table 7.2) was lower than those found 

in sediments (142 ± 59 ng/g) (Pait et al., 2013) indicating 

that coral tissue integrate 

less PAHs than sediment in 

the surrounding area. The 

mean of 22.0 ± 8.6 ng/g 

in STEER P. astreoides

tissues was comparable, 

but more variable, than 

the mean concentration of 

total PAHs in the tissues 

of P. astreoides (15.0 ± 0.6 

ng/g) found in Vieques, 

Puerto Rico (Pait et al., 

2010) (Table 7.3 ), the 

closest geographical 

location where we have 

comparable data. The highest total PAH concentration in 

coral tissues, 80.4 ng/g was found at the HBI23P site in 

stratum 3 (Figure 7. 1). Pait et al. (2013) calculated a mean 

total PAH concentration of 46.9 ± 18.5 ng/g in P. astreoides

from southwest Puerto Rico, comparable to corals from 

both STEER and Vieques, Puerto Rico. Looking at the 

means of total PAHs across four NCCOS Caribbean 

studies, the STEER falls above the means of Guanica Bay 

and Jobos Bay. 

Table 7.2. Summary of means, standard error, and maximum values for organic chemical

contaminants analyzed in STEER coral, conch and fish.

Contaminant/Class

Mean ±SE Maximum Mean ±SE Maximum Mean ±SE Maximum

Total PAHs 22.0 ±8.6 80.4 32.7 ±9.07 113 15.0 ±0.97 18.9

Monobutyltin 0.13 ±0.04 0.29 5.11 ±2.77 23.2 2.60 ±0.63 5.39

Dibutyltin 0.03 ±0.02 0.16 1.07 ±0.45 4.27 5.47 ±1.95 14.2

Tributyltin 0.08 ±0.03 0.29 0.12 ±0.03 0.38 9.37 ±5.73 48.7

Total BTs 0.24 ±0.08 0.74 6.30 ±3.24 27.9 17.4 ±7.66 68.3

Total DDT 0.01 ±0.01 0.08 0 0 2.32 ±2.02 16.5

Mirex 0 0.04 0 0 0.42 ±0.11 0.64

Total Chlordane 0.01 ±0.01 0.05 0 0 1.41 ±0.44 3.92

Total PCBs 0 0 0 0 65.9 ±50.1 416

BTs, butyltins; SE. standard error

Coral (ng/g) Conch (ng/g) Fish (ng/g)
STEER Integrated Environmental Assessment Report

151Chapter 7: Contaminants in Coral, Conch and Fish

PAHs in Conch. The concentrations of total PAHs found 

in conch tissues are presented in Figure 7.3 . The mean 

concentration of total PAHs in the tissues of the queen 

conch (32.7 ± 9.07 ng/g) were similar to those found in 

corals (22.0 ± 8.6 ng/g) (Table 7.2). In their global survey 

of mollusk tissues, Vorkamp et al. (2010) found that total 

PAH ranged between 177 and 5,966 ng/g, calculated from 

30 PAHs (versus the 59 used in this study). In the STEER, 

the sum of our 59 PAHs in general fell well below this 

range, with the highest concentration of total PAHs in L. 

gigas tissues being 113 ng/g at site S4-CB (Table 7.2 and 

Figure 7.3).

PAHs in Fish. The 

mean concentration 

of total PAHs (Table 

7.2) in the tissues 

of all fi sh (15.0 ± 

0.97 ng/g) were not 

signifi cantly different 

(nonparametric

Kruskal-Wallis) 

than those found in 

sediments (142 ± 59 

ng/g), corals (22.04 ± 

8.57 ng/g), or conch 

(32.7 ± 9.07 ng/g). The 

mean concentration 

of total PAHs in the 

tissues of schoolmaster 

snapper was 16.5 

± 1.16 ng/g while 

those for longspine 

squirrelfi sh were 13.5 

± 1.20 ng/g. None of 

the values exceeded 

EPA recommended 

screening values 

(SVs) for PAHs in fi sh tissues for recreational fi shers (EPA, 

2000).

Polychlorinated Biphenyls (PCBs)

PCBs or polychlorinated biphenyls are a group of synthetic 

compounds that have been used in numerous applications 

ranging from electrical transformers and capacitors, to 

hydraulic and heat transfer fl uids, to pesticides and in 

paints. Although no longer manufactured in the U.S., 

ecosystem contamination by PCBs is widespread due 

to their environmental persistence and tendency to 

bioaccumulate. 

Figure 7.3. Total PAHs detected in the conch Lobatus gigas.

Table 7.3. PAHs, TBT and total butyltins in coral tissues from NOAA Caribbean studies.

Location

Mean SE Maximum Mean SE Maximum Mean SE Maximum

Guanica Bay, Puerto Ricoa 4.96 ± 0.48 10.1 ND N/A ND ND N/A ND

Jobos Bay, Puerto Ricob 5.61 ± 0.31 8 ND N/A ND ND N/A ND

Southwest Puerto Ricoc 46.9 ± 18.5 158.9 ND N/A ND 2.62 ± 0.25 3.53

Vieques, Puerto Ricod 15.0 ± 0.64 24.9 0.08 ± 0.07 2.36 4.65 ± 0.45 9.37

STEER, USVI 22.04 ± 8.57 80.4 0.08 ± 0.03 0.29 0.24 ± 0.08 0.74

a

Whitall et al., 2013; bWhitall et al., 2011; cPait et al. , 2007; dPait et al. , 2010. TBT, tributyltin; SE, standard error. 

Units for PAHs are ng/g for TBT, and total butyltins ng Sn/g.

PAHs TBT Total Butyltins
STEER Integrated Environmental Assessment Report

152Chapter 7: Contaminants in Coral, Conch and FishPCBs in Coral. 

No detectable 

levels of PCBs 

were found in 

any of the coral 

samples from 

the STEER.

PCBs in Conch. 

No detectable 

levels of PCBs 

were found 

in any of the 

conch samples 

from the 

STEER.

PCBs in Fish.

PCBs were 

detected in 

all the fi sh 

analyzed; 

the mean 

concentration 

was 65.9 ± 

50.1 ng/g 

(Table 7.2). 

The highest 

concentration 

of total PCBs 

in fi sh tissues in the STEER was found in the fi sh caught 

at site SQ-S2 (Figure 7.4). The concentration in fi sh SQS2 (longspine squirrelfi sh) was 419.2 ng/g (150.9 ng/g wet 

weight) which is in the top 10th percentile of all National 

Status and Trends (NS&T) data for PCBs. This sample 

also exceeded the EPA screening value (SV) for PCBs 

in fi sh tissues for recreational fi shers for noncarcinogens 

of 80 ng/g wet weight (EPA, 2000). Exposure to PCBs 

in fi sh has been linked to reduced growth, reproductive 

impairment and vertebral abnormalities (EPA 1997).

Organochlorine Pesticides

A series of man-made chlorine-containing hydrocarbon 

pesticides (insecticides and herbicides) were developed and

used from the 1940s through the 1970s. Organochlorine 

pesticides are toxic to varying degrees to aquatic life 

including crayfi sh, shrimp and fi sh. One of the best 

known organochlorine pesticides was the insecticide DDT 

(dichlorodiphenyltrichloroethane). The use of many of the 

organochlorine pesticides, including DDT, was banned 

in the U.S. due to their environmental persistence and 

toxicity to nontarget species (ATSDR, 2002). Because 

of their persistence and heavy use in the past, residues of 

many organochlorine pesticides can still be found in the 

environment (Butler, 1973). 

DDT in Coral. Only the coral sample from the HBI14P site 

in stratum 4 (Figure 7.1), had a detectable concentration 

of both DDT and its metabolites, and only then at a total 

concentration of 0.08 ng/g. In comparison, the mean 

concentration of total DDT in coral tissues found in 

Vieques, Puerto Rico was 0.13 ± 0.07 ng/g. The mean 

concentration of total DDT in the sediments in the STEER 

was 0.047 ± 0.025 ng/g (Pait et al., 2013).

DDT in Conch. None of the conch analyzed from the 

STEER contained detectable levels of total DDT. 

DDT in Fish. Only the squirrelfi sh sample collected at 

the site SQ-S2 in stratum 2 had a DDT level above the 

detection limit. The total DDTs concentration in the fi sh 

was 16.5 ng/g, which was comprised solely of DDT 

breakdown products (56.7% 2,4 – DDD, 6.1% 4,4 – DDD, 

and 37.2% 4,4 – DDE). The absence of the parent DDT 

compounds (2,4’-DDT or 4,4’-DDT) likely indicates an 

Figure 7.4. Total PCBs detected in fi sh in the STEER.
STEER Integrated Environmental Assessment Report

153Chapter 7: Contaminants in Coral, Conch and Fish

older source of the contamination as DDT was phased out 

for use in the U.S. beginning in 1972.

Other Pesticides. A number of additional chlorinated 

pesticides were analyzed, however with only one exception 

(chlordane), there were no detectable concentrations in 

coral and conch. Total chlordane was detected at HBI14P 

at a concentration of 0.05 ng/g in coral. In comparison, the 

mean concentration of total chlordane detected in coral 

tissues in Vieques, Puerto Rico was 0.12 ± 0.03 ng/g (Pait 

et al., 2010). 

Chlordane was detected in fi sh tissues in the STEER. The 

mean total chlordane concentration in fi sh was 1.41 ± 0.44 

ng/g. The mean total chlordane concentration in the tissues 

of longspine squirrelfi sh was 1.32 ±0.87 ng/g, while the 

mean tissue concentration in schoolmaster snapper was 

1.51 ± 0.35 ng/g.

Endosulfan, mirex, and dieldrin were also detected in fi sh 

tissues collected from the STEER. Mirex was detected in 

two squirrelfi sh samples at sites SQ-S2 (0.64 ng/g) and 

SQ-S3 (1.11 ng/g). Dieldrin was detected in a squirrelfi sh 

from site SQ-S4 (0.53 ng/g) and in a snapper from site 

SN-S4 (3.58 ng/g). Endosulfan was detected in only one 

squirrelfi sh from SQ-S2 (0.69 ng/g).

Butyltins

A class of organometallic compounds, butyltins have had a 

variety of uses ranging from biocides in antifoulant paints 

to catalysts and glass coatings (Birchenough et al. 2002; 

Bennett, 1996). In the environment, tributyltin or TBT 

degrades to dibutyltin (DBT), then monobutyltin (MBT), 

and fi nally to inorganic tin. Tetrabutyltin is an intermediate 

in the manufacture of TBT. Experiments have shown that 

the half -life of TBT is on the order of days; degradation 

to monobutyltin takes approximately a month, however in 

deeper anoxic sediments, the half-life of TBT appears to be 

on the order of 2-4 years or longer (Batley, 1996). 

The presence of TBT has been linked to endocrine 

disruption, specifi cally an imposex (females developing 

male characteristics) condition in marine gastropods, 

while in other mollusks (e.g., oysters), abnormal shell 

development, and poor weight gain have been seen (Batley, 

1996; Strand et al. 2009). TBT has also been shown to 

have effects on larval growth of fi sh at concentrations 

below 100 ng/L in water (Newman and McIntosh, 1991). 

Beginning in 1989, the use of TBT as an antifouling agent 

was banned in the U.S. on non-aluminum vessels smaller 

than 25 meters in length (Gibbs and Bryan, 1996). Because 

of its widespread use in the past, TBT and its metabolites 

continue to be detected in many components of the 

environment. Recent work by Titley-O’Neil et al. (2011) 

showed that high concentrations of antifouling paint-based 

butyltin compounds were linked to imposex in conch. 

Negri et al. (2002) investigated the effects of TBT in 

sediments on the coral Acropora microphthalma. They 

found that the effective concentration of TBT which caused 

50 percent inhibition (EC50) of fertilization after four hours 

was 200 μg/L, and the concentration needed to inhibit 50 

percent larval metamorphosis was only 2 μg/L.

Total Butyltins in Coral. The sum of the three butyltins 

(total butyltins), was calculated to better visualize total

butyltin exposure to corals in the STEER (Figure 7.5). The 

mean concentration in coral was 0.24 ng Sn/g. The highest 

concentration of total butyltins (0.74 ng Sn/g) was found in 

stratum 2 just outside of Benner Bay at site HBI28P. The 

mean concentrations of total butyltins in coral tissues in 

the STEER appeared somewhat lower than that detected in 

southwest and Vieques, Puerto Rico in studies conducted 

by NOAA (Table 7.3). 

Total Butyltins in Conch. The mean concentration of 

butyltins in conch tissues increased from TBT (0.12 ng 

Sn/g), to DBT (1.07 ng Sn/g), and the highest being MBT 

(5.11 ng Sn/g) (Table 7.2). This appears to follow the 

natural degradation pattern of TBT in the environment 

(Batley, 1996). The two highest concentrations of total 

butyltins of 27.9 ng Sn/g and 23.3 ng Sn/g were both found 

in stratum 2 in Benner Bay (Figure 7.6). This appears to 

correlate with the elevated concentrations of butyltins 

found in the sediments of STEER in northern Benner Bay 

(Pait et al., 2013; Chapters 4 and 5), which has a number of 

marinas and boatyards. 

The two highest total butyltin concentrations are at least 

seven times higher than the next highest concentration 

(3.25 ng Sn/g) found in stratum 5. Strand et al. (2009) 

looked at total butyltins in different non -L. gigas conch 

species in the U.S. Virgin Islands. They found a mean 

concentration of total butyltins in tissues collected from 

St. Thomas of 104.7 ± 44.8 ng Sn/g, however, none of 

the samples collected by Strand et al. (2009) were from 

the STEER. In contrast, the mean concentration of total 

butyltins in L. gigas tissues from the STEER in the current 

study was much lower, 6.30 ng Sn/g ± 3.24. 

Total Butyltins in Fish. The mean concentration of total 

butyltins in all fi sh was 17.4 ng Sn/g (Table 7.2). For 

schoolmaster snapper, the mean concentration of total 

butyltins was 24.9 ng Sn/g while the mean concentration 
STEER Integrated Environmental Assessment Report

154Chapter 7: Contaminants in Coral, Conch and Fish

Figure 7.5. Total butyltins detected in the coral Porites astreoides.

of total butyltins for 

longspine squirrelfi sh was 

10.0 ng Sn/g. The highest 

concentration of total 

butyltins (68.3 ng Sn/g) 

was at site SN-S4.

TBT in Coral. The 

highest concentration 

of TBT in P. astreoides

tissues collected from 

the STEER was 0.29 

ng Sn/g at site HBI28P 

just outside Benner Bay 

(Figure 7.7). The mean 

concentration of TBT 

in STEER corals was 

0.08 ng Sn/g ± 0.03 

(Table 7.2). The average 

concentration of TBT 

in the sediments in the 

STEER found by Pait 

et al. (2013) was 1.85 

±1.30 ng Sn/g. The 

highest concentration of 

TBT detected in STEER 

sediments from the same 

study using a stratifi edrandom sampling 

design was in Benner 

Bay, at 31 ng Sn/g. The 

mean concentration of 

TBT in coral tissues 

in the STEER was the 

same as that found in 

Vieques, Puerto Rico 

(Table 7.3). From the 

NOAA NCCOS studies, 

only Vieques, Puerto 

Rico and STEER had 

detectable TBT in P. 

astreoides. The higher 

detection of TBT in 

coral in Benner Bay, 

may be associated 

with the elevated 

concentrations found in 

the sediments of STEER 

in this same area (Pait et 

al., 2013). There was a 

signifi cant relationship 

between TBT in coral Figure 7.6 Total butyltins detected in the conch Lobatus gigas.
STEER Integrated Environmental Assessment Report

155Chapter 7: Contaminants in Coral, Conch and Fish

Figure 7.8 Tributyltin detected in the conch Lobatus gigas.

tissues in the STEER 

and a basic inshore vs. 

off shore designation, 

with the inshore being 

signifi cantly higher 

than the offshore 

using a nonparametric 

Wilcoxon’s rank sums 

test (p = 0.0304).

TBT in Conch. The 

highest concentration of 

TBT in L. gigas tissues 

in the STEER was 0.38 

ng Sn/g in stratum 2 at 

site Conch 2B (Figure 

7.8). There was also a 

signifi cant relationship 

between TBT in conch 

tissues in the STEER 

and a basic inshore vs. 

offshore designation, 

using nonparametric 

Wilcoxon’s rank sums 

(p = 0.0304). 

TBT in Fish. The 

highest concentration 

of TBT was 48.7 ng 

Sn/g at site SN-S4 

(Figure 7.9). The 

mean concentration 

of butyltins in all fi sh 

tissues decreased from 

TBT (9.37 ng Sn/g), to 

DBT (5.47 ng Sn/g), to 

MBT (2.60 ng Sn/g). 

This relationship is 

inverse of that found 

in conch and may 

be caused by fi sh 

being exposed more 

recently to TBT. For 

schoolmaster snapper, 

the mean concentration 

of butyltins followed 

the same pattern, 

decreasing from TBT 

(16.95 ng Sn/g), to 

DBT (5.18 ng Sn/g), to 

MBT (2.75 ng Sn/g). 

However, in longspine 

Figure 7.7. Tributyltin detected in the coral Porites astreoides.
STEER Integrated Environmental Assessment Report

156Chapter 7: Contaminants in Coral, Conch and Fish

Figure 7.9 Distribution of tributyltin (TBT), dibutyltin (DBT), and monobutyltin 

(MBT) from fi sh sampled in the STEER. 

squirrelfi sh the mean for DBT (5.77 ng Sn/g) 

was higher than MBT (2.46 ng Sn/g), or TBT 

(1.79 ng Sn/g). TBT is broken down in fi sh 

tissues usually on the scale of days to weeks 

(Newmann and McIntosh, 1991) suggesting 

the presence of TBT in fi sh tissues was from 

a more recent exposure. Figure 7.9 shows the 

distribution of TBT, DBT, and MBT in fi sh 

tissues collected from the STEER.

While there was no statistically signifi cant 

differences in the concentrations of TBT or 

any of its metabolites between the two fi sh 

species, there was a statistically signifi cant 

difference (non-parametric Wilcoxon) between 

the percentage of TBT as compared to total 

butyltins, with schoolmaster snapper having 

a signifi cantly higher percentage of TBT 

in their tissues than longspine squirrelfi sh. 

It is not clear why the distribution of TBT, 

DBT and MBT differed between the two fi sh 

species. One possibility is that the longspine 

squirrelfi sh are more effi cient at metabolizing 

TBT than the schoolmaster snapper. 

Trace and Major Elements

All 14 of the trace and major elements (Table 7.1) analyzed 

in the samples were detected in coral, conch and fi sh. Coral 

tissue body burdens for each element varied broadly from 

one collection site to another within the STEER. With 

the exception of arsenic, copper, zinc, lead and the major 

elements (Al, Fe, Mn), the trace metal concentrations in 

coral are illustrated in Tables 7.4a and 7.4b. A summary 

of average concentrations of individual trace and major 

elements are presented in Figures 7.10 - 7.13, to show the 

relative abundance of each metal. 

Silver

Silver in Corals. Body burdens of silver in P. astreoides 

were relatively low; the maximum value of 0.02 μg/g 

(Table 7.4a, Figure 7.10) was found in coral from HBI42A 

site in stratum 5. In coral from various bays in Puerto Rico 

Pait et al., (2009 and 2010) and Whitall et al. (2011), have 

documented comparable ranges of silver in P. astreoides

tissues. Because silver was not detected in sediment from 

the STEER (Pait et al., 2013), the results suggest naturally 

low silver concentration related to the geological formation 

of the island. 

Silver in Conch. Silver body burdens in conch samples 

from the STEER varied from 0.16 μg/g to 3.75 μg/g, with 

a mean value of 0.88 μg/g (Table 7.6, Figure 7.11). Mean 

values of silver were similar in conch across all strata in 

the STEER with the exception of stratum 5 where silver 

was found to be nearly an order of magnitude higher 

(Table 7.7). Glazer et al. (2008) investigated heavy metal 

concentrations in queen conch from south Florida, and 

found a mean body burden for silver of 1.03 μg/g in 

conch from the offshore habitats, and 2.54 μg/g in conch 

from nearshore habitats. Although causative effects were 

not established, these authors hypothesized that reduced 

reproductive fi tness of conch in the nearshore habitats in 

south Florida was due to elevated metal concentrations 

including silver. 

Silver in Fish. Silver was detected at only three of the eight 

fi sh sites (Table 7.8). The maximum concentration of silver 

in any fi sh tissue was only 0.04 μg/g observed in snappers 

from SN-S1 site (Table 7.8). The mean concentration of 

silver for all fi sh was 0.01 ± 0.005 μg/g (0.01 ± 0.009 

μg/g in schoolmaster snapper, 0.01 ± 0.005 μg/g in 

longspine squirrelfi sh). The mean concentration of silver 

in fi sh tissues from the STEER were similar to the mean 

concentration of silver in fi sh tissues from Vieques, Puerto 

Rico (Table 7.9). 

Aluminum

Aluminum in Corals. In the STEER, P. astreoides had 

aluminum body burdens ranging from zero to a maximum 
STEER Integrated Environmental Assessment Report

157Chapter 7: Contaminants in Coral, Conch and Fish

value of 201 μg/g (Table 7.4a). Figure 7.12 shows the 

overall mean of aluminum in coral tissue, however, the 

results indicated that aluminum concentrations were below 

the detection limit at most of the sampling locations in 

the STEER except at HBI28P where the maximum value 

was detected. Pait et al. 

(2010) and Whitall et al. 

(2011) have respectively 

reported maximum values 

of 37 μg/g in coral from 

Vieques, Puerto Rico and 

333 μg/g in Jobos Bay, 

Puerto Rico indicating that 

concentrations found in 

the STEER were within 

the range of aluminum 

concentration in coral from 

the Caribbean.

Aluminum in Conch. In L. 

gigas, aluminum ranged 

from 38.5 to 828 μg/g 

(Table 7.6). The highest 

concentration of aluminum 

occurred in one of the conch 

collected from stratum 4 

(Table 7.7). 

Aluminum in Fish. Aluminum concentrations in the tissue 

of all fi sh in the STEER ranged from 1.67 μg/g to 14.4 μg/g 

(Table 7.8) with a mean of 6.32 ± 2.03 μg/g. The highest 

concentration of aluminum was found in snappers at site 

SN-S3. Similar ranges of aluminum concentrations were 

Figure 7.10. Concentrations (mean ±SE) of metals detected in the coral Porites astreoides. 

0

0.5

1

1.5

2

2.5

3

3.5

Ag As Cd Cr Hg Ni Pb Se Sn

μg/g dry weight (coral tissue)

Table 7.4a. Summary statistics for contaminants (μg/g) in coral tissue, including comparison with other studies. 

Species Location Reference

Porites astreoides STEER Maximum 0.0202 201 1.76 0.0467 1.52 4.07 275 This study

Porites astreoides STEER Mean 0.01293 22.33333 1.255 0.011867 0.389111 2.692222 72.31111 This study

Porites astreoides STEER Minimum 0 0 0.611 0 0 1.96 27.9 This study

Porites astreoides Southwest Puerto Rico Mean 0 37.8 0 0 0 2.06 90.8 Pait et al., 2009

Porites astreoides Vieques, Puerto Rico Mean 0.013 30.75 0.241 0.194 0.183 0.757 51.2 Pait et al., 2010

Porites astreoides Jobos Bay, Puerto Rico Range 0 100-333 0.94-2.44 0.21-0.31 0 2.37-97.2 110-480 Whitall et al., 2011

Porites astreoides Punta brava, Venezuela Range 1.32-369 Bastidas and Garcia, 1999

Bajo Caiman, Venezuela Range nd-88.7

Porites sp. Misima Island, Papua NG Fallon et al., 2002

Porites lobata Ulan Reef, Philipines Mean 3.1 David, 2003

Porites sp. Dafangji Island, China Peng et al., 2006

Porites sp. Daya Bay, China Range 41.4-226.4 Chen et al., 2010

Table 7.4b. Summary statistics for contaminants (μg/g) in coral tissue, including comparison with other studies.

Species Location Reference

Porites astreoides STEER Maximum 0.003 19.6 8.33 0.42 0.116 0.0393 14.8 This study

Porites astreoides STEER Mean 0.001 10.1 2.18 0.16 0.012889 0.004367 5.983333 This study

Porites astreoides STEER Minimum 0 7.25 0 0.07 0 0 1.87 This study

Porites astreoides Southwest Puerto Rico Mean 0 3.01 1.32 0 0.05 0.02 6.09 Pait et al., 2009

Porites astreoides Vieques, Puerto Rico Mean 2.66 0.9 0.07 0.096 0.246 3.43 Pait et al., 2010

Porites astreoides Jobos Bay, Puerto Rico Range 0.001-.004 8.33-24.6 0.8-6.84 0.08-12.5 0.13-0.26 nd-0.10 2.56-16.9 Whitall et al., 2011

Porites astreoides Punta brava, Venezuela Range 3.59-42.5 Bastidas and Garcia, 1999

Bajo Caiman, Venezuela Range 0.83-23.1

Porites sp. Misima Island, Papua NG 0.19-1.6 0.68-36.5 Fallon et al., 2002

Porites lobata Ulan Reef, Philipines Mean 1 1.8 David, 2003

Porites sp. Dafangji Island, China 2.76-6.85 4.2-55.1 Peng et al., 2006

Porites sp. Daya Bay, China Range 0.79-5.38 0.02-22.3 Chen et al., 2010

Hg Mn

Value Ag Al As

Value Ni Zn

Cr Cu

Pb Se Sn

Cd Fe
STEER Integrated Environmental Assessment Report

158Chapter 7: Contaminants in Coral, Conch and Fish

Table 7.5. Mean metal body burden (μg/dry g) in coral by stratum.

Element

Ag 0.0138 0.0134 0.0131 0.0169 0.0134

Al 0 201 0 0 0

As 0.611 1.76 1.57 0.984 1.11

Cd 0 0 0 0.0177 0.0205

Cr 0 0 0 0 1.52

Cu 2.37 4.07 2.06 2.44 2.77

Fe 54.7 275 82.6 32.3 42

Hg 0 0.00227 0 0 0

Mn 8 19.6 11.8 8.07 7.25

Ni 1.58 2.3 0.954 1.78 2.28

Pb 0.111 0.415 0.217 0.0693 0.0741

Se 0 0 0.116 0 0

Sn 0 0.0393 0 0 0

Zn 2.04 14.8 10.2 1.87 2.38

n = 2 for each stratum except for stratum 1 (only one site located). 

Stratum 1 Stratum 2 Stratum 3 Stratum 4 Stratum 5

found in fi sh tissues from Vieques, Puerto 

Rico (Table 7.9).

Arsenic

Arsenic in Corals. Arsenic body burdens 

in P. astreoides varied from 0.61 μg/g to 

1.76 μg/g. Table 7.4a indicates that the 

overall range of arsenic concentrations 

were similar to those reported elsewhere 

in southwest Puerto Rico and Jobos Bay, 

Puerto Rico (Pait et al., 2009 and Whitall 

et al., 2011). Sublethal thresholds for 

arsenic in coral have not been established, 

but Pichler et al. (1999) found that coral 

in Ambide Island, Papua New Guinea, 

exposed to elevated concentrations of 

arsenic in seawater from hydrothermal 

vents did not show any obvious toxic 

effects. 

Arsenic in Conch. Arsenic was detected 

in the tissue of all L. gigas collected in the 

STEER. Body burdens varied from 17.6 

μg/g to 67.6 μg/g (Table 7.6). The highest 

concentrations in conch were found in stratum 4 (Table 

7.7). With a mean value of 32.7 μg/g, arsenic had the 

second highest concentration of the trace metals measured 

in conch after copper (Figure 7.11). Said et al. (2013) 

assessed elemental concentrations including arsenic in the 

conch S. canarium in the western region of Johor Straits, 

Malaysia, and reported an arsenic value of 0.125 μg/g 

wet weight (Table 7.6). Using the average 76% moisture 

content measured in the 

conch from the STEER, 

we derived an equivalence 

maximum concentration of 

16.9 μg/g wet weight (ww) 

and minimum of 8.2 μg/g 

ww of arsenic in L. gigas. 

The sublethal threshold 

toxicity of arsenic for 

conch is unknown at this 

time. For human protection 

however, the U.S. FDA 

(FDA, 2009) has set the 

maximum permissible 

action level of 86 μg/g 

arsenic wet weight (ww) 

in shellfi sh. The derived 

wet weight equivalence 

of the maximum arsenic 

concentration value found 

in conch from the STEER (16.9 μg/g ww) was low relative 

to the FDA criterion. 

Arsenic in Fish. Arsenic was also detected in all tissue 

samples of both fi sh species with concentrations ranging 

from 4.7 μg/g to 27.9 μg/g (Table 7.8). The highest 

concentration was found at site SQ-S2 just outside of 

Benner Bay. The mean concentrations of arsenic for both 

TI (nearshore)

Ag 0.88 0.16 3.75 1.03 (1.4) 2.54 (3.4)

As 32.7 17.6 67.6 0.125 (0.17)

Cd 1.96 0.89 3.75 2.62 (3.5) 24.14 (31.9) 0.01 (0.01)

Hg 0.24 0.05 0.88 0.01 (0.01) 0.00 (0) 

Al 229 38.5 828

Cr 3.41 1.45 8.57

Fe 785 284 1720

Mn 113 40 355

Ni 5.79 3.03 13.6 16.28 (21.53) 9.59 (12.7)

Zn 484 170 1320 30.53 (40.39) 660.32 (873.6)

Cu 84.7 36 122 14.06 (18.6) 84.34 (111.6) 1.36 (1.8)

Pb 0.61 0.21 1.32

Se 1.19 0.68 2.38

Sn 5 0.03 12.7 0.00 (0) 0.00 (0)

Min. Conc., minimum concentration; Max. Conc., maximum concentration; TI, Tingler Island; PS = Pelican Shoal. 

Values in parentheses are dry weight equivalence of the wet weight concentrations; ww, wet weight.

Johor Straits, Malaysia

STEER Glazer, 2008 (ww) Metal

Mean Min. Conc. Max. Conc. PS (offshore)

Said et al., 2013 (ww)

Table 7.6. Summary statistics for contaminants (μg/g) in conch tissue (n=10), including comparison with mean concentration values derived from study of conch contamination in South Florida 

(Glazer et al., 2008) and Johor Straits, Malaysia (Said et al., 2013). 
STEER Integrated Environmental Assessment Report

159Chapter 7: Contaminants in Coral, Conch and Fish

fi sh species was 11.8 

± 2.8 μg/g (9.7 ± 2.7 

μg/g for schoolmaster 

snapper, 13.8 ± 5.1 

μg/g for longspine 

squirrelfi sh). The 

mean concentrations 

of arsenic in fi sh 

tissues from the 

STEER were 

similar to the mean 

concentration of 

arsenic found in fi sh 

tissues from Vieques, 

Puerto Rico (Table 

7.9). 

Using the laboratory 

recorded percent dry 

and percent moisture 

for each sample, a wet 

weight concentration 

of arsenic for each 

sample was calculated 

for comparison to 

EPA’s recreational 

fi shers recommended screening values (SVs) (EPA, 

2000). Based on the SV of 1.2 μg/g inorganic arsenic, 

all of the STEER samples exceeded the threshold by at 

least 0.15 μg /g. However, it is important to note that our 

numbers represent total arsenic, including both organic and 

inorganic fractions. According to the EPA 

(2012), inorganic arsenic makes up only 

2% of total arsenic in marine organisms. 

Given that 2%, our inorganic arsenic 

concentrations in wet weight would range 

from 0.027 μg/g to 0.185μg/g with a mean 

concentration of 0.079 ± 0.051 μg/g wet 

weight (schoolmaster snapper 0.054 ± 0.028 

μg/g, longspine squirrelfi sh 0.104 ± 0.061 

μg/g). As such all of the fi sh samples from 

the STEER would fall below the EPA SV of 

1.2 μg/g wet weight.

Cadmium

Cadmium in Corals. Cadmium 

concentrations in coral tissues ranged 

from zero to a maximum of 0.047 μg/g 

(Table 7.4a), in stratum 5, at HBI42A. As 

with the other trace metals, the coral body 

burdens of cadmium were low (Figure 

7.10). Cadmium body burdens in coral from 

the STEER were virtually an order of magnitude lower 

than concentrations reported by Whitall et al. (2011) in 

Jobos Bay, Puerto Rico (Table 7.4a). These authors linked 

the high cadmium concentrations observed in coral from 

Jobos Bay to elevated concentrations observed in bed 

sediments in the vicinity of the reef. Laboratory studies 

Table 7.7. Mean metal body burden in conch collected from the five strata.

in the STEER (μg/g).

Element Stratum 5

Ag 0.238 0.172 0.8755 0.985 2.116

Al 113 141.5 38.65 767.5 77.1

As 25.3 19.9 32.25 51.4 38.1

Cd 1.45 1.044 2.66 2.725 1.745

Cr 3.03 1.81 3.085 6.33 3.16

Cu 48.8 113 62.2 114.5 85.5

Fe 783 776 389 1625 380

Hg 0.054 0.097 0.298 0.196 0.549

Mn 55.8 258 86.2 103.9 69.55

Ni 5.18 6.06 4.08 11.045 3.545

Pb 0.424 1.26 0.29 0.7415 0.3305

Se 0.758 0.962 1.22 1.19 1.845

Sn 1.74 4.75 12.25 4.011 0.03765

Zn 307 920.5 670 235.5 288.5

n = 2 from each stratum.

Stratum 1 Stratum 2 Stratum 3 Stratum 4

Figure 7.11. Concentrations (mean ±SE) of metals detected in the conch Lobatus gigas. 

0

5

10

15

20

25

30

35

40

Ag As Cd Cr Hg Ni Pb Se Sn

μg/g dry weight (conch tissue)
STEER Integrated Environmental Assessment Report

160Chapter 7: Contaminants in Coral, Conch and Fish

Table 7.8. Trace and major element concentrations (μg/g) in fish from the STEER. 

All Fish

Mean Mean Mean Maximum

Ag 0.0084 0.0087 0 0.0349 0.0080 0 0.0174

As 11.76 9.72 4.70 17.00 13.80 6.34 27.90

Cd 0.0283 0.0226 0.0178 0.0318 0.0339 0.0173 0.0472

Hg 0.2548 0.2953 0.1970 0.4660 0.2144 0.0496 0.5020

Al 6.32 5.40 1.67 14.40 7.24 1.64 13.50

Cr 20.1 24.6 11.1 35.2 15.5 11.5 18.1

Fe 177.1 203.5 119 276 150.8 131 192

Mn 2.52 2.73 2.16 3.48 2.32 1.94 2.77

Ni 2.575 3.758 0.911 10.100 1.392 0.966 1.880

Zn 65.8 40.8 35.8 43.8 90.8 25.3 217.0

Cu 3.07 2.32 1.79 2.96 3.83 1.86 6.87

Pb 0.0865 0.0482 0 0.0653 0.1247 0.0590 0.2600

Se 2.69 1.71 1.53 2.11 3.67 1.18 9.84

Sn 0.0436 0.0511 0.0231 0.0930 0.0360 0 0.1040

Note - all values in dry weight; whole fish analysis.

Element Schoolmaster Snapper Longspine Squirrelfish

Minimum Maximum Minimum

have shown that cadmium 

can affect coral metabolic 

processes by inhibiting 

photosynthetic electron 

transport in symbiotic 

zooxanthellae (Kuzminov 

et al., 2013). Additionally, 

cadmium has been shown 

to impair development and 

reproduction in several 

invertebrate species 

including coral (Eisler, 1985; 

Mitchelmore et al., 2007). 

Cadmium in Conch. 

Cadmium body burdens in 

conch tissues ranged from 

0.89 μg/g to a maximum of 

3.75 μg/g (Table 7.6) which 

was found in stratum 3. The 

results showed little variation 

between strata for cadmium 

body burden in conch relative to the STEER-wide mean 

value of 1.96 μg/g (Table 7.7; Figure 7.11). Cadmium body 

burdens found in the STEER were similar to concentrations 

reported by Glazer et al. (2008) in L. gigas collected from 

the offshore environment in south Florida. However, the 

same authors reported concentrations of 31.9 μg/g in conch 

collected from nearshore environments in Florida (Table 

7.6). Cadmium’s toxicity to aquatic organisms is well 

documented (Lin and Dunson, 1993; Omer et al., 2012). 

However, threshold guidelines for cadmium sublethal 

effects in conch are unknown at this time. The FDA 

action level for cadmium in molluscan shellfi sh is 4 μg/g 

wet weight. Using the measured 76% moisture content 

in conch, we derived an equivalence value of 0.94 μg/g 

(ww) for cadmium in STEER conch. The concentrations of 

cadmium in conch from the STEER were below the FDA 

threshold. 

Cadmium in Fish. Cadmium was detected in all fi sh tissues 

collected in the STEER and ranged from 0.017 μg/g up 

to 0.047 μg/g. The highest concentration of cadmium 

was detected at site SQ-S3. The mean concentration of 

cadmium for all fi sh in the STEER was 0.028 ± 0.004 

μg/g (0.023 ± 0.003 μg/g in schoolmaster snapper, 0.034 

± 0.008 μg/g in longspine squirrelfi sh) (Table 7.8). Using 

the laboratory recorded percent dry and percent moisture 

for each sample, a wet weight concentration of cadmium 

for each sample was calculated for comparison to EPA’s 

recreational fi shers recommended screening value (SV) 

(EPA, 2000). Based on the SV of 4.0 μg/g, all detections of 

cadmium were two to three orders of magnitude below the 

SV.

Cadmium concentrations in fi sh tissues in the STEER 

were an order of magnitude lower than those found in the 

sediments. Cadmium concentrations in fi sh and corals 

were two orders of magnitude lower than those observed in 

conch in the STEER. The mean concentration of cadmium 

in fi sh tissues in the STEER were similar to the mean 

Table 7.9. Comparison of average elemental 

composition in fish tissues (μg/g) in STEER and Vieques.

Element STEER* 

(NOAA)

Vieques 

(ATSDR)

Aluminum (Al) 2.15 7.66

Arsenic (As) 3.95 3.95

Cadmium (Cd) 0.01 0.08

Chromium (Cr) 6.62 0.16

Copper (Cu) 1.07 0.56

Iron (Fe) 58.8 6.81

Lead (Pb) 0.04 0.27

Manganese (Mn) 0.85 0.33

Mercury (Hg) 0.08 0.05

Nickel (Ni) 0.81 0.81

Selenium (Se) 0.91 0.98

Silver (Ag) 0.01 0.08

Zinc (Zn) 22.7 3.13

*Note - STEER means converted to approximate

wet weight concentrations.
STEER Integrated Environmental Assessment Report

161Chapter 7: Contaminants in Coral, Conch and Fish

concentration of cadmium 

found in fi sh tissues in 

Vieques, Puerto Rico (Table 

7.9).

Chromium

Chromium in Corals. The 

average concentration of 

chromium in P. astreoides

was 0.39 μg/g (Table 7.4a), 

and ranged from zero to a 

maximum of 1.52 μg/g, at 

sampling location HBI7P in 

stratum 5. Mean chromium 

body burdens in coral tissue 

from the STEER were 

similar to the mean value 

reported in coral from Puerto 

Rico (Table 7.4a), although 

the maximum level found 

at HBI7P was nearly an 

order of magnitude higher 

than concentrations found in 

Vieques, Puerto Rico. 

Chromium in Conch. Summary statistics for the 

concentrations of chromium in L. gigas from the STEER 

are presented in Table 7.6. Mean chromium concentrations 

in conch varied from 1.81 μg/g to a maximum value of 6.33 

μg/g. Relative to the STEER-wide mean concentration of 

3.41 μg/g, chromium appeared to be fairly well distributed 

across the strata in the STEER except in Stratum 4 where 

the maximum values were measured (Table 7.7). 

Chromium effects in conch are unknown. To limit human 

exposure to chromium through seafood consumption, 

the U.S. FDA (FDA, 2009) has set a chromium action 

level in molluscan shellfi sh at 2.14 μg/g wet wt. Using 

the measured 76% moisture content in conch, we derived 

an FDA equivalence value of 17.2 μg/g chromium (dry 

weight) in mollusks. Levels of chromium found in conch 

tissue from the STEER (maximum of 8.57 μg/g) are below 

the FDA action levels. Chromium has been shown to 

reduce survival and fecundity in the cladoceran Daphnia 

magna, and result in reduced growth in fi ngerling chinook 

salmon (Oncorhynchus tshawytscha) (Eisler, 1986).

Chromium in Fish. Chromium was detected in all fi sh 

samples from the STEER and ranged from 11.5 μg/g 

to 35.2 μg/g with a mean concentration of 21.4 ± 3.04 

μg/g (schoolmaster snapper 24.6 ± 5.92 μg/g, longspine 

squirrelfi sh 15.5 ± 1.49 μg/g) (Table 7.8). The highest 

concentration of chromium was detected at site SN-S3. 

The mean concentration of chromium in fi sh tissues in 

the STEER were an order of magnitude higher than the 

mean concentration of chromium found in fi sh tissues in 

Vieques, Puerto Rico (Table 7.9). Compared to sediment 

concentrations in the STEER chromium in fi sh tissues are 

similar in range. 

Copper 

Copper in Corals. Copper body burdens in P. astreoides

ranged from 1.96 μg/g to 4.07 μg/g, with a mean of 2.69 

μg/g (Table 7.4a and Figure 7.12). Like a number of the 

other metals measured, the highest copper concentration 

was found at HBI28P within stratum 2 in Benner Bay 

(Figure 7.1). A number of metals (e.g. Al, Fe, Mg, As, Cu, 

and Zn) were more elevated in the coral at this site than 

coral from other sites, and this may be related to inputs 

from point and nonpoint sources in the area, including 

runoff from terrestrial areas (e.g., roads and boatyard 

activities), and the resuspension of sediments as a result of 

boat traffi c. 

Copper found in P. astreoides from the STEER were in the 

range of concentrations found in southwest and in Vieques, 

Puerto Rico (Table 7.4a). However, in P. astreoides from 

Jobos Bay, Puerto Rico, Whitall et al. (2011) reported a 

higher median value, 69 μg/g. These authors suggested 

there have been copper contamination problems in Jobos 

Bay. 

The toxicity of copper to corals is well demonstrated 

(Downs et al., 2005; Reichelt-Brushett and Harrison, 1999, 

Figure 7.12. Concentrations (mean ±SE) of metals detected in the coral Porites astreoides. 

0

20

40

60

80

100

120

Al Cu Fe Mn Zn

μg/g dry weight (coral tissue)
STEER Integrated Environmental Assessment Report

162Chapter 7: Contaminants in Coral, Conch and FishGoh and Chou, 1997; Reichelt-Brushett and MichalekWagner, 2005). Downs et al. (2005) showed that copper 

as cuprous oxide affected cell vitality and mitochondrial 

function. Reichelt-Brushett and Michalek-Wagner 

(2005) investigated the effects of copper on the soft 

coral Lobophytum compactum. A signifi cant reduction in 

fertilization success was found at a copper concentration 

of 117 μg/L. Also, in corals, Reichelt-Brushett and 

Harrison (2004) found that a copper concentration of 20 

μg/L signifi cantly reduced fertilization success in brain 

coral Goniastrea aspera. Goh and Chou (1997) found that 

a copper concentration of 40 μg/L in the zooxanthellae 

Symbiodinium microadriaticum, isolated from the rice coral 

Montipora verrucosa resulted in growth inhibition in the 

symbiotic dinofl agellate. Goh and Chou (1997) noted a 

synergistic effect when the zooxanthellae were exposed to 

both copper and zinc.

Copper in Conch. Copper body burdens in L. gigas

from the STEER ranged from 36 μg/g to 122 μg/g with 

a mean of 84.7 μg/g (Table 7.6 and Figure 7.13). Mean 

concentration of copper found in conch from the STEER 

were similar to concentrations found in conch from 

nearshore environments in south Florida (Table 7.6). 

However, the mean copper value measured in conch from 

the STEER was elevated relative to published values by 

Glazer et al. (2008) and Said et al. (2013), in conch from 

offshore environments of south Florida and Johor Straits, 

Malaysia (Table 7.6), respectively. 

While an essential element especially for mollusks, which 

use copper as the oxygen carrier in their blood, elevated 

concentrations of copper can impact aquatic organisms, 

including the functioning of gills, along with reproduction 

and development in fi sh and mollusks (Eisler, 1998a; 

Spade et al., 2010). Spade et al. (2010) found copper 

concentrations of 34.8 μg/g ww (46 μg/g dw) and 84.0 

μg/g (111 μg/g dw) respectively in the testis and digestive 

gland of conch from south Florida, and speculated that 

copper may be contributing to testis regression, and hence 

to reproductive failure of the conch in the nearshore 

environment of south Florida. Note, our data is whole body 

burden, and not tissue specifi c.

Copper in Fish. Copper was detected in all fi sh tissues from 

the STEER with body burdens ranging from 1.79 μg/g to 

6.87 μg/g and a mean of 3.07 ± 1.66 μg/g (schoolmaster 

snapper 2.32 ± 0.27 μg/g, longspine squirrelfi sh 3.83 ± 1.08 

μg/g) (Table 7.8). The highest concentration of copper was 

found in the squirrelfi sh caught at site SQ-S2. The mean 

concentration of copper in fi sh tissues from the STEER was 

an order of magnitude higher than the mean concentration 

of copper in fi sh tissues from Vieques, Puerto Rico (Table 

7.9). However, in the STEER, the mean concentration 

of copper in conch tissues was elevated relative to mean 

copper concentration found in fi sh tissues. 

As mentioned above, copper can impact the functioning 

of gills in fi sh and mollusks (Eisler, 1998a; Spade et al., 

2010). Reduced hatching rates in seabass Dicentrarchus 

labrax has also been seen with concentrations of copper as 

low as 5 μg/L in seawater (Newman and McIntosh, 1991). 

Overall in the STEER, less copper was found in fi sh and 

coral tissues relative to copper concentrations found in 

conch tissue (non-parametric Kruskal-Wallis test, p-value =

<0.0001). 

Iron

Iron in Coral. The major element iron ranged from a 

minimum of 27.9 μg/g to a maximum of 275 μg/g in P. 

astreoides (Table 7.4a). Similar to copper, the maximum 

iron body burden in coral was found at the HBI28P in 

stratum 2. The STEER-wide mean of iron of 72.3 μg/g 

indicates that iron is the most abundant metal in coral from 

the STEER (Figure 7.12). 

Similar coral body burden ranges of iron were reported in 

southwest Puerto Rico, Vieques, Puerto Rico and in Daya 

Bay, China (Table 7.4a). Like aluminum and manganese, 

iron is regarded as a marker of metals from terrestrial 

sources (Chen et al. 2010). However, there was no 

signifi cant correlation between iron and other trace metals 

to infer any reasonable source identifi cation aside from that 

of natural sources. 

Iron in Conch. Iron detected in conch ranged from 284 

to 1,720 μg/g, with a mean of 785 μg/g (Table 7.6). As 

with coral, iron had the highest mean concentration of any 

element measured in conch in this study. 

Iron in Fish. The range of iron detected in fi sh tissues 

in the STEER ranged from 119 μg/g to 276 μg/g with a 

mean of 177 ± 21 μg/g (schoolmaster snapper 204 ± 36 

μg/g, longspine squirrelfi sh 151 ± 14 μg/g) (Table 7.8). 

The highest concentration of iron measured in fi sh in the 

STEER was found in the snapper caught at site SN-S1. As 

with coral and conch, iron was the most abundant metal 

measured in fi sh tissues. The mean iron concentration in 

fi sh tissues from the STEER was an order of magnitude 

higher than the mean concentration of iron from fi sh tissues 

in Vieques, Puerto Rico (Table 7.9).
STEER Integrated Environmental Assessment Report

163Chapter 7: Contaminants in Coral, Conch and Fish

Mercury

Mercury in Coral. 

Mercury was detected 

at low concentrations 

in P. astreoides (Figure 

7.10) in the STEER 

with concentrations 

ranging from zero 

to 0.003 μg/g (Table 

7.4b). Similar 

concentration ranges 

were reported for 

mercury in coral from 

Puerto Rico (Table 

7.4b). The ecotoxicity 

of mercury includes 

neurological effects 

in vertebrates, which 

are well documented 

(Murphy et al. 2008). 

Bastidas and Garcia 

(2004) found reduced 

zooxanthellae density 

in Porites astreoides

exposed to mercury as well reduced levels of symbiotic 

algae either through death or expulsion.

Mercury in Conch. Mercury body burdens in conch were 

elevated in the STEER (ranging from 0.05 μg/g to 0.88 

μg/g) relatively to other studies (Table 7.6). Mercury was 

detected in all conch specimens collected. With a STEERwide mean of 0.24 μg/g, conch in the STEER appeared to 

have a slightly higher mercury tissue content than conch 

from south Florida, which averaged 0.01 μg/g in a study 

published by Glazer et al. (2008).

Mercury in Fish. Mercury was detected in all fi sh tissues 

in the STEER with body burdens ranging from 0.050 μg/g 

to 0.502 μg/g and a mean concentration of 0.255 ± 0.056 

μg/g (schoolmaster snapper 0.295 ± 0.061 μg/g, longspine 

squirrelfi sh 0.214 ± 0.100 μg/g) (Table 7.8). The highest 

concentration of mercury in fi sh tissues in the STEER was 

found in the squirrelfi sh caught at site SQ-S2 (0.502 μg/g) 

followed by the snappers caught at site SN-S1 (0.466 μg/g). 

The mean concentration of mercury was elevated relative 

to the mean concentration of mercury in fi sh from Vieques, 

Puerto Rico (Table 7.9). Relative to the coral and conch 

tissues that were measured, there was more mercury in fi sh 

tissue in the STEER.

Using the laboratory recorded percent dry and percent 

moisture for each sample, a wet weight concentration of 

mercury for each sample was calculated for comparison to 

EPA’s recreational fi shers recommended screening values 

(SVs) (EPA, 2000). Based on the SV of 0.4 μg/g methyl 

mercury, none of our total mercury (methyl mercury plus 

inorganic mercury) concentrations exceeded the threshold. 

According to Kannan (1998), methyl mercury makes up 

83% of total mercury in marine organisms. 

Due to the low number of fi sh collected from the STEER,

comparison between individual strata was not possible.

However, by pooling the strata into two groups, Western

(strata 1 and 2) and Eastern (strata 3, 4, and 5), a 

comparison was possible. Using a non-parametric 

Wilcoxon test, concentrations of mercury in pooled fi sh 

tissues were signifi cantly higher in fi sh from the Western 

region than the Eastern region (p-value = 0.0253). While no 

guidelines for mercury were exceeded in sediments from 

the STEER, the same spatial pattern of the Western region 

being signifi cantly higher than the Eastern region exists 

in sediments as it does for fi sh (nonparametric Wilcoxon, 

p-value = 0.0012). For the coring portion of this study (see 

Chapter 5), surfi cial sediments in Benner Bay (BB-2) were 

an order of magnitude higher than those nearby suggesting 

that, while below all guidelines and thresholds, Benner Bay 

may be a source of mercury for the STEER.

Mercury has no known biological function, and is 

hazardous to exposed organisms. Accumulation of mercury 

at high concentrations in aquatic systems can pose serious 

Figure 7.13. Concentrations (mean ±SE) of metals detected in the conch Lobatus gigas. 

0

100

200

300

400

500

600

700

800

900

1000

Al Cu Fe Mn Zn

μg/g dry weight (conch tissue)
STEER Integrated Environmental Assessment Report

164Chapter 7: Contaminants in Coral, Conch and Fishenvironmental threats to wildlife (EPA, 1997; Murphy et 

al., 2008). Signs of neurological effects including abnormal 

behavior, convulsions, reduced fi tness and death, have 

been observed in wildlife exposed to mercury (EPA, 1997; 

Murphy et al., 2008). 

Manganese 

Manganese in Coral. Manganese body burdens in P. 

astreoides varied from a minimum value of 7.25 μg/g to a 

maximum value of 19.6 μg/g (Table 7.4b). In the STEER, 

manganese was detected in all the coral samples, with the 

maximum concentration measured in stratum 2. Manganese 

concentrations were similar in range to reported values 

in P. astreoides from Puerto Rico (Table 7.4b). However, 

these values were nearly an order of magnitude higher 

than concentrations reported in Misima Island, Papua New 

Guinea, Ulan Reef, Philippines, and Daya Bay, China 

(Table 7.4b). With a mean body burden value of 10.1 μg/g, 

manganese had the third highest elemental concentration in 

coral after iron and aluminum. 

Accumulation of metals in coral tissue refl ects the 

environmental condition, and because manganese is also 

considered a marker of terrigenous metal inputs in the 

aquatic environment (Chen et al., 2010), manganese-tometal ratio in coral tissue could indicate possible metal 

enrichment. A non-parametric Spearmen correlation test 

indicated that, in the STEER, with the exception of lead, all 

other metals were correlated with manganese (Figure 7.14). 

However, because there were no such positive correlations 

with aluminum and iron, which are also terrigenous marker 

elements, the indication is that rather than enrichment, lead 

along with the other metals are of natural origin. More 

research is needed to understand uptake processes of metals 

in coral species. 

Manganese in Conch. In L. gigas, manganese was also 

detected in all samples. The highest concentration detected 

was 355 μg/g, in conch from stratum 2 (Table 7.7). There 

does not currently appear to be any research available on 

the effects of manganese in conch. 

Manganese in Fish. Manganese was detected in all fi sh 

sampled in the STEER with body burden concentrations 

ranging from 1.94 μg/g to 3.48 μg/g and a mean 

concentration of 2.52 ± 0.49 μg/g (schoolmaster snapper 

2.73 ± 0.28 μg/g, longspine squirrelfi sh 2.32 ± 0.18 μg/g) 

(Table 7.8). The highest concentration of manganese found 

in fi sh tissues in the STEER was in the fi sh caught at site 

SN-S3. The mean manganese concentration was elevated 

relative to the mean concentration of manganese found in 

fi sh tissues from Vieques, Puerto Rico (Table 7.9). On a 

STEER-wide basis, there was less manganese in fi sh tissue 

than in both coral and conch.

Manganese can be toxic to aquatic organisms (Reimer, 

1999). The most manganese sensitive aquatic organism that 

Reimer (1999) studied had a 48 hour LC50 at 0.8 mg/L 

manganese while the majority of other aquatic fi shes had 

LC50s between 2.1 mg/L up to 94 mg/L.

Nickel

Nickel in Coral. Body burdens of nickel in coral tissues 

ranged from zero to a maximum value of 8.33 μg/g, found 

at the HBI42A in stratum 5. Nickel was detected in all coral 

samples with concentrations that were elevated relative to 

other trace metals measured (Figure 7.10). Whitall et al. 

(2011) reported a maximum body burden of 6.84 μg/g in P. 

astreoides for nickel, indicating that concentrations found 

in the STEER were within the regional range. 

Reichelt-Brushett and Harrison (2005) exposed the gametes 

of Goniastrea aspera to nickel concentrations ranging 

from 5 to 2,000 μg/L. Concentrations of nickel at or above 

100 μg/L resulted in decreased fertilization success. In 

another study, Goh (1991) exposed larvae of the coral 

Pocillopora damicornis to nickel. The larvae were exposed 

to concentrations ranging from 1 to 25 mg/L (ppm) for 

durations of 12 to 96 hours. After the exposure, the larvae 

were placed in natural fi ltered seawater, and settlement 

success was followed over a period of days. Goh (1991) 

found signifi cantly lower settlement success of the larvae 

nine days after the recovery period in all concentrations, 

regardless of the duration of the treatment. In experimental 

settings, nickel was found to cause serious toxicity to 

sea anemones Condylactis gigantea and Stichodactyla 

Figure 7.14. Scatter plot showing relationship between manganese and lead in coral. 
STEER Integrated Environmental Assessment Report

165Chapter 7: Contaminants in Coral, Conch and Fish

helianthus (Shimek, 2008). The author reported that nickel 

ambient concentrations as low as 4 ppb could induce 

sublethal effects such as reduced carbonic anhydrase 

activity. Sea anemones are sometimes used as a lab model 

for coral (Tolleter et al. 2013).

Nickel in Conch. Body burdens of nickel in conch tissues 

ranged from 3.03 μg/g to 13.6 μg/g (Table 7.6). Nickel was 

detected in conch from all strata. The mean concentrations 

of nickel in L. gigas tissue by stratum are shown in Table 

7.7. While in all other strata, nickel body burdens in conch 

were fairly similar, relative to the STEER-wide mean, high 

nickel concentrations (~14 μg/g) were observed in stratum 

4. Glazer et al. (2008) reported concentrations of 9.59 

μg/g ww in conch from the nearshore coastal environment 

in Florida. Using the measured 76% moisture content in 

conch, we derived a maximum wet weight value of 3.4 

μg/g, indicating that nickel concentrations in conch from 

the STEER were low relative to values reported by Glazer 

et al. (2008). For nickel, the FDA action level in shellfi sh 

of 80 μg/g (ww), is much higher than the wet weight 

nickel concentration of 3.4 μg/g derived for conch from the 

STEER. 

Nickel in Fish. Nickel was detected in all fi sh sampled in 

the STEER with body burdens ranging from 0.911 μg/g 

to 10.1 μg/g and a mean concentration of 2.57 ± 1.09 

μg/g (schoolmaster snapper 3.76 ± 2.13 μg/g, longspine 

squirrelfi sh 1.39 ± 0.20 μg/g ) (Table 7.8). The highest 

concentration of nickel found in fi sh tissues in the STEER 

was in the fi sh caught at site SN-S3. The mean nickel 

concentration was the same as that in Vieques, Puerto 

Rico (Table 7.9), and was higher than the mean nickel 

concentration in coral but lower than that of conch.

Nickel toxicity in aquatic organisms varies by species 

with the concentration necessary to cause negative effects 

decreasing as exposure time increases (Eisler, 1998b; 

Svecevicius, 2010). Eisler (1998b) found that for most 

non-human mammals, concentrations of nickel in the liver 

above 3.0 μg/g and 10.0 μg/g in the kidneys was evidence 

of signifi cant nickel exposure. Our highest concentration 

of 10.1 μg/g falls above those ranges, but represents whole 

body burden nickel and is not tissue specifi c. Nickel 

concentrations above 40 μg/L, have no effect on larval or 

embryonic survival in fi shes, but have been shown to delay 

hatching time (Eisler, 1998b).

Lead

Lead in Coral. Lead body burdens in P. astreoides from 

the STEER ranged from 0.07 μg/g to 0.42 μg/g (Table 

7.4b). With a mean value 0.16 μg/g, lead was detected 

in coral from all fi ve strata (Table 7.5). The highest lead 

concentration in P. astreoides from the STEER was found 

at HBI28P (0.415 μg/g ). A lead body burden as high as 

12.50 μg/g was reported in P. astreoides from Jobos Bay, 

Puerto Rico (Whitall et al., 2011). However, other studies 

in southwest and Vieques, Puerto Rico have reported lead 

mean values of below detection to 0.07 in P. astreoides

(Pait et al., 2009 and 2010). In a laboratory experiment, 

Reichelt-Brushett and Harrison (2004) demonstrated that 

a seawater concentration of lead of 2,900 μg/L seriously 

impacted coral larvae survival. When lead concentrations 

in water exceeded 500 ppb, enzymes needed for 

photosynthesis in the algae were inhibited (Taub, 2004).

Lead in Conch. The lead body burden in L. gigas from 

the STEER ranged from 0.21 μg/g to 1.32 μg/g (Table 

7.6). With a mean value of 0.61 μg/g, lead was detected in 

conch from all fi ve strata (Table 7.7). The highest lead body 

burden in conch from the STEER was found in stratum 2 at 

1.32 μg/g. In a 48h laboratory study, toxicity of lead to the 

shellfi sh Meretrix meretrix embryogenesis was observed 

with an EC50 of 297 μg/L in water (Wang et al. 2009). The 

FDA action level for lead in molluscan shellfi sh is 1.7 

μg/g (ww). Using the measured 76% moisture content in 

conch, we derived an equivalence maximum value of 0.33 

μg/g lead ww, indicating that lead concentrations in conch 

from the STEER were lower than the FDA action level for 

shellfi sh. 

Lead in Fish. Lead was detected in all but one fi sh sampled 

in the STEER at concentrations ranging from 0.086 μg/g 

to 0.027 μg/g and a mean concentration of 0.0865 ± 

0.0268 μg/g (schoolmaster snapper 0.0483 ± 0.0161 μg/g, 

longspine squirrelfi sh 0.1247 ± 0.0459 μg/g ) (Table 7.8). 

The highest concentration of lead found in fi sh tissues in 

the STEER was at site SQ-S4. Lead tissue concentrations 

in the STEER appear to be on the low end of the normal 

range of coastal marine fi shes in the U.S. (Eisler, 1988). 

Mean lead concentrations in the STEER were an order of 

magnitude lower than those in Vieques, Puerto Rico (Table 

7.9) and were also lower than mean concentrations found 

in coral and conch in the STEER. Rainbow trout (Salmo 

gairdneri) had an LC50 at 72 hours after exposure to 3.5 

μg Pb/L of water (Eisler, 1988). Other deleterious effects of 

high concentrations of lead on fi sh include anemia, reduced 

stamina, vertebral deformities, caudal fi n erosion, and 

inhibition of hatching (Eisler, 1988).

Selenium

Selenium in Coral. The body burden of selenium in P. 

astreoides varied from zero to 0.12 μg/g. Selenium was 

only detected in coral samples from stratum 3 (Table 7.5). 
STEER Integrated Environmental Assessment Report

166Chapter 7: Contaminants in Coral, Conch and FishSimilar concentration values were observed elsewhere in P. 

astreoides from the Caribbean (Pait et al., 2009 and 2010; 

Whitall et al., 2011). 

Selenium in Conch. Selenium body burdens in L. gigas 

varied from 0.68 μg/g to 2.38 μg/g in the STEER (Table 

7.6). The highest selenium concentration was found in 

stratum 5 (Table 7.7). There is no FDA action level for 

selenium in shellfi sh tissue.

Selenium in Fish. Selenium was detected in all fi sh 

tissues in the STEER and ranged from 1.18 μg/g to 

9.84 μg/g with a mean concentration of 2.69 ± 1.03 

μg/g (schoolmaster snapper 1.71 ± 0.14 μg/g, longspine 

squirrelfi sh 3.67 ± 2.06 μg/g ) (Table 7.8). The highest 

concentration of selenium found in fi sh tissues in the 

STEER was in snappers caught at site SQ-S2 and exceeded 

the EPA selenium criterion (EPA, 2015). It is important to 

note that the EPA criterion is for freshwater fi sh, but there 

currently is no EPA selenium criterion for saltwater fi sh. All 

other measured selenium detections in fi sh were below the 

EPA freshwater selenium criterion of 8.0 μg/g dry weight. 

Mean selenium concentrations in the STEER were similar 

to those found in fi sh tissues in Vieques, Puerto Rico (Table 

7.9). However, elevated concentrations were found in coral 

and conch tissues in the STEER. High concentrations of 

selenium (> 50 μg/L) in water an cause adverse effects to 

aquatic organisms (Taylor et al., 1992), and exposure to 

fi sh larvae can cause skeletal anomalies, decreased growth, 

and mortality (Newman and McIntosh, 1991). Studies 

in both marine and fresh water show mortality and other 

adverse effects at or above 50 ug/L selenium (Hamilton 

et al., 1986; Phillips, 1988). Some data indicate effects at 

lower concentrations, for example hematological effects in 

freshwater trout (15-53 ug/L) (Hodson et al., 1980).

Zinc

Zinc in Coral. In the STEER, P. astreoides body burdens 

ranged from 1.87 μg/g to a maximum value of 14.8 

μg/g (Table 7.4b), with an overall average of 5.98 μg/g. 

Zinc was detected in all fi ve strata (Table 7.5). Zinc 

body burdens in P. astreoides from the STEER were 

similar to reported values (Table 7.4b). Mean zinc body 

burdens of 6.09 μg/g and 8.59 μg/g were reported by 

Pait et al. (2009) and Whitall et al. (2011) in P. astreoides

from southwest Puerto Rico and Jobos Bay, Puerto 

Rico, respectively. These published data indicate that 

zinc concentrations found in the coral from the STEER 

are within the concentration ranges seen in the region. 

However, higher zinc body burdens (Table 7.4b) have been 

reported elsewhere in Punta Brava, Venezuela (Bastidas 

and Garcia, 1999), Misima Island, Papua New Guinea 

(Fallon et al, 2002), and Dafangji Island, China (Peng et 

al. 2006). Zinc is an essential element, however at elevated 

concentrations, it can be toxic to coral (Chen et al., 2010). 

Several studies have linked excess zinc to harmful effects 

in zooxanthellae (Goh and Chou, 1997) and fertilization 

impairments in coral (Reichelt-Brushett and Harrison, 

2005).

Zinc in Conch. In the STEER, L. gigas body burdens 

ranged from 170 μg/g to a maximum value of 1,320 μg/g 

(Table 7.6). With an overall average of 484 μg/g, zinc was 

detected in all fi ve strata (Table 7.7). Concentration ranges 

of 40.4 μg/g to 874 μg/g have been reported in L. gigas 

from south Florida (Glazer et al. 2008), indicating that zinc 

concentrations found in conch from the STEER are within 

the concentration range seen in Florida. Zinc has been 

associated with reproductive inhibition in mollusks. Spade 

et al. (2010) reported that zinc concentrations of 84 μg/g 

in testis have been linked to testis regression in gastropods 

such as L. gigas from the Florida Keys. 

Zinc in Fish. Zinc was detected in all fi sh tissues in the 

STEER and ranged from 25.3 μg/g to 217 μg/g with a 

mean concentration of 65.79 ± 22.0 μg/g (schoolmaster 

snapper 40.75 ± 1.73 μg/g, longspine squirrelfi sh 90.83 

± 40.87 μg/g ) (Table 7.8). The highest concentration 

of zinc found in fi sh tissues in the STEER was in the 

snappers caught at site SQ-S2. Mean zinc concentrations 

in the STEER were an order of magnitude higher than 

those found in fi sh tissues in Vieques, Puerto Rico (Table 

7.9), and in coral tissues in the STEER. Mean zinc 

concentrations in conch were higher than those found in 

fi sh however.

7.4. CONCLUSIONS

In general, organic contaminant concentrations in the tissues of coral, conch, and fi sh in the STEER appeared to be 

relatively low, and similar to results seen in other studies 

from the region. A signifi cant correlation between higher 

TBT concentrations closer to shore (inshore vs. offshore) 

existed for both coral and conch. The correlation was not 

signifi cant for fi sh tissues. Total butyltins in fi sh tissues 

were signifi cantly higher than those found in coral (nonparametric Kruskal-Wallis, p-value = <0.0001) but not 

conch, yet did not seem to follow the spatial patterns observed in sediments. This may be a factor of the number of 

fi sh we were able to collect or the temporal difference between when the sediments and fi sh tissues were collected, 

among other confounding factors. The percentage of TBT 

as compared to its breakdown products DBT and MBT in 

fi sh tissues was signifi cantly higher in schoolmaster snapper than in longspine squirrelfi sh, possibly pointing to long-
STEER Integrated Environmental Assessment Report

167Chapter 7: Contaminants in Coral, Conch and Fish

spine squirrelfi sh being more effi cient at breaking down 

TBT into its metabolites than schoolmaster snapper.

With the exception of the fi sh caught at SQ-S2, total PCBs 

concentrations in the tissues of fi sh caught in the STEER 

were generally an order of magnitude lower than those 

observed by NS&T in the round gobi caught in the Great 

Lakes. The fi sh at site SQ-S2 had a sum total PCB value of 

150.9 ng/g wet weight (419.2 ng/g dry weight) which exceeded EPA’s screening value for noncarcinogenic PCBs of 

80 ng/g wet weight (EPA, 2000).

Trace and major elements are incorporated into corals, 

conch, and fi sh tissue by a variety of pathways. In coral, 

metal accumulation can occur by direct replacement of calcium by dissolved metals in the aragonite lattice, inclusion 

of detritus materials into skeletal pore spaces, uptake of 

organic materials, incorporation of metals into coral skeletons, or coral feeding (Howard and Brown, 1984). Bioaccumulation of metals in conch can occur via exposure to 

dissolved metals in the gills, through feeding, and by direct 

contact through the skin. Conch have been shown to ingest 

considerable amounts of sediment particles (Brownell and 

Stevely, 1981). It has been observed that corals (David, 

2003; Chen et al., 2010) and conch (Glazer et al., 2008 and 

Said et al., 2013) from polluted areas show much higher 

concentrations of trace metals in their tissues than corals 

from unpolluted areas. In the STEER, the most elevated 

metal concentrations in corals (skeleton and tissue) were 

found in strata 1 and 2, which are the strata where sediments had the most elevated concentration of metals (see 

Chapter 4). This pattern was not observed in conch. The 

most elevated metal concentrations seen in conch were 

from stratum 4 instead of strata 1 and 2, where elevated 

metal concentrations were seen in sediment. It is unclear 

why there is a difference in the relative metals concentrations in conch tissues as compared to coral and fi sh. Based 

on the concentrations of metal body burdens found, the coral and conch tissues do not appear to be very contaminated. 

Since there are currently no ecotoxicity thresholds, and the 

fact that trace and major element concentrations were similar to published data from many other coastal areas in the 

Caribbean, we conclude that concentrations of the trace and 

major elements in the coral and conch tissue were background concentrations. More research is needed to understand ecotoxic processes of metals in coral species.

Trace and major elemental contamination in the tissues of 

fi sh were not able to be statistically analyzed by individual 

stratum due to the low number of samples collected. For 

mercury there appears to be signifi cantly higher mean concentrations in the western region (pooling strata 1 and 2) 

than in the eastern region (pooling strata 3, 4, and 5). Mean 

metals concentrations in the tissues of all fi sh in the STEER 

were comparable to those found in Vieques, Puerto Rico by 

ATSDR (2003) with the exception of chromium, copper, 

iron, lead, and zinc which had means an order of magnitude 

higher than those found in Vieques. No metal concentrations in any fi sh tissue exceeded any health guidelines or 

thresholds.

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171Chapter 7: Contaminants in Coral, Conch and Fish

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172Chapter 7: Contaminants in Coral, Conch and Fish
173Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

CHAPTER 8: HISTOLOGICAL EXAMINATION OF CORAL TISSUE SAMPLES FROM ST. THOMAS 

EAST END RESERVES (STEER), USVI

Esther C. Peters, Ph.D.

Principal, Pathobiology Consulting Services, 4107 Parkedge Lane, Annandale, VA 22003

8.1. INTRODUCTION

Samples of the coral Porites astreoides (Figure 8.1) were 

obtained from the same sites and colonies from which the 

coral tissue samples were taken for chemical contaminant 

analyses (see Chapter 7). Sampling sites were located on 

a transect from most suspected contaminant exposure near 

the Bovoni Landfi ll (Stratum 1), nearshore shallow Benner Bay (Stratum 2) and Nazareth Bay (Stratum 3), to least 

exposure in deeper water Jersey Bay (Stratum 4) or shallow 

Great Bay (Stratum 5). 

This encrusting to massive species is widespread and considered to be relatively hardy (Szmant 1986; Fauth et al., 

2011); it was found in varying abundances at the STEER 

stations. This species has also been used in recent studies on biomarkers of contaminant or stressor exposure (by 

measuring physiological or biochemical changes) indicating 

functional or molecular changes (Downs et al., 2011, Fauth 

et al., 2011, Kenkel et al., 2011). 

Changes in an organism’s health can also be evaluated using histopathological examination, a biomarker of effect, 

based on microscopic anatomy that is related to changes in 

molecular composition and function of the cells and tissues 

(Yevich and Yevich 1994; Jagoe 1996; Peters et al., 2005). 

Some histological studies of P. astreoides have been conducted to describe its structure, reproduction, and suspected 

diseases (Peters, 1984a, 1984b; Szmant, 1986; Chornesky, 

and Peters, 1987). Toxicant exposures are anticipated to 

affect this coral’s health, which might be refl ected in its microscopic anatomy (structure = function), since other coral 

species have been adversely affected by fi eld and laboratory exposures to oil hydrocarbons, heavy metals, and pesticides, as well as sedimentation (e.g., Peters et al., 1981, 

Peters and Pilson 1985; Peters et al., 1997; Downs, 2005; 

Downs et al., 2005, 2006; Rotchell and Ostrander, 2011).

Downs et al. (2011) identifi ed site-specifi c changes in cellular-stress marker proteins in P. astreoides sampled from St. 

John, U.S. Virgin Islands, indicating DNA lesions, which 

were associated with polyaromatic hydrocarbons (PAHs), 

biocides, and semi-volatile organochlorines, as well as fecal contamination. These were not detected in their control 

population, furthest removed from anthropogenic activities. Fauth et al. (2011) collected samples of P. astreoides

Figure 8.1. Map of the St. Thomas East End Reserves showing site locations (in red circles) where the samples for histopathological 

examination were collected in June 2012. Coral samples for tissue chemistry analyses were also collected at all sample sites.
174Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

from sites near an ocean 

outfall, inlets, and reefs 

off Broward County, 

FL, and also observed 

increased frequencies 

of DNA damage and 

higher concentrations of 

the antioxidant enzymes 

catalase and copper/zinc 

superoxide dismutase 

at mid-water stations 

near Port Everglades 

and Hillsborough Inlets, 

and an overall indication 

of intermittent, chronic 

stress from land-based 

sources of pollution. 

However, no histopathological examinations 

were included in those 

reports. 

8.2. METHODS

Samples of P. astreoides were collected by 

NOAA divers from fi ve 

sites (Figure 8.1) in the 

STEER on June 18 and 

June 22, 2012, according 

to “Standard Operating 

Procedure: Collecting 

Coral Samples with a Coring Tube for Histology”, provided by the author of this chapter. One or two cores were 

obtained from each coral colony (“head”) by driving a 

2.2-cm diameter stainless steel coring tube into the colony 

with a sledge hammer and placing the tube and sample into 

a clean labeled 50-mL plastic centrifuge tube with ambient 

seawater. In some cases, portions of a colony were removed 

by chisel and sledge hammer and placed in a tube. On return to the surface, the seawater was replaced with fi xative 

solution, 1 part Z-Fix Concentrate (Anatech, Ltd.) mixed 

with 4 parts 35 ppt seawater prepared from marine salts and 

deionized water (about 4% formaldehyde). 

Sample Preparation

The 44 samples from 23 coral colonies (specimens) were 

left in the fi xative, shipped to Dr. Peters at George Mason University (GMU), and received on June 26, 2012. 

Samples were photographed in the laboratory (Figure 8.2) 

and then decalcifi ed using ImmunocalTM, a 5% formic acid 

decalcifying solution, to remove the aragonite exoskeleton 

from the polyps. Some samples needed only 24 hours to 

completely decalcify, but most required 48–72 hours. 

Endolithic algae and fungal fi laments and sponge tissue 

remaining with the sample were removed only when it was 

easy to do so (most samples had visible endolithic communities).When decalcifi ed, samples were put in a running tap 

water rinse bath for 30 minutes or more to remove the solution and placed in 70% undenatured ethanol. Each sample 

was trimmed into three or more pieces to fi t into one or two 

tissue processing cassettes. 

The approximate locations where the tissue was sectioned 

were marked on the gross undecalcifi ed images which 

had been printed out to document the trimming. For those 

samples that had broken into pieces when collected in the 

fi eld, the largest piece(s) were retained; smaller ones were 

discarded as they were probably damaged, and grossly 

damaged margins were trimmed away when feasible. In 

general, one or more 2–3 mm wide strips were cut from the 

middle of the sample core for examining the polyps sagittally, and the ends of the core were placed in the cassette 

oral and aboral sides up to prepare cross (transverse) sections of the polyps. 

Figure 8.2. Examples of fi xed coral samples as photographed in the GMU Histology Laboratory. (a) 

MLC 01 Head 1, small portion from edge of colony, note abundant algae underneath the sample. (b) 

HBI 15P Head 5 B, intact core sample. (c) HBI 23P Head 2A, two pieces received, note surface mucus 

and sediment on larger piece, and green endolithic community (d) HBI 23P Head 3B, three smallest 

shattered pieces were discarded, two largest pieces were decalcifi ed and trimmed for embedding, slides 

read but data not used in fi nal evaluation, because the other core from the colony was intact.
175Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

Tissue samples were processed through a graded series of 

diluted undenatured ethanol (two changes of 70%, one each 

of 80% and 95%), three changes of 100% reagent alcohol, 

three changes of SafeClear II (xylene substitute), and three 

changes of molten Paraplast® Plus. They were then embedded in Paraplast® Xtra in stainless steel molds and cooled 

to solidify into blocks. Blocks were sectioned on a rotary 

microtome set at 5-μm thickness. Sections were fl oated 

on a warm-deionized water bath and one or two sections 

were mounted on clean microscope slides. Two slides were 

prepared from each block. The fi rst slide for each block was 

stained with Harris’s hematoxylin and alcoholic eosin procedure (H&E) and coverslipped with PermountTM mounting 

medium. The second slide was stored unstained, if needed 

for a special staining procedure later.

The H&E-stained histoslides were examined with a Zeiss 

microscope and photomicrographs were taken using an 

attached Nikon COOLPIX 5000 camera. Histoslides of P. 

astreoides collected from reference sites (Jamaica, Belize, 

1980s) were used to develop the “within normal limits” 

criteria for coral tissue condition and zooxanthellae condition/abundance scores, specifi c parameters thought to 

indicate sampling damage or exposure to environmental 

stressors, and suspect parasites or pathogenic microorganisms (protozoans from the phylum Apicomplexa and bacterial aggregates previously reported in this species, Peters, 

1984; Rickettsiales-like bacteria, Casas et al., 2004, C. S. 

Friedman, pers. comm; and three “unknowns”). Sections 

were fi rst scanned at 100x magnifi cation to obtain data on 

larger features (e.g., general condition, epidermal ruptures, 

gonads, planulae, endolithic organisms) and then scanned at 

250x to obtain data on smaller features (e.g., zooxanthellae 

condition, epithelial necrosis, suspect bacteria, protozoan 

parasites). 

Sample Analysis

Semi-quantitative data were collected from each sample 

based on relative condition (0=Excellent, 1=Very Good, 

2=Good, 3=Fair, 4=Poor, 5=Very Poor) or the severity or 

intensity of tissue changes from normal (0=Within Normal Limits, 1=Minimal, 2=Mild, 3=Moderate, 4=Marked, 

5=Severe). The extent of the lesions was also recorded 

(1=Focal, 2=Multifocal, 3=diffuse or systemic). Only presence was recorded for the three “unknowns” (unusual cells 

or metazoans whose identity is unknown and were rarely 

found). 

The developmental stages of gonads were noted and number of planulae in the sections were counted, if present. 

The criteria for these data are presented in Table 8.1. Data 

for each colony sample were entered into a spreadsheet, 

grouped by Stratum. The approach for analyzing the data 

was simply exploratory, because no one has done this sort 

of histopathological examination of a population of P. 

astreoides to determine effects of environmental stressors 

on the coral. A mean score for each parameter for each 

colony was calculated from the observations made on the 

two cores (A and B) or from multiple histoslides of tissue 

sections, if available, but damaged (broken) core scores 

were not used. 

For gonad development and “unknowns,” percentage of 

colonies containing gonads, planulae, or “unknowns” in 

each stratum were determined. For changes related to 

suspect sampling damage, epidermis, gastrodermis, calicodermis, skeleton, and suspect apicomplexa, the severity was 

multiplied by the extent to obtain a fi nal score in the range 

of 0–15 (= not present to the most severe and widespread) 

for each parameter. These fi nal scores were summed for 

each sample to provide a Specifi c Condition Scores Sum 

as an indicator of the colony’s health status. Means and 

standard deviations were calculated for the scores for each 

parameter from the samples for each Stratum. The frequency distributions of data for all the colonies sampled from 

the STEER were plotted to determine whether the scores 

were normally distributed. 

Quality Assurance and Quality Control

Preparation of the histoslides included frequent checks that 

samples had been carried through all steps of the procedures, including gross photography (images were retaken if 

they were not in focus), decalcifi cation and trimming (damaged fragments were noted and some discarded, marked on 

the trimming sheets), processing and embedding (clearing 

and infi ltration with paraffi n occurred, tissues placed in bottom center of molds as they had been trimmed into the

cassettes), microtomy (sectioned at 5 microns, one section 

mounted on each of two microscope slides, dried), and 

staining with H&E (procedure followed and staining quality of each rack checked microscopically). 

Histoslides were briefl y reviewed for staining quality and 

to detect any lesions that should be included in the spreadsheet for analysis. Then each sample was examined in 

more depth to record lesion and reproduction data. Sections 

were viewed at 100x to note general condition and zooxanthellae distribution, then at 250x to detect lesions, and 

400x to confi rm observations. After recording the data for 

all histoslides, the spreadsheet columns were adjusted to 

separate lesions that were probably associated with sample 

collection and handling from those that might be indicative 

of site-specifi c stressors. Randomly selected histoslides 

were reexamined to confi rm the data or make corrections 
176Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

Table 8.1. Characteristics and scoring of changes noted in cells and tissues using light microscopic examination of P. astreoides

samples collected during this study.

Parameter Viewed at 100x or 

250+x, Description of “Normal”

0 (No Change) 12345

Low Magnification Very Good Good Fair Poor Very Poor

General Condition

0 = Excellent, similar to reference 

samples, thick and intact epithelia 

and mesoglea, highly cellular, 

polyp and coenenchyme 

architecture well developed

Similar to reference 

samples, but epithelia and 

mesoglea not as thick, 

epidermal mucocytes 

slightly hypertrophied

Hypertrophy of epidermal 

mucocytes, intact epithelia 

and mesoglea not 

attenuated, mesentery and 

filament architecture still 

normal

Hypertrophy of epidermal 

mucocytes, minimal to mild 

attenuation of epithelia and 

mesoglea noted, damage to 

epithelia noted (lysing cells)

Loss of mucocytes, 

moderate attenuation of 

epithelia and mesoglea, 

mesentery and filament 

architecture degenerating, 

vacuolation of basal body 

wall epithelia

Severe attenuation of 

epithelia and mesoglea, 

vacuolation of mesogleal 

pleats, necrosis and 

dissociation of mesenterial 

filaments, necrosis and 

lysing of epithelial cells

Zooxanthellae

0 = Gastrodermal cells packed 

with well-stained algal symbionts in 

surface body wall, tentacles; 

scattered algal symbionts deeper 

in gastrovascular canals

Similar to reference 

samples, slightly fewer wellstained algal symbionts in 

gastrodermis of surface 

body wall, tentacles, and 

scattered cells in 

gastrovascular canals

Layer of well- stained algal 

symbionts, but less 

abundant than in reference 

samples

Algal symbionts fewer in 

gastrodermis which is mildly 

attenuated, most still stain 

appropriately, some may be 

degenerating

Even fewer algal symbionts 

in surface body wall 

gastrodermis and in tentacle 

gastrodermis, some have 

lost acidophilic staining as 

proteins no longer produced 

or nucleus/cytoplasm lysed, 

vacuole enlarged compared 

to algal cell

No zooxanthellae present in 

gastrodermis of colony 

(bleached)

Low or High Magnification Minimal Mild Moderate Marked Severe

Melanin-like Granular 

Amoebocytes, Surface Body Wall

0 = None present

One to a few noted in some 

areas of surface body wall 

(epidermis or gastrodermis)

About one-quarter of 

epithelial area contains 

these cells

About half of epithelial area 

contains these cells

About three-quarters of 

epithelial area contains 

these cells

Both epidermis and 

gastrodermis are heavily 

infiltrated by these cells

Melanin-like Granular 

Amoebocytes, Mesenteries and 

Mesenterial Filaments 0 = None 

present

One to a few noted in some 

areas of mesenterial lobes 

or cnidoglandular bands of 

mesenterial filaments

About one- quarter of the 

area of mesenterial lobes or 

cnidoglandular bands 

contains these cells

About half of the area of 

mesenterial lobes or 

cnidoglandular bands 

contains these cells

About three-quarters of the 

area of mesenterial lobes or 

cnidoglandular bands 

contains these cells

Area of both lobes and 

mesenterial filaments 

heavily infiltrated by these 

cells

High Magnification Minimal Mild Moderate Marked Severe

Suspect Sampling Damage, 

Surface Body Wall Ruptures 0 = 

Epithelia and mesoglea intact

One or a few breaks in 

epithelia noted on sagittal 

sections

About one- quarter of area 

of epithelia has gaps with 

missing epithelia and 

mesoglea, mucus discharge

About one-half of area of 

epithelia has gaps with 

missing epithelia and 

mesoglea, mucus discharge

About three-quarters of area 

of epithelia has gaps with 

missing epithelia and 

mesoglea, mucus discharge

Entire surface body wall 

dissociated, extensive 

release of mucus

Suspect Sampling Damage, 

Lysing Gastrodermal Cells 0 = 

Gastro-dermis of

surface body wall and lining basal 

body wall of oral coenenchyme 

gastrovascular canals intact

One or a few areas of 

gastrodermal cells have 

lysed, mucus filling 

gastrovascular canals or 

gastrovascular cavity, 

granular gland cells, 

holotrichous isorhiza 

nematocysts, zooxanthellae 

also released

About one- quarter of the 

areas of gastrodermal cells 

have lysed, mucus filling 

gastrovascular canals or 

gastrovascular cavity, 

granular gland cells, 

holotrichous isorhiza 

nematocysts, zooxanthellae 

also released

About one-half of the areas 

of gastrodermal cells lysed, 

mucus filling gastrovascular 

canals and gastrovascular 

cavities, granular gland 

cells, holotrichous isorhiza 

nematocysts, zooxanthellae 

also released

About three-quarters of the 

area of gastrodermal cells 

lysed, mucus filling 

gastrovascular canals and 

gastrovascular cavities, 

granular gland cells, holotrichous isorhiza 

nematocysts, zooxanthellae 

also released

All gastrodermal cells have 

lysed, mucus filling 

gastrovascular canals and 

gastrovascular cavities, 

granular gland cells, holotrichous isorhiza 

nematocysts, zooxanthellae 

also released

Numerical Score Intensity or Severity Score
177Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

Table 8.1. Characteristics and scoring of changes noted in cells and tissues using light microscopic examination of P. astreoides

samples collected during this study (continued).

Parameter Viewed at 100x or 

250+x, Description of “Normal”

0 (No Change) 1 2 3 4 5

Epidermis, Epidermal Mucocytes 

Hypertrophy

0 = In reference sample, short 

columnar cells, uniform distribution 

and not taller than ciliated 

supporting cells, pale mucus

Slightly hypertrophied, 

numerous, pale- staining 

frothy mucus

Many cells hypertrophied, 

abundant release of palestaining mucus

Uneven appearance of 

mucocytes, some 

hypertrophied but some 

reduced in size and 

secretion, darker staining 

mucus

Some epidermal foci lack 

mucocytes entirely, 

attenuation of epidermis 

evident, darker staining and 

stringy mucus

Loss of many mucocytes, 

epidermis is attenuated to at 

least half of normal 

thickness or more, if mucus 

present stains dark, thick

Epidermis, Necrosis or Apoptosis?

0 = None present

Single cells rarely seen 

having pycnotic or blebbed 

nuclei in the epidermis

Single cell necrosis or 

apoptosis present in about 

one- quarter of area of 

epidermis

Single cell necrosis or 

apoptosis present in about 

one-half of the area of 

epidermis

About three-quarters of the 

area of epidermis contains 

necrotic or apoptotic cells

Complete necrosis of 

epidermis

Gastrodermis, Black Particles in 

Released Mucus of Gastrovascular 

Canals

0 = None present

One or a few black 

spherules present in mucus 

within gastrovascular canals 

of oral region

Cluster of black spherules 

present in mucus within 

gastrovascular canals of 

oral region

Two clusters of black 

spherules present in mucus 

within gastrovascular canals 

of oral region

Three clusters of black 

spherules present in mucus 

within gastrovascular canals 

of oral region

Multiple clusters of black 

spherules scattered in 

mucus with gastrovascular 

canals of oral region

Gastrodermis, Necrosis or 

Apoptosis?

0 = None present

Single cells rarely seen 

having pycnotic or blebbed 

nuclei in the gastrodermis 

(surface body wall or 

elsewhere)

Single cell necrosis or 

apoptosis present in about 

one- quarter of area of 

gastrodermis

Single cell necrosis or 

apoptosis present in about 

one-half of the area of 

gastrodermis

About three-quarters of the 

area of gastrodermis 

contains necrotic or 

apoptotic cells

Complete necrosis of 

epidermis

Calicodermis, Attenuation, Lack of 

Acidophilic Granules 0 = 

squamous to low columnar 

calicodermis, fine acidophilic 

granules of organic matrix proteins 

present

Slight thinning of 

calicodermis or fewer 

acidophilic granules

More variable in thinning of 

calicodermis, fewer 

acidophilic granules, more 

areas affected

Calicodermis squamous, 

fewer acidophilic granules, 

lysing in some areas

Squamous calicodermis, 

necrotic or lysing, no 

acidophilic granules

Loss of calicoblasts along 

mesoglea, necrotic or lysing

Calicodermis, Suspect Bacteria on 

Apical Surface or Necrosis?

0 = None present

Fine basophilic granules 

rarely seen along apical 

surface of calicodermis

About one- quarter of 

calicoblasts attenuated, 

fewer acidophilic proteins in 

cytoplasm, increase in 

basophilic granules on 

surface

About half of calicoblasts 

attenuated, fewer in 

number, thin layer of 

basophilic granules on 

apical surface on about half 

of calicodermis, some nuclei 

may be pycnotic

Most calicoblasts 

attenuated, fewer in 

number, calicoblasts 

cytoplasm basophilic, fine 

darker purple granules 

present, nuclei swollen and 

pale or pycnotic

Calicoblasts attenuated or 

vacuolated, cytoplasm 

basophilic, fine darker 

purple granules present and 

being released from cells, 

forming thick layer, nuclei 

swollen and pale or absent

Skeleton, Endolithic Algae and 

Fungi

0 = None present

A few filaments or suspect 

hyphae (special stain must 

be done to confirm fungi) 

present in subcalicodermal 

spaces where skeleton was 

removed

About one- quarter of 

subcalicodermal space 

where skeleton was 

removed contain filaments 

or suspect hyphae

About half of 

subcalicodermal space 

where skeleton was 

removed contain filaments 

or suspect hyphae

About three-quarters of 

subcalicodermal space 

where skeleton was 

removed contain filaments 

or suspect hyphae

Thick tangle of filaments or 

suspect hyphae present in 

subcalicodermal spaces 

where skeleton was 

removed

Numerical Score Intensity or Severity Score
178Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

Table 8.1. Characteristics and scoring of changes noted in cells and tissues using light microscopic examination of P. astreoides

samples collected during this study (continued).

Parameter Viewed at 100x or 

250+x, Description of “Normal”

0 (No Change) 1 2345

Apicomplexa, Coccidia? Oocysts 

in gastrodermal cells in lobes of 

mesenterial filaments; Sporozoites 

(stage hatching from oocysts) and 

Sporozoa (four-celled organism, 

one cell resembles sporozoite 

nucleus) in gastrodermis of basal 

body wall lining gastrovascular 

canals and polyps

One to a few oocysts, 

sporozoites, or sporozoa 

rarely seen in specific cells, 

deep aboral region of tissue

About one- quarter of 

specific cells in deep aboral 

region contain oocysts, 

sporozoites, or sporozoa, 

scattered

About half of specific cells in 

deep aboral region contain 

oocysts, sporozoites, or 

sporozoa, scattered

About three-quarters of 

specific cells in deep aboral 

region contain oocysts, 

sporozoites, or sporozoa, 

scattered

Specific cells contain one or 

more oocysts, sporozoites, 

or sporozoa throughout 

entire deep aboral region of 

tissue

Bacterial Aggregates in Tentacles 

(Peters 1984)

0 = Not present

One bacterial aggregate in 

mesoglea/ gastrodermis of 

tentacle section of sample 

(rare)

One bacterial aggregate in 

tentacle tissue sections of 

more than one polyp on 

slide (occasional)

Density increases, one 

bacterial aggregate in 

tentacle tissue of all polyps 

on slide (common)

Density increases, multiple 

bacterial aggregates in 

tentacle tissue of polyps on 

slide (frequent)

Numerous bacterial 

aggregates present in 

tentacle tissue, multiple 

adjacent aggregates 

(abundant)

Other Suspect Bacteria (RLOs, 

CGB)

0 = Not present

One infected cell in 

cnidoglandular bands of 

mesenterial filaments of 

sample (rare)

One infected cell in a few 

cnidoglandular bands of 

mesenterial filaments of 

sample (occasional)

One or more infected cells 

in about half of 

cnidoglandular band 

sections of sample 

(common)

Multiple infected cells in 

about three- quarters of 

cnidoglandular band 

sections of sample 

(frequent)

Infected cells in all 

cnidoglandular band 

sections of sample 

(abundant)

Unknown Cells?

Calicodermis/skeleton Unknown 

Metazoan

Skeletal Space Containing “Blobs”

Gonad Staging

0 = None present 1 2 345

Oocytes Single germ cell surrounded 

by mesoglea in mesentery

Early oocyte, nucleus with 

distinct nucleolus but little 

development of lipid and 

protein in cytoplasm

Mid-development, uniform 

distribution of lipid droplets 

and protein granules, 

nucleus and cytoplasm 

enlarge

Mature, development of 

cortical granules and 

vitelline membrane, 

beginning to separate from 

mesoglea

Spawned, hole present 

where ovum released to 

gastrovascular cavity

Spermaries Germ cells aggregate in 

mesoglea, forming one or a 

few clusters

Early spermaries, 

multiplication of germ cells, 

mitotic figures present

More spermaries present, 

spermatocytes undergo 

meiosis, spermatids fill 

lumen

Mature spermatozoa fill 

lumen, may still have earlier 

stages surrounding these, 

but eventually all change to 

spermatozoa

Spawned, remnants of 

spermatozoa endocytosed 

by absorptive gastro- dermal 

cells on mesentery

In spaces where skeleton should be at tips of septa, small (about twice the size of a zooxanthella or about 20 μm), ovoid to irregularly shaped cells 

with pink cytoplasm, single nucleus does not seem to be present, but fine dark purple granules scattered in cytoplasm, have been seen in other 

species (Renegar et al.

2008, Peters unpubl. observ.), unidentified

Numerical Score Intensity or Severity Score

Ovoid multicellular organism, pink cuticle, present in a space adjacent to calicodermis (next to skeleton?), one end appears to be ciliated, seen in 

P. astreoides occasionally from other areas (e.g., Belize, Florida Keys, Peters unpubl. observ.), unidentified

Spherical cells containing two or three cells packed within, each has large dark-staining nucleus, pale pink cytoplasm, multiple paler vacuoles

Unknowns - Presence only noted of these organisms – one to a few seen in some samples
179Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

to the spreadsheet. Photomicrographs of selected structures 

and conditions were taken; a couple of them were sent to 

experts to obtain additional diagnosis insights (the project 

name, species, and sampling locations were not provided to 

the experts). A complete review of the histopathology data 

by another comparative histopathologist (the most common 

QC approach in anatomic pathology) has not been conducted.

Samples that had broken or were grossly visibly damaged 

during collection were removed from the calculations. 

Condition scores between the A and B subsamples were 

usually close in value, if not the same. Calculations were 

rechecked and reviewed.

Statistical Analysis

A single-factor analysis of variance was calculated to 

determine whether the mean parameter scores and condition sums of samples collected for each stratum were equal. 

Because of the small sample sizes and nonnormality of 

some of the data, a Kruskal-Wallis test was also run on the 

Specifi c Condition Scores Sums for each stratum. 

8.3. RESULTS AND DISCUSSION

A total of 23 colonies of P. astreoides were sampled from 

the STEER stations, with duplicate cores or fragments 

obtained from most specimens. The colonies were widely 

scattered at the station nearest to shore, and only three colonies were sampled at this station (MLC 0). Five colonies 

were sampled at each of the other four stations (HBI7P, 

15P, 23P, 28P). On examination of the gross specimens, 

most appeared to be apparently healthy—having a covering of uniformly brown pigmented tissue and polyps, with 

normal morphology for the species and no visible lesions—

and in good condition, except for obvious breakage during 

sampling. Many, however, had mild to moderate mucus and 

sediment particles visible on the tissue surface.

Samples taken from the growing edge of colonies often 

had green fi lamentous or calcifi ed algae attached to the 

skeleton (e.g., Figures 8.2a and 8.2c). After decalcifi cation, 

endolithic fungi, algae, and suspect boring sponge tissue 

were found in most samples, deep within the gastrovascular 

canal region of coenosteum between the polyps. This mat 

community was removed if it could be done easily without 

tearing the coral tissue, because this material often harbors 

siliceous sponge spicules, which can cause knicks in the 

microtome blades and tears in tissue sections. None of the 

sampled colonies were judged to be in excellent condition 

microscopically under low magnifi cation, even disregarding what was probably the result of sampling damage: 

surface body wall ruptures and lysing of gastrodermal cells 

in the oral region of the polyp and coenenchyme tissue 

(Figure 8.3a-d).

It appeared that crushing of the sample margins by the 

stainless steel corers released mucus into the gastrovascular cavity and canals throughout each sample. On closer 

examination, the impact of hitting the corer with the sledge 

hammer caused lysing of gastrodermal cells, largely

mucocytes, which line the basal body wall and gastrovascular canals below the surface body wall. Only the primitive 

connective tissue, the mesoglea, and calicodermis remained 

to mark where the epithelium should have been. The epidermis of the surface body wall was usually thin, resting on 

a thinner layer of mesoglea and having a thicker gastrodermal epithelium underneath it fi lled with zooxanthellae, and 

this surface body wall often remained intact. 

Most samples, however, had multifocal areas of rupture 

of the epidermis and release of mucus, nematocysts, and 

zooxanthellae over the surface from the hammering. No 

changes in zooxanthellae condition were noted at any station (intact, not misshapen, no vacuolation, no necrosis, 

no enlargement of the gastrodermal cell vacuoles containing the algae) and all samples contained these symbiotic 

algae; some colonies might have fewer than others, but 

this could not be reliably detected in the histopathological 

examinations. The relative amount of melanin-like granular amoebocytes (formerly known as chromophore cells, 

Peters, 1984a) was noted for each sample (Figure 8.4), with 

differences found in their distribution. These cells support 

the coral’s immune system (Palmer et al., 2008). Some of 

the samples had high levels of these cells in the epidermis/

gastrodermis and tentacles of the polyps, some had fewer 

cells there but more in the mesenteries and mesenterial fi laments, and in others they were distributed among the basal 

body wall epithelial cells. 

Toward the base of the tissue layer (polyps with associated 

gastrovascular canals) in this perforate coral, these amoebocytes become rounded and dark, indicating that the cells 

have died, and are present within gastrodermal cells of the 

basal body wall as residual bodies, remnants of pigment 

that are only slowly broken down. Although it appears that 

the number and distribution of these cells changes with 

exposure to stressors, such as fungi (Domart-Coulon et 

al., 2006), it could also be related to genetics as individual 

expression of their innate immune system.

The distribution and size of epidermal mucocytes also 

varied greatly, and some samples had markedly hypertrophied mucocytes. This might be related to sedimentation 

(Peters and Pilson, 1985) or contaminant exposure as a 
180Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

response to a 

toxic substance, 

but other studies 

will be needed 

to determine 

this. Probably 

the most unusual 

fi nding was minute particles of 

basophilic cell 

debris in the basal portion of the 

epidermal cells 

or in gastrodermal cells of the 

surface body 

wall, which 

was otherwise 

intact and had 

normal-appearing nuclei in the 

columnar cells 

and mucocytes 

(Figure 8.5). The 

condition of the 

calicodermis 

was often poor, 

degenerating, 

or appeared to 

have basophilic 

debris or suspect 

bacteria on the 

surface of calicoblasts. Occasionally such particles appeared to be sequestered within phagocytic amoebocytes. 

More often, the particles were present in that region and 

did not appear to have been phagocytosed. This could mean 

that mild necrosis of cells was occurring chronically. It 

did not seem to be associated with the sampling damage, 

Figure 8.4. Melanin-like granular amoebocytes (brown cells) infi ltrating between cells of the epidermis and gastrodermis of tentacles (arrow), rated severe (= 5). (a) Sagittal section, 10x. (b) Cross section, 40x.

Figure 8.3. Examples of surface body wall and gastrodermis ruptures and lysing. (a) Intact surface body wall, but 

gastrovascular canal is fi lled with discharged mucus and lysed cells (M) from basal body wall gastrodermis (arrow), 10x. (b) Sagittal view of surface body wall rupture, discharge of mucus containing holotrichous isorhiza nematocysts, zooxanthellae, and cell debris, 10x. (c) Cross-sectional view of gastrovascular cavity and canals fi lled 

with mucus, lysed gastrodermis from basal body wall surrounding an area where skeleton was removed, 10x. (d) 

Lysed gastrodermal cells along mesentery, mesogleal pleats in lower right-hand corner, 40x.

F G
181Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

although a delay in putting the cores into the fi xative might 

begin this process; however, no delay was reported.

Dr. Taylor Reynolds of Johns Hopkins University, a boardcertifi ed veterinary pathologist, was consulted on this 

phenomenon and she noted that mild necrosis and apoptosis 

might be diffi cult to distinguish using light microscopy. 

She further stated, “There is, as you say, single cell necrosis within the epidermis and calicodermis. Within the 

gastrodermis, there is segmental necrosis. The single cells 

undergoing necrosis have not lost membrane integrity, but 

have several nuclear blebs which are each 1/3 to 1/10 the 

size of an intact nucleus. These cells are sometimes also 

swollen. Typically, an apoptotic cell has nuclear blebbing, 

and is also shrunken, instead of swollen. It is very diffi cult 

to make the distinction between apoptosis and necrosis 

using light microscopy. I would indicate in the report that 

there are individual cells undergoing necrosis / apoptosis, 

within otherwise normal epidermal and calicodermal layers. 

Within the segments of necrotic gastrodermis, there is loss 

of cells and scant evidence of nuclear remnants, i.e. the

necrosis in this region is more pronounced.”

The calicodermis, the epithelium forming the aragonite 

exoskeleton of the coral on the basal body wall of the 

polyps and gastrovascular canals, should appear as a squamous, but substantial layer (Figure 8.6a) and the calicoblasts should contain fi ne acidophilic granules (believed to 

be proteins for the organic matrix of the skeleton) (Figure 

8.6b). It should be cuboidal to short columnar in areas of 

more active calcifi cation (Figure 8.6c). In multiple samples, 

the calicoblasts were attenuated, lacked the acidophilic 

granules, or were lysing (Figure 8.6d). Sometimes the epithelium had small circular spots of basophilic material on 

cell surfaces (possibly staining this way due to an association with calcium and a degenerative process); in some cases darker basophilic-staining coccoid masses were associated with the surface of this epithelium (possibly bacteria). 

Dr. Reynolds noted that the cells were undergoing necrosis. 

Because of the high levels of boring endolithic fungi in the 

skeleton, and suspect apicomplexan parasites burrowing 

in the epithelium with associated vacuolation and necrosis 

within the gastrodermis, the calicodermal condition might 

have been related to these stressors. Although the mechanism of action is uncertain, any susceptibility of cells to 

mechanical or toxic stress could lead to necrosis, and then 

lysing of the other epithelium (the gastrodermis) could occur as enzymes were released by the degrading cells.

As has been noted in recent literature, the coral holobiont—

all of the associated organisms living on, within tissues, or 

boring through the skeleton—must be taken into consideration (Wegley et al., 2007). In this study, zooxanthellae, 

bacterial aggregates (Figure 8.7a and b) (Rohwer et al.,

2002), endolithic pigmented or nonpigmented fungi or 

fi lamentous algae (Figure 8.7c and d) (e.g., Ostreobium 

quekettii), boring sponges, suspect apicomplexan protozoan parasites (Upton and Peters 1986), and other suspect 

bacteria were seen in tissue sections. The role of most of 

these organisms is unknown. Although the bacterial aggregates of Porites spp. have not been associated with any 

tissue damage (Peters, unpub. observ.), observations made 

during this study and others indicated that the protozoans, 

fungi, and suspect RLOs can be detrimental to the coral 

(Upton and Peters, 1986; Bentis et al., 2000; Peters unpub. 

observ.). The samples provided additional histological data 

to assist in understanding this species of coral, since most 

studies have been on its biochemistry or microbiology. In 

particular, the susceptibility of the coral to biotic factors 

can be mediated by exposure to abiotic factors when levels 

Figure 8.5. Examples of apoptosis in the epidermis (at arrows). (a) Surface body wall, 40x. (b) High magnifi cation of 

apoptotic cells, 100x.
182Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

exceed the limits to which the organism is adapted, causing stress (Stebbing, 1981). In addition, it is possible that 

some of the biotic commensals or parasites may succumb 

to abiotic stressors sooner than the coral (e.g., Cook et al., 

1990; Williams and MacKenzie, 2003). This study provided 

new data that will be useful in understanding these interrelationships, although caution in their interpretation is 

warranted at this time because so little is known.

The fi rst apicomplexan parasite discovered in the scleractinian corals was described by Peters (1984b). Upton and 

Peters (1986) identifi ed one of the tissue parasites as a 

cocidian and this included oocysts found in the lobes of the 

mesenterial fi laments of P. astreoides. Later, sporozoites 

that hatched from the oocysts were detected in the gastrodermis of other samples of this species and in other corals. 

Dr. Upton had proposed a life cycle in that paper for this 

parasite, suggesting that it might continue to cycle within 

the coral host and not have an alternate host, although 

whether this is true is unknown. What has been identifi ed in the current STEER P. astreoides samples appears 

to be a different endoparasite. Oocysts similar to the ones 

originally found were present in some of the samples in the 

lobes of the mesenterial fi laments, but might be larger in 

size. A single-celled elongated organism with eosinophilic 

cytoplasm was detected in the basal body wall gastrodermis 

of some samples, never seen in the surface body wall. The 

most unusual related stage also found in the basal body 

wall was not single-celled, but was a chain of four cells, 

with one end cell resembling the single-celled elongated 

organism. The other three cells had prominent nuclei (same 

size and nuclear details as the single-celled organism’s 

nucleus) and appeared to be fi lled with circular vacuoles, 

possibly containing lipid. These were identifi ed as “sporozoan” for data collection. Although gregarines, also apicomplexan parasites, have a two-cell stage, they also have 

a thick-walled sporocyst stage, which was not seen in these 

samples.

Figure 8.6. Examples of calicodermis condition. (a) Squamous calicoblasts (arrow), 40x. (b) Deeper calicodermis fi lled with fi ne 

acidophilic granules of calcifi cation proteins (arrow), 40x. (c) Apical extensions on calicoblasts in more actively calcifying region 

(arrow), 40x. (d) Necrosis and lysing calicodermis (arrow), 40x.
183Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

A photomicrograph was sent to Dr. Nathan Kirk, Oregon 

State University, who has done extensive studies of the 

coral coccidia for his dissertation. He researched this question and found a couple of references to septate Eugregarines that form chains while in syzygy. He noted that “The 

two taxa are Hirmacystis and Nematopsis spp. Hirmacystis 

polymorpha can form chains of 10–15 individuals in a row 

in syzygy. Interestingly, Nematopsis (a genus that you detected in Porites samples in the 1984 paper) can also form 

chains (straight or forked) of up to 10 individual trophozoites prior to reproduction. However, the cartoon pictures 

from the illustrated guide do NOT look like the image you 

sent me. However, the zoite in the far left looks almost 

exactly like the pictures from your 1986 paper with Steve 

Upton. There are very few cases of coccidians undergoing 

syzygy (where they form chains) so that is an extremely 

interesting result as well if these are truly coccidians.” The 

molecular analyses he performed of numerous coral species 

tissue samples “suggested that some of these apicomplexans are quite different from each other.”

However, due to their numbers and movement through the 

basal body wall gastrodermis (Figure 8.8c), these organisms are capable of causing damage to the coral. It is possible that they, and the fungi, help to break down the basal 

body wall cells that the coral can no longer support nutritionally (Figure 8.9). Although how the coral tissue remains 

on the surface of the skeleton— a proposed mechanism is 

that it detaches from the skeleton and moves up—perhaps 

in the perforate corals the deepest cells simply die as those 

of the surface epithelia proliferate to continue forming the 

polyps and coenenchyme. Bacteria may contribute to this 

(Figure 8.10a). Some of the brooded planula larvae contained one or a few of the sporozoites in their lipid-fi lled 

gastrodermis, indicating that these may be acquired at the 

same time as the zooxanthellae from the parent’s tissue. 

Dr. Kirk noted he had found evidence of larval uptake of 

coccidians in his molecular studies, but he has not done 

histopathological examinations. More work will need to be 

done on this, of course, but this sample set is valuable for 

apicomplexan research.

Figure 8.7. Examples of bacterial aggregates in mesoglea of tentacles (a and b), 25x; calicodermis reaction to suspect fungal hyphae 

(c), 40x; endolithic algae or fungi where skeleton was removed along basal gastrovascular canals (d), 10x.
184Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

Several other structures that have been found previously or 

were new observations were also present in these samples, 

including suspect rickettsia-like organisms (RLOs) that 

were identifi ed by sequencing only as 90% similar to an 

organism in the Ricketsiales (Casas et al., 2004), a circular 

cell containing up to four nuclei (“unknown cell”) (Figure 

8.10c), a metazoan that has been consistently seen next to 

the calicodermis deep in the coral tissue (Figure 8.10c) (Peters, unpub. observ. of other Porites from the Caribbean), 

and clusters of multiple single cells having an eosinophilic 

cytoplasm and minute basophilic particles but no defi nitive 

nucleus apparently residing in spaces where septal skeleton 

should have been (Figure 8.10d). The latter cells have been 

found in other corals (Peters 1978, Renegar et al., 2008), 

but their true nature has not been investigated. Gonad 

development and brooding of planula larvae varied among 

the sites (Figure 8.11). However, this observation must also 

be cautiously interpreted. Gonad development might be 

affected by exposure to toxicants (e.g., Peters et al., 1981), 

but location 

of the sample in the colony can also affect whether gonads 

will be present. Chornesky and Peters (1987) noted that 

colony age and size can affect this, and younger polyps on 

the margins of colonies or small colonies can lack gonad 

development. Thus, the results must be compared with the 

size of the colonies and location of tissue sampled to be 

sure they represent what was happening at each site. Only 

females and hermaphrodites were found in the STEER, 

consistent with previous research on this species. Numbers 

of planulae larvae present varied with the site.

Summary statistics for all of the parameters examined in 

this study grouped by stratum are presented in Table 8.2. A 

summary of observations for each sampling site is presented below:

Stratum 1: Site MLC 0

Samples 12-180, 12-181, 12-182: 12-180 had algae growing underneath the coral margin, 12-181 had larger polyps 

and more space between the polyps on the larger piece, 

Figure 8.8. Examples of apicomplexan parasites of P. astreoides. (a) Suspect oocysts in lobes of mesenterial fi laments (arrow), 40x). 

(b) Suspect sporozoite stages in basal body wall gastrodermis, 40x). (c) Numerous sporozoan stages in degraded basal body wall 

gastrodermis. (d) Suspect 4-cell sporozoan stage, 40x.
185Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

12-182A was broken in 

sampling, 12-182B had 

boring sponge. This 

location was closest to 

the St. Thomas municipal dump. The general condition of these 

colonies was good 

to fair, with minimal 

to moderate surface 

body wall ruptures and 

moderate to severe 

lysing of gastrodermal 

mucocytes along the 

oral surface. These 

colonies also had mild 

to marked hypertrophy 

and numbers of epidermal mucocytes. One colony had diffuse single cell necrosis 

or apoptosis characterized by fi ne basophilic particles in 

the bases of epidermal and gastrodermal cells. This same 

colony had minimal changes in the calicodermis, whereas 

the other two had moderate to marked reduced acidophilic 

Figure 8.9. Examples of apparent destruction of the basal body wall of most aboral gastrovascular canals 

in the tissue layer of the perforate coral, P. astreoides. (a) Fungal hyphae next to break in basal body wall 

(arrow), 10x. (b) Necrosis and lysing of calicodermis, mesoglea, and gastrodermis adjacent to suspect 

fungal hyphae, 40x.

Figure 8.10. Examples of other unknowns present in the STEER samples. (a) Suspect bacteria on surface of calicodermis, 100x. 

(b) Unknown multinucleated cell, 100x. (c) “Blobs” in skeletal space of septal ridge on oral surface, 40x. (d) Metazoan adjacent to 

basal body wall, 40x.
186Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

granules, lysing, and suspect bacteria or necrosis of this 

epithelium, but this was not correlated with the amount of 

endolithic suspected fungi or algae. None of the samples 

contained suspect apicomplexan oocysts, sporozoites, or 

sporozoans. Only one sample had a single early developing 

oocyte, none had spermaries or planulae. These samples 

were collected from a shallow site (4 ft depth) subjected 

to high temperatures, salinity changes, and land-based 

sources of pollution and the species was diffi cult to fi nd at 

this site. The lack of gonad development and apicomplexan 

parasites (found at all other sites) is intriguing, but may 

not be related to contaminant exposures, as colony size or 

age (Chornesky and Peters, 1987), and isolation might also 

control these factors.

Stratum 2: Site HBI28P

Samples 12-198, 12-199, 12-200, 12-201, 12-202: All 

samples were grossly apparently healthy but with some 

surface mucus and sediment, except 12-201A, which broke 

into fragments and was not included in the calculations. 

This location was farther east away from the Municipal

Landfi ll, in shallow water of Cas Cay Mangrove Lagoon, 

close to a developed shoreline, seaward of the Compass 

Point Marina corridor. The general condition of these 

colonies was fair to poor, with minimal to severe, diffuse 

surface body wall ruptures and marked to severe, diffuse

lysing of gastrodermal mucocytes along the oral surface. 

These colonies also had mild to severe hypertrophy and 

numbers of epidermal mucocytes. All subsamples had minimal to moderate single cell necrosis or apoptosis characterized by fi ne basophilic particles in the bases of epidermal 

and gastrodermal cells. 12-201 had small clusters of variably sized focal to multifocal black particles of unknown 

nature in the mucus of the surface gastrovascular canals 

(Figure 8.12). The calicodermis of all the subsamples had 

minimal to mild attenuation and reduced acidophilic

Figure 8.11. Examples of reproductive structures present in the STEER samples. (a) Multiple oocytes developing in mesenteries, 10x. 

(b) Two mature oocytes in mesentery, 25x. (c) Spermary in mesentery, 40x. (d) Planula larva in cross section through oral surface of 

polyp, 10x.
187Chapter 8: Histologic Analysis of Porites astreoides

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Table 8.2. Summary statistics for histopathological observations for each parameter for each stratum.

Range Range Mean St.Dev. Range

2.0–

3.0

3.0–

3.3 3.2 0.4 3.0–4.0

0.0–

0.0

0.0–

0.0 0.4 0.5 0.0–1.0

1.5–

3.0

2.0–

3.7 4.2 0.7 3.0–5.0

1.0–

4.0

1.5–

2.0 2.2 1.3 1.0–4.0

2.0–

7.5

6.0–

12.0 4.2 1.8 2.0–6.0

9.0–

15.0

9.0–

12.0 10.5 1.5

9.0–

12.0

8.0–

12.0

3.0–

12.0 6.2 2.8 3.0–9.0

0.0–

3.8

0.0–

0.2 1.8 4.0 0.0–9.0

0.0–

1.5

0.0–

0.3 0.2 0.4 0.0–1.0

0.0–

7.5

0.0–

6.7 3.0 4.2 0.0–9.0

2.5–

9.0

6.0–

10.5 12.9 2.5

9.0–

15.0

4.0–

12.0

2.0–

12.0 9.1 4.4

2.0–

12.0

1.0–

10.5

6.0–

10.5 8.5 4.1

2.0–

12.0

0.0–

0.0

0.2–

8.0 0.0 0.0 0.0–0.0

0.0–

0.0

0.0–

2.0 0.5 0.9 0.0–2.0

0.0–

0.0

2.0–

11.0 10.2 3.4

6.0–

15.0

0.0–

1.0

1.5–

4.0 4.0 2.9 2.0–9.0

0.0–

0.0

0.1–

2.0 0.0 0.0 0.0–0.0

0–0 0 0 20 45 0–100

0–0 0–100 0 0 0–0

0–0 0–100 0 0 0–0

0–100

100–

100 60 55 0–100

0–0 0–100 20 45 0–100

0–0 0.0–

22.0 Planulae, Count 0 0 0.4 0.5 0–1.0 0.2 0.4 11.0 9.6 0.6 0.9 0.0–2.0 0.0–

1.0

100 0

Gonads, Spermaries 

(Stages) 0 0 0 0 0–100 60 55 0–100 40 55

Gonads, Oocytes (Stages) 33 58 100 0100–

100 80 45 0–100

80 45

Skeletal Space Containing 

“Blobs” 0 0 0 0 0–0 20 45 0–100 40 55

Calicodermis/Skeleton 

Unknow n Metazoan 0 0 0 0 0–0 0 0 0–0

0.8 0.8

Percent Containing

Unknow n Cells 0 0 0 0 0 0 0 0 0–0 0 0

Other Bacteria (rickettsialike organisms in 

cnidoglandular bands)

0.0 0.0 1.8 1.7

0.3–

4.0 0.3 0.7

0.0–

1.5

5.5 3.4

Bacterial Aggregates in 

Tentacles

0.3 0.6 3.0 1.0 2.0–

4.0

4.7 1.2 3.0–

6.0

2.8 1.0

Apicomplexa, Sporozoa 0.0 0.0 3.3 1.9

2.0–

6.3 9.8 3.0

6.3–

13.5

3.2 3.0

Apicomplexa, Sporozoites 0.0 0.0 1.2 1.3

0.0–

3.0 6.1 3.1

2.0–

9.0 1.6 0.9

Apicomplexa, Oocysts 0.0 0.0 0.0 0.0

0.0–

0.0 1.3 1.7

0.0–

3.9

6.6 3.6

Skeleton, Endolithic Algae 

and Fungi 6.8 5.1 2.7 3.1 0.0–6.0 10.8 2.0 9.0–13.5 8.2 1.7

Calicodermis, Suspect 

Bacteria on Apical Surface 

or Necrosis?

8.0 4.0 5.5 1.6

3.8–

7.5 6.8 1.3

6.0–

9.0

1.8 2.9

Calicodermis, Attenuation 

and Lack of Acidophilic 

Granules

6.8 3.8 3.2 1.6

2.0–

6.0 7.9 5.9

0.5–

15.0 8.3 1.8

Gastrodermis, Necrosis or 

Apoptosis? 3.2 3.9 4.2 2.0 1.5–6.0 1.5 3.1 0.0–7.0

0.0 0.1

Gastrodermis, Black 

Particles in Released Mucus, 

Gastrovascular Canals

0.5 0.9 0.2 0.4 0.0–

1.0 1.2 2.7 0.0–6.0 0.1 0.1

Epidermis, Necrosis or 

Apoptosis? 1.3 2.2 5.7 1.6

3.0–

7.5 0.1 0.1

0.0–

0.3

11.0 1.4

Epidermis, Epidermal 

Mucocytes Hypertrophy 9.6 2.1 11.5 3.2

6.3–

15.0 5.8 3.1

2.0–

9.0 7.5 3.4

Suspect Sampling Damage, 

Lysing Gastrodermal Cells 12.0 3.0 13.2 1.6

12.0–

15.0 9.3 0.7

9.0–

10.5

1.9 0.2

Score = Severity or Intensity (1–5) x Extent (1–3)

Suspect Sampling Damage, 

Surface Body Wall Ruptures 4.5 2.8 11.3 4.3

4.0–

15.0 6.3 4.6

0.5–

12.0 9.0 2.7

Melanin-like Granular 

Amoebocytes, Mesenteries 

and Mesenterial Filaments

2.5 1.5 3.2 0.8 2.0–

4.0 1.6 0.8 1.0–2.5

0.0 0.0

Relative Quantity (0 = None to 5 = Maximum)

Melanin-like Granular 

Amoebocytes, Surface Body 

Wall

2.3 0.8 3.3 0.8

2.0–

3.0 3.7 0.7

2.5–

4.0 2.8 0.6

General Microscopic 

Condition Zooxanthellae 

(100x)

0.0 0.0 0.0 0.0

0.0–

0.0 0.0 0.0

0.0–

0.0

0 = Excellent, 1 = Very Good, 2 = Good, 3 = Fair, 4 = Poor, 5 = Very Poor

General Microscopic 

Condition Coral (100x) 2.7 0.6 3.5 0.5

3.0–

4.0 3.4 0.4

3.0–

4.0 3.1 0.1

Parameter

Stratum 1 Stratum 2 Stratum 3 Stratum 4 Stratum 5

Mean St.Dev. Mean St.Dev. Range Mean St.Dev. Range Mean St.Dev.
188Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

granules, and diffuse mild suspect bacteria or necrosis of 

this epithelium. Endolithic suspected fungi or algae were 

not detected in three of the subsamples and minimal to

moderate levels in the others with limited in extent. Suspect 

apicomplexan developmental stages were found in all of 

the subsamples, but no oocysts, and minimal to mild focal 

infections of sporozoites and sporozoans; moderate, diffuse 

amounts of the latter in 12-199A. All of the subsamples 

contained oocytes in middle to mature development, two 

contained small spermaries, and none had planulae. These 

results suggest the colonies were under some stress leading 

to the single cell necrosis, but were still producing gonads.

Stratum 3: Site HBI23P

Samples 12-193, 12-194, 12-195, 12-196, 12-197: All 

samples were grossly apparently healthy (uniform covering of pigmented tissue and polyps) but with mild to 

moderate surface mucus and sediment, except 12-195B, 

which broke into fragments and was not included in the 

calculations. This location was nearshore in the St. James 

Reserve, downstream of the developed Jersey Bay watershed. The general condition of these colonies was good 

to poor, with no to marked severity of surface body wall 

ruptures and moderate to marked lysing of gastrodermal 

mucocytes along the oral surface. These colonies also had 

minimal to marked hypertrophy and numbers of epidermal 

mucocytes. Only one colony had focal minimal single cell 

necrosis or apoptosis of the epidermal cells and two had 

minimal, diffuse to mild, multifocal single cell necrosis of 

the gastrodermal cells. All of the colonies had degradation 

of the calicodermis, including marked to severe, diffuse 

attenuation, lack of acidophilic granules, and cell lysing in 

12-194A, 12-195, and 12-197; and all had mild to moderate, multifocal to diffuse suspect bacteria or necrosis of 

this epithelium. They all had more severe and extensive 

proliferation of endolithic organisms in the skeleton. All of 

the samples contained suspect apicomplexan oocysts, sporozoites, or sporozoans; the latter were marked to severe, 

diffuse infections of the deep basal body wall gastrodermis. 

Two colonies lacked gonads, the others had developing oocytes or spermaries, but none contained planula larvae. The 

presence of hypertrophied mucocytes and minimal necrosis 

of the surface body wall suggests the sampled colonies 

were stressed.

Stratum 4: Site HBI15P

Samples 12-188, 12-189, 12-190, 12-191, 12-192: The 

cores from this site grossly appeared to be healthy except 

for mild to moderate mucus or sediment particles on the 

surfaces, but three subsamples (12-189B, 12-190B, 12-

191A-2) were broken in fragments and not included in the

calculations. Samples were collected from a hardbottom 

site farther offshore and deeper (42 ft) than the other stations (4–8 ft), at the entrance to Jersey Bay. The general 

condition of these colonies was fair to poor, with multifocal 

to diffuse, mild to marked surface body wall ruptures

and moderate to marked lysing of gastrodermal mucocytes 

along the oral surface. One sample had minimal hypertrophy of epidermal mucocytes, the others had mild to marked 

hypertrophy and numbers of epidermal mucocytes. One 

colony had diffuse, severe necrosis or apoptosis of the 

gastrodermis, with minimal changes noted in two other 

colonies, and only one had multifocal minimal single cell 

Figure 8.12. Example of black particles trapped in mucus secretions (arrows), 40x.

Table 8.3. Summary of results of the histopathological examinations, means of Specifi c Condition Scores Sum and 

percent of colonies with selected condition at each site.

Stratum

1 (n=3)

2 (n=5)

3 (n=5)

4 (n=5)

5 (n=5) 35.0 ± 5.8 100 20 40 100 60 100

51.1 ± 10.5 100 20 40 100 80 100

42.8 ± 5.8 100 20 40 100 100 100

36.2 ± 3.6 100 33 67 100 33 0

37.3 ± 5.5 100 100 100 100 100 100

Mean 

Condition 

Scores ± St. 

Dev.

Sampling 

Damage

%

Epidermal 

Necrosis or 

Apoptosis 

%

Gastrodermal 

Necrosis or 

Apoptosis %

Calicodermis 

Degeneration

%

Gonads and 

Larvae

%

Apicomplexan 

Parasites

%
189Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

necrosis of the epidermis. The calicodermis of all the colonies had diffuse, 

moderate to marked attenuation and 

lack of acidophilic granules, and 

most also had mild to marked suspect 

bacteria or necrosis, except the calicodermis had only minimal changes 

in 12-191. Mild to marked levels of 

endolithic organisms were noted in 

these samples throughout the deep 

tissue. All of the samples contained 

suspect apicomplexan oocysts, sporozoites, or sporozoans, with marked 

levels of oocysts in 12-190 and of 

sporozoans in 12-192. All of the 

colonies were developing gonads, but 

only one with spermaries was found; 

all but one colony also were brooding 

larvae—more larvae here than at any 

of the other sites. The sample with 

severe necrosis of the gastrodermis 

also had marked epidermal mucocyte 

hypertrophy, numerous suspect sporozoans in the deep gastrodermis and 

endolithic organisms in the skeleton, 

and one area of black particles in the gastrovascular canal 

mucus, but still contained developing oocytes and planula 

larvae. This illustrates the challenges in determining the 

health of a colony.

Stratum 5: Site HBI7P

Samples 12-183, 12-184, 12-185, 12-186, 12-187: Sampling damage was present on all of the cores collected at 

this site, with mucus and sediment on their surfaces, but 

otherwise were grossly apparently healthy. Subsamples 12-

189B, 12-190B, and 12-191A-2 were broken and not

included in the analyses. This sampling location was near 

shore, but the farthest east from MLC 0, in Great Bay. The 

general condition of these colonies was good to poor, with 

minimal to moderate surface body wall ruptures and moderate to marked lysing of gastrodermal mucocytes along 

the oral surface. These colonies also had mild to moderate 

hypertrophy and numbers of epidermal mucocytes. One 

colony (12-186) had moderate single cell necrosis or apoptosis characterized by fi ne basophilic particles in the bases 

of epidermal and gastrodermal cells (also seen in 12-183, 

mild). Two subsamples had black particles in released mucus. The calicodermis of all of the subsamples had marked 

to severe attenuation, lack of acidophilic granules, and 

lysing of the epithelium, and multifocal to diffuse, minimal 

to marked bacteria or necrosis occurring. All of the subsamples had mild to marked amounts of endolithic algae and 

fungi. Suspect apicomplexan sporozoans were found in 

all the subsamples, most numerous in 12-186 and 12-187; 

no or minimal amounts of oocysts and sporozoites. Only 

60% of the samples had developing gonads, one colony 

with spermaries, and 40% had planulae in their polyps. The 

sporozoan infections of the gastrodermis might be most 

responsible for the condition of these colonies. 

The means of the Specifi c Condition Scores Sums of the 

samples, which ranged from 30–61.8 (out of a possible 

total of 180 points for worst severity of 5 and most extensive distribution of 3 for all 12 parameters) are presented by 

site and observations of percentage of affected colonies for 

selected data are summarized in Table 8.3. A comparison 

of the mean Specifi c Condition Scores Sums by Stratum is 

presented in Figure 8.13. Based on these summed scores, 

the samples from Stratum 3 were in worse condition than 

the other sites. A single-factor analysis of variance for those 

data indicated signifi cant differences among the strata (p = 

0.011), with t-tests revealing the differences to be between 

Stratum 1 or 5 and 3. However, the Kruskal-Wallis analysis 

barely revealed these differences (p = 0.057). Stratum 2 

samples were signifi cantly different from all other strata for 

epithelial necrosis or apoptosis, but at low intensities.

8.4. CONCLUSIONS

In conclusion, the most widely seen effect across all of 

the sites was the lysing of the gastrodermis along the oral 

gastrovascular canals and cavities, fi lling these lumens with 

mucus and also epidermal ruptures releasing mucus and 

Figure 8.13. Comparison of means of Specifi c Condition Scores Sum with standard 

deviations among the fi ve strata.

0.0

10.0

20.0

30.0

40.0

50.0

60.0

70.0

12345

6WUDWXP

6SHFLILF&RQGLWLRQ6FRUHV6XP
190Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report

other lysed cells and zooxanthellae onto the subsample surface. Similar lesions have been observed in other species, 

but not to such a level of severity and extent. 

The impact of hammering the stainless steel coring tube 

into the coral colony to remove the tissue and skeleton 

biopsy probably needs to be reconsidered and a method 

with less vibration used (e.g., more manual pressing of the 

coring tube, less intense pounding, or a diamond-tipped 

rock coring device on a pneumatic drill). The presence 

of hypertrophied mucocytes and single cell or segmental 

necrosis or apoptosis in some of the colonies, and reproduction capabilities indicate that some of the sampled corals 

might be experiencing stress, but associating the effects 

with exposures will require additional observations and 

measurements of environmental parameters. The presence 

of suspect apicomplexan parasites, particularly the sporozoan stage that was burrowing through the gastrodermis of 

the deep basal body wall, could be contributing to colony 

condition, as well, because that epithelium was becoming 

vacuolated and necrotic, potentially in concert with proliferation of fungi in the skeleton. 

Because of lack of knowledge of how the polyps remain 

on the surface of the skeleton in these nonperforate corals, perhaps a cyclical breakdown of deep tissue occurs as 

the surface tissues continue to grow. More observations of 

growth patterns in the scleractinian corals, including the 

histopathology of the tissues, is needed to examine this 

question. 

The STEER P. astreoides colony samples are valuable 

because the effects of other environmental stressors, especially biotic associations of parasites and endolithic organisms, were detected by light microscopy and will assist in 

interpreting the results of toxicology analyses.

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fungi in reef-building corals (Order: Scleractinia) are common, cosmopolitan, and potentially pathogenic. Biological 

Bulletin. 198:254–260.

Casas, V., D.I. Kline, L. Wegley, Y. Yu, M. Breitbart, and F. 

Rohwer. 2004. Widespread association of a Rickettsialeslike bacterium with reef-building corals. Environmental 

Microbiology. 6(11):1137-1148.

Chornesky, E.A., and E.C. Peters. 1987. Sexual reproduction and colony growth in the scleractinian coral Porites 

astreoides. Biological Bulletin. 172: 161-177.

Cook, C.B., A. Logan, J. Ward, B. Luckhurst, and C. Berg, 

Jr. 1990. Elevated temperatures and bleaching on a high 

latitude coral reef: the 1988 Bermuda event. Coral Reefs. 

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Domart Coulon, I.J., N. Traylor Knowles, E. Peters, D. 

Elbert, C.A. Downs, K. Price, J. Stubbs, S. McLaughlin, 

E. Cox, G. Aeby, P.R. Brown, and G.K. Ostrander. 2006. 

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Toxicology, Volume 2, ed. G.K. Ostrander, pp. 181-207. 

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Downs, C.A., E. Mueller, S. Phillips, J.E. Fauth, and C.M. 

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Bulletin. 51:558–569.

Downs, C.A., R.H. Richmond, W.J. Mendiola, L. Rougee, 

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G.A. Ostrander. 2011. A survey of environmental pollutants 

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Fauth, J.E., C. Calestani, P. Dustan, D. Wham, K. Banks, 

A. Moulding, and C.A. Downs. 2011. Biomarker Study to 

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and C.H. Jagoe, Lewis Publishers, Boca Raton, FL.
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Kenkel, C.D., G. Aglyamova, A. Alamaru, R. Bhagooli, R. 

Capper, R. Cunning, A. DeVillers, J.A. Haslun, L. Hédouin, 

S. Keshavmurthy, K.A. Kuehl, H. Mahmoud, E. McGinty, 

P.H. Montoya-Maya, C. Palmer, R. Pantile, J.A. Sánchez, T. 

Schils, R.N. Silverstein, L.B. Squiers, PC. Tang, T.L. Goulet, and M.V. Matz. 2011. Development of gene expression 

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Lond. B, Biological Bulletin. 275(1652):2687-2693.

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Coral Manicina areolata (Linne, 1758) to Water Soluble 

Oil Extracts. M.S. Thesis, University of South Florida.

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Effects of Sedimentation Stress. Ph.D. Dissertation, University of Rhode Island.

Peters, E.C. 1984b. A survey of cellular reactions to environmental stress and disease in Caribbean scleractinian corals. Helgoländer Wissenschaftliche Meeresuntersuchungen. 

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of the effects of sedimentation stress on symbiotic and 

asymbiotic colonies of the coral Astrangia danae Milne 

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Biology and Ecology. 92:215-230.

Peters, E.C., N.J. Gassman, J.C. Firman, R.H. Richmond, 

and E.A. Power. 1997. Ecotoxicology of tropical marine 

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Peters, E.C., K.L. Price, and D.J. Borsay Horowitz. 2005. 

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contaminant effects. In: Techniques in Aquatic Toxicology, Volume 2, ed. G.K. Ostrander, pp. 653-686. Taylor & 

Francis, Boca Raton, FL.

Renegar, D.A., P.L. Blackwelder, J.D. Miller, D.J. Gochfeld, and A.L. Moulding. 2008. Ultrastructural and histological analysis of dark spot syndrome in Siderastrea 

siderea and Agaricia agaricites. Proc. 11th International 

Coral Reef Symposium, Ft. Lauderdale, Florida, 7-11 July 

2008, pp. 185-189.

Rohwer, F., V. Seguritan, F. Azam, and N. Knowlton. 2002. 

Diversity of coral-associated bacteria. Marine Ecology 

Progress Series. 243:1-10. 

Rotchell, J.M., and G.K. Ostrander. 2011. Molecular 

toxicology of corals: A review. Journal of Toxicology and 

Environmental Health, Part B. 14:571-592.

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Marine Pollution Bulletin. 12(10):326–329.

Szmant, A.M. 1986. Reproductive ecology of Caribbean 

reef corals. Coral Reefs 5:43–53.

Upton, S.J., and E.C. Peters. 1986. A new and unusual 

species of coccidium (Apicomplexa: Agamococcidiorida) 

from Caribbean scleractinian corals. Journal of Invertebrate 

Pathology. 47:184-193.

Wegley, L., R. Edwards, B. Rodriguez-Brito, H. Liu, and 

F. Rohwer. 2007. Metagenomic analysis of the microbial 

community associated with the coral Porites astreoides. 

Environmental Microbiology. 9(11):2709-2719.

Yevich, P.P., and C.A. Yevich. 1994. Use of histopathology 

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Coastal Waters and Estuaries, ed. K.J.M. Kramer, pp. 179-

204. CRC Press, Boca Raton, FL.
192Chapter 8: Histologic Analysis of Porites astreoides

STEER Integrated Environmental Assessment Report
STEER Integrated Environmental Assessment Report

193Chapter 9: Nutrients, Sedimentation and TSS

9.1. INTRODUCTION

This chapter contains the results of the monthly monitoring 

of nutrients and total suspended solids (TSS) in the water 

column, along with sedimentation using sediment traps, as 

part of the project in the STEER. The monthly monitoring 

was carried out by project partners at the University of the 

Virgin Islands (UVI) from 2012 through 2013. 

Nutrients were identifi ed as a 

major environmental concern in 

the STEER Management Plan 

(STEER, 2011). While dissolved 

nutrients are essential to productivity in aquatic systems, an overabundance of nutrients can help 

trigger macroalgae and phytoplankton blooms, resulting in degradation of water quality and habitat. 

In coral reef systems, algal blooms 

can lead to algae out-competing 

and then smothering juvenile and 

adult corals, ultimately resulting in 

the loss of those corals (Fabricius, 

2005; D’Angelo and Wiedenmann, 

2014; Box and Mumby, 2007). 

It has also been shown that nutrients can have direct effects 

on corals. Ammonium and phosphate in parts per billion (μg/L or ppb) concentrations can impact fertilization 

success (Harrison and Ward, 2001), while nitrate has been 

shown to decrease calcium deposition in corals (Marubini 

and Davis, 1996). 

Sediments can be deposited on coral reefs as a result of 

surface water transporting eroded soils, as might occur 

during a storm, or through the resuspension of bottom 

sediments. Sedimentation has been shown to impact coral 

reefs (Fabricius, 2005; Burke et al., 2011; Waddell et al., 

2005). The deposition of sediments in reef areas can act to 

smother corals and physically abrade coral tissues. At the 

very least, sediments “raining” down on corals results in 

the organisms having to expend energy to remove sediment 

particles, meaning there is less energy available for other 

functions including growth and reproduction. Elevated 

sedimentation has been linked to less coral cover, lower 

coral diversity and recruitment, along with lower growth 

and calcifi cation rates (Fabricius, 2005; Weber et al., 2012; 

ISRS, 2004; Rogers, 1990). Like 

nutrients, the input of sediment 

was identifi ed as a major threat 

in the STEER Management Plan 

(STEER, 2011).

The presence of total suspended 

solids or TSS in the water column acts to decrease the amount 

of light available for corals as 

well as seagrasses. Nemeth and 

Nowlis (2001) suggested that 

excessive levels of suspended 

sediments led to increased coral 

bleaching, specifi cally along the 

north shore of St. Thomas. 

9.2. METHODS

The locations for the monitoring sites (Figure 9.1) were 

selected non-randomly by project partners at the University 

of the Virgin Islands (UVI) and the USVI Department of 

Planning and Natural Resources (DPNR), in order to target 

potential sources of land based pollution. These sites were 

used to assess terrestrial inputs from the surrounding watershed, including residential areas surrounding Benner Bay, 

and the Bovoni Landfi ll, which is adjacent to Mangrove 

Lagoon. Samples for nutrient analysis, TSS and sedimentation were collected monthly from fi ve targeted sites from 

January 2012 to November 2013. A sixth site, at Little St. 

James (LSJ, Figure 9.1) Island, was added and then sampled beginning in March 2012. The methods used for the 

collection and analysis are described below. 

CHAPTER 9: AN ASSESSMENT OF NUTRIENTS, SEDIMENTATION, AND TOTAL SUSPENDED SOLIDS 

(TSS) IN THE ST. THOMAS EAST END RESERVES (STEER)

Anthony S. Pait1

, Francis R. Galdo, Jr.2, S. Ian Hartwell1, Andrew L. Mason1 , Dennis A. Apeti1, Christopher F. G. Jeffrey1,3, Anne M. Hoffman4

, and Simon J. Pittman1,5

1

NOAA/NOS/National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment (CCMA), 

1305 East/West Highway, Silver Spring, MD 20910

2

The University of the Virgin Islands, St. Thomas, USVI

3

CSS-Dynamac Consolidated Safety Services, Fairfax, VA 22030, under CSS-Dynamac Contract #EA-133C-14-NC-1384

4

The Nature Conservancy, St. Thomas, USVI

5

The Marine Institute, Plymouth University, United Kingdom

Diver installing a sediment trap in the STEER. 
STEER Integrated Environmental Assessment Report

194Chapter 9: Nutrients, Sedimentation and TSS Nutrients

At each site, duplicate samples were collected for the 

analysis of dissolved nutrients. Nitrile gloves were worn by 

personnel, in order to prevent contamination of the water 

samples. In the fi eld, samples were kept in the dark and 

then fi ltered into acid-washed 125 ml high density polyethylene (HDPE) bottles, using 60 ml syringes equipped 

with disposable Millipore Sterivex 0.22 μm fi lter units. 

The syringe was fi rst rinsed with several full volumes 

of site water. Next, the syringe was refi lled, the Sterivex 

fi lter attached, and a full volume of site water was pushed 

through the fi lter. The sample bottles were rinsed three 

times with fi ltered site water. The fi lter was removed and 

the syringe refi lled with site water. After replacing the fi lter, 

the syringe/fi lter process was repeated until the bottles were 

fi lled, leaving adequate headspace to allow for expansion 

during freezing. Samples were then immediately packed 

on ice for transport to UVI. On return to the laboratory, the 

water samples were frozen until shipped. 

Water samples were analyzed by the Geochemical and 

Environmental Research Group (GERG) at the Texas 

A&M University, through a subcontract with TDI-Brooks, 

International. The following is a brief summary of methods used for the analysis of nutrients in the water samples. 

Nitrate and nitrite analyses were based on the methodology of Armstrong et al. (1967) and use a ground cadmium 

column for reduction of nitrate to nitrite. Orthophosphate 

was measured using the methodology of Bernhardt and 

Wilhelms (1967), with the modifi cation of hydrazine as a 

reductant. Silicate determination was accomplished following the methods of Armstrong et al. (1967) using stannous 

chloride. 

Ammonium analysis was based on the method of Harwood 

(Harwood and Kuhn, 1970) using dichloroisocyanurate as 

an oxidizer. Urea was measured using diacetyl-monoximine 

and micarbozide. Total nitrogen and total phosphorus 

concentrations were determined after an initial decomposition step. This method involves persulfate oxidation while 

heating the sample in an autoclave (Hansen and Koroleff 

1999). After oxidation of the samples, nutrient determinations were conducted on a Technicon® II analyzer. 

As the water samples were fi ltered for this project, reported 

values are for dissolved nutrient species. Proposed nutrient thresholds for coral reefs for dissolved organic nitrogen 

(DIN), and for orthophosphate (also referred to as soluble 

reactive phosphorus or SRP), are compared with the results 

from the STEER.

Figure 9.1. Sampling sites for nutrients, sedimentation, and TSS along with the STEER boundary. 
STEER Integrated Environmental Assessment Report

195Chapter 9: Nutrients, Sedimentation and TSS

Sedimentation

Sediment trap arrays were deployed at fi ve sites located 

throughout the STEER, and included Great St. James (SJ), 

Cowpet Bay (CB), Rotto Cay (RC), Benner Bay (BB), and 

Mangrove Lagoon (ML). In March 2012, at the request 

of DPNR, an additional station was added near Little St. 

James Island (LSJ), to address concerns related to major 

ongoing construction activities on this island. GPS coordinates were recorded for each station, and are shown in 

Table 9.1. 

Each sediment trap consisted of a two-inch diameter PVC 

cylinder, sealed at one end, with a minimum height-todiameter ratio of 4:1, the same as those already in use by 

the University of the Virgin Islands (Smith et al., 2008). 

This height:diameter ratio has been shown to minimize the 

resuspension and escape of trapped sediments under normal 

fl ow conditions (Smith et al., 2008). The cylinders were 

deployed vertically, affi xed to metal posts at a height of 

approximately 60 cm above the seafl oor, and approximately 

30 cm for very shallow sites (Benner Bay and Mangrove 

Lagoon). The cylinders were affi xed to the posts with 

combinations of Velcro and plastic zip-ties, allowing for 

monthly exchange of the traps. Three replicate cylinders 

were spaced approximately one meter apart, in order to 

minimize the effects of water fl ow disturbances between 

replicates, thus helping to ensure independence of replicate 

samples (Butman, 1984). 

At four sites (Little St. James, St. James, Cowpet Bay, and 

Rotto Cay), traps were exchanged by divers using SCUBA. 

For trap arrays located in the shallowest sites (Benner Bay 

and Mangrove Lagoon), the exchange was generally accomplished by wading, taking care to minimize disturbance 

to bottom sediments. During sediment trap exchanges, each 

trap was carefully removed from its post, and sealed with a 

tight-fi tting cap. Due to the fact that a variety of small fi sh 

and invertebrates were attracted to the refuge provided by 

the sediment traps, cylinders were checked for the presence 

of marine organisms prior to being capped. 

Replacement traps were cleaned thoroughly between deployments, and rinsed just prior to deployment at each site. 

Newly deployed traps were visually inspected just before 

divers departed a site, in order to ensure that no sediment 

entered during the exchange process. If sediment was observed in a newly deployed trap, the cylinder was removed 

from the post, cleaned, and replaced. 

Beginning in April 2012, Pettit (Kop-Coat, Inc.) infl atable 

boat anti-fouling paint was applied to the upper 5 cm of 

the traps due to concerns that fouling of trap apertures at 

several sites, could signifi cantly affect trap performance.

Efforts were taken to ensure that traps were retrieved and 

replaced at all sites within a period of no more than 24 

hours, however on several occasions, extenuating circumstances (e.g., storms), resulted in delays of several days 

between sites. Such occasions have been noted and were 

taken into account when calculating sedimentation rates. 

Following retrieval, the sealed sediment traps were stored 

upright until decanted and fi ltered.

Sediment samples were decanted, fi ltered, rinsed with 

freshwater to remove salts, then dried completely at 70 °C. 

Samples were then cooled to room temperature in a desiccator, and weighed to the nearest 0.001 g to obtain total dry 

weight of accumulated sediments for each trap.

An analysis of sediment composition (organic/carbonate/

terrigenous fractions) was carried out using loss on ignition (LOI) at 550 °C and 950 °C, following the techniques 

described by Heiri et al. (2001). To determine organic 

content, homogenized sediment sub-samples were placed 

into clean, labeled, and pre-weighed porcelain crucibles. 

Crucibles and sediments were then dried at 105 °C, cooled, 

Table 9.1. Location of sites and mean water quality values from STEER sites.

Site Name

Site 

Code

Latitude 

(DD)

Longitude 

(DD)

Salinity 

(ppt)

Turbidity 

(NTU) pH Depth (m)

Chlorophyll a 

(μg/l)

DO 

(mg/l)

Temperature 

(°C)

Mangrove Lagoon ML 18.31385 -64.87988 35.6 ±0.3 4.07 ±0.71 8.09 ±0.03 1.3 ±0.1 1.86 ±0.17 6.79 ±0.13 29.3 ±0.3

Benner Bay BB 18.31670 -64.8674 36.0 ±0.1 10.7 ±1.4 8.13 ±0.03 1.2 ±0.1 1.12 ±0.08 6.18 ±0.12 29.3 ±0.2

Rotto Cay RC 18.31331 -64.86423 35.8 ±0.1 1.41 ±0.20 8.13 ±0.02 2.1 ±0.1 0.37 ±0.03 6.37 ±0.16 28.6 ±0.2

Cowpet Bay CB 18.31487 -64.84267 35.9 ±0.1 0.91±0.13 8.17 ±0.02 1.7 ±0.1 0.32 ±0.02 6.54 ±0.03 28.3 ±0.2

Saint James SJ 18.30302 -64.83671 35.9 ±0.1 1.03 ±0.16 8.16 ±0.02 1.8 ±0.1 0.28 ±0.03 6.42 ±0.02 28.0 ±0.1

Little St. James LJ 18.30069 -64.83003 35.8 ±0.1 1.52 ±0.13 8.15 ±0.02 1.6 ±0.1 0.28 ±0.03 6.51 ±0.02 28.4 ±0.1

Values are ± standard error. Abbreviations: DD, decimal degrees; ppt, parts per thousand; NTU, nephelometric turbidity units; m, meters; 

DO, dissolved oxygen; mg/l, milligrams/ liter; °C, degrees Celsius. Note that depth is the water depth at which the water quality 

measurements were made, and not the depth of the site.
STEER Integrated Environmental Assessment Report

196Chapter 9: Nutrients, Sedimentation and TSSand weighed to the nearest 0.001 g prior to combustion at 

550 °C in a muffl e furnace (Fisher Scientifi c Isotemp 550 

series). Samples were held at 550° C for four (4) hours, 

then cooled to room temperature. Samples were again 

dried in a desiccator, and re-weighed post-combustion. To 

determine carbonate content, the subsamples were returned 

to the muffl e furnace and combusted at 950 °C for two (2) 

hours. After cooling to room temperature, the weighing 

process was repeated a fi nal time to obtain dry weight postcombustion. Organic and carbonate contents of samples 

were calculated by the following equations, respectively:

%LOI 550° C = ((DW 105 °C - DW 550 

°C)/DW 105 °C)*100 

%LOI 950 °C = ((DW 550 °C - DW 950 

°C)/DW 105 °C)*100

Total Suspended Solids

At each site, a one (1) liter water sample was collected for analysis of total 

suspended solids (TSS) each month. A 

clean, pre-labeled bottle was uncapped 

and submerged approximately one half 

meter below the water surface. The bottle 

was fi lled and rinsed out twice with site 

water, then fi lled, capped, and placed on 

ice for transport back to UVI. The water 

samples for TSS were stored refrigerated 

for a period of no longer than one month 

from collection until analysis. Each 

one liter sample was fi ltered through a 

pre-weighed glass fi ber fi lter mounted in 

a suction fl ask apparatus. (if less than one liter was used, 

the exact volume of water fi ltered was noted). The fi ltered 

sample was rinsed several times with deionized water in 

order to remove salts, then dried at 105° C, and weighed to 

the nearest 0.001 g. Calculation of TSS was as follows: 

TSS (mg/L) = ([A-B]*1000)/C

Where A = End weight of the fi lter in grams (g)

 B = Initial weight of the fi lter in grams (g)

 C = Volume of water fi ltered in liters (l).

Statistical Analysis

The data collected were analyzed using JMP® statistical 

software. Because the data were not normally distributed, 

nonparametric tests (e.g, Spearman’s nonparametric multivariate correlation) were used. When needed, pairwise 

comparisons were made using the Wilcoxon Rank-Sum 

Method.

9.3. RESULTS AND DISCUSSION

Water Parameters

In addition to the site location information for the monthly 

monitoring, Table 9.1 also contains a summary of the water 

parameters measured. Note that depth refers to the depth 

made for the water quality measurements, and not the depth 

of the water at the site. More detailed results for these and 

other parameters measured in this part of the project can be 

found in Pait et al. (2015).

The mean (average) turbidity was highest at the Benner 

Bay site (10.7 NTU). A nonparametric (Wilcoxon RankSum) comparison between sites 

indicated that the turbidity at the 

Benner Bay site was signifi cantly (p 

< 0.0001) higher than all the other 

sites sampled monthly in the STEER, 

including Mangrove Lagoon. 

For chlorophyll a, the mean for 

Mangrove Lagoon (1.86 μg/L) was 

significantly (p < 0 .0001) higher 

than all other sites, including Benner 

Bay (p = 0.0005), using a Wilcoxon 

nonparametric pairwise comparison 

test. Nonpoint source inputs from surrounding residential areas, along with 

inputs from the horse racetrack, which 

are adjacent to the northern border of 

Mangrove Lagoon, are likely contributing nutrients, leading to increased 

phytoplankton growth (and correspondingly higher chlorophyll a concentrations) seen in 

Mangrove Lagoon. For pH, salinity, and temperature, the 

average readings between sites were fairly similar.

Nutrients

A summary of the results from the nutrient monitoring 

can be seen in Table 9.2, and in Figures 9.2 to 9.8. The 

intervals in the maps were derived using the Jenks Natural 

Breaks Classification Method. In general, higher nutrient 

concentrations were found in the western portion of the 

study area, specifically in Mangrove Lagoon and Benner 

Bay. 

Differences by Site 

Nonparametric analyses indicated that ammonium (NH4

+

), 

nitrite (NO2

-

), and dissolved inorganic nitrogen (DIN) 

varied significantly by site. The variation of the combined 

nitrate/nitrite (sum of NO3

-

 and NO2

-

), however, was not 

significant. Mangrove Lagoon and Benner Bay had significantly higher (p < 0.05) mean concentrations of NH4

+ 

Sediment traps deployed in the STEER. 

Larger cylinder is a passive water chemistry sampler used in another part of the 

project (see Chapter 6).
STEER Integrated Environmental Assessment Report

197Chapter 9: Nutrients, Sedimentation and TSS

and DIN than at Cowpet Bay, Rotto Cay, Saint James, and 

Little St. James. For nitrite, Benner Bay had significantly 

higher mean values than all other sites, except for Mangrove Lagoon. Finally, Mangrove Lagoon and Benner 

Bay did not differ significantly from each other for any of 

the nutrient species analyzed, indicating elevated levels of 

the nutrients analyzed at both of these locations. Figures 

9.2 to 9.8 show the mean and maximum values recorded 

at the sites during the monthly sampling. From these 

figures as well, it can be seen that the Mangrove Lagoon 

and Benner Bay sites, had higher concentrations (both the 

mean and maximum values), for a number of the nutrients 

analyzed. The watershed surrounding the western portion 

of the study area includes the higher density residential 

areas of Estate Bovoni and Anna’s Retreat, along with the 

active Bovoni Landfill, and are likely contributing nutrients 

to the STEER. In addition, there appear to be a number of 

live-aboard boats in Benner Bay, which are also potential 

sources of nutrients. The east to west gradients seen with 

nitrogen compounds was not seen with orthophosphate 

and total phosphate, which indicates a different matrix of 

sources and/or forcing functions that drive distributions of 

these nutrients. 

Approximately 70% of the residential housing adjacent to 

Mangrove Lagoon and Benner Bay are on septic systems, 

many of which are failing (Horsley Witten, 2013). There is 

also a deteriorating sewer infrastructure for those connected 

to the public sewer system (Horsley Witten, 2013). The 

STEER Management Plan (STEER, 2011) cited nutrients 

as a high to very high threat in the STEER. An assessment of fecal coliform bacteria (FCB) in Mangrove Lagoon 

and Benner Bay (Tetra Tech, 2005), indicated a variety of 

sources including improperly functioning septic systems, 

urban runoff and discharges from recreational vessels in 

the area. The highest concentrations of the sewage marker 

Clostridium perfringens was found in Mangrove Lagoon, 

adjacent to where Turpentine Gut empties into the lagoon 

(Chapter 4). 

Variation by Latitude and Longitude 

Nutrient concentrations were assessed to determine if they 

varied by longitude (east/west orientation) and latitude 

(onshore/offshore orientation). A non parametric analysis 

(Spearman’s) revealed a significant (p < 0.05) and negative 

correlation between longitude and ammonium, nitrite, DIN, 

and total phosphorus, indicating that moving east to west, 

Table 9.2. Summary statistics for nutrients measured in the STEER. All units are expressed as mg/L N or mg/L P. 

Mean Median Max Mean Median Max Mean Median Max

NO3

-

 + NO2

- 0.04 ±0.023 0.016 0.422 0.013 ±0.004 0.008 0.075 0.007 ±0.002 0.004 0.022

NH4

+ 0.020 ±0.003 0.017 0.055 0.016 ±0.003 0.011 0.042 0.007 ±0.002 0.002 0.039

Urea 0.004 ±0.001 0.003 0.017 0.007 ±0.003 0.005 0.056 0.004 ±0.001 0.003 0.023

DIN 0.061 ±0.024 0.031 0.442 0.029 ±0.005 0.022 0.08 0.014 ±0.003 0.005 0.059

DON 0.305 ±0.048 0.312 0.652 0.280 ±0.040 0.239 0.62 0.258 ±0.037 0.289 0.467

Total N 0.366 ±0.060 0.347 1.094 0.309 ±0.040 0.286 0.701 0.272 ±0.037 0.305 0.526

HPO4

= 0.004 ± 0.001 0.006 0.012 0.006 ±0.001 0.006 0.012 0.005 ±0.001 0.004 0.011

Total P 0.012 ±0.001 0.011 0.027 0.012 ±0.001 0.011 0.022 0.017 ±0.006 0.009 0.116

Mean Median Max Mean Median Max Mean Median Max

NO3

-

 + NO2

- 0.007 ±0.002 0.005 0.021 0.009 ±0.002 0.004 0.024 0.007 ±0.002 0.003 0.024

NH4

+ 0.006 ±0.002 0.003 0.022 0.006 ±0.001 0.004 0.017 0.006 ±0.001 0.004 0.015

Urea 0.003 ±0.001 0.003 0.01 0.003 ±0.001 0.004 0.007 0.003 ±0.001 0.002 0.008

DIN 0.014 ±0.003 0.011 0.034 0.015 ±0.003 0.008 0.036 0.013 ±0.003 0.007 0.036

DON 0.251 ±0.032 0.257 0.502 0.255 ±0.037 0.267 0.438 0.297 ±0.036 0.36 0.45

Total N 0.265 ±0.031 0.262 0.504 0.270 ±0.036 0.276 0.469 0.310 ±0.036 0.385 0.463

HPO4

= 0.005 ±0.001 0.005 0.011 0.005 ±0.001 0.007 0.013 0.005 ±0.002 0.003 0.018

Total P 0.013 ±0.003 0.009 0.047 0.011 ±0.002 0.008 0.05 0.009 ±0.001 0.008 0.022

Abbreviations: NO3

-

, nitrate; NO2

-

, nitrite; NH4

+

, ammonium; DIN, dissolved inorganic nitrogen; DON, dissolved organic nitrogen; 

HPO4

=

, orthophosphate. Mean is ±SE. 

Nutrient

Nutrient

Mangrove Lagoon Benner Bay Rotto Cay

Cowpet Bay Saint James Little Saint James
STEER Integrated Environmental Assessment Report

198Chapter 9: Nutrients, Sedimentation and TSS Table 9.3. Comparison of STEER nutrient results with those from other U.S. Caribbean locations. 

Min Mean Max Min Mean Max Min Mean Max Min Mean Max Min Mean Max

NO3 + NO2 0 0.014 0.426 ND 0.001 2.664 ND 0.001 3.936 ND 0.001 0.289 0 0.14 3.68

NH4 0 0.01 0.055 ND 0.004 0.175 ND 0.0039 0.2335 ND 0.010 0.978 0 0.05 6.45

Orthophosphate 0 0.005 0.018 ND 0.002 0.158 ND 0.0016 1.8176 ND 0.002 1.234 0 0.05 1.48 1

Data from Smith et al, 2013. 2Data from Whitall et al., 2013. 

Abbreviations: NO3, nitrate; NO2, nitrite. NH4, ammonium; ND, not detected. 

Nutrient

STEER

St. Thomas Puerto Rico2 St. Croix1 St. John1

Lameshur Bay Coral Bay Teague Bay Guanica

concentrations of these nutrients tended to increase. For 

latitude, there was a significant (p < 0.05) positive correlation for these same nutrients, indicating that as latitude 

increased (i.e., moving towards the more populated shores), 

there was an associated increase in concentrations. These 

results provide some evidence that land-based activities 

may be sources of the elevated nutrient concentrations in 

the STEER. The sites further offshore tended to have lower 

levels for a number of the nutrient species. Although there 

were construction activities observed on Little St. James Island during the field work, nutrient concentrations around 

this island were lower than in the Mangrove Lagoon and 

Benner Bay areas.

 

Comparison with Other U.S. Caribbean Studies

A number of projects in the U.S. Caribbean have examined 

the concentration of various nutrients in nearshore waters. 

Summarized results from these studies, along with those 

from the current work in the STEER, are presented in Table 

9.3. From this table, it can be seen that for most of the 

nutrient species, the mean concentrations appeared to be 

somewhat higher in the STEER compared to the locations 

monitored in St. John and St. Croix (Smith et al., 2013), 

although lower than that found in and around Guanica Bay, 

Puerto Rico. Data from Guanica Bay includes both coastal 

embayments (similar to the STEER), and an enclosed estuary. The maximum concentrations found in these other 

studies, however, were almost always higher than that 

recorded in the STEER (Table 9.3). These data indicate 

that the nutrient concentrations in the STEER were similar 

to what has been found in other parts of the USVI and also 

in southwest Puerto Rico. 

Nutrient Concentrations and Rainfall 

Ideally, streamflow gauge data would be used to help 

assess nutrient delivery to the STEER. There are, however, no active streamflow gauges in the Turpentine Gut 

watershed, the largest watershed that drains directly to the 

STEER. The record of the USGS stream gauge data in 

Turpentine Gut appears to have ended in 2008. Because 

of this, rainfall data was used in place of streamflow, as 

a proxy to assess the relationship between the amount of 

rainfall (precipitation) and variations in nutrient concentrations in the STEER. The rationale for using this data is that 

higher rainfall would be expected to result in additional 

runoff and nutrients entering streams that flow into the 

STEER, and also directly into the STEER through runoff 

from streets and hillsides, which would not be accounted 

for from the stream gauge data. The closest rainfall gauge 

to the STEER is located at Redhook Bay in St. Thomas. 

Unfortunately, nearly 40% of the data were missing from 

the records for the time period that the nutrient monitoring 

was conducted for this project. On those days when water 

samples were collected for nutrient analysis, missing data 

for rainfall was over 80%. As a result, precipitation records 

from the Cyril E. King Airport in West Charlotte Amalie, 

with a more complete data set, were used. Daily rainfall 

records for the Cyril E. King Airport were accessed through 

NOAA’s National Climatic Data Center. Daily rainfall estimates were plotted against concentrations for each nutrient 

species at each of the six sites in the STEER. 

Nonparametric tests (Spearman’s) failed to show a significant positive correlation between rainfall and nutrients in 

the STEER. An example of the data for nitrite + nitrate 

(NO2

 + NO3) plotted against rainfall for Benner Bay is 

presented in Figure 9.9. The highest concentration of nitrite 

+ nitrate was found in the May 2013 sampling, however, 

rainfall for that day along with the day before was 0 mm. 

During the period of highest rainfall (1,364 mm) in September 2013, there were unfortunately no water samples 

taken for nutrient analysis. Additional graphs for nutrients 

and rainfall can be seen in Pait et al. (2015). 

 

It’s unclear why there wasn’t a positive correlation between nutrient concentrations and rainfall in the STEER, 

although there are a number of possibilities. One of these 

is the lack of more complete rain gauge data adjacent to the 
STEER Integrated Environmental Assessment Report

199Chapter 9: Nutrients, Sedimentation and TSS

Figure 9.2. Mean and max concentrations of ammonium (NH4+) detected in water samples from the STEER.

LSJ 

RC 

BB 

CB 

SJ 

LSJ 

ML 

Mean 

0.020 

Max 

0.055 

0.016 0.042 

Mean Max 

0.007 0.039 

Mean Max 0.006 0.022 

Mean Max 

0.006 0.017 

Mean Max 

Mean 

0.006 0.015 

Mean Max 

NH4+ (mg/l N) 

Mean Max  0 – 0.007 0 – 0.022  0.08 – 0.020 0.023 – 0.042  0.043 – 0.055 
STEER Integrated Environmental Assessment Report

200Chapter 9: Nutrients, Sedimentation and TSS

Figure 9.3. Mean and max concentrations of nitrate (NO3-) and nitrite (NO2-) detected in water samples from the STEER.

LSJ 

LSJ 

RC 

BB 

CB 

SJ 

LSJ 

ML 

0.040 0.422 

Mean Max 

0.013 0.075 

Mean Max 

Mean Max 

0.007 0.021 

Mean Max 

Mean 

0.009 0.024 

Mean Max 

Mean 

0.007 0.024 

Mean Max 

NO3 + NO2 (mg/l N) 

Mean Max 

 0 – 0.009 0 – 0.024  0.010 – 0.013 0.024 – 0.075  0.014 – 0.040 0.076 – 0.422 

0.007 

Max 

0.022 

Mean 
STEER Integrated Environmental Assessment Report

201Chapter 9: Nutrients, Sedimentation and TSS

Figure 9.4. Mean and max concentrations of urea detected in water samples from the STEER.

LSJ 

RC 

BB 

CB 

SJ 

LSJ 

ML 

0.004 0.017 

Mean Max 

0.007 0.056 

Mean Max 

0.004 0.023 

Mean Max 

Mean Max 

0.003 0.011 

Mean Max 

0.003 0.007 

Mean Max 

Mean 

0.003 0.008 

Mean Max 

Urea (mg/l N) 

Mean Max  0 – 0.002 0 – 0.011  0.003 – 0.004 0.012 – 0.023  0.005 – 0.007 0.024 – 0.056 
STEER Integrated Environmental Assessment Report

202Chapter 9: Nutrients, Sedimentation and TSS

Figure 9.5. Mean and max concentrations of dissolved inorganic nitrogen (DIN) detected in water samples from the STEER.

RC 

BB 

CB 

SJ 

LSJ 

ML 

0.061 0.442 

Mean Max 

0.014 0.059 

Mean Max 

Max 

Mean Max 

0.014 0.034 

Mean Max 

0.015 0.036 

Mean Max 

Mean 

0.013 0.036 

Mean Max 

Dissolved Inorganic Nitrogen (DIN) (mg/l N) 

Mean Max  0 – 0.015 0 – 0.036  0.016 – 0.028 0.037 – 0.079  0.029 – 0.061 0.080 – 0.442 

Max 

0.029 0.080 

Mean 
STEER Integrated Environmental Assessment Report

203Chapter 9: Nutrients, Sedimentation and TSS

Figure 9.6. Mean and max concentrations of total nitrogen (TN) detected in water samples from the STEER.

LSJ 

RC 

BB 

CB 

SJ 

LSJ 

ML 

0.366 1.094 

Mean Max 

0.309 0.701 

Mean Max 

0.272 0.526 

Mean Max 

Max 

Mean Max 

0.265 0.504 

Mean Max 

Mean Max 

0.270 0.469 

Mean Max 

Mean 

0.310 0.463 

Mean Max 

Total Nitrogen (TN) (mg/l N) 

Mean Max  0 – 0.272 0 – 0.526  0.273 – 0.310 0.527 – 0.701  0.311 – 0.366 0.702 – 1.094 
STEER Integrated Environmental Assessment Report

204Chapter 9: Nutrients, Sedimentation and TSS

Figure 9.7. Mean and max concentrations of orthophosphate (HPO4=) detected in water samples from the STEER.

RC 

BB 

CB 

SJ 

LSJ 

ML 

0.005 0.012 

Mean Max 

0.006 0.012 

Mean Max 

0.005 0.011 

Mean Max 

Mean Max 

0.005 0.011 

Mean Max 

Mean 

0.005 0.013 

Mean Max 

Mean 

0.005 0.018 

Mean Max 

Orthophosphate (HPO4=) (mg/l P) 

Mean Max  0 - 0.005 0 - 0.011  0.006 0.012 – 0.013  0.0.14 – 0.018 
STEER Integrated Environmental Assessment Report

205Chapter 9: Nutrients, Sedimentation and TSS

Figure 9.8 Mean and max concentrations of total phosphorus (TP) detected in water samples from the STEER.

LSJ 

RC 

BB 

CB 

SJ 

LSJ 

ML 

0.012 0.027 

Mean Max 

0.012 0.022 

Mean Max 

0.017 0.116 

Mean Max 

Mean Max 

0.013 0.047 

Mean Max 

Mean Max 

0.011 0.050 

Mean Max 

Mean 

0.009 0.022 

Mean Max 

Total Phosphorus (TP) (mg/l P) 

Mean Max 

 0 – 0.013 0 – 0.027  0.014 – 0.017 0.028 – 0.050  0.051 – 0.116 
STEER Integrated Environmental Assessment Report

206Chapter 9: Nutrients, Sedimentation and TSS STEER. Rainfall data near the STEER might reveal better 

correlations between rainfall and nutrient concentrations. 

Rainfall patterns on St. Thomas can be highly localized, 

and more complete rainfall data near the STEER might 

help better elucidate any relationships between rainfall, the 

mountainous terrain, and nutrients. Another possibility is 

that discharges from septic systems into the STEER either 

from streams like Turpentine Gut, or via groundwater to the 

STEER, are providing a continuous source of nutrients, independent of rainfall. Another factor may be the influence 

of winds or tides on the resuspension of sediments into the 

water column containing nutrients. There is also significant 

boating activity including some liveaboards, particularly in 

the Benner Bay area, which are a likely source of nutrients 

to the STEER. There did not appear to be any significant 

differences in the nutrient concentrations between the wet 

and dry seasons. Finally, sampling for this project was not 

designed to be during or just after heavy rainfall events, 

which might have provided a better correlation between 

rainfall and nutrient levels. 

Relationships Between Nutrients 

Whitall et al. (2013) examined correlations between nutrient species, leaving out those that are autocorrelated (e.g., 

orthophosphorus and total phosphorus), and found that 

ammonium, urea and orthophosphorus were associated 

with runoff, while the oxidized forms of nitrogen tended to 

percolate into soils during rainfall events, and eventually 

into groundwater. Spearman’s rank correlation coefficient 

analysis for the STEER also indicated significant correlations between ammonium, urea and orthophosphorus, and 

that these species were not correlated with the more oxidized forms of nitrogen, particularly nitrate plus nitrite. 

Nutrients and Coral Reefs 

Lapointe (1997) suggested nutrient thresholds for marine 

waters, above which macroalgae and phytoplankton were 

more likely to flourish on coral reefs, in the greater Caribbean. While it needs to be acknowledged that coral species 

respond differently to elevated nutrient concentrations, and 

that there has been some controversy regarding the use 

of thresholds (Hughes and Connell, 1999; Szmant, 2002) 

proposed by Lapointe (1997) and others, these thresholds 

provide an opportunity to assess nutrient levels that may be 

of concern. Thresholds were proposed for orthophosphate 

(0.003 mg/L as P), and dissolved inorganic nitrogen (DIN, 

0.014 mg/L as N). DIN is the summation of nitrate, nitrite 

and ammonium. 

Figure 9.9. Nitrate and nitrite concentrations versus rainfall in Benner Bay during the study period.

0

0.01

0.02

0.03

0.04

0.05

0.06

0.07

0.08

0.09

0.1

0

200

400

600

800

1000

1200

1400

1600

1/16/20122/16/20123/16/20124/16/20125/16/20126/16/20127/16/20128/16/20129/16/2012

10/16/201211/16/201212/16/2012

1/16/20132/16/20133/16/20134/16/20135/16/20136/16/20137/16/20138/16/20139/16/2013

10/16/201311/16/2013

Nitrite + Nitrate (mg/LͲN)

Daily Rainfall (mm)

Rainfall

NO2 + NO3

Figure 9.10. Percent exceedances of DIN threshold by site in the 

STEER.

0

10

20

30

40

50

60

70

80

90

100

% Exceedences of DIN threshold
STEER Integrated Environmental Assessment Report

207Chapter 9: Nutrients, Sedimentation and TSS

Using the values proposed by Lapointe 

(1997), 58% of the samples analyzed from 

the STEER were above the threshold for 

orthophosphate, with a slightly higher number (61%) within the western portion of the 

study area. For DIN (Figure 9.10), the mean 

exceedance across the STEER was 55%. A 

nonparametric analysis using the Wilcoxon 

method indicated that DIN varied by sampling site, with DIN at Mangrove Lagoon and 

Benner Bay signifi cantly higher (p < 0.01) 

In Figure 3.13 from Chapter 3, it appears that 

macroalgae may be somewhat abundant in 

Mangrove Lagoon. In addition, Figure 9.11 

shows herbivore biomass at the sites sampled 

in the STEER. There does not appear to be 

an overabundance of herbivores, particularly in Mangrove 

Lagoon, and perhaps in the western portion of Benner 

Bay. Some areas of the STEER may be at risk, to blooms 

of macroalgae which could outcompete and eventually 

smother corals in the area. There is also concern regarding 

the direct effects of nutrients on corals, including reduced 

fertilization and reduced calcifi cation rates (Harrison and 

Ward, 2001; Marubini and Davis, 1996). The likely source 

of these nutrients are inputs from the developed areas 

around the STEER. 

Sedimentation 

A summary of the results from the monthly monitoring of 

sediment traps in the STEER (January 2012 to November 

2013) can be seen in Figures 9.12 to 9.17. 

Differences by Site 

The average percent deposition of 

sediments by weight is presented 

in Figure 9.12. For all sites, terrigenous material was dominant, 

accounting for 60 to 70% of total 

sediment in the traps, highlighting 

the role of terrestrial inputs to the 

STEER. Conversely, it can also be 

seen that carbonate inputs appeared 

somewhat smaller in Mangrove Lagoon and Benner Bay, compared to 

the more offshore sites, as might be 

expected. Also, the organic fraction 

tended to be higher at the Mangrove 

Lagoon, Benner Bay and perhaps 

the Rotto Cay sites. Organic inputs, 

however, can be from terrestrial or 

marine sources. 

The percent terrigenous material in the sediment traps in 

the STEER was significantly higher (p < 0.05) in Mangrove Lagoon, Benner Bay, and Rotto Cay compared to the 

other locations in the STEER. In addition to fresh inputs 

from the surrounding watershed, resuspended bed sediments from within the STEER can enter the traps as well, 

as a result of storms (wave and wind activity), or from boat 

traffic in Benner Bay. The contribution from new versus 

resuspended materials can not be determined using the 

traps deployed. 

The percent carbonate deposition in the sediment traps was 

significantly higher (p < 0.05) at Rotto Cay, Cowpet Bay 

and Saint James, further away from the land-based inputs 

in the Benner Bay and Mangrove Lagoon areas. Carbonate sediments are derived primarily from marine skeletons 

(e.g., coral) and shells. 

 

Figure 9.11. Herbivore biomass in the STEER.

D

D

D D D D

Habitat strata

Coral Reef and Hardbottom

Unconsolidated Sediments

Mangrove

Reef/Hardbottom outside STEER

Land

STEER boundary

Excluded from survey

Herbivore biomass (g/100 m2)

D 0

0.1 - 1000

1000.1 - 2000

2000.1 - 4000

4000.1 - 18159.9

012 0.5

Kilometers  ̄

Figure 9.12. Bulk deposition of sediment in traps placed in the STEER.

0

10

20

30

40

50

60

70

80

90

100

% deposition by weight

% Carbonate

% Organic

% Terrigenous
STEER Integrated Environmental Assessment Report

208Chapter 9: Nutrients, Sedimentation and TSSThe sediment trap site adjacent to Little St. James Island 

(Figure 9.1), arguably the site 

furthest away from Benner 

Bay and Mangrove Lagoon, 

appeared to have a somewhat 

higher terrigenous fraction 

(Figure 9.12), and a correspondingly lower carbonate 

input. The difference in the 

percent carbonate fraction 

between the Little St. James 

and Saint James sites was 

significant. During the course 

of the sediment trap work, 

substantial earth moving 

activities were observed on 

Little St. James Island (Figure 

9.13), which would likely be 

a significant source of terrigenous sediments entering the 

adjacent waters.

A comparison of the mean 

daily accumulation rates in 

the sediments traps by site is 

presented in Figure 9.14. The 

mean accumulation rate (9.02 

mg/cm2

/day) in the Benner Bay 

sediment traps was significantly 

(p < 0.001) higher than the trap 

accumulation rates at all other 

sites in the STEER. Similar to 

the bulk deposition of sediments, 

the highest accumulation rates 

were seen for the terrigenous 

fraction. The mean terrigenous 

accumulation rate (6.45 mg/

cm2

/day) was also higher (p 

< 0.0001) in Benner Bay than 

the other sediment traps in the 

STEER, including Mangrove 

Lagoon. Although Mangrove 

Lagoon receives input from Turpentine Gut, the only perennial 

stream on St. Thomas, the highest rate of terrigenous sediment 

input occurred in Benner Bay. 

There are likely two sources 

of input to the traps placed at 

Benner Bay: terrestrial materials 

washed off the roads and hillsides from the surrounding 

landscape, and resuspended 

sediments from within Benner Bay. The hillsides in 

the watershed surrounding 

Benner Bay are fairly steep, 

and in some areas bare soils 

are exposed. These factors, 

along with widespread construction activities, and periodic torrential downpours, 

can lead to the transport of 

soils into the STEER (Horsley Witten, 2013). Pait et 

al. (2013) found that sediments in northern Benner 

Bay had some of the highest 

silt and clay fractions (31 

- 56%) in the STEER. Silt 

and clay sediments are typically derived from terrestrial 

sources. Sediment coring 

in northern Benner Bay 

by NCCOS in 2013 (see 

Chapter 5), revealed a thick 

layer of silt and clay over a 

deeper layer of shell hash, 

Figure 9.13. Excavation activity on Little St. James Island, a possible source of terrigenous sediments found in the sediment traps 

at this site.

Figure 9.14. Average accumulation rates at the sediment trap sites in the STEER.

0

1

2

3

4

5

6

7

8

9

10

Mean Organic Accumulation Rate

Mean Carbonate Accumulation Rate

Mean Terrigenous Accumulation Rate

Trap accumulation rate (mg/cm2/day)
STEER Integrated Environmental Assessment Report

209Chapter 9: Nutrients, Sedimentation and TSS

indicating that changes 

in land use over time 

have resulted in higher 

amounts of terrigenous 

materials transported 

to the STEER. 

Variation by Latitude 

and Longitude 

A nonparametric analysis revealed a significant negative correlation (Spearman’s Rho 

= -0.6686, p < 0.0001) 

between longitude and 

mean trap accumulation rate, and between 

the terrigenous accumulation rate and 

longitude (Spearman’s 

Rho = -0.6625, p < 0.0001), indicating that moving east to 

west, the deposition rate of terrigenous sediments tended to 

increase. 

There was also a significant (Spearman’s Rho = 0.5047, p 

< 0.001) positive correlation between latitude and mean 

trap accumulation rate, along with the terrigenous accumulation rate, indicating that deposition tended to increase 

moving from the more offshore sites to the nearshore locations. 

Comparison with Other U.S. Caribbean Studies 

The mean terrigenous accumulation in sediments traps 

found by Sherman et al. (2013) within Guanica Bay Puerto 

Rico, was roughly 58%, less but somewhat similar to what 

was found in the STEER. Outside of Guanica Bay, the percent terrigenous was only 24%. As noted, the mean percent 

terrigenous sediment in the traps in the STEER was higher, 

approximately 66% terrigenous and 20% carbonate. Within 

the STEER, Mangrove Lagoon (73%) and Benner Bay 

(71%) were even higher. Working in St. John, Gray et al.

(2012), found that terrigenous input into the sediment traps 

in Coral Bay located near the shore accounted for 56%. 

Out on the reefs in Coral Bay, that value fell to roughly 

21% (Gray et al., 2012). In Lameshur Bay, terrigenous 

sediment accounted for approximately 32% of the material 

in the nearshore sites, and fell to roughly 15% out on the 

reefs in this Bay. Terrigenous input into the sediment traps 

in the STEER was quite high. Additional work is needed 

to better characterize the inputs of fresh material from the 

surrounding watershed versus resuspended sediments. 

Sediment Deposition and Rainfall 

As with nutrients, there did not appear to be a good correlation between sediment deposition and rainfall. A plot of 

the sediment trap accumulation rate and rainfall for Benner 

Bay can be seen in Figure 9.15. A plot of the terrigenous 

accumulation rate showed similar results. Nonparametric 

(Spearman’s) analyses of the results between sedimentation and daily and monthly rainfall (Cyril E. King Airport) 

failed (Spearman’s Rho = 0.0747, p = 0.4491) to show any 

significant relationship, either across the STEER or for 

each site. 

On the northwestern coast of St. Thomas, Nemeth and 

Nowlis (2001) found that sedimentation closely tracked 

rainfall during a period of early construction at a new resort 

near Caret Bay, however, once the earth-moving phase had 

been completed, that relationship disappeared, resulting in 

an overall lack of significance between rainfall and sedimentation during their study. In the STEER, it would likely 

take sustained rainfall over a period of days in order to alter 

the amount of sediment accumulating in the traps from 

surface water runoff, and so correlations with daily rainfall 

might not be particularly useful. However, monthly rainfall 

amounts did not correlate with the sediment deposition 

rates either. It may be that other factors are involved with 

increases in sedimentation, including increased wave action 

resuspending sediments already within the STEER.

Sediment Deposition Over Time

Plots of sediment deposition over time, both in terms of 

percent deposition and by sedimentation rate for three of 

the sites in the STEER are shown in Figure 9.16. Graphs 

for Rotto Cay, Cowpet Bay, and Saint James can be seen 

Figure 9.15. Bulk deposition in Benner Bay sediment traps plotted against rainfall.

0

5

10

15

20

25

0

200

400

600

800

1000

1200

1400

1600

1/16/20122/16/20123/16/20124/16/20125/16/20126/16/20127/16/20128/16/20129/16/2012

10/16/201211/16/201212/16/2012

1/16/20132/16/20133/16/20134/16/20135/16/20136/16/20137/16/20138/16/20139/16/2013

10/16/201311/16/2013

Trap accumulation (rate mg/cm2/d)

Daily Rainfall (mm)

Rainfall

Trap accumulation rate D.W. (mg/cm2/d)
STEER Integrated Environmental Assessment Report

210Chapter 9: Nutrients, Sedimentation and TSS

in the appendices in Pait et al. (2015). In Figure 9.16, 

the contributions from terrestrial, carbonate and organic 

sources were fairly constant over time for both Mangrove 

Lagoon (a) and Benner Bay (b). In both cases, terrigenous 

material was the major component (~70%) found in the 

sediment traps. The lack of substantial variation in the 

sources (terrestrial versus carbonate) in Mangrove Lagoon 

and Benner Bay sediment traps could indicate a continuous 

input of terrestrially-derived sediments at these two sites 

as a result of new input, resuspension of sediments into the 

water column from storms, tides and boats (in Benner Bay), 

or a combination of these phenomena. On the right hand 

side of Figure 9.16, for Mangrove Lagoon (d) and Benner 

Bay (e), there is substantial variation in the daily rate of 

terrigenous and carbonate deposition (organic material can 

be derived from terrestrial or marine sources) over time. In 

March 2012, there was a sharp increase in the terrigenous 

fraction found in the sediment traps in Mangrove Lagoon 

(Figure 9.16d). Specifically, the rate increased from 2.79 

mg/cm2

/day to 6.10 mg/cm2/day, a factor of 2.18. However, 

at the same time, the carbonate deposition rate went from 

0.141 to 0.456 mg/cm2

/day, a factor of 3.23, higher than the 

rate increase for the terrigenous fraction. While the increase in the terrigenous sediment deposition rate may have 

been related to rainfall during this period, other factors such 

as the movement of tides or winds that could have led to a 

resuspension of sediments cannot be ruled out. In addition, 

there does not appear to be a corresponding increase in the 

rate of sediment deposition in the adjacent Benner Bay site 

in March 2012, as might be expected if rainfall had resulted 

Figure 9.16. Percent and rates of deposition for terrigenous, carbonate and organic materials in the sediment traps in the STEER 

over time for Mangrove Lagoon (a, d), Benner Bay (b, e), and Little St. James (c, f).

0

10

20

30

40

50

60

70

80

Percent Deposition

Mangrove Lagoon

Mean % terrigenous

Mean % carbonate

Mean % organic

a.

0

1

2

3

4

5

6

7

Deposition Rate (mg/cm2/d)

Mangrove Lagoon

Mean Terrigenous Accumulation Rate

Mean Carbonate Accumulation Rate

Mean Organic Accumulation Rate

d.

0

10

20

30

40

50

60

70

80

90

Percent Deposition

Benner Bay b.

0

2

4

6

8

10

12

Deposition Rate (mg/cm2/d)

Benner Bay e.

0

10

20

30

40

50

60

70

80

90

Percent Deposition

c. Little St. James

0

2

4

6

8

10

12

14

Deposition Rate (mg/cm2/d)

Little St. James f.
STEER Integrated Environmental Assessment Report

211Chapter 9: Nutrients, Sedimentation and TSS

in higher surface water runoff from the steep hillsides, carrying terrestrially derived materials to the STEER. 

For Little St. James (Figure 9.16c), deposition appeared 

more variable, and may be related to weather and wave 

patterns. In Figure 9.16f, it can be seen that there was a 

spike in terrigenous, organic and carbonate deposition into 

the Little St. James sediment traps sampled in September 

2012. In August 2012, sediment traps in the STEER were 

sampled around the middle of the month. In late August 

2012, Hurricane Isaac passed to the south of the USVI, and 

appears likely responsible for the increased rates of sedimentation found when the sediment traps were retrieved in 

September. Further evidence of this is presented in Figure 

9.17. Total monthly deposition of sediment in the traps 

is plotted from January 2012 through October 2012. The 

average deployment of the sediment traps during this period was 30 days. Daily rainfall records from the Cyril E. 

King Airport are shown in Figure 9.17b. Wave height data 

(Figure 9.17c) were obtained from the Caribbean Coastal 

Ocean Observing System (CariCOOS), for a site south 

of St. John (Station 41052 ), and accessed online through 

NOAA’s National Data Buoy Center data base (http://www.

ndbc.noaa.gov/station_page.php?station=41052). Although 

the station is not within the boundaries of the STEER 

(there appear to be no wave stations in the STEER), it does 

provide an indication of likely increases in wave height, at 

least entering the southern portion of the STEER.

In Figure 9.17a, there was increased deposition in the traps 

found during the September 2012 sampling, particularly in 

the more offshore traps at Little St. James and Saint James 

(identified in red circle). The amount of sediment in the 

traps at Little St. James (17.3 g) in September 2012, was 

actually higher than in the traps at Benner Bay. Also, the 

amount of sediment in the traps at Little St. James in September 2012 was higher by a factor of 14 from the previous 

month at this site. At Saint James, the amount of sediment 

in the traps was 12.7 g, an increase in sediment deposition 

by a factor of 12 from the previous month. As mentioned, 

Hurricane Isaac passed to the south of the USVI in late 

August 2012. While there did not appear to be a substantial 

amount of rainfall (Figure 9.17b) in St. Thomas associated 

with this system, wave height increased to nearly 4 meters 

(Figure 9.17c) at the CariCOOS wave station just south of 

St. John. It seems likely that waves from Hurricane Isaac, 

moving into the southern portion of the STEER, resulted in 

the remobilization of bed sediments that were subsequently 

deposited into the sediment traps at both Saint James and 

Little St. James. As can be seen in Figure 9.16, the percent 

contribution from terrigenous versus carbonate during this 

time did not appear to change appreciably. During the 

same period, the Benner Bay traps also accumulated more 

sediment, however, the percent terrigenous contribution 

also did not change. 

Sedimentation and Coral Reefs 

Rogers (1990) suggested that sedimentation rates above 

10 mg/cm2

/day on coral reefs may be excessive, and that 

heavy sedimentation on reefs has been associated with 

Figure 9.17. Plots of mean sediment deposition (a), rainfall (b) 

and wave height at Station 41052 (c).

0

2

4

6

8

10

12

14

16

18

20

Sediment Deposition (g)

Benner Bay Cowpet Bay

Little Saint James Mangrove Lagoon

Rotto Cay Saint James

0

100

200

300

400

500

600

Rainfall (mm)

0

0.5

1

1.5

2

2.5

3

3.5

4

Wave Height (m)

c.

b.

a.

Hurricane Isaac
STEER Integrated Environmental Assessment Report

212Chapter 9: Nutrients, Sedimentation and TSS fewer coral species, less live coral, 

reduced recruitment 

and slower accretion 

rates among other 

effects. Research by 

Smith et al. (2008) 

and Nemeth and 

Nowlis (2001) have 

shown this value 

may be useful at 

least in the USVI, 

for determining 

when coral reefs 

are at risk to being 

impacted by chronic 

sedimentation.

Using the rate of 10 

mg/cm2

/day, none of the sites had a mean rate above this, 

although Benner Bay (Figure 9.14) (9.02 mg/cm2/day) was 

fairly close. There were nine occasions, however, during 

the course of the monthly monitoring when a site exceeded 

this threshold. Benner Bay exceeded the threshold on six 

occasions, and Rotto Cay, St. James (September 2012) 

and Little St. James (September 2012) each exceeded the 

threshold once. Although none of the sites had a mean 

sedimentation rate above the suggested threshold, sedimentation in Benner Bay appears to be high enough to put the 

corals in this area at some risk. Additional work is needed 

to better describe sedimentation throughout Benner Bay. In 

addition, it would also be useful to understand the association between coral species richness/diversity and sedimentation in Benner Bay and throughout the Reserves, in order 

to assess how sedimentation and perhaps the chemical 

contaminants present may be affecting the distribution of 

individual coral species.

Total Suspended Solids (TSS)

A summary of the results from TSS monitoring in the 

STEER is presented in Figure 9.18. TSS includes silts 

which can settle out onto reefs impacting the health of corals, along with plankton and other materials, some naturally 

occurring while others are derived from human activities. 

TSS also impacts corals and seagrasses by decreasing the 

amount of light available for photosynthesis. In northern 

Benner Bay (in addition to northern Mangrove Lagoon), 

the biological survey by SCUBA divers could not be conducted, due in part to poor visibility.

Differences by Site

Nonparametric analysis (Wilcoxon Rank-Sum) revealed 

that the mean TSS value (8.32 ±0.88 mg/L) in Benner Bay 

was significantly (p < 0.01) higher than the other sites, with 

the exception of Mangrove Lagoon. As was seen earlier, 

the Benner Bay site had a signifi cantly different (higher) 

mean turbidity than the other sites in the STEER (Table 

9.1). Finally, TSS at Rotto Cay, Cowpet Bay, Saint James, 

and Little Saint James were not significantly different from 

each other. 

Variation by Latitude and Longitude

Like the results from the sediment traps, a nonparametric analysis indicated there was a significant and negative (Spearman’s Rho = -0.5466, p < 0.0001) correlation 

between longitude and TSS, indicating that moving east to 

west, concentrations of TSS tended to increase. In addition, 

there was a positive and significant (Spearman’s Rho = 

0.4725, p < 0.0001) correlation between latitude and TSS, 

indicating that TSS was higher in the more nearshore sites. 

Minimum Mean Maximum

St. Thomas

STEER 0.5 4.7 18.6

St. John1

Lameshur Bay 0.4 6.5 22.0

Coral Bay 1.0 6.5 22.0

Fish Bay 0.8 6.8 24.0

St. Croix1

Teague Bay 1.0 6.4 28.0

1

Data from Smith et al. , 2013. 

TSS (mg/l)

Table 9.4. Comparison of TSS in the STEER with other 

locations in the USVI.

 Figure 9.18. Total suspended solids (TSS) means (±SE) at sampling sites in the STEER. Sites with 

the same letter were not statistically different. 

0

1

2

3

4

5

6

7

8

9

10

Mangrove Lagoon Benner Bay Rotto Cay Cowpet Bay Saint James Little Saint James

TSS (mg/L)

A

A

B B

B

B
STEER Integrated Environmental Assessment Report

213Chapter 9: Nutrients, Sedimentation and TSS

Comparison with Other U.S. Caribbean Studies 

Table 9.4 presents a comparison of the TSS results from 

work in the STEER, with that of measurements made in St. 

John and St. Croix; (Smith et al., 2013). From this table, it 

can be seen that the STEER sites were similar to the sites 

sampled on St. John and St. Croix, for both the mean and 

maximum values. The highest TSS value recorded in the 

STEER was 18.6 mg/L, in Benner Bay in January 2012. 

TSS Concentrations and Rainfall

A nonparametric correlation analysis (Spearman Rank Correlation) 

was first run on TSS versus daily 

rainfall. The results (Spearman’s 

Rho = -0.0844, p = 0.3535, ) indicated no significant relationship 

between daily rainfall and TSS in 

the STEER throughout the course of 

the study. The lack of a significant 

relationship with rainfall was similar to that found for the sediment 

traps. As with those results, it is not 

clear why there wasn’t a significant 

relationship between TSS and rainfall in the STEER. Although stream 

flow data was not available, higher 

rainfall might be expected to result in higher levels of TSS. 

As with sedimentation, it is possible that at least some of 

the TSS was the result of resuspension of sediments. It 

could also be that there is a lag time between a large rain 

event and when that water empties into the STEER. This 

second possibility seems unlikely though, given the steep 

slopes in much of the watershed. Additional work is 

needed to assess the relationship between rainfall, streamflow and sediment delivery to the STEER. 

TSS and Coral Reefs

Rogers (1990) suggested that suspended sediment concentrations above 10 mg/L on coral reefs may be excessive, 

and that heavy sedimentation on reefs has been associated 

with fewer coral species, less live coral, reduced recruitment and slower accretion rates among other effects. None 

of the sites in the STEER had a mean TSS value above 10 

mg/L, however, the mean for Benner Bay during the study 

was 8.32 mg/L. 

There were 19 occasions during the monthly monitoring 

when TSS exceeded 10 mg/L. The highest TSS value recorded was 18.6 mg/L in Benner Bay. Forty-seven percent 

of the exceedances of the threshold occurred in Benner 

Bay, followed by Mangrove Lagoon with 26%. Similar to 

the results for sedimentation, corals in the Benner Bay area 

would appear at some risk as a result of suspended solids. 

While there were a number of exceedances in Mangrove 

Lagoon, there appear to be very few corals in this area; corals were only found in the extreme southern portion of the 

lagoon. 

Relationships Between Parameters 

Finally, a series of nonparametric analyses (Spearman Rank 

Correlation) were carried out to assess relationships between parameters measured in this part of the project in the 

STEER. The mean sediment trap 

accumulation rate was highly correlated with TSS. This is perhaps 

not surprising, as some of the 

TSS eventually settles out of the 

water column. Areas with higher 

levels of TSS might also be areas 

of higher sediment deposition, 

as a result of transport from the 

watershed, or from resuspension 

within the STEER. A number of 

the nutrients, particularly the nonoxidized forms (e.g., ammonium, 

urea, and orthophosphate) were 

correlated (p < 0.05) with both 

TSS and sediment deposition, 

again suggesting areas with higher 

inputs of sediments were associated with higher inputs of 

specific nutrient classes

9.4. CONCLUSIONS

The monitoring of nutrients, sedimentation and total suspended solids (TSS) for 23 months was part of the project 

in the STEER to assess the presence and effects of landbased sources of pollution, and a characterization of the 

biological communities within the STEER. The results 

indicated elevated levels of nutrients in the western portion 

(Mangrove Lagoon and Benner Bay) of the STEER. These 

areas contain higher densities of residential housing, most 

of which have septic systems, and many that are likely failing. There is also a horse racetrack along with the Bovoni 

Landfill which border Mangrove Lagoon on the north and 

west sides, as well as live-aboard boats in Benner Bay, all 

of which have the potential to contribute nutrients, leading 

to higher concentrations in this part of the STEER. Ammonium, nitrite and dissolved inorganic nitrogen (DIN) 

were higher in Benner Bay and Mangrove Lagoon than the 

other sites in the STEER. For DIN, both Mangrove Lagoon 

and Benner Bay had significantly higher levels than the 

other four sites. 

A significant relationship between rainfall and nutrients, 

although expected, was not found. Because there are no active stream gauges in the watershed draining to the STEER, 

Apparatus for fi ltering water samples for measuring 

TSS in the STEER.
STEER Integrated Environmental Assessment Report

214Chapter 9: Nutrients, Sedimentation and TSSrainfall was used a proxy for streamflow. The reason for 

the lack of correlation between rainfall and nutrients was 

not clear. It would be useful to have an active stream gauge 

in the watershed that could be used to assess the relationship between stream flow and concentrations of nutrients. 

If a stream gauge is not possible, then more complete rainfall data at Redhook would be helpful. 

The concentrations of the nutrients measured in the STEER 

were similar to other sites recently monitored in the U.S. 

Caribbean. Nutrient values in the STEER appeared slightly 

higher than in St. John and St. Croix, USVI, but lower than 

in Guanica Bay in Puerto Rico. Approximately 60% of the 

nutrient samples analyzed from the STEER were above a 

proposed threshold for coral reefs for orthophosphate, with 

a slightly higher number within the western portion of the 

study area. 

Results from the monitoring of sedimentation indicated that 

terrigenous material accounted for roughly 60 - 70% of the 

material found in the sediment traps, highlighting the role 

of terrestrial inputs to the STEER. Terrigenous inputs to 

the sediment traps in the STEER appeared higher than in 

studies that have been conducted in nearby St. John, USVI, 

and also in the Guanica Bay area in Puerto Rico, highlighting the magnitude of terrigenous input to the STEER. The 

percent terrigenous material in the sediment traps was higher in both Mangrove Lagoon and Benner Bay compared to 

the other locations in the STEER. It is likely that in addition to inputs of sediment from the surrounding watershed, 

resuspended sediments as a result of storm (wave and wind 

activity) or boat traffic (Benner Bay) are likely contributing 

to the material found in the traps as well. 

The average daily accumulation rates in the sediments traps 

were higher in Benner Bay then at all the other sites in the 

STEER, including Mangrove Lagoon. The mean accumulation rate and the terrigenous accumulation rate were 

negatively correlated with longitude, and positively correlated with latitude, indicating rates tended to be higher in 

the western and nearshore portions of the study area. 

There are steep hillsides in the area around northern Benner 

Bay, that contribute terrigenous materials to the STEER 

through surface water runoff. Follow up work in 2013 for 

another part of the STEER project (Chapter 5), in which 

sediment cores were taken, revealed a thick layer of silt and 

clay over older shell hash in sediment cores from northern 

Benner Bay, testifying to historic changes in land use that 

have resulted in increased transport of terrigenous material 

to the STEER. In addition, this area contains numerous 

marinas and boat yards. The boat traffic in and out of this 

portion of the STEER may be resuspending sediments into 

the water column as well. 

As with nutrients, there did not appear to be a good correlation between sediment deposition and rainfall. A stream 

gauge in the watershed would help with understanding the 

relationship between streamflow, rainfall and sediment 

delivery. 

The percent deposition of sediment over time by source 

(i.e., terrigenous, carbonate and organic) was fairly constant, particularly for Mangrove Lagoon and Benner Bay, 

with terrigenous material being the major component 

(~70%) found in the sediment traps. It would appear that 

the lack of substantial variation in the sources (terrestrial 

versus carbonate) in the Mangrove Lagoon and Benner 

Bay traps could indicate a continuous input of terrestriallyderived sediments at these two sites as a result of runoff, 

resuspension of sediments from storms, tides or boats, or a 

combination of these phenomena. 

A comparison of the sedimentation rates in the STEER with 

a proposed threshold for coral reefs (10 mg/cm2

/day), indicated that none of the sites monitored in the STEER had an 

average above this value, although Benner Bay (9.02 mg/

cm2

/day) was close. 

Results from the monthly monitoring indicated that like 

the nutrient and sedimentation monitoring, the western and 

more nearshore portions of the STEER had higher levels of 

TSS. Benner Bay and Mangrove Lagoon had higher TSS 

levels than the other sites monitored in the STEER. Results 

indicated that the TSS levels in the STEER were similar to 

those found in studies in St. John and St. Croix. As with 

sedimentation, there was no correlation between TSS and 

rainfall. 

None of the sites in the STEER had a mean value that 

exceeded a proposed TSS threshold for coral reefs of 10 

mg/L. The highest was Benner Bay with a mean of 8.32 

mg/L. 

The results from this part of the project in the STEER show 

that nutrients in particular, along with sedimentation are 

frequently elevated. The Mangrove Lagoon and Benner 

Bay areas are of particular concern and in need of additional management efforts to reduce the input of these environmental stressors in order to ensure a healthy, functioning 

ecosystem. 
STEER Integrated Environmental Assessment Report

215Chapter 9: Nutrients, Sedimentation and TSS

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1967. Th e measurement of upwelling and subsequent 

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381-389.

Bernhardt, H. and A. Wilhelms. 1967. Th e continuous 

determination of low level iron, soluble phosphate and total 

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Box, S. J. & Mumby, P. J. 2007. Eff ect of macroalgal competition on growth and survival of juvenile Caribbean corals. 

Marine Ecology Progress Series 342, 139–149.

Burke, L., and J. Maidens. 2004. Reefs at Risk in the

Caribbean. World Resources Institute. Washington,

D.C. 80pp.

Butman (Hannan), C.A. (1984). Initial Settlement of Marine 

Invertebrate Larvae: Th e Role of Passive Sinking in a Nearbottom Turbulent Flow Environment. Doctoral Dissertation, Woods Hole Oceanographic Institution/Massachusetts 

Institute of Technology, WHOI-84-18, 535 pp.

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217Chapter 10: Summary and Conclusions

STEER Integrated Environmental Assessment Report

CHAPTER 10: SUMMARY AND CONCLUSIONS

NOAA’s National Centers of Coastal Ocean Science along 

with local partners, and with funding from NOAA’s Coral 

Reef Conservation Program (CRCP), conducted a three 

year chemical and biological assessment of the St. Thomas 

East End Reserves or STEER, in St. Thomas, USVI. The 

STEER, located on the southeastern end of the island, is a 

collection of four reserves and sanctuaries, and was established in order to manage the area as one comprehensive 

ecological unit, rather than separate management areas. 

The project was requested by local partners in order to 

assess the presence of anthropogenic stressors suspected 

of impacting living resources within the STEER, characterize the biological communities within the STEER, and 

establish a baseline that can be used to measure progress in 

restoring affected habitats. 

Components of the project included: 1) development of 

an updated high resolution benthic habitat map for the 

STEER; 2) characterization of fi sh communities and associated benthic habitats throughout the STEER; 3) quantifi cation of a suite of 185 organic (e.g., hydrocarbons) and 

inorganic (i.e., metals) chemical contaminants in sediment, 

coral, conch and fi sh; 4) follow-up fi eld work to further 

quantify contaminants in surface sediments and in sediment 

cores from areas in Benner Bay found to have elevated levels of contaminants in the initial survey; 5) assessment of 

water-soluble chemical contaminants using passive water 

samplers; 6) determination of sediment toxicity using a set 

of established sediment toxicity bioassays; 7) characterization of the benthic infaunal community (organisms living 

within the sediments); 8) histologic examination of tissues 

from the coral Porites astreoides and fi nally; 9) monitoring of nutrients, sedimentation and total suspended solids 

(TSS) throughout the STEER. 

The STEER contains a variety of habitats including coral 

reefs, seagrass beds and mangroves. Patch reefs are scattered throughout the STEER, interspersed with areas of unconsolidated sediments consisting primarily of sand, along 

with areas of gravel and of silt. Seagrasses are abundant 

throughout the STEER, and the largest remaining stand of 

mangroves in St. Thomas can be found in the STEER. 

The STEER watershed contains high-density residential areas, the Bovoni Landfi ll that serves both St. Thomas and St. 

John, marinas and boat yards, various commercial/industrial activities, a number of resorts, and an EPA Superfund 

site, all of which have the potential to contribute a variety 

of land-based sources of pollution or LBSP, including 

chemical contaminants, nutrients and sediments. Liveaboard boats moored within the STEER are also a likely 

source of pollution.

 

For the biological survey (fi sh communities and benthic 

habitats) of the STEER, a total of 80 sites were surveyed. 

Unfortunately, due to low visibility (high turbidity) and 

concerns for the health of divers related to water quality, 

a survey of the upper third of Mangrove Lagoon and also 

northern Benner Bay could not be carried out. These areas 

appear to be particularly impacted by LBSP. Results from 

other areas in the STEER indicated that coral cover and 

coral community structure were similar to that of coral 

reef areas in St. John and St. Croix in the USVI, and with 

selected locations in Puerto Rico. The low coral cover 

(5.2%) observed in the STEER is in line with values from 

similar studies and surveys in St. Croix (2.9%) and St. John 

(4.5%) found by NOAA NCCOS, and likely refl ects the decline of coral reefs in the Caribbean as a whole. The high 

density urban population along with other activities within 

the watershed contributing LBSP, are additional stressors in 

the STEER. 

 

Fish metrics in the STEER were similar to other U.S. 

Caribbean monitoring locations, using the same methodology. Biomass for grunts and snapper were higher in St. 

Croix than in the STEER, and may refl ect the role that the 

extensive mangroves in the Mangrove Lagoon/Benner Bay 

area play, as nursery areas for juvenile fi shes. The functioning of this part of the STEER as an important nursery 

area highlights the need to conserve and restore Mangrove 

Lagoon, which along with northern Benner Bay, appears to 

be the area in the STEER most impacted by LBSP. Had the 

divers been able to conduct their surveys within northern 

Mangrove Lagoon and northern Benner Bay, it seems likely 

that the impacts of LBSP in these areas on fi sh metrics and 

benthic habitats would have been seen. 

Chemical contaminants in sediments sampled in the 

STEER were elevated in the Mangrove Lagoon and 

northern Benner Bay areas. A number of contaminants, 

particularly copper and tributyltin (TBT), were found at 

higher concentrations in the western part of the STEER, 

particularly in northern Benner Bay. Copper at one site in 

northern Benner Bay was above a NOAA sediment quality 

guideline indicating that effects on benthic organisms were 

likely. Tributyltin, banned for use as a boat hull antifoulant 

in the US, was found at the third highest concentration in 

the history of NOAA’s National Status and Trends (NS&T) 

Program. Levels of several other metals were also elevated 

in Mangrove Lagoon. In addition, the benthic infaunal 
218Chapter 10: Summary and Conclusions

STEER Integrated Environmental Assessment Report

community in both of these areas appeared to be severely 

diminished. Finally, the results of the bioassays indicated 

signifi cant sediment toxicity in Mangrove Lagoon and Benner Bay using multiple tests. 

From these results, the western portion of the STEER 

appears to be the most impacted by the chemical contaminants present. During the planning phase of the project, 

partners felt that Mangrove Lagoon would likely have high 

or very high concentrations of chemical contaminants in 

sediments, particularly metals, due to the proximity of the 

unlined Bovoni Landfi ll, located on the shores of Mangrove 

Lagoon. Somewhat surprisingly, however, northern Benner Bay had concentrations for a number of contaminants 

(e.g., copper, chromium, lead, zinc, TBT, total DDT, and 

total PCBs) that were as high if not higher than in Mangrove Lagoon. As noted in Chapter 4, other research has 

found evidence that the mangroves and the clay sediments 

in this area may be acting as a buffer, somewhat protecting 

Mangrove Lagoon for now from contaminants, particularly 

trace elements, originating from Bovoni Landfi ll, making their way into the lagoon. It should also be noted, that 

there may be areas within Mangrove Lagoon with high 

chemical contaminant concentrations (above sediment quality guidelines, for example), but because of the stratifi ed 

random sampling design, were not sampled. Additional 

work within Mangrove Lagoon would help address inputs 

and impacts from the landfi ll. In particular, it would be 

useful to target areas within Mangrove Lagoon that appear 

to be receiving inputs of runoff directly from the landfi ll. 

It would be useful to sample not only sediments in these 

areas, but also deploy passive water samplers capable of 

sequestering trace elements (e.g., Chemcatcher®) from 

the water column, to see if they are being transported into 

Mangrove Lagoon and beyond from the landfi ll. 

Following the initial assessment of chemical contaminants 

in sediments from the STEER, additional work was requested by the USVI Department of Planning and Natural 

Resources (DPNR), to further assess levels of TBT and 

trace elements in northern Benner Bay, particularly in the 

areas adjacent to the marinas and boat yards, which were 

found to be elevated during the initial assessment. DPNR 

noted that there had been a request to dredge the navigation 

channels leading to the marinas and boat yards in northern 

Benner Bay, in order to accommodate larger vessels. NCCOS scientists recommended that in addition to surface 

samples, sediment cores also be taken and analyzed to 

assess concentrations of contaminants in deeper, older sediments. Results from the follow-up chemical contaminant 

analysis indicated that some of the sediment cores were 

highly contaminated. Copper, for example, was found as 

high as 1,540 μg/g in a sediment core, which is more than 

fi ve times higher than the NOAA sediment quality guideline (SQG) concentration associated with toxic effects on 

benthic organisms. In addition, TBT was found at greater 

than 5,000 ng Sn/g, nearly an order of magnitude higher 

than the highest concentration (550 ng Sn/g) ever recorded 

in NOAA’s NS&T Program, and over an order of magnitude higher than an upper screening value established 

to help determine when additional testing or assessments 

would be advisable at EPA Superfund sites (see Chapter 

4). In sediments, TBT degrades to dibutyltin (DBT) and 

then monobutyltin (MBT), and fi nally to elemental tin, 

primarily through microbial action. The sum of TBT, DBT, 

and MBT is sometimes referred to as total butyltins. The 

total butyltins concentration was over 9,000 ng Sn/g in one 

sample from a sediment core in northern Benner Bay, eight 

times higher than the highest total butyltins concentration 

recorded by NOAA’s NS&T Program. In addition, in those 

sediment cores from Benner Bay containing high levels of 

butyltins, the highest contribution was from TBT, which 

may indicate that in the deeper sediments from these cores, 

environmental conditions are such (e.g., anoxic sediments) 

that degradation of the TBT is proceeding very slowly. 

The results from the follow-up contaminants work raises 

serious concerns regarding the effects that would occur 

from dredging the navigation channels or pile driving in the 

northern Benner Bay area. If the channels are dredged, the 

resuspension of highly contaminated sediments into the water column would likely impact biota in the area, particularly those in the adjacent mangroves, which has been shown 

through this project and others to be a valuable nursery 

area for juvenile fi shes. In addition, once the sediments are 

dredged, the question becomes where and how to dispose 

of the highly contaminated dredge spoil, without impacting 

other environments, either marine or terrestrial.

The results of the deployment of the passive water samplers in the STEER indicated a fairly typical mix of water 

soluble contaminants, including those associated with detergents, personal care products such as DEET, indole and 

menthol, and plasticizers such as DEHP and DEP. The only 

compound found that exceeded water quality criteria was 

the plasticizer DEHP. In 1988, an EPA Superfund site was 

established in the STEER watershed, due to contamination 

of groundwater and wells by chlorinated volatile organic 

compounds (CVOCs), including tetrachloroethylene. As 

part of the remediation effort, groundwater treatment 

systems were put in place to remove CVOCs, including tetrachloroethylene. Signifi cantly, there were no detections of 

tetrachloroethylene in the passive water samplers deployed 

in Turpentine Gut, Mangrove Lagoon or Benner Bay. 

 
219Chapter 10: Summary and Conclusions

STEER Integrated Environmental Assessment Report

The results of the analysis of biota indicated that levels of 

chemical contaminants in conch were below FDA action 

guidelines for molluscan shellfi sh consumption. However, 

PCBs in one fi sh analyzed exceeded an EPA guideline for 

recreational fi shers. Given the elevated contaminant levels 

found in sediments in portions of the STEER, more work 

is needed to assess contaminant levels in fi sh and also in 

invertebrates, in order to better understand the effects the 

contaminants in the STEER are having, not only in terms 

of human health, but also the effects on larvae and juvenile 

fi sh and other biota, particularly those that inhabit the western portion of the STEER. Trace and major elements along 

with concentrations of TBT would be candidate contaminants for additional investigations. 

The histological analysis of coral tissue (Porites astreoides) 

in the STEER showed some pathologies (e.g., necrosis or 

apoptosis) in colonies from Benner Bay. However, there 

was no clear pattern between pathologies and sites. Also, 

there were almost no corals in Mangrove Lagoon, and the 

only ones found there were at the extreme southern end 

of the lagoon. The effects of low visibility, pollution, and 

slightly lower salinities likely precludes coral from existing 

in most of Mangrove Lagoon. 

The monitoring of nutrients and sedimentation in the 

STEER indicated, as with a number of the other stressors 

measured during this project, that the western portion had 

higher inputs than the eastern and southern portions of the 

study area. Nutrient levels were signifi cantly higher at the 

sites in the western portion, specifi cally in Benner Bay and 

Mangrove Lagoon. Comparisons with proposed coral reef 

criteria for nutrients indicated that approximately 50-60% 

of the samples collected during the course of the study, particularly in Mangrove Lagoon and Benner Bay, had levels 

above a suggested threshold for orthophosphate and dissolved inorganic nitrogen (DIN). It has been suggested that 

levels above the threshold can sustain macroalgal blooms 

on Caribbean coral reefs, which increases the risk of corals 

being outcompeted and ultimately overgrown by macroalgae. In addition, sedimentation rates appeared to be highest 

in the area of Benner Bay, and were close to a suggested 

rate, above which impacts to the structure and function of 

coral reefs have been associated. 

The STEER contains multiple anthropogenic stressors. 

The evidence was strongest in the western portion of the 

STEER, where elevated concentrations of chemical contaminants in sediments, higher concentrations of watersoluble chemical contaminants, elevated nutrient and 

sedimentation rates and total suspended solids were found. 

Effects included evidence of reduced reproductive fi tness 

in corals from Mangrove Lagoon and increased necrosis in 

coral tissue in Benner Bay, and reduced and in some cases, 

severely reduced benthic infaunal communities (Mangrove 

Lagoon), all of which point to the impacts of these stressors 

on the STEER. Although fi sh metrics in the STEER were 

similar to other U.S. Caribbean monitoring locations in the 

STEER, that was for the areas where divers could conduct 

surveys. Had the divers been able to conduct the biological surveys in these areas, it seems likely that the biological 

communities there would have been diminished. All of 

these results point to the effects that anthropogenic stressors are having in the STEER. The impacts of LBSP on the 

western portion of the STEER is of particular concern as 

the mangroves and associated habitats serve as important 

nursery areas for a variety of vertebrate and invertebrate 

marine species. Loss of suitable habitat further impacts 

the ability of the STEER to be a source of new recruits of 

marine resource species for St. Thomas and beyond. 


U.S. Department of Commerce

Rebecca Blank, Deputy Secretary

National Oceanic and Atmospheric Administration

Kathryn Sullivan, Acting Under Secretary for Oceans and Atmosphere

National Ocean Service

Holly Bamford, Assistant Administrator for Ocean Service and Coastal Zone Management

The mission of the National Centers for Coastal Ocean Science is to provide managers with scientifi c 

information and tools needed to balance society’s environmental, social and economic goals. For 

more information, visit: http://www.coastalscience.noaa.gov/.