Marine Sanctuaries Conservation Series ONMS-09-02

U.S. Department of Commerce

National Oceanic and Atmospheric Administration

National Ocean Service

Office of Ocean and Coastal Resource Management

Office of National Marine Sanctuaries March 2009

A Comparison of Seafloor Habitats and 

Associated Benthic Fauna in Areas Open and 

Closed to Bottom Trawling Along the Central 

California Continental Shelf
About the Marine Sanctuaries Conservation Series

The National Oceanic and Atmospheric Administration’s Office of National Marine Sanctuaries (ONMS) 

administers the Office of National Marine Sanctuaries. Its mission is to identify, designate, protect and 

manage the ecological, recreational, research, educational, historical, and aesthetic resources and qualities of 

nationally significant coastal and marine areas. The existing marine sanctuaries differ widely in their natural 

and historical resources and include nearshore and open ocean areas ranging in size from less than one to over 

5,000 square miles. Protected habitats include rocky coasts, kelp forests, coral reefs, sea grass beds, estuarine 

habitats, hard and soft bottom habitats, segments of whale migration routes, and shipwrecks.

Because of considerable differences in settings, resources, and threats, each marine sanctuary has a tailored 

management plan. Conservation, education, research, monitoring and enforcement programs vary accordingly. 

The integration of these programs is fundamental to marine protected area management. The Marine 

Sanctuaries Conservation Series reflects and supports this integration by providing a forum for publication 

and discussion of the complex issues currently facing the Office of National Marine Sanctuaries. Topics of 

published reports vary substantially and may include descriptions of educational programs, discussions on 

resource management issues, and results of scientific research and monitoring projects. The series facilitates 

integration of natural sciences, socioeconomic and cultural sciences, education, and policy development to 

accomplish the diverse needs of NOAA’s resource protection mandate.
A Comparison of Seafloor Habitats and Associated Benthic 

Fauna in Areas Open and Closed to Bottom Trawling Along 

the Central California Continental Shelf

J. de Marignac1, J. Hyland2, J. Lindholm3, A. DeVogelaere1, W.L. Balthis2, and D. Kline3

1 NOAA/NOS Office of National Marine Sanctuaries (ONMS), Monterey Bay National 

Marine Sanctuary, 299 Foam Street, Monterey, CA 93940

2 NOAA/NOS National Centers for Coastal Ocean Science (NCCOS), Center for Coastal 

Environmental Health and Biomolecular Research (CCEHBR), 219 Fort Johnson Road, 

Charleston, SC 29412-9110

3 Institute for Applied Marine Ecology, California State University Monterey Bay, 100 

Campus Center, Building 53, Seaside, CA 93955

Silver Spring, Maryland

March 2009

U.S. Department of Commerce

Otto Wolff, Acting Secretary

National Oceanic and Atmospheric Administration

Dr. Bill Brennan, Acting Administrator Under Secretary

of Commerce for Oceans and Atmosphere

National Ocean Service

Jack Dunnigan, Assistant Administrator

Office of National Marine Sanctuaries

Daniel J. Basta, Director
DISCLAIMER

Report content does not necessarily reflect the views and policies of the Office of 

National Marine Sanctuaries or the National Oceanic and Atmospheric Administration, 

nor does the mention of trade names or commercial products constitute endorsement or 

recommendation for use.

REPORT AVAILABILITY

Electronic copies of this report may be downloaded from the National Marine Sanctuaries 

Program web site at www.sanctuaries.nos.noaa.gov. Hard copies may be available from 

the following address:

National Oceanic and Atmospheric Administration

Office of National Marine Sanctuaries

SSMC4, N/ORM62

1305 East-West Highway

Silver Spring, MD 20910

COVER 

NOOA Ship McArthur II (Credit: NOAA)

SUGGESTED CITATION

de Marignac, J., J. Hyland, J. Lindholm, A. DeVogelaere, W.L. Balthis, and D. Kline. 

2008. A comparison of seafloor habitats and associated benthic fauna in areas open and 

closed to bottom trawling along the central California continental shelf. Marine 

Sanctuaries Conservation Series ONMS-09-02. U.S. Department of Commerce, National 

Oceanic and Atmospheric Administration, Office of National Marine Sanctuaries, Silver 

Spring, MD. 44 pp. 

CONTACT

Jean de Marignac, SIMoN Scientist 

Monterey Bay National Marine Sanctuary, 299 Foam Street, Monterey, CA 93940.

E-mail: Jean.deMarignac@noaa.gov
1

EXECUTIVE SUMMARY

A number of studies have shown that mobile, bottom-contact fishing gear (such as otter trawls) 

can alter seafloor habitats and associated biota. Considerably less is known about the recovery 

of these resources following such disturbances, though this information is critical for successful 

management. In part, this paucity of information can be attributed to the lack of access to 

adequate control sites – areas of the seafloor that are closed to fishing activity. Recent closures 

along the coast of central California provide an excellent opportunity to track the recovery of 

historically trawled areas and to compare recovery rates to adjacent areas that continue to be 

trawled. In June 2006 we initiated a multi-year study of the recovery of seafloor microhabitats 

and associated benthic fauna inside and outside two new Essential Fish Habitat (EFH) closures 

within the Cordell Bank and Gulf of the Farallones National Marine Sanctuaries. Study sites 

inside the EFH closure at Cordell Bank were located in historically active areas of fishing effort, 

which had not been trawled since 2003. Sites outside the EFH closure in the Gulf of Farallones 

were located in an area that continues to be actively trawled. All sites were located in 

unconsolidated sands at equivalent water depths. Video and still photographic data collected via 

a remotely operated vehicle (ROV) were used to quantify the abundance, richness, and diversity 

of microhabitats and epifaunal macro-invertebrates at recovering and actively trawled sites, 

while bottom grabs and conductivity/temperature/depth (CTD) casts were used to quantify 

infaunal diversity and to characterize local environmental conditions.

Analysis of still photos found differences in common seafloor microhabitats between the 

recovering and actively trawled areas, while analysis of videographic data indicated that biogenic 

mound and biogenic depression microhabitats were significantly less abundant at trawled sites. 

Each of these features provides structure with which demersal fishes, across a wide range of size 

classes, have been observed to associate. Epifaunal macro-invertebrates were sparsely 

distributed and occurred in low numbers in both treatments. However, their total abundance was 

significantly different between treatments, which was attributable to lower densities at trawled

sites. In addition, the dominant taxa were different between the two sites. Patchily-distributed 

buried brittle stars dominated the recovering site, and sea whips (Halipteris cf. willemoesi) were 

most numerous at the trawled site though they occurred in only five of ten transects. Numerical 

classification (cluster analysis) of the infaunal samples also revealed a clear difference between 

benthic assemblages in the recovering vs. trawled areas due to differences in the relative 

abundances of component species. There were no major differences in infaunal species richness, 

H′ diversity, or J′ evenness between recovering vs. trawled site groups. However, total infaunal 

abundance showed a significant difference attributable to much lower densities at trawled sites. 

This pattern was driven largely by the small oweniid polychaete Myriochele gracilis, which was 

the most abundant species in the overall study region though significantly less abundant at 

trawled sites. Other taxa that were significantly less abundant at trawled sites included the 

polychaete M. olgae and the polychaete family Terebellidae. In contrast, the thyasirid bivalve 

Axinopsida serricata and the polychaetes Spiophanes spp. (mostly S. duplex), Prionospio spp., 

and Scoloplos armiger all had significantly to near significantly higher abundances at trawled

sites. As a result of such contrasting species patterns, there also was a significant difference in 

the overall dominance structure of infaunal assemblages between the two treatments.
2

It is suggested that the observed biological patterns were the result of trawling impacts and 

varying levels of recovery due to the difference in trawling status between the two areas. The 

EFH closure was established in June 2006, within a month of when sampling was conducted for 

the present study, however, the stations within this closure area are at sites that actually have 

experienced little trawling since 2003, based on National Marine Fishery Service trawl records. 

Thus, the three-year period would be sufficient time for some post-trawling changes to have 

occurred. Other results from this study (e.g., similarly moderate numbers of infaunal species in 

both areas that are lower than values recorded elsewhere in comparable habitats along the 

California continental shelf) also indicate that recovery within the closure area is not yet 

complete. Additional sampling is needed to evaluate subsequent recovery trends and persistence 

of effects. Furthermore, to date, the study has been limited to unconsolidated substrates. 

Ultimately, the goal of this project is to characterize the recovery trajectories of a wide spectrum 

of seafloor habitats and communities and to link that recovery to the dynamics of exploited 

marine fishes.

KEY WORDS

Fishing gear impacts, bottom trawling disturbances, benthic fauna, seafloor microhabitats, 

habitat recovery, central California continental shelf, National Marine Sanctuaries.
3

TABLE OF CONTENTS

Topic Page

EXECUTIVE SUMMARY ............................................................................................................ 1

KEY WORDS................................................................................................................................. 2

TABLE OF CONTENTS................................................................................................................ 3

INTRODUCTION .......................................................................................................................... 4

METHODS ..................................................................................................................................... 5

Study area and sampling locations.............................................................................................. 5

ROV Survey of Seafloor Microhabitats and Epifaunal Macro-Invertebrates............................. 6

Benthic Grab and CTD Survey................................................................................................... 8

RESULTS AND DISCUSSION................................................................................................... 10

Water Quality Characteristics................................................................................................... 10

Sediment Grain Size, TOC, and Depth..................................................................................... 10

Seafloor Microhabitats.............................................................................................................. 11

Epifaunal Macro-invertebrates.................................................................................................. 11

Benthic Infauna......................................................................................................................... 13

CONCLUSIONS AND RECOMMENDATIONS ....................................................................... 16

ACKNOWLEDGMENTS ............................................................................................................ 17

REFERENCES ............................................................................................................................. 17

FIGURES and TABLES............................................................................................................... 21
4

INTRODUCTION

There is no doubt that mobile, bottom-contact fishing gear (such as otter trawls and scallop 

dredges) alters seafloor communities (Jones 1992, Auster et al. 1996, Jennings and Kaiser 1998, 

Hall 1999, Auster and Langton 1999, Collie et al. 2000, National Research Council 2002, Barnes 

and Thomas 2005, Løkkeborg 2005). In fact, fishing has been described as the dominant direct 

anthropogenic impact to marine ecosystems worldwide (Dayton et al. 1995). Watling and Norse 

(1998) have suggested that below the effective depth of storm penetration, fishing is the 

prominent disturbance to the marine environment. Mobile fishing gear reduces seafloor 

complexity through the removal of attached and emergent fauna that provide structure (e.g., 

corals and sponges), the removal of other sediment-associated megafauna that produce pits and 

burrows (e.g., crabs, fish), and the smoothing of bedforms (e.g., sand waves; Lindholm et al. 

2004). In addition to the removal of targeted species, such operations can cause a variety of 

incidental biological impacts to non-targeted benthic organisms including changes in population 

densities, species diversity, community structure and composition, trophic structure, and 

productivity (Thrush and Dayton 2002, Hixon and Tissot 2007).

The spatial scale and temporal duration of impacts from fishing activity are of particular interest 

to the National Marine Sanctuaries, where conservation and protection of natural resources are 

mandated goals. Developing related information to support protective habitat zoning has been 

identified as a high research priority for a majority of National Marine Sanctuaries along the 

west coast of the U.S. (Gittings et al. 2002). As part of its recent (2001-2002) management plan 

review process, the Monterey Bay National Marine Sanctuary (MBNMS), in particular, has 

emphasized the need for additional research on the potential effects of bottom trawling on 

benthic habitats and associated living resources. Based on recommendations of a working group 

addressing this issue, the sanctuary developed an Action Plan with strategies for assessing such 

impacts and applying related protective measures as necessary (MBNMS 2006). One of the key 

research strategies recommended in the plan (Strategy BH-5) is to use recent fishing closures on 

the continental shelf as a basis for monitoring the recovery of disturbed benthic habitats within 

these areas relative to comparable habitats still being trawled. Results of an earlier 1998 study 

(Engel and Kvitek 1998) demonstrated impacts of bottom trawling on benthic fauna within 

MBNMS, yet still very little is known with respect to the extent and length of recovery following 

the cessation of fishing in such areas.

The primary objective of the present study was to evaluate recovery of seafloor microhabitats 

and associated benthic fauna from trawling-related impacts in National Marine Sanctuaries along 

the central California continental shelf. This objective is being addressed by comparison of the 

condition of these resources at previously trawled sites within an Essential Fish Habitat (EFH) 

ground-fish closure area, located within Cordell Bank National Marine Sanctuary (CBNMS), to 

actively trawled sites of comparable habitat type (unconsolidated fine sediments at depths of 

113-152 m) outside the closure area (Figure 1). The EFH closure area was established in June 

2006, though study sites within this area have experienced no trawling since 2003, based on 

trawl records from the National Marine Fisheries Service (NMFS). Currently trawled sites 

outside the closure area are within the adjacent Gulf of Farallones National Marine Sanctuary 

(GFNMS). The results of this study are intended to assist the MBNMS in fulfilling its Benthic 
5

Habitat Action Plan and revised 2006 Draft Sanctuary Management Plan requirements, which 

call for such studies, and to contribute to a related long-term goal aimed at maintaining the 

natural state of biological communities and ecological processes while promoting the 

sustainability of local fisheries. Results also will be made available to address related 

management issues of adjacent CBNMS and GFNMS where the actual sampling sites are 

located.

The study consisted of two components: (1) a remotely operated vehicle (ROV) sampling effort 

to collect videographic and still photographic data on seafloor microhabitats and epifaunal 

macro-invertebrates at 10 stations within each of the trawling-effort treatments; and (2) a 

sediment-grab and CTD companion effort to collect data on condition of benthic macro-infaunal 

assemblages and other abiotic environmental characteristics of the sediment and water column at 

corresponding sites. The sampling strategy for both study components includes an initial survey 

conducted in June-July 2006 and at least one more follow-up field effort (schedule pending) to 

assess any persistent impacts or recovery trends. The present report provides results of the initial 

2006 baseline survey.

METHODS

Study area and sampling locations

Study sites were selected using data on trawling effort provided by the NMFS. Data were 

analyzed, first as aggregated effort in 0.25 km2 blocks to determine high trawling activity areas, 

and then as individual trawl tracks to select a study area with intense bottom trawling effort. 

Stations were systematically sited within the CBNMS EFH closure in an area that was intensely 

trawled through 2003, while stations adjacent to the GFNMS EFH closure were similarly sited in 

an area that continued to be actively trawled through 2005 (the most recent effort data available 

at the time). Due to the proprietary nature of the information on specific fishing vessels and the 

location of their activities, we were unable to publish either the aggregated or individual trawl 

track data.

Keeping depth variations to a minimum between the two treatment categories was an important 

criterion of this study to control for natural depth-related variations in benthic fauna that could 

otherwise interfere with our ability to evaluate trawling-related impacts. The nearest sites that fit 

such sampling-design requirements were the above-mentioned EFH closure sites within the 

neighboring CBNMS and corresponding trawled sites of similar depths and bottom type located 

outside the EFH within GFNMS (Figure 1).

The resulting sampling framework consists of a balanced factorial design to test for differences 

in microhabitat and biological response variables between the 10 stations within the Cordell 

Bank EFH closure area (hereafter referred to as “recovering” sites) and the 10 stations located in 

GFNMS at actively trawled sites outside the closure area (hereafter referred to as “trawled” 

sites). Comparisons of response variables between recovering and trawled sites provided a basis 
6

for evaluating the extent of recovery from any trawling impacts within the EFH conservation 

area since the decline of trawling in 2003 and subsequent 2006 closure.

ROV Survey of Seafloor Microhabitats and Epifaunal Macro-Invertebrates

Still Photographic and Videographic Data Acquisition

The ROV survey was conducted at 20 stations, 10 each in the recovering and trawled areas, on 

Leg 3 of NOAA Ship McArthur II Cruise AR06-08, June 22-27, 2006. A single combined video 

and still photographic transect was conducted at each station (Figure 2) using the X2 ROV 

(operated by Deep Ocean Exploration and Research, Alameda, CA; Figure 3). The ROV was 

configured with two video cameras (forward and down-looking), a down-looking digital still 

camera, and two down-looking lasers for image calibration and estimating height off the bottom. 

Quartz halogen HMI lights provided illumination for the video and lighting for still photographs. 

The ROV was flown at an altitude of approximately 0.5 m above the seafloor. Each transect 

consisted of 20 min of continuous video and 20 digital-still photographs recorded on DVD. Still 

photographs were taken at approximately 1-min intervals throughout each transect.

Seafloor Microhabitats

Seafloor microhabitats were defined as features of the seafloor that occur at the scale at which 

individual fish associate, including physical substrata (such as boulders and sand waves), 

biogenic structure (such as erect sponges or anemones), and structures of biogenic origin (such 

as depressions and mounds formed by mobile fishes and invertebrates). Digital-still photographs 

were used to assess the relative abundance of ‘common’ microhabitat types. Additional 

photographs were taken to document habitat features and organisms and were not used for 

quantitative analyses. Down-looking video was quantified for computing the relative abundance 

of ‘rare’ habitat types. Note that the term rare is used in the numerical sense based on underrepresentation in the photographs rather than in a population context. Paired parallel lasers (20-

cm spacing) were used to indicate a consistent height for taking still photographs (to maintain 

constancy in area of coverage for each image) and for maintaining altitude for video transects. 

Still photographs were taken from a camera height of approximately 0.75 m off the seafloor and 

covered an area of approximately 0.42 m

2

.

Data on the percent relative abundance of 15 common microhabitats were derived from images 

using a classification system based on abiotic and biotic seafloor features that fishes have been 

shown to use for cover (Auster 1998, Lindholm et al. 2004). Data were produced from the still 

photographs using a series of 50 randomly distributed dots overlaid on each photograph (Figure 

4). The microhabitat feature under each dot was counted and apportioned to a particular 

microhabitat type. New random patterns were used for each photograph from each transect. The 

percent relative abundance of a given microhabitat was calculated as the number of each habitat 

type divided by the total number of occurrences for all microhabitats for that transect.

Imagery from the down-looking video camera was used to characterize the relative abundance of 

rare microhabitats (i.e. biogenic depressions and biogenic mounds). These two microhabitat 

types were not well represented by the still photographs and were subsequently removed from 
7

those analyses. However, both depressions and mounds were obviously present from qualitative 

viewing of the video.

Each video transect was treated as a series of non-overlapping video frames (Auster et al. 1991, 

Lindholm et al. 2004). The size of a down-looking video frame at a height of 0.75 m from the 

seafloor was 0.48 m2

. The relative abundances for depressions and mounds were calculated 

based on the number of video frames in which the microhabitat type occurred divided by the 

transect distance in meters (i.e., frames m–1

). The paired 20-cm lasers were used to distinguish 

two size classes for each microhabitat: 10 – 20 cm and 21+ cm. Each measurement was based 

on the maximum width of a depression or mound that was discernable from the video. No effort 

was made to quantify either depressions or mounds < 10 cm in width, nor was any effort made to 

quantify the depth of depressions or the height of mounds.

Epifaunal Macro-Invertebrates

Digital-still photographs were also used to assess the relative abundance, diversity, and species 

richness of epifaunal, macro-invertebrate species. Analyses were conducted using individual 

transects as replicate sampling units. Counts of all individuals distinguishable to major taxa, and 

identified to lowest possible taxonomic level, were made by overlaying each image with a 10-cm 

grid (Figure 5). Total counts for each species were made at least twice and, if the two counts 

differed, a third count was made. If two counts were in agreement, that number was recorded. If 

counts differed after three attempts, the photo was reevaluated at a later date until two of three 

counts were in agreement. Individual photos were eliminated if greater than 20% of the photo 

was obscured by sediment disturbance from the ROV or focus was too poor to identify taxa 

present.

Multiple measures were used to compare trawled and recovering sites to test for differences 

between epifaunal communities. Species richness (S) was calculated as the total number of 

species per transect for each site. Means were compared using a t-test assuming either equal or 

unequal variance, as appropriate after initial estimates of variance were calculated. T-tests were 

used to evaluate the null hypothesis that there was no difference in abundance, species richness, 

or diversity between trawled and recovering sites using transects as replicates. The ShannonWeaver index (H’) was used to calculate diversity (Pielou 1966, Krebs 1999). This index 

incorporates both numbers of species and their proportional abundance as an estimate of 

diversity:

H′ = ∑-pi * ln(pi)

where i = 1-S and i represents the ith species of a total of S species; pi is the fraction of total 

individuals made up of species i. Means were compared using a t-test assuming equal or unequal 

variance after initial estimates of variance were calculated.

A series of analysis of covariance (ANCOVA) and non-parametric analysis of similarity 

(ANOSIM; Clarke 1993) tests were conducted to determine if there were significant differences 

in species richness, diversity, and abundance between sites and whether depth differences 

between sites significantly influenced the response variables. Both non-parametric and 
8

parametric tests were used because species distributions were unknown. In addition, for the less 

frequently observed taxa, residuals from ANCOVAs did not appear to be normally distributed 

due to a high number of zero counts. To assess whether residuals were normally distributed, 

histograms of fitted model residuals were plotted and diagnostic graphs including normal 

quantile/quantile (Q-Q) plots were examined in the statistical program R (Dalgaard 2002).

Percent frequency of occurrence was calculated for each species in both trawled and recovering 

sites by dividing the number of transects at each site within which the species occurred by the 

total number of transects represented in each area. Percent frequency of occurrence within 

photos was calculated for each species by dividing the number of photos within which the 

species occurred by the total number of photos.

Community comparison of species composition and relative abundance between trawled and 

recovering sites were measured using the Percent Similarity Index (PSI; Wolda 1981, Krebs 

1999). PSI was calculated using the following formula:

 S

PSI = ∑ minimum (p1i, p2i) x 100

 1

where p1i = percentage of species i in community sample 1 and p2i = percentage of species i in 

community sample 2 and for each species represented i represents the ith species of a total of S 

species (Krebs 1999).

The zero-adjusted Bray-Curtis measure of dissimilarity (D; Bray and Curtis 1957, Clarke et al. 

2006; 0 = similar, 1 = dissimilar) was also used to evaluate area resemblance in community 

composition:

∑( )

∑

+ +

− = −

Xij Xik

Xij Xik

DB Cadj

jk 2

| | 100*

where Xij and Xik = number of individuals in species i in each area j or k (Krebs 1999). The zeroadjustment was used to moderate the erratic behavior of Bray-Curtis for near-denuded samples. 

As one of the sites was a fishery closure area and the other continues to be trawled using mobile 

bottom fishing gear, and both contained few species, this adjustment was considered appropriate.

Benthic Grab and CTD Survey

The sediment-grab and CTD sampling was conducted on the companion Leg 5 of NOAA Ship 

McArthur II Cruise AR06-08, July 2-5, 2006. Mapped locations and coordinates of the sampling 

stations are identified in Figure 1 and Table 1, respectively. The stations were located as the 

centroids of the 20 ROV transects completed during the previous Leg 3 of Cruise AR06-08 

(Figure 2).

Sediment grab samples for the analysis of macro-infaunal assemblages were collected in 

duplicate at each of the 20 stations (10 recovering and 10 trawled) using a Van Veen bottom grab 

(0.1 m2

). Sediment samples were live-sieved in the field through a 1.0-mm mesh screen and 

preserved in 10%-buffered formalin with rose bengal. As part of the QA/QC procedures, 
9

samples that showed significant slumping or loss of material through the jaws of the grab (e.g., 

samples with a sediment layer < 5 cm) were rejected. All samples were appropriately labeled 

with pertinent information on the project, station/replicate ID, and sample type. Also, prior to 

sampling at a station, all sampling equipment was washed with in-situ seawater to minimize 

contamination with sediment from prior stations. All infaunal samples were transferred to 70% 

ethanol after returning to the laboratory, where animals were sorted from sample debris under a 

microscope and identified to the lowest practical taxon (usually to species). Resulting data were 

entered into an electronic database as numbers of individuals by species and sample.

The upper 3-5 cm of sediment from an additional 1-2 grabs also was taken at each station, 

combined into a single station composite, and then sub-sampled for analysis of total organic 

carbon (TOC) content and grain-size distribution. As part of this process, the surface layer of 

sediment was removed from the grab with a scoop, placed in a bowl, and mixed. A TOC subsample was then removed from the homogenized sample and placed in a 125-mL plastic jar with 

lid and stored frozen. An additional sub-sample for grain-size analysis was removed from the 

homogenate and placed in a 500-mL plastic jar with lid and stored frozen. TOC and grain-size 

samples were processed using protocols modified from Plumb (1981). TOC content of sediment 

was measured on a carbon:hydrogen:nitrogen (CHN) elemental analyzer at 950 °C combustion 

temperature.

A CTD unit (Sea-Bird SEACAT, SBE 19 plus), equipped with additional dissolved oxygen (DO) 

and pH sensors, was used to acquire vertical profiles of conductivity/salinity, temperature, 

pressure, DO, and pH at six of the 20 stations, including three in the recovering area and three in 

the trawled area (Table 3).

A variety of data-analysis methods were used to characterize benthic communities and examine 

patterns in relation to other measured environmental variables and potential trawling-related 

impacts. Spatial patterns in the distributions of benthic communities, including differences 

between the two trawling categories, were examined using normal (Q mode) cluster analysis 

(Boesch 1977). Group-average sorting (= unweighted pair-group method, Sneath and Sokal 

1973) was used as the clustering method and Bray-Curtis similarity (Bray and Curtis 1957) was 

used as the resemblance measure. Analyses were run on double-square-root transformed 

abundances using the PRIMER software package (Clarke and Gorley 2001). Results were 

expressed as a dendrogram in which samples were ordered into groups of increasingly greater 

similarity based on resemblances of component-species abundances. Spatial patterns in 

community structure also were examined using non-metric multidimensional scaling ordination 

(MDS) (Kruskal and Wish 1978) on the Bray-Curtis similarity matrix of double-square-root 

transformed species abundance data. The latter analysis also was performed with the PRIMER 

software package.

Student t-tests were performed in conjunction with the above analyses to examine statistical 

differences in benthic and abiotic environmental variables among resulting site groups. Benthic 

variables included number of species, H′ diversity derived with base-2 logarithms (Shannon and 

Weaver 1949), the associated evenness component J′ (Pielou 1966), density (m-2

) of total fauna 

(all species combined), density (m-2) of major taxonomic groups, and density (m-2) of 
10

numerically dominant fauna. All t-tests and supporting statistical analyses (e.g., tests for 

homogeneity of variances, normality, etc.) were based on procedures in SAS (2004).

RESULTS AND DISCUSSION

Water Quality Characteristics

Water-quality characteristics (Table 2) were typical of offshore oceanographic conditions for the 

area and time of year, with near-bottom temperature, salinity, DO, and pH ranging from 8.71-

9.22 °C, 33.90-34.05 psu, 9.26-9.35 mg/L, and 7.61-7.73 respectively among the various 

stations. There were slight differences between near-bottom and near-surface conditions, with 

near-bottom water having lower temperature (mean of 8.91 °C on bottom vs. 11.59 °C at 

surface), higher salinity (mean of 33.99 psu on bottom vs. 33.43 at surface), higher DO (mean of 

9.32 mg/L on bottom vs. 8.81 mg/L at surface), and lower pH (mean of 7.67 on bottom vs. 8.08 

at surface). There were no apparent differences between recovering stations in CBNMS vs. 

trawled stations in GFNMS.

Sediment Grain Size, TOC, and Depth

The seafloor throughout the study area consisted of coarse to very fine sands with median 

particle size ranging from 0.934 to 3.761 phi on the Udden-Wentworth scale (Wentworth 1922) 

and with moderate amounts of silt-clay (10.2 to 43.6% and < 30% at all but one site) (Table 1). 

Sediments (also referred to as “sands” hereafter) were moderately to very poorly sorted, with 

sorting coefficients ranging from 0.719 to 3.348 phi. There were no obvious differences in these 

parameters between stations in the recovering vs. trawled areas (Table 3).

The TOC content of sediment averaged 3.7 mg/g at the 10 recovering stations and 5.2 mg/g at 

the 10 trawled stations (Table 3). The difference, statistically significant at P < 0.001, may be a 

signal of trawling-related physical disruption of the seafloor. For example, elevated levels of 

TOC in surficial sediments could result from the transport of organic matter buried in the 

sediment to the surface due to physical mixing by contact with the trawl gear (Stone and Masuda 

2003). However, note that the TOC values for both areas are still at relatively low levels well 

below a reported range (> 35 mg/g) associated with high risks of impaired benthic condition 

(e.g., reduced species diversity and abundance) from organic over-enrichment (Hyland et al. 

2005).

Station depths ranged from 113 to 152 m overall (Table 1) and averaged 140 m at the 10 

recovering sites and 130 m at the 10 trawled sites (Table 3). The statistically significant 

difference between the two groups (P < 0.001) is a result of the relatively tight within-group 

variances and is not likely to be of major biological significance given their common offshore 

outer-shelf locations (Figure 1) within a relatively small depth range (see further infaunal 

discussion below).
11

Seafloor Microhabitats

Analysis of common microhabitats from still photographs (Table 4) indicated that both trawled 

and recovering sites were dominated by unconsolidated sands (with a noticeable fine fraction) 

with mean percent relative abundance of 99.66% and 100%, respectively. Cobble habitat 

occurred in one transect within the actively trawled site but none was observed at the recovering 

site. Small proportions of the sandy substrate also contained attached and mobile epifauna or 

biogenic debris. Five of the ten transects (transect #’s 1-4 and 8 in Figure 2B) conducted at the 

actively trawled area adjacent to the GFNMS contained living sea whips Halipteris cf.

willemoesi (identified initially by Scott McEuen, Pacific Marine Taxonomy, and confirmed by 

Gary Williams, California Academy of Sciences). While little is known about these organisms, 

they are considered to be sensitive to some mobile fishing gear (Troffe et al. 2005, Brodeur 

2001, Wilson et al. 2002) especially due to their exposed structure extending vertically above the 

seafloor. As such, we interpreted the presence of these organisms at the above five transects as 

an indication that these particular locations (all positioned in close proximity of one another and 

inshore of the remaining five) may not have been actively trawled in the recent past.

ANCOVA results identified significant differences between trawled and recovering sites for all 

habitat categories except featureless sands (Table 5). Depth was a significant influence in 

featureless sand, sand with sessile epifauna, and sand with mobile fauna. The interaction 

between site and depth was significant for only the sand with sessile epifaunal category of 

microhabitats.

Analysis of rare microhabitats from video data (Table 6) indicated that significant differences 

were present between trawled and recovering areas in all categories except small (10-20 cm) 

depressions. Both small (10-21 cm) and large (>21 cm) biogenic mounds and large (>21 cm) 

depressions were significantly more abundant at the recovering area than at the trawled area 

(p<0.05).

Epifaunal Macro-invertebrates

Differences between trawled and recovering sites were minor but distinct. A total of eight

epifaunal taxa were observed at both sites combined. Two taxa occurred in both areas, decapod 

crustaceans (crabs) and polychaetes (fanworms), though different crab species were found at the 

two sites. A Brachyuran crab, Cancer sp., was observed at the recovering site and an Anomuran 

crab, possibly Lopholithodes sp., was observed. at the recovering site. Trawled transects were 

populated by Pannatulaceans (sea whips) and gastropods whereas transects within the recovering 

site were consistently populated by ophiuroids (brittle stars; Table 8). Tentative species 

identifications (without specimen collection) were based on literature and field guides and 

internet sources (Smith and Carleton 1975, Gotshall 1994, Kozloff 1996, Lambert 2007). The 

dominant taxa within trawled transect photos was a sea whip, identified by a recovered specimen 

as Halipteris cf. willemoesi (Octocorallia: Pannatulacea).
12

Trawled-transect photo analyses included 195 photos from ten transects. Twenty photos were 

eliminated due to either poor focus (9) or mud cloud obscurity (11) of at least 20% of the photo. 

A total of only 189 individuals from six taxa were identified, the dominant organism was the sea 

whip Halipteris cf. willemoesi. In addition, three distinct species of gastropod were recorded, the 

most common a Conus species. In addition, one moon snail (unknown species) and two cowries 

(possibly Cypraea spadicea, the chestnut cowrie known to occur in the area) were observed. 

Fanworms were observed in the photos from both sites but were likely underrepresented due to 

retraction.

Data collected from the ten recovering site transects included a total of 182 photos. Thirteen

photos were eliminated due to either poor focus (12) or mud cloud obscurity (1) of at least 20% 

of the photo leaving 169 photos for analyses. Three macro-invertebrate taxa, totaling 3220 

individuals, were identified. Recovering transects were dominated by patchily distributed 

ophiuroids, evidenced by single brittle star arms (n = 3190) emerging from the sediment, 

unidentifiable to species level. Invertebrates other than ophiuroids were sparsely distributed and 

occurred in very low numbers in all of the recovering-area transect photos. 

Macrofaunal species richness was very low for both actively trawled and recovering sites. The 

trawled site contained only six distinct species and the recovering site only three. Differences 

between the two areas were not significant at the level of transects (Table 9). Diversity was low 

in both actively trawled and recovering sites (Table 9). Differences in mean diversity between 

the two sites were significant (n = 10, p = 0.0095).

Dominant taxa differed between the two areas and overall numbers were significantly lower at 

the trawled site. Abundance was relatively high at the recovering site, due to the presence of 

patchily distributed ophiuroids. Differences in mean number of individuals were highly 

significant at the scale of transects (n = 10, p = 0.0012). The two sites were statistically different 

using both parametric and non-parametric tests for abundance (F = 16.475, p = 0.0009, n = 10) 

and species diversity (F = 8.539, p = 0.014) and the depth influence was significant as well (F = 

5.484, p = 0.0325, n = 10). Differences were not significant between sites for species richness (F 

= 3.2615, p = 0.0898, n = 10). ANOSIM tests confirmed the findings of the ANCOVAs.

Overlap in epifaunal macroinvertebrate species composition between actively trawled and 

recovering sites was low. Two taxa were present at both sites, decapod crustaceans of different 

species and Sabellid fanworms, probably multiple species. Percent similarity between sites was 

low (S = 0.96). Dissimilarity between sites was very high (zero-adjusted Bray-Curtis 

dissimilarity D = 98.89).

The two crab species that were observed each occurred in a single photo, an anomuran crab in a 

photo from the actively trawled site and a cancer crab in a photo from the recovering site (Tables 

8 and 10), though both were more numerous in complete video footage. The most commonly 

occurring species was the ophiuroid, which occurred in 100% of the recovering site transects and 

96.5% of photos. Ophiuroids were not observed in any photos within the actively trawled area. 

Fanworms were the only species observed at both sites and occurred in nearly all transects, 50% 

of trawled and 90% of recovering, but infrequently. They were captured in 8.57% of photos 

from the trawled site and 14.2% of photos from the recovering site. Sea whips and gastropods 
13

were not observed in any photos from the recovering transects, but occurred in 39.43% 

and11.42% of photos from the trawled site respectively.

Benthic Infauna

Results of multivariate cluster analysis of benthic infaunal data from the 10 recovering stations at 

CBNMS and 10 trawled stations at GFNMS are presented as a dendrogram in Figure 6. Each 

station is represented by two combined replicate samples. There is a distinct separation of 

recovering vs. trawled sites (at Bray-Curtis dissimilarity level of 0.36). A two-dimensional plot 

of the MDS results (Figure 7) shows a consistent pattern based on individual replicate samples. 

Contour lines drawn around samples having similar benthic composition at a Bray-Curtis 

dissimilarity level< 0.48 yield the same two recovering vs. trawled site groups.

To explore whether the previously mentioned depth-related variation between the two trawlingstatus categories (Section on grain size, TOC, and depth) may have influenced this site-group 

separation, an additional cluster analysis was performed on a subset of the data from individual 

samples at Stations 1-7 in the recovering area (depths of 133-139 m) and Stations 15-17 at 

corresponding depths in the trawled area (130-141 m). Results (Figure 8) show that the same 

pattern is maintained, with a clear separation of the trawled and recovering areas, even after 

removing any potential depth-related influence from the analysis. Thus, the pattern that emerged 

from the full cluster analysis (all stations included) is not likely to be the result of a major depthrelated break in benthic community structure and composition, particularly within such common 

outer-shelf locations and the relatively small depth range overall (average of 140 m for the 10 

recovering stations and 123 m for the 10 trawled stations). The small difference in average 

depths between the two trawling-status groups (only 17 m) was detectable statistically because of 

tight within-group variances. Hyland et al. (1991) reported depth-related patterns in the structure 

and composition of benthic macroinfaunal assemblages along the Santa Maria Basin portion of 

the California outer continental shelf and slope; however they found little variation in these 

assemblages within a depth range of 145-161 m, a comparable difference of 16 m, compared to 

deeper stations with depths > 200 m. Species richness, diversity, and abundances declined 

precipitously at mid-slope (409-410 m) and sea valley (595 m) stations compared to stations 

shallower than 200 m.

There were no major differences in measures of species richness, H′ diversity, or J′ evenness 

between trawled vs. recovering site groups (Table 11). Type 1 error probabilities from t-tests of 

the significance of mean differences in these variables between the two site groups (n1 = n2 = 10) 

were all in a range of p > 0.1. However, total faunal abundance showed a significant difference 

at the 10% level (p = 0.065) attributable to much lower densities at trawled sites. This pattern 

was driven largely by the small oweniid polychaete Myriochele gracilis, which was the most 

abundant species in the overall study region though significantly less abundant (p = 0.010) at 

trawled sites (Table 11). Polychaeta as a group also had significantly lower abundances (p = 

0.045) at trawled sites, due similarly to the influence of M. gracilis (Table 11). In fact, when M. 

gracilis are removed from the analysis, the pattern shifts to significantly higher abundances at 

trawled sites for all fauna combined and polychaeta as a group.
14

Two other major taxonomic groups, mollusca and non-pennatulacean anthozoans (i.e., 

ceriantharians and sea anemones), displayed an opposite pattern with significantly higher 

abundances at trawled sites (p ≤ 0.001, Table 11). Pennatulacean anthozoans (sea whips), 

though slightly more abundant at trawled sites, were not significantly different between the two 

treatment groups (p = 0.220). Crustacea and two of the three echinoderm classes — Echinoidea 

(sea urchins) and Holothuroidea (sea cucumbers) — also did not reveal any discernable 

differences between the recovering and trawled areas (at p < 0.1). It has been predicted that 

densities of longer-lived and lesser-mobile animals such as bivalves, echinoids, and anemones 

should decrease following trawling disturbances, while faster-growing, regenerative, and more 

mobile groups such as polychaetes, crustaceans, and ophiurids should increase (see discussion by 

Hansson et al. 2000 with relevant citations therein). Our results are consistent with the evolving, 

alternative realization that patterns of biological response to trawling effects may vary in 

complex ways among different types of organisms (Hansson et al. 2000, Currie and Parry 1996, 

Tuck et al. 1998).

Table 12 provides a comparison of the densities of major individual taxa (i.e., each representing 

> 1% of total faunal abundance) between the recovering and trawled areas. Cumulatively these 

taxa accounted for 75% of the abundances of all fauna combined. The two oweniid polychaetes, 

Myriochele gracilis and M. olgae, and the polychaete family Terebellidae all had significantly 

lower densities (p = 0.004 to 0.01, n1 = n2 = 10) at trawled sites. Similar response patterns for 

related taxa have been observed in other studies as well. For example, Hansson et al. (2000) 

observed a 43% decrease in abundances of Myriochele oculata at trawled sites, compared to a 

127% increase at control sites, following an experimental shrimp-trawling disturbance in 

Gullmarsfjorden, Sweden. In this same study, terebellid polychates decreased at trawled sites by 

an average of 62% in comparison to only 28% at control sites (Hansson et al. 2000). Although 

these authors caution that such differences cannot be unambiguously attributed to trawling, the 

directions of the patterns are suggestive of at least partial trawling influences that are consistent 

with the present study. Similarly, the abundance patterns of M. gracilis and M. olgae in the 

present study are consistent with the results of Flåten et al. (2007) who found highest abundances 

of a related oweniid polychaete, Owenia fusiformis, at reference sites furthest from an oilfield in 

the North Sea. The authors also noted that this species is not known to have strong opportunistic 

properties. Terrebellids and many oweniids including Myriochele are tubicolous, sessile to 

relatively sessile, polychaetes that probably do not move around to any great extent (Fauchald 

and Jumars 1979). Thus these animals may not be able to recover readily from physically 

disturbed sediment.

In contrast to the above patterns, the thyasirid bivalve Axinopsida serricata and the polychaetes 

Spiophanes spp. (97% of which were S. duplex and the remaining 3% S. bombyx), Prionospio

spp., and Scoloplos armiger all had significantly to near-significantly higher abundances (p < 

0.001 to 0.080, n1 = n2 = 10) at trawled sites (Table 12). Similarly, Hansson et al. (2000) 

observed a proportionally higher increase in abundances of thyasirid bivalves at trawled sites 

(average of 239%) following an experimental disturbance by shrimp trawling than at control 

sites (average of 137%). Axinopsida serricata also has been reported in high abundance in 

organically enriched areas of Puget Sound, WA (Nichols 2002, Armstrong et al. 1980) and as an 

abundant member of altered benthic assemblages in organically enriched areas of Santa Monica 

Bay, CA (Bergen et al. 2000). Other members of the family Thyasiridae (e.g., Thyasira flexuosa, 
15

T. sarsi), as well as the polychaete Scoloplos armiger and several members of the polychaete 

genus Prionospio, are well known initial to second-stage colonizers in polluted sediments 

(Pearson and Rosenberg 1978). The polychaete Spiophanes duplex is a common dominant in 

outer-shelf habitats off the California coast, e.g. as reported by Bergen et al. (2001) at depths of 

115-200 m in the Southern California Bight. However, we are not aware of studies that suggest 

an affinity of this species for disturbed substrates.

There also was a significant difference in the dominance structure of infaunal assemblages from 

the two areas (Table 13). The highest ranked (most abundant) dominant in the recovering area 

was the polychaete Myriochele gracilis. This species did not appear as a dominant (i.e., among 

the five most abundant species) in the trawled area, though it was present there at much lower 

densities. In comparison, the bivalve Axinopsida serricata, while not ranked as a dominant in 

the recovering area, appeared as the second most dominant species in the trawled area. 

Spiophanes (mostly S. duplex) was dominant in both areas. Kendall’s concordance test (Kendall 

1975) showed no significant concordance (at P < 0.01) in the ranking of these dominants 

between the two areas (coefficient of concordance W = 0.4225, Χ2= 5.63, 7 df), thus revealing a 

significant difference in the dominance hierarchy of these assemblages.

The above results, based on both multivariate and univariate techniques, revealed a clear 

difference between benthic infaunal communities in the recovering vs. trawled areas due to 

differences in the relative abundances of component species. An important question is whether 

such differences are attributable to a trawling effect or whether the benthic fauna of the two areas 

have always been different due to other natural environmental factors. The two areas are in 

similar oceanographic regimes with common outer-shelf locations off the central California coast 

(only about 35 km apart) and with similar ranges in other measured environmental variables 

(salinity, DO, temperature, pH, sediment grain size). There was a small, yet statistically 

significant, difference in the average TOC content of sediments between the two areas 

(recovering sites: 3.7 mg/g, trawled sites: 5.2 mg/g; Table 3). While these values are well 

below a TOC range (>35 mg/g) associated with impaired benthic condition (Hyland et al. 2005), 

the slightly higher levels of TOC in the fished area could be a sign of recent trawling interactions 

with the seafloor which in turn may have caused physical disruption of benthic communities. 

Stone and Masuda (2003) similarly found higher levels of TOC in trawled area than in closed 

areas in the Gulf of Alaska, and attributed the result to the transport of TOC from within the 

sediments to the surface due to physical mixing by contact with the trawl gear. There also was a 

small, yet statistically significant, difference in the average sampling depth between our two 

study areas (closed: 140 m, trawled: 123 m; Table 3), but this variation is minor relative to the 

generally deep, outer-shelf locations and appeared to have little influence on the separation of 

recovering vs. trawled site groups in the numerical classification (cluster) analysis of infaunal 

abundance.

Given these points, it is suggested that the observed biological patterns are the result of trawling 

impacts and varying levels of recovery due to the difference in trawling status between the two 

areas. The EFH closure was established in June 2006, within a month of when sampling was 

conducted for the present study, however the stations within this closure area are at sites that 

actually have experienced little trawling since 2003, based on NMFS trawl records. Thus, the 

three-year period would be sufficient time for some post-trawling changes to have occurred. The 
16

significantly higher densities of suspected stress-sensitive species (e.g., the owenid polychaetes,

Myriochele gracilis and M. oglae, and the polychaete family Terebellidae) and lower densities of 

suspected or known stress-tolerant species (e.g., the bivalve Axinopsida serricata and the 

polychaetes Prionospio spp. and Scoloplos armiger) in the closure area at CBNMS seem to 

suggest that recovery is occurring.

Other measures also indicate that recovery within the closure area is not yet complete. Both 

areas had similar, moderate numbers of infaunal species (mean of 62 species/0.1m2 at recovering 

sites and 65 species/0.1m2 at trawled sites) that are lower than values recorded elsewhere in 

comparable habitats along the California continental shelf. For example, Bergen et al. (2001) 

reported an overall mean of 87 species/0.1 m2 (1.0 mm sieve size) at comparable sandy, outershelf sites (115-200 m) throughout the Southern California Bight. Hyland et al. (1991) also 

reported means of 85-123 species/0.1m2 at depths of 145-161 m in the Santa Maria Basin, off the 

central California coast between Pt. Arguello and Pt. San Luis (though these samples were 

processed on finer-mesh 0.5 mm sieves). Data from a recent survey of ecological conditions in 

coastal-ocean waters along the western U.S. continental shelf (from Straits of Juan de Fuca, WA 

to Channel Islands, CA), as part of the U.S. Environmental Protection Agency’s National Coastal 

Assessment Program, show an average of 83.7 species/0.1 m2 (1.0 mm sieve size) at comparable 

depths (102-123 m) in the central to northern California portion of the study area (unpublished 

data, U.S. Environmental Protection Agency, Newport OR). Tuck et al. (1998) showed that 

physical effects of an experimental trawling disturbance on seabed topography were almost 

indistinguishable by 18 months of recovery, although there were clear longer-term effects on 

infaunal communities that persisted beyond that time and the life of the study. Lindholm et al. 

(2004) also demonstrated measurable differences in microhabitat resources between trawled and 

non-trawled sites on Georges Bank after 4.5 years of closure.

CONCLUSIONS AND RECOMMENDATIONS

Our results indicate that significant differences existed between an actively trawled area and an 

area that had been recovering from trawling impacts for three years at the time of sampling. 

These differences were manifest in the micro-topographic structure that fish utilize for protection 

from predation and as refugia from currents, as well as in invertebrate epifaunal and infaunal 

communities. Each of the differences is consistent with the literature dealing with gear impacts 

to seafloor communities (Jones 1992, Auster et al. 1996, Jennings and Kaiser 1998, Hall 1999, 

Auster and Langton 1999, Collie et al. 2000, National Research Council 2002, Barnes and 

Thomas 2005, Løkkeborg 2005). However, this first year of sampling was intended as a point of 

departure for a multi-year study rather than an end in itself. Additional sampling is needed to 

evaluate subsequent recovery trends and persistence of effects over time and to further 

investigate any differences between our experimental treatments that may be due to factors other 

than trawling activity. Furthermore, to date, the study has been limited to unconsolidated 

substrates. Ultimately, a goal of this type of project would be to characterize the recovery 

trajectories of a wide spectrum of seafloor habitats, and to link that recovery to the dynamics of 

exploited marine fishes.
17

A final important recommendation based on our efforts to date relates to the need for better 

control areas in the field in which studies like this one can be conducted (see similar discussion 

in Engel and Kvitek 1998). From our earliest efforts at designing this experiment through our 

analysis of the first year’s data, we were forced to adjust repeatedly to variables that were 

beyond our experimental control due to the lack of a well-designed research closure. The 

importance of understanding the impacts of mobile fishing gear to seafloor communities is 

increasingly clear to managers and policy-makers alike. A network of well-designed research 

closures, which encompass a variety of seafloor substrata and biological communities, will allow 

for a robust, statistically sound quantification of seafloor recovery from impacts due to fishing 

with mobile gear. Ultimately, such data will allow for the zoning of the seafloor analogous to 

existing zoning efforts on land in the interest of all those who manage and/or utilize marine 

resources.

ACKNOWLEDGMENTS

This work was conducted through a partnership agreement between NOAA’s Office of National 

Marine Sanctuaries (ONMS) and National Centers for Coastal Ocean Science (NCCOS) and 

supported largely by FY06 Ocean Assessment Program (OAP) funds directed to NCCOS. 

Additional funding support was provided through the MBNMS’s “Sanctuary Integrated 

Monitoring Network (SIMoN)” program. Special recognition is extended to Marine Taxonomic 

Services (Corvallis, OR) for the analysis of macroinfaunal samples and to Barry Vittor and 

Associates (Mobile, AL) for TOC and grain size analyses. Field operations were supported by 

the NOAA Ship McArthur II (Cruise AR06-08: Legs 3 and 5) and the Ocean Explorer X2 ROV 

(owned and operated by Deep Ocean Exploration and Research, Alameda CA). We also wish to 

thank the following members of the scientific sampling teams for their invaluable field support: 

JD Dubick (NCCOS), Erica Burton (MBNMS), Lorraine Anglin (MBNMS), Ashley Knight 

(Pfleger Institute of Environmental Research), Bob Lea (Natural History Museum of Los 

Angeles County), Lisa Uttal (Moss Landing Marine Laboratories), Dan Howard (CBNMS), and 

Tom Laidig (NMFS, Santa Cruz). We are grateful for the valuable comments of three dedicated 

anonymous reviewers.

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21

FIGURES and TABLES

Figure 1. Study area showing stations inside the 2006 Essential Fish Habitat (EFH) Closure 

Area within the Cordell Bank National Marine Sanctuary (“recovering”) and in a currently 

trawled area outside the EFH Closure Area within the Gulf of Farallones National Marine 

Sanctuary (“trawled”).
22

A. Recovering stations (R1-10) in CBNMS EFH Closure.

B. Trawled stations (F1-10) in GFNMS outside EFH Closure

Figure 2. Locations of ROV transects: A) Recovering stations within CBNMS EFH Closure area 

(R1-10), and B) Trawled stations in GFNMS outside closure area (F1-10).
23

Figure 3. The X2 ROV configured with forward and down-looking video cameras and downlooking digital still camera and paired 20 cm lasers.
24

Figure 4. Still photographic image taken by the X2 ROV, including an overlay with 50 

randomly distributed dots used for the quantification of common seafloor microhabitat 

abundance. “OV1D” is a unique overlay photo identifier.
25

Figure 5: Still photographic image taken by the X2 ROV, including a 10 cm grid overlay used 

to quantify epifaunal invertebrates abundance. The “OV1B” is a unique overlay identifier. 

Linear red features are brittle star arms (possibly Ophiothrix spiculata) and the crab is a Cancer 

sp. (possibly Cancer magister or Cancer productus).
26

Figure 6. Dendrogram resulting from clustering of the 10 trawled and 10 recovering 

stations using group-average sorting and Bray-Curtis dissimilarity. Each station is 

represented by two combined replicate infaunal samples (0.1 m2 each) sieved through a 

1.0 mm screen. The analysis was performed on double-square-root transformed 

abundances. Two major site groups, trawled vs. recovering, are distinguished at a BrayCurtis dissimilarity level of 0.36.
27

Figure 7. Results of non-metric, two-dimensional MDS ordination on the Bray-Curtis 

dissimilarity matrix of double-square-root transformed infaunal species abundance data from 

individual replicate samples at the 10 recovering and 10 trawled stations. Boundaries are 99% 

confidence ellipses. Encircled samples are Bray-Curtis dissimilarity < 0.48.
28

Figure 8. Dendrogram resulting from clustering of individual replicate infaunal samples from 

Stations 1-7 (depths of 133-139 m) in the EFH closure area at CBNMS (recovering stations) and 

Stations 15-17 at corresponding depths (130-141 m) in the actively trawled area at GFNMS, 

using group-average sorting and Bray-Curtis dissimilarity. Each sample is represented by a 

single replicate (0.1 m2

) sieved through a 1.0 mm screen. The analysis was performed on 

double-square-root transformed abundances.
29

Table 1. Station locations, depths, and sediment characteristics of the 10 recovering sites (1-10) and 10 trawled sites (11-20).

Infaunal

Stationa Latitude Longitude

ROV

Transect

Avg. 

Depth 

(m)b

TOC

(mg/g)

Gravel

(%)

Sand

(%)

Silt

(%)

Clay

(%)

Silt+Clay

(%)

Size 

Classd

Median

Particle

Size 

(phi)

Sorting

Coeff.

Moisture

(%)

1 37.91628 123.42535 R1 137 3.82 0.00 81.86 13.40 4.74 18.14 VF Sand 3.393 0.853 26.66

2 37.91384 123.42313 R2 137 3.96 0.00 79.98 12.33 7.69 20.02 VF Sand 3.543 0.759 28.48

3 37.91136 123.42042 R3 135 3.87 0.00 78.16 18.13 3.20 21.33 VF Sand 3.440 0.907 27.81

4 37.91152 123.42487 R4 139 3.96 0.00 56.39 32.93 10.68 43.61 VF Sand 3.761 1.850 28.09

5 37.90585 123.41937 R5 136 3.62 0.00 83.39 12.50 4.11 16.61 VF Sand 3.321 1.810 24.19

6 37.90256 123.41597 R6 135 4.26 0.00 87.32 6.40 6.25 12.65 “Sand” c c 21.90

7 37.89974 123.41236 R7 133 2.89 0.65 89.18 7.65 2.52 10.17 C Sand 0.934 1.983 18.20

8 37.89859 123.41761 R8 147 3.56 0.00 90.60 4.49 4.91 9.40 VF Sand 3.090 1.735 24.02

9 37.89540 123.41394 R9 152 3.86 0.00 79.78 17.32 2.90 20.22 VF Sand 3.348 1.717 24.97

10 37.89269 123.41133 R10 147 2.91 0.00 79.86 14.53 5.61 20.14 F Sand 2.736 2.213 20.74

11 37.71712 123.13581 F1 117 5.58 0.00 77.17 19.93 2.90 22.83 VF Sand 3.362 2.720 31.93

12 37.71294 123.13077 F2 114 5.47 0.00 77.06 16.13 6.81 22.94 VF Sand 3.537 0.807 30.23

13 37.71054 123.12737 F3 113 5.20 0.00 87.66 9.45 2.90 12.35 F Sand 2.498 0.719 29.46

14 37.70827 123.12462 F4 114 4.92 0.00 75.13 17.65 7.22 24.87 VF Sand 3.587 0.755 41.54

15 37.71504 123.14156 F5 133 5.30 0.00 83.88 12.55 3.57 16.12 VF Sand 3.441 3.348 29.32

16 37.71223 123.13770 F6 130 4.46 0.00 84.57 10.35 5.08 15.43 VF Sand 3.268 0.782 29.48

17 37.71010 123.13509 F7 141 4.72 0.00 83.62 13.88 2.50 16.38 VF Sand 3.273 0.805 30.27

18 37.70776 123.12658 F8 117 5.19 0.00 80.36 13.95 5.69 19.64 VF Sand 3.419 0.883 29.90

19 37.69317 123.11181 F9 123 5.44 0.00 71.99 25.03 2.98 28.01 VF Sand 3.701 1.080 29.01

20 37.69148 123.10952 F10 124 5.28 0.00 82.55 12.35 5.10 17.45 VF Sand 3.372 0.835 29.42

a Infaunal station locations are the centroids of each corresponding ROV epifaunal transect. b Recorded where bottom grabs taken.

c Insufficient data for statistics.

d Udden-Wentworth grain-size scale (Wentworth 1922). VF = very fine, C = coarse, F = fine.
30

Table 2. Summary of water-quality measurements taken at three of the 10 infaunal stations in the recovering area (2, 6, 9) and three 

in the trawled area (12, 16, 19).

Temp. (C) Salinity (PSU) D.O. (mg/L) pH 

Station Depth (m)a Surface Bottom Surface Bottom Surface Bottom Surface Bottom

2 130 10.85 9.04 33.47 34.00 8.95 9.29 7.97 7.69

6 129 11.04 8.99 33.45 33.96 8.92 9.3 7.98 7.68

9 122 11.01 9.22 33.46 33.9 8.92 9.26 7.99 7.73

Mean 127 10.97 9.08 33.46 33.95 8.93 9.28 7.98 7.70

12 109 12.16 8.72 33.41 34.03 8.71 9.35 8.17 7.63

16 117 12.14 8.77 33.38 34.01 8.68 9.35 8.16 7.61

19 117 12.31 8.71 33.43 34.05 8.68 9.35 8.19 7.66

Mean 114 12.20 8.73 33.41 34.03 8.69 9.35 8.17 7.63 a Depth of CTD sensors at bottom of profile
31

Table 3. Comparison of abiotic environmental variables at recovering (n = 10) vs. trawled (n = 10) sampling sites

Trawling Status Statistical Results

Variable Recovering Trawled t-value a df b p

TOC (mg/g) 3.7 5.2 8.21 17.1 <0.001

% Sand 80.6 80.4 0.07 13.4 0.942

% Silt/Clay 19.2 19.6 0.11 13.4 0.915

Median Particle Size (Phi) 3.06 3.35 0.94 10.1 0.369

Sorting coefficient 1.54 1.27 0.75 14.6 0.464

% Moisture 24.5 31.1 4.06 17.8 0.001

Depth (m) c 140 123 4.75 15.9 <0.001 a Student’s t-test performed under the assumption of unequal variances.

b Degrees of freedom computed using Satterthwaite’s (1946) approximation.

c Mean of average recorded station depth where bottom grabs were taken.
32

Table 4. Mean percent relative abundance of common microhabitat types from still photographs 

taken in 2006 at trawled sites in GFNMS and recovering sites in CBNMS. Microhabitat 

classification was based on Greene et al. (1999).

Mean percent relative abundance

Microhabitat type Trawled Recovering

 Combined cobble 0.34% 0%

Cobble 0.31 0

Cobble, sessile epifauna 0.03 0

 Combined sand 99.66% 100%

Featureless sand 97.16 98.87

Sand, sessile epifauna 1.99 0.01

Sand, mobile epifauna 0.06 0.83

Sand, debris 0.45 0.26
33

Table 5. Results of ANCOVA used to test for site effects (trawled vs recovering), water depth, 

and site-depth interactions on mean transect abundance of common microhabitats from still 

photographs (n = 426). All data were square-root arcsine transformed prior to analysis. 

Microhabitat classifications were based on Greene et al. (1999). (* = significantly different at 

P=0.05.)

Source Df Mean square F p

Featureless sand

 Site 1 0.0021 0.0547 0.818

 Depth 1 0.0176 4.601 0.0477*

 Site x depth 1 0.0046 1.1981 0.290

 Error 16 0.0038

Sand, sessile epifauna

 Site 1 5.7764 2866.4129 < 2e-16 *

 Depth 1 3.7061 1839.0987 < 2e-16 *

 Site x depth 1 0.0125 6.2271 0.0239 *

 Error 16 0.0020

Sand, mobile epifauna

 Site 1 0.0175 19.5282 0.0004*

 Depth 1 0.0075 8.4141 0.0104* 

 Site x depth 1 0.0005 0.5054 0.4874

 Error 16 0.0009

Sand, debris

 Site 1 0.0096 6.5046 0.0214 *

 Depth 1 0.0003 0.2020 0.6591 

 Site x depth 1 0.0001 0.0345 0.8551

 Error 16 0.0015
34

Table 6. Mean percent relative abundance of rare microhabitat types, biogenic mounds, and 

depressions at recovering and trawled transects in 2006, based on the number of video frames per 

ROV transect.

Mean percent relative abundance

Microhabitat type Trawled Recovering

 Biogenic Mounds

 Combined 11.9 28.3

 10-20 cm 11.1 23.5

 21 + cm 0.78 4.9

 Biogenic Depressions

 Combined 12.9 31.6

 10-20 cm 11.4 22.8

 21 + cm 1.6 8.8
35

Table 7. Results of ANCOVA used to test for site effects (trawled vs recovering), water depth, 

and site-depth interactions on mean transect abundance of uncommon microhabitats from video 

records. All data were square-root arcsine transformed prior to analysis. Microhabitat 

classifications were based on Greene et al. (1999). (* = significantly different at P=0.05, ** 

P=0.01, *** P=0.001.)

Source Df Mean square F p

Biogenic mounds 10-20 cm

 Site 1 0.0232 5.4305 0.0332 * 

 Depth 1 0.1072 25.0631 0.0001 ***

 Site x depth 1 0.0117 2.7399 0.1173 

 Error 16 0.0043

Biogenic mounds 20+ cm

 Site 1 0.0306 7.9197 0.0125 * 

 Depth 1 0.1010 26.1682 0.0001 ***

 Site x depth 1 0.0050 1.3004 0.2709

 Error 16 0.0039

Biogenic mounds, combined

 Site 1 0.0403 6.9028 0.01830 * 

 Depth 1 0.1720 29.4323 5.61e-05 ***

 Site x depth 1 0.0209 3.5785 0.0768

 Error 16 0.0058

Biogenic depressions 10-20 cm

 Site 1 0.0319 3.6572 0.0739

 Depth 1 0.0849 9.7243 0.00662 **

 Site x depth 1 0.0019 0.2228 0.64326

 Error 16 0.0087

Biogenic depressions 20+ cm

 Site 1 0.0560 7.3119 0.0156 * 

 Depth 1 0.1608 20.9840 0.0003 ***

 Site x depth 1 0.0010 0.1326 0.7205

 Error 16 0.0077

Biogenic depressions, combined

 Site 1 0.0806 5.5066 0.0322 *

 Depth 1 0.1892 12.9220 0.0024 **

 Site x depth 1 0.0014 0.0945 0.7624

 Error 16 0.0146
36

Table 8. Occurrence of epifaunal macro-invertebrate taxa from ten trawled (A) and ten recovering (B) transects in 2006.

A.

Trawled

Transect #

# 

Photos

Sea whip

(Halipteris 

cf. 

willemoesi)

Crab

(Lopholithoides 

sp.) 

Fan 

worm 

(Sabellid) 

Gastropod 

A

(Conus sp.)

Gastropod 

B

Gastropod 

C Richness

(Number of Species )

ShannonWeaver

Diversity 

Index

(H’)

06-1F-01 10 14 0 0 0 0 0 1 0

06-2F-01 16 37 0 0 0 1 0 2 0.1217

06-3F-01 20 34 0 0 2 0 0 2 0.2146

06-4F-01 25 43 0 0 9 0 2 3 0.6021

06-5F-01 20 0 0 0 1 0 0 1 0

06-6F-01 16 0 1 5 0 0 0 2 0.4506

06-7F-01 18 0 0 2 0 0 0 1 0

06-8F-01 16 4 0 7 21 0 0 3 0.8688

06-9F-01 19 0 0 2 2 0 0 2 0.6931

06-10F-01 15 0 0 1 1 0 0 2 0.6931

TOTAL 175 132 1 17 36 1 2 6 0.8868

 B.

Recovering

Transect # # Photos

Crab

(Cancer sp.) 

Fan worm 

(Sabellid) 

Brittle star

(Ophiothrix 

spiculata?)

Richness

(Number of Species 

)

Shannon-Weaver

Diversity Index

(H’)

06-1R-01 20 0 4 680 2 0.0359

06-2R-01 19 0 2 568 2 0.0233

06-3R-01 14 0 2 349 2 0.0351

06-4R-01 20 0 1 523 2 0.0139

06-5R-01 18 0 1 283 2 0.0234

06-6R-01 18 1 7 237 3 0.1562

06-7R-01 8 0 1 23 2 0.1732

06-8R-01 16 0 0 90 1 0

06-9R-01 18 0 6 132 2 0.1788

06-10R-01 18 0 5 275 2 0.0896

TOTAL 169 1 29 3190 3 0.0546
37

Table 9. Macrofaunal richness (A), diversity (B), and abundance (C) comparisons for ten trawled and ten recovering benthic transects 

in 2006. Probability values from ANCOVAs are given for site effects, depth effects, and interaction of site and depth. (* = 

significantly different at P=0.05, ** P=0.01, *** P=0.001.)

A. Richness (Number of species)

Transect as replicate ANCOVA (parametric)

Site Mean SE n T-test (P) Source df F P

Trawled 1.9 0.233 10 0.722 Site 1 3.2615 0.0898

Recovering 2 0.149 10 Depth 1 1.746 0.2050

S x D 1 0.3707 0.5512

Residuals 16

B. Diversity (Shannon-Weaver Index)

Transect as replicate ANCOVA (parametric)

Site Mean SE n T-test (P) Source df F P

Trawled 0.3644 0.150 10 0.0095** Site 1 3.8975 0.0659

Recovering 0.0154 0.005 10 Depth 1 5.9717 0.0265

S x D 1 0.0419 0.8404

Residuals 16

C. Abundance (Number of individuals)

Transect as replicate ANCOVA (parametric)

Site Mean SE n T-test (P) Source df F P

Trawled 18.9 1.46 10 0.0012* Site 1 16.475 0.0009***

Recovering 319 23.02 10 Depth 1 5.484 0.0325*

S x D 1 2.231 0.1547

Residuals 16
38

Table 10. Percent frequency of occurrence in transects by taxa/species (genus identifications are tentative as none were collected by 

sampling) within ten trawled and ten recovering benthic transects in 2006 determined by counts from still photos (n = 175 trawled

photos, n = 169 recovering photos, total = 344 photos). Numbers in parentheses are percent frequency of occurrence in photos within 

the transects.

Trawling Status

Recovering Trawled Percent frequency in all photos combined

Sea whip (Halipteris cf.) 0 50 (39.43) 20.1

Crab (Lopholithodes sp.) 0 10 (0.57) 0.29

Crab (Cancer sp.) 10 (0.59) 0 0.29

Fan worm (Sabellidae) 90 (14.2) 50 (8.57) 11.34

Gastropod A (Conus sp.) 0 60 (9.71) 4.94

Gastropod B (mud snail) 0 10 (0.57) 0.29

Gastropod C (cowrie) 0 10 (1.14) 0.58

Ophiuroid (brittle star, (Ophiothrix sp.) 100 (96.5) 0 47.38
39

Table 11. Comparison of benthic infaunal community characteristics at recovering sites (n=10 sites x 2 reps each) vs. trawled sites 

(n=10 sites x 2 reps each).

Trawling Status Statistical Results

Benthic Variable Recovering Trawled df b t-value a P

Mean # taxa grab-1 62 65 18 0.93 0.365

Mean # taxa station-1 (pooled replicates) 87 89 17.8 0.34 0.736

Mean H′ grab-1 3.4 4.0 9.44 1.26 0.237

Mean J′ grab-1 0.57 0.67 9.32 1.15 0.2795

Mean density grab-1 (# m-2):

 All fauna 8626 5023 9.41 -2.09 0.065

 All fauna (Myriochele gracilis removed) 3326 4945 18 4.99 <0.001

Polychaeta 7684 3689 9.36 -2.31 0.045

Polychaeta (M. gracilis removed) 2384 3611 18 4.17 0.001

Crustacea 275 249 17 -0.53 0.604

Mollusca 477 737 14.8 8.43 <0.001

Ophiuroidea 114 112 12.6 -0.09 0.931

Holothuroidea 14 41 9.59 1.28 0.232

Echinoidea 8 12 17.9 0.95 0.353

Pennatulacea 1 3 14.7 1.28 0.220

Other Anthozoans 11 55 12.1 4.07 0.001 a Student’s t-test were performed under the assumption of unequal variances. Replicates were combined for each of the 20 sites, thus n = 10 for each of the two treatment groups. b Degrees of freedom computed using Satterthwaite’s (1946) approximation.
40

Table 12. Comparison of benthic infaunal species abundances at recovering sites (n = 10 sites x 2 reps each) vs. trawled

sites (n = 10 sites x 2 reps each). Included are species each representing at least 1% of total faunal abundance of all 

species combined (75% of cumulative abundance collectively).

Mean density grab-1 (# m-2) % difference 

relative to 

recovering 

area

Statistical Results

Taxon Recovering Trawled df b t-value a p

Myriochele gracilis 5300 77 -99 9.0 -3.27 0.010

Spiophanes spp.c 279 1894 579 11.9 11.71 <0.001

Myriochele olgae 618 127 -79 14.9 -3.36 0.004

Cirratulidae 196 218 11 17.6 1.32 0.205

Axinopsida serricata 102 273 168 11.9 7.79 <0.001

Maldanidae 104 149 43 11 0.82 0.431

Terebellidae 152 40 -74 10.1 -3.46 0.006

Prionospio spp. 76 149 96 18 4.14 0.001

Ophiuroidea juv. 114 112 -2 12.6 -0.09 0.931

Decamastus gracilis 75 64 -15 18 -0.41 0.685

Scoloplos armiger 59 92 56 18 1.86 0.080 a t-tests were performed under the assumption of unequal variances. Replicates were combined for each of the 20 sites, thus n = 10 for each of the two 

treatment groups..

b Degrees of freedom computed using Satterthwaite’s (1946) approximation.

c Mostly S. duplex (97%).
41

Table 13. Dominant (five most abundant) infaunal species, listed in decreasing order of abundance, at 

recovering sites (n = 10 sites x 2 reps each) vs. trawled sites (n = 10 sites x 2 reps each).

Recovering Sites Trawled Sites

Taxon Mean 

Density (m-2

)

Frequency* 

(%) Taxon Mean Density (m-2)

Frequency* 

(%)

Myriochele gracilis 5300 100 Spiophanes spp. 1894 100

Myriochele olgae 618 100 Axinopsida serricata 273 100

Spiophanes spp. 279 100 Cirratulidae 247 100

Cirratulidae 196 100 Maldanidae 149 100

Terebellidae 152 100 Prionospio spp. 149 95

*Percentage of samples (individual replicates) in which species occurred.
42

NMSP CONSERVATION SERIES PUBLICATIONS

To date, the following reports have been published in the Marine Sanctuaries Conservation 

Series. All publications are available on the Office of National Marine Sanctuaries Web site 

(http://www.sanctuaries.noaa.gov/).

Chemical Contaminants, Pathogen Exposure and General Health Status of Live and Beach-Cast 

Washington Sea Otters (Enhydra lutris kenyoni) (ONMS-09-01)

Caribbean Connectivity: Implications for Marine Protected Area Management (ONMS-08-07)

Knowledge, Attitudes and Perceptions of Management Strategies and Regulations of FKNMS by 

Commercial Fishers, Dive Operators, and Environmental Group Members: A Baseline 

Characterization and 10-year Comparison 

(ONMS-08-06)

First Biennial Ocean Climate Summit: Finding Solutions for San Francisco Bay Area's Coast and 

Ocean 

(ONMS-08-05)

A Scientific Forum on the Gulf of Mexico: The Islands in the Stream Concept (NMSP-08-04)

M/V ELPIS Coral Reef Restoration Monitoring Report Monitoring Events 2004-2007 Florida 

Keys National Marine Sanctuary Monroe County, Florida (NMSP-08-03)

CONNECTIVITY Science, People and Policy in the Florida Keys National Marine Sanctuary 

(NMSP-08-02) 

M/V ALEC OWEN MAITLAND Coral Reef Restoration Monitoring Report Monitoring Events 

2004-2007 Florida Keys National Marine Sanctuary Monroe County, Florida (NMSP-08-01)

Automated, objective texture segmentation of multibeam echosounder data - Seafloor survey and 

substrate maps from James Island to Ozette Lake, Washington Outer Coast. (NMSP-07-05) 

Observations of Deep Coral and Sponge Assemblages in Olympic Coast National Marine 

Sanctuary, Washington (NMSP-07-04) 

A Bioregional Classification of the Continental Shelf of Northeastern North America for 

Conservation Analysis and Planning Based on Representation (NMSP-07-03) 

M/V WELLWOOD Coral Reef Restoration Monitoring Report Monitoring Events 2004-2006 

Florida Keys National Marine Sanctuary Monroe County, Florida (NMSP-07-02) 

Survey report of NOAA Ship McArthur II cruises AR-04-04, AR-05-05 and AR-06-03: Habitat 

classification of side scan sonar imagery in support of deep-sea coral/sponge explorations at the 

Olympic Coast National Marine Sanctuary (NMSP-07-01) 

2002 - 03 Florida Keys National Marine Sanctuary Science Report: An Ecosystem Report Card 

After Five Years of Marine Zoning (NMSP-06-12) 

Habitat Mapping Effort at the Olympic Coast National Marine Sanctuary - Current Status and 

Future Needs (NMSP-06-11) 
43

M/V CONNECTED Coral Reef Restoration Monitoring Report Monitoring Events 2004-2005 

Florida Keys National Marine Sanctuary Monroe County, Florida (NMSP-06-010) 

M/V JACQUELYN L Coral Reef Restoration Monitoring Report Monitoring Events 2004-2005 

Florida Keys National Marine Sanctuary Monroe County, Florida (NMSP-06-09)

M/V WAVE WALKER Coral Reef Restoration Baseline Monitoring Report - 2004 Florida Keys 

National Marine Sanctuary Monroe County, Florida (NMSP-06-08) 

Olympic Coast National Marine Sanctuary Habitat Mapping: Survey report and classification of 

side scan sonar data from surveys HMPR-114-2004-02 and HMPR-116-2005-01 (NMSP-06-07) 

A Pilot Study of Hogfish (Lachnolaimus maximus Walbaum 1792) Movement in the Conch Reef 

Research Only Area (Northern Florida Keys) (NMSP-06-06) 

Comments on Hydrographic and Topographic LIDAR Acquisition and Merging with Multibeam 

Sounding Data Acquired in the Olympic Coast National Marine Sanctuary (ONMS-06-05) 

Conservation Science in NOAA's National Marine Sanctuaries: Description and Recent 

Accomplishments (ONMS-06-04)

Normalization and characterization of multibeam backscatter: Koitlah Point to Point of the 

Arches, Olympic Coast National Marine Sanctuary - Survey HMPR-115-2004-03 (ONMS-06-03) 

Developing Alternatives for Optimal Representation of Seafloor Habitats and Associated 

Communities in Stellwagen Bank National Marine Sanctuary (ONMS-06-02) 

Benthic Habitat Mapping in the Olympic Coast National Marine Sanctuary (ONMS-06-01) 

Channel Islands Deep Water Monitoring Plan Development Workshop Report (ONMS-05-05) 

Movement of yellowtail snapper (Ocyurus chrysurus Block 1790) and black grouper 

(Mycteroperca bonaci Poey 1860) in the northern Florida Keys National Marine Sanctuary as 

determined by acoustic telemetry (MSD-05-4) 

The Impacts of Coastal Protection Structures in California's Monterey Bay National Marine 

Sanctuary (MSD-05-3) 

An annotated bibliography of diet studies of fish of the southeast United States and Gray's Reef 

National Marine Sanctuary (MSD-05-2) 

Noise Levels and Sources in the Stellwagen Bank National Marine Sanctuary and the St. 

Lawrence River Estuary (MSD-05-1) 

Biogeographic Analysis of the Tortugas Ecological Reserve (MSD-04-1) 

A Review of the Ecological Effectiveness of Subtidal Marine Reserves in Central California 

(MSD-04-2, MSD-04-3) 

Pre-Construction Coral Survey of the M/V Wellwood Grounding Site (MSD-03-1) 
44

Olympic Coast National Marine Sanctuary: Proceedings of the 1998 Research Workshop, Seattle, 

Washington (MSD-01-04) 

Workshop on Marine Mammal Research & Monitoring in the National Marine Sanctuaries 

(MSD-01-03) 

A Review of Marine Zones in the Monterey Bay National Marine Sanctuary (MSD-01-2) 

Distribution and Sighting Frequency of Reef Fishes in the Florida Keys National Marine 

Sanctuary (MSD-01-1) 

Flower Garden Banks National Marine Sanctuary: A Rapid Assessment of Coral, Fish, and Algae 

Using the AGRRA Protocol (MSD-00-3) 

The Economic Contribution of Whalewatching to Regional Economies: Perspectives From Two 

National Marine Sanctuaries (MSD-00-2) 

Olympic Coast National Marine Sanctuary Area to be Avoided Education and Monitoring 

Program (MSD-00-1) 

Multi-species and Multi-interest Management: an Ecosystem Approach to Market Squid (Loligo 

opalescens) Harvest in California (MSD-99-1)