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Chapter 2 Program Design, Operational Background, Data Collection, and 

 Processing Methodologies

The Pacific Reef Assessment and Monitoring Program (RAMP) field collection methodologies 

produce a series of integrated, comprehensive, and multidisciplinary ecosystem observations 

for the ~ 50 islands, atolls, and shallow-water banks of the United States (U.S.)-affiliated 

Pacific Islands. The data collections are designed to characterize the spatial and temporal 

variability of the distribution, abundance, and diversity of fish, corals, other invertebrates, 

and algae in the context of their benthic and oceanographic habitats. Though most of the 

ecological and oceanographic observations are collected every 2 years during Pacific RAMP 

research cruises, time series observations of key environmental conditions influencing reef 

processes are also made continuously by an array of moored oceanographic and bioacoustic 

instruments deployed and maintained as part of the National Oceanic and Atmospheric 

Administration (NOAA) Coral Reef Watch (CRW) program. These biological and 

environmental observations are further complemented by a suite of benthic habitat mapping 

products produced collaboratively by the NOAA Pacific Islands Fisheries Science Center 

(PIFSC) Coral Reef Ecosystem Division (CRED) and the Center for Coastal Monitoring and 

Assessment (CCMA) Biogeography Program of the NOAA National Centers for Coastal 

Ocean Science. Collectively, CRED’s Pacific RAMP, CRW, and benthic habitat mapping 

are part of the NOAA Coral Reef Conservation Program’s (CRCP’s) Coral Reef Ecosystem 

Integrated Observing System (CREIOS) in the Pacific Islands.

The primary objectives of these CRED-led activities in the U.S.-affiliated Pacific Islands 

are:

To conduct benthic habitat mapping of reefs and submerged banks using ship- and 

launch-based multibeam echosounders, underwater towed-camera systems, and 

towed-diver surveys for characterizing the benthic environments that provide habitat 

and shelter for reef biota;

To conduct near and offshore oceanographic and water quality surveys and deploy 

a variety of surface and subsurface oceanographic and bioacoustic instruments, to 

quantify, assess, and gain a better understanding of the overall hydrographic and 

bioacoustic environments (e.g., water temperature, salinity, nutrients, waves, tides, 

currents, and ambient sound levels) influencing reef biota;

To employ complementary and overlapping methods, collectively referred to as Rapid 

Ecological Assessment (REA) surveys to assess and monitor species composition, 

abundance, percent cover, size distribution, diversity, and general health of fish, 

corals, other invertebrates, and algae in shallow-water (< 35 m) habitats;

To monitor coral and coralline algal diseases in conjunction with continued long-term 

monitoring of fish, coral, invertebrates, and algae;

To conduct broad-scale towed-diver surveys that provide a spatial assessment 

of the composition and condition of shallow-water benthic habitats, and general 

distribution and abundance patterns of ecologically and/or economically important 

macroinvertebrates and reef fish (> 50 cm total length); and

To ascertain the existence of threats to the health of coral reef resources from natural 

and/or anthropogenic sources.

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Ecosystem observations and monitoring of this scope and detail are unprecedented and 

unequaled in the waters of American Samoa. As such, the initial years of these multidisciplinary 

Pacific RAMP research expeditions were exploratory in nature, often providing the first-ever 

baseline assessments of reef resources in these mostly remote and uninhabited regions of 

the Pacific. As the analyses of initial baseline assessments have progressed, the program 

has shifted from an assessment phase to a long-term ecosystem monitoring phase. With this 

shift, the suite of methods used by the program has slowly evolved to continually improve 

the quality of the data and ability to detect temporal changes in ecosystem processes and 

community structure.

To qualify the nature and temporal variation of the data gathered during Pacific RAMP cruises 

and to provide a context for how surveys were performed, the operational background of the 

three American Samoa RAMP (ASRAMP) cruises conducted to date and details on the suite 

of assessment and monitoring methods employed are presented in the following sections.

2.1 Operational Background

As part of the Pacific-wide monitoring effort, CRED conducted its first ASRAMP cruise in 

2002 with subsequent cruises in 2004 and 2006. Partners from the local management agencies, 

including the scientists and managers from American Samoa’s Department of Marine and 

Wildlife Resources (DMWR), the Department of Commerce (DOC), the National Park of 

American Samoa (NPAS), and NOAA’s Fagatele Bay National Marine Sanctuary (FBNMS) 

worked alongside CRED scientists to plan the surveys, determine and establish monitoring 

sites, and conduct surveys. Specific individuals from American Samoa who participated in 

the planning and/or implementation of ASRAMP cruises included:

2002: Tony Beeching (DMWR), Dr. Andrew Cornish (DMWR), Dr. Peter Craig 

(NPAS), Nancy Daschbach (FBNMS), Gene Brighouse (DOC), Eva Pasko-DiDonato 

(NPAS), Dr. Douglas Wilson (DMWR), Joshua Seamon (DMWR), Saiofoi Fa`aumu 

(DMWR), Dr. Ray Tulafono (DMWR), Lelei Peau (DOC), Wallace Thompson 

(Swains Island Representative)

2004: Dr. Douglas Fenner (DMWR), Dr. Peter Craig, Christopher Hawkins (DOC), 

Nancy Daschbach, Gene Brighouse, Dr. Ray Tulafono, Lelei Peau, Fatima Sauafea 

(DMWR), Francesca Riolo (DMWR), Wallace Thompson, Penekosova Peau 

(student)

2006: Dr. Douglas Fenner, Dr. Peter Craig, Nancy Daschbach, Gene Brighouse, Dr. 

Karl Brookins (DMWR), Dr. Ray Tulafono, Lelei Peau, Wallace Thompson, Merideth 

Speicher (DOC), Dr. Bill Keine (FBNMS), Fatima Sauafea

•

•

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Figure 2.1a. The NOAA ships used to conduct ASRAMP cruises in 2002, 2004, and 2006. From left to right: 

Townsend Cromwell, Oscar Elton Sette, and the Hi`ialakai. (Photographs provided by NOAA PIFSC CRED)
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The first three ASRAMP expeditions were conducted from the NOAA Ships Townsend 

Cromwell between February 9 and March 3, 2002, Oscar Elton Sette between February 3 and 

26, 2004, and Hi`ialakai between February 9 and March 10, 2006 (Fig. 2.1a). Each of these 

research vessels, as well as their officers and crews, had different capabilities and limitations. 

In its 39th year of service supporting NOAA missions, the aging Townsend Cromwell was 

significantly smaller (50 m) than the other two vessels (69 m). The smaller size restricted 

the vessel’s ability to carry, launch, and recover small boats and also limited the maximum 

scientific complement to 12 scientists. With the addition of the larger Oscar Elton Sette in 

2003, the capacity to support Pacific RAMP requirements increased significantly. The Oscar 

Elton Sette can accommodate a complement of 20 scientists and has the ability to carry and 

deploy larger small boats. The addition of the Hi`ialakai in 2005 increased the maximum 

complement to 22 scientists and significantly improved the ability of CRED to conduct 

benthic habitat mapping missions because of the ship’s hull-mounted shallow- and deepwater multibeam systems and the ability to carry CRED’s 8-m multibeam survey launch R/V 

Acoustic Habitat Investigator (AHI). The Hi`ialakai is also equipped with diesel-powered 

8-m and 10-m small boats, a cascade Nitrox compressor system, and a permanently installed 

diving recompression chamber.

Concurrent with changes in vessels from 2002 to 2006, CRED increased its small-boat and 

dive-support capabilities with the addition of two 6-m SAFEboats and a portable cascade 

Nitrox compressor system. During this period, support of diving operations was enhanced as 

the NOAA Dive Center endorsed the transition from exclusive use of decompression tables 

to the standard use of dive computers and began providing a portable recompression chamber 

aboard the Oscar Elton Sette during cruises requiring extensive diving operations.

2.2 Benthic Habitat Mapping

Accurate, high-resolution benthic habitat maps are essential tools for the effective 

conservation and management of coral reef ecosystems. CRED, through its Pacific Islands 

Benthic Habitat Mapping Center (PIBHMC), supports mapping operations during dedicated 

mapping cruises, combined RAMP/mapping cruises, and cruises with other missions on 

which mapping is piggybacked. The data collected during these missions were used to create 

a set of comprehensive map products that are available to resource management agencies, 

researchers, and the general public.

High-resolution multibeam echosounder bathymetric data serve as the primary base layer 

for CRED’s benthic habitat mapping. The highly accurate and detailed maps generated 

from these data are useful for a number of management and research applications. Maps 

illustrating or highlighting other seafloor characteristics, including slope, rugosity (a measure 

of topographic roughness and convolutedness), and bathymetric position index structures 

and zones, are derived from the bathymetric data.

In addition to bathymetric and derived data products, modern multibeam echosounders 

produce backscatter intensity data which provide an indication of the acoustic roughness 

and/or hardness of the seafloor. Used in various combinations, depth, slope, rugosity, and 

backscatter intensity can yield significant information about seafloor characteristics that 
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are important to specific groups of organisms and can be used to identify and delineate the 

benthic habitats they use (Fig. 2.2a).

To fully interpret and understand the wealth of data from multibeam echosounders, additional 

optical data are needed to validate (ground-truth) interpretations of the acoustically derived 

information. Towards this end, towed-camera surveys using a Towed Optical Assessment 

Device (TOAD) and towed-diver habitat surveys were routinely conducted to collect 

observations, still photographs, and video imagery of the seafloor. Towed-camera systems 

covered depths between 20 and 150 m and towed-diver surveys covered depths between 3 

and 30 m.

2.2.1 Operational Background and Logistics

In The National Action Plan to Conserve Coral Reefs, the U.S. Coral Reef Task Force 

identified mapping of all U.S. coral reef habitats as one of their highest priorities. The 

NOAA CRCP established a goal to map all U.S. coral reef areas to support conservation 

and management of U.S. coral reefs. In support of these goals, CRED and the CCMA 

Biogeography Program have been leading efforts to produce benthic habitat maps of coral 

Figure 2.2a. Multibeam bathymetry (a), slope (b), rugosity (c), and multibeam backscatter (d) data provide 

valuable information about seafloor characteristics.

a b

c d
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reef areas from the shoreline to moderate depths (≤ 1000 m). The Biogeography Program 

has been leading collaborative efforts to develop shallow-water benthic habitat maps using 

aerial and satellite-based methods. As a result of visibility constraints, these techniques are 

best suited for shallow-water habitats (≤ 20 m deep). CRED has been leading efforts using 

multibeam acoustic echosounders and optical assessment technologies to extend the existing 

shallow-water maps to moderate depths (~ 20–1000 m) where aerial- and satellite-based 

techniques are less suitable.

As stated above, three different NOAA ships were used to support mapping operations in 

American Samoan waters between 2002 and 2006. These include the NOAA Ships Townsend 

Cromwell (2002), Oscar Elton Sette (2004), and the Hi`ialakai (2006). In addition, the CRED 

R/V AHI, an 8-m survey launch, was deployed in 2004 and 2006 to conduct shallow-tomoderate depth habitat mapping.

A variety of operational scenarios have been developed to optimize the efficiency of mapping 

operations. During cruises aboard the Hi`ialakai, shipboard multibeam mapping surveys 

were conducted primarily during nighttime hours to avoid interfering with daytime reef 

ecosystem monitoring and nearshore oceanographic surveys requiring small boat and diverbased operations. R/V AHI-based mapping operations were conducted during daylight hours 

to perform multibeam surveys in shallow, nearshore waters inaccessible to the Hi`ialakai.

During previous cruises aboard the Townsend Cromwell and Oscar Elton Sette, optical 

validation data were typically collected using a towed camera sled deployed from the ships in 

deeper waters (20–150 m) during nighttime hours and by towed-diver surveys in shallower 

waters (3–30 m) during daylight hours.

Operationally, depth limitations existed for both multibeam surveying and optical data 

collection. As a general rule, multibeam surveys by CRED have focused on collecting data 

at depths between approximately 20 and 1000 m. The 20-m inshore limit is based on: (1) 

safety concerns relating to increased risks in shallow water as a result of possible groundings 

and/or breaking waves, and (2) significant decreases in mapping efficiencies because the area 

mapped decreases proportionally to water depth. Combined, these factors meant that survey 

work in waters shallower than 20 m would have required increasingly larger amounts of time 

that were spent working in potentially dangerous conditions, particularly in areas with steep 

forereef slopes.

Similarly, ship-based towed-camera optical data collection has been limited to depths 

between approximately 20 and 150 m based on the depth limitations of the instruments. 

Towed-diver surveys provide optical data to about a 30-m maximum depth. Below this depth, 

the divers would be subject to increased risk of decompression sickness. Ship- and launchbased multibeam surveying, as well as towed-camera and towed-diver optical assessment 

data collection procedures adhere strictly to NOAA safety policies applicable to ship, small 

boat, and scuba diving operations.
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2.2.2 Acoustic Mapping

Equipment

Aboard the Townsend Cromwell, acoustic mapping was conducted using a Simrad EQ-50 

(50 kHz) single-beam echosounder that was integrated with a Quester Tangent Corporation 

(QTC) View data acquisition and bottom classification system. This system was subsequently 

transferred to the Oscar Elton Sette, where the QTC View was interfaced to one quadrant 

of a 38 kHz split-beam transducer used in conjunction with a Simrad EK-60 echosounder. 

Acoustic seafloor classification systems such as QTC are best used in reasonably flat areas 

such as the continental shelf off the eastern seaboard of the continental U.S. It was found 

that in areas where the seafloor is quite steep, including much of the seafloor around the 

islands of American Samoa, classification results are not very reliable. For this and other 

reasons, acoustic surveying transitioned to multibeam echosounder technology at the earliest 

opportunity.

The Hi`ialakai is equipped with two multibeam sonars: a Kongsberg 300 kHz EM3002 

multibeam echosounder that can map at depths between roughly 20 and 150 m, and a 

Kongsberg 30 kHz EM300 multibeam that is capable of mapping in depths ranging from 

about 50 to 3000 m. The AHI is equipped with a 240 kHz RESON 8101ER multibeam 

echosounder capable of mapping at depths between approximately 10 and 250 m. When 

used in conjunction with the Hi`ialakai, the AHI can be deployed and recovered in locations 

far from sheltered harbors, allowing shallow-water surveys to be conducted throughout the 

remote U.S.-affiliated Pacific Island areas (Fig. 2.2.2a).

Survey Design

The quality and geographic coverage of existing bathymetric data, as well as consultation 

with key resource managers and stakeholders, were used to determine survey priorities. Data 

collected on previous cruises were typically combined with existing datasets, allowing the 

mapping team to develop survey plans to most effectively target gaps in the bathymetry 

coverage.

Prior to 2002, only a 

few, limited shallowand moderate-depth 

bathymetry datasets existed 

for the nearshore waters of 

American Samoa. Existing 

nautical charts of Tutuila 

Island showed surrounding 

banks (0–60 m) with an 

area of approximately 300 

km2, but little was known 

about the coral reef and 

other shallow habitats 

that existed on these 

banks. Almost no shallow 

bathymetric information 

Figure 2.2.2a. Survey launch R/V AHI and NOAA Ship Hi`ialakai are 

outfitted with three multibeam echosounders that facilitate mapping in 

depths ranging from ~ 20 to 3000 m. (Photograph provided by NOAA 

PIFSC CRED)
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existed around Ofu, Olosega, Ta`u, and Swains Islands or Rose Atoll. Aside from nautical 

charts, the available limited data (Wright, 2002) served as the primary base for the 2004 

planning process.

In early 2004, shallow-water multibeam surveying was conducted around Tutuila and the 

Manu`a Islands using the R/V AHI. During the ASRAMP 2004 cruise, the AHI operated 

independently of the Oscar Elton Sette and was based out of Pago Pago Harbor and the Ofu 

small boat harbor. During that deployment, the shallow waters surrounding Ofu, Olosega and 

Ta`u were completely surveyed, as were approximately 60% of the banks surrounding Tutuila. 

Substantial amounts of deeper multibeam data were collected in American Samoan waters 

during a variety of academic research deployments between 2004 and 2006. These datasets 

were collated in the online Seamount Catalog (http://earthref.org), and also incorporated 

more recent data obtained from NOAA and University of Hawaii (UH) research activities 

aboard the R/V Kilo Moana and the R/V Kaimi`kai O Kanaloa. These data, combined with 

multibeam data collected from previous CRED cruises, formed the base for the 2006 survey 

planning. In 2006, the AHI was deployed from the Hi`ialakai and surveyed the shallow 

waters surrounding Rose and Swains while the ship surveyed the deeper flanks. Surveys of 

the banks surrounding Tutuila were completed by a combination of the two vessels.

Data Collection and Processing

Though the QTC habitat classification system can be used with a variety of sonar systems 

and different frequencies, data collected at different sonar frequencies or transmission 

characteristics cannot be easily integrated. Unfortunately, this meant that QTC classifications 

acquired during the 2002 surveys aboard the Townsend Cromwell could not be compared 

with QTC classifications acquired during the 2004 surveys aboard the Oscar Elton Sette. 

Nevertheless, the spatial variability of the habitat classifications, rather than the classifications 

themselves, was determined to be a good predictor of bottom type for use in targeting areas 

for optical ground-truth surveys.

Since 2004, the R/V AHI and Hi`ialakai have been the exclusive platforms for CRED multibeam 

mapping missions. Real-time data acquisition and processing often occurred concurrently 

and involved several processing steps and software packages. See the Documentation section 

of PIBHMC’s web site (http://www.soest.hawaii.edu/pibhmc) for more details.

Data Acquisition

Multibeam data were collected using the ISS-2000 collection module. Sensors were interfaced 

to the system through a software module called a Data Transaction Center (DTC) that was 

used to set sensor settings, calibration parameters, quality control parameters, input formats, 

and output file formats. Each of the DTC modules stored the data from its corresponding 

sensor in the appropriate file formats and assigned the appropriate names to each file. Most 

data were ASCII text files, but binary Generic Sensor Format (GSF; Ferguson and Chayes, 

1995; SAIC, 2007) were used specifically for multibeam data. Each filename was unique and 

based on the sensor collecting the data, the collection date, and a sequential extension.

A benefit of ISS-2000 was that all echosounder correctors were applied in real-time during data 

collection. All data were displayed in real-time for quality control purposes and for guidance 

of the progress of the survey. Each GSF echosounder file not only stored all information 

necessary to provide the depth for each beam, but each file also contained a record of every 
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action taken on the data file.

Data Processing

Data collected using the ISS-2000 software were fully corrected for ship’s motion, navigation, 

sound velocity, and predicted tides (if selected). Predicted tidal correctors were applied 

(using data from the NOAA Center for Operational Oceanographic Products and Services) 

to multibeam data during collection to minimize apparent errors which may be caused by tide 

offsets or other system problems. Using Science Applications International Corporation’s 

(SAIC’s) compatible Survey Analysis and area Based EditoR (SABER) processing package, 

many of these corrections can be reapplied or changed, if desired. The following four 

processing steps were needed for the majority of multibeam bathymetric data collected:

The application of alternate sound velocity profiles to a limited number of multibeam 

swath files;

The application of corrected tides (if available and/or needed) to some or all multibeam 

swath files to replace the predicted tides applied in real-time;

The visual editing of individual multibeam swath data files in GSF; and

The assembly of all data in a given area within a Pure File Magic (PFM) grid and 

visual editing using an area-based editor.

After edits were made to the PFM grid the data were downloaded back to the GSF files, where 

flags were set to indicate the edits. These processed GSF files were used for data synthesis 

work at PIBHMC and were documented with metadata; the GSF files with metadata were 

sent to the NOAA National Geophysical Data Center on a cruise-by-cruise basis.

After the grid editing was complete, the PFM grid was downloaded to ASCII, Cartesian or 

other grid formats, or the original GSF files were regridded and output to these formats. The 

GSF files, ASCII, Cartesian, and/or grid files were then transferred to other data processing 

and visualization packages, including:

MBSystem: an open-source software package for the processing and display of 

bathymetry and backscatter imagery data derived from multibeam, interferometry, 

and sidescan sonars (http://www.mbari.org/data/mbsystem/). MBSystem is supported 

by the National Science Foundation (NSF); and

Generic Mapping Tools (GMT): GMT is an open-source collection of about 60 tools 

for manipulating geographic and Cartesian datasets and producing output in the 

encapsulated postscript format. It is supported by the NSF (http://www.soest.hawaii.

edu/gmt/).

2.2.3 Optical Validation Surveys

TOAD

CRED’s initial TOAD integrated a digital still camera, an underwater video camera, lights, 

and parallel scaling lasers on a Guideline Minibat tow body (Fig. 2.2.3a). The Minibat design 

allowed limited control of the vehicle’s position while towing by changing the angle of the 

Minibat wings. The TOAD operator entered the estimated layback distance into the Minibat 

software, which integrated it with the ship’s position to provide an estimated position of the 

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tow body along the survey track. Estimated positional accuracies using this method were on 

the order of 50 m. Various operational scenarios were tested, including towing the TOAD at 

speeds of 1 to 3 kn and using it in a drift mode. After several cruises, it was determined that 

the drift technique was most effective and presented the least overall risk to both the tow 

body and shipboard personnel operating the winch, particularly over high relief terrain.

Seafloor videography collected during TOAD deployments were analyzed using a series of 

five small circles extending in a straight horizontal line marked on a video monitor screen. 

The types of substrate (sand, rock, etc.) and living cover (macroalgae, scleractinian coral, 

hydrocorals or other benthic fauna, etc.) that fell within these circles were identified at 20-m 

or 30-sec increments along the camera’s trackline. Other biologically relevant observations 

were made as well. The full listing of benthic habitat classifications is shown in Appendix I, 

Table I. i. TOAD habitat classifications are incorporated in attribute tables associated with 

Arc© shapefiles that show the location of TOAD tracks over the seafloor.

Towed-diver Benthic Habitat Characterization

Data characterizing the benthic habitats around American Samoa in depths between 3 and 30 

m were collected during towed-diver surveys. These benthic habitat characterizations provide 

background for analyses of biological data collected during the towed-diver surveys and also 

can be used to validate (ground-truth) habitat maps created by acoustic and/or satellite-derived 

information. The benthic characterization data collected during benthic towed-diver surveys 

are discussed in Section 2.4.2, Towed-diver Surveys. Only a brief overview of towed-diver 

surveys and details on the benthic habitat categories used to make habitat characterization 

maps are presented in this section.

The towed-diver methodology involved towing two divers/observers approximately 60 m 

behind a small boat while they each maneuver their towboard to maintain their position 

about 1 m above the bottom. A typical survey covered approximately 2 linear km of habitat 

and lasted about 50 min. Surveys were divided into ten 5-min segments (~ 200 m in length) 

during which the benthic diver/observer recorded visual estimates of habitat complexity and 

benthic substrate cover within a 10-m swath (5 m on either side of the tow line). In addition 

to visual estimates of benthic cover, continuous video imagery of the benthos was collected 

in 2002 and still camera photographs of the benthos were taken at 15-sec intervals in 2004 

and 2006. The photos and video imagery have been archived for future analyses.

Classification of habitat 

complexity was a subjective 

assessment of topographical 

diversity and complexity over 

a large scale (~ 2000 m2) 

based on six categories: low, 

medium-low, medium, mediumhigh, high, and very high. For 

example, a sandy bottom with 

scattered macroalgae has low 

habitat complexity. In contrast, 

a shallow reef with numerous 

Figure 2.2.3a. TOAD. (Photograph provided by NOAA PIFSC CRED)
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growth forms of corals and three-dimensional structure providing shelter for reef fish of 

various size categories would be rated medium-high to very high. See Figure 2.4.2b in 

Section 2.4.2: Towed-diver Surveys for visual examples of each complexity category.

Benthic cover was estimated for four different types of substrate: hard substrate/pavement, 

sand, rubble, and live hard (scleractinian) coral. A description of each substrate type is given 

in Table 2.2.3a. It is important to note that in 2006 the definition of rubble changed to include 

only unconsolidated fragments of coral skeleton or reef rock not visibly encrusted by fleshy 

or calcareous algae or corals. Also in 2006, the hard substrate/pavement category was not 

recorded. All other benthic substrate definitions remained the same for towed-diver surveys 

from 2002 to 2006.

Towed-diver benthic data were used to make habitat characterization maps for complexity, 

sand, hard substrate/pavement, rubble, and live hard (scleractinian) coral. For each habitat 

characterization map, estimates of respective benthic features were plotted in ArcGIS 9.2 

using the midpoint of each 5-min towed-diver segment. Results from the 2002, 2004, and 

2006 surveys were combined and then an inverse distance weighting (IDW) interpolation 

function (ArcGIS 9.2) was applied to the combined dataset. The IDW function produced a 

continuous plot of the salient benthic features around each island.

Table 2.2.3a. Benthic cover categories used to create habitat characterization products from towed-diver 

surveys, 2002-2006 (Kenyon et al., 2006a).

Benthic Cover

Category Description

Live Hard Coral Colonies or portions of colonies, of live pigmented tissue. 

Sand

Unconsolidated sediment, ranging in texture and size from fine 

to course. Origins are both inorganic (eroded rock) and organic 

(eroded fragments of calcareous organisms).

Rubble* Unconsolidated fragments of coral skeleton or reef rock whose 

sizes are larger than sand.

Hard Substrate/

Pavement**

Consolidated substrate, typically composed of calcareous and/or 

basaltic elements that have become cemented together by biogenic 

and physical processes.

* In 2006 the definition changed to include only rubble that was not visibly encrusted by macroalgae, calcareous algae or 

corals.

** In 2006 the hard substrate/pavement category was not recorded.

2.3 Oceanography and Water Quality

Knowledge of local oceanographic processes and water quality parameters is fundamental 

to understanding the natural dynamics and anthropogenic influences controlling many 

environmental aspects of coral reef ecosystems, including organism distribution, abundance, 

and biodiversity; biological productivity; larval dispersal and recruitment; localized and 

large-scale patterns of coral bleaching and disease; and degrees of disturbance from episodic 

storms and human-related activities. To assess the oceanographic and water quality conditions 

influencing the environmental aspects of coral reef ecosystems in American Samoa, CRED 

collected and integrated five key data streams, including: (1) deep-water oceanographic 
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surveys characterizing prevailing water properties and ocean currents around the islands of 

American Samoa; (2) intensive closely spaced nearshore oceanographic and water quality 

surveys conducted concurrently with REA and towed-diver biological surveys; (3) an array 

of surface and subsurface moored instruments providing continuous, high-resolution time 

series observations; (4) satellite remote sensing products providing spatial time series 

observations of key oceanographic properties (e.g., sea surface temperature [SST], sea surface 

height, surface winds, chlorophyll-a, and other derived products), and (5) numerical models 

(e.g., Wave Watch III) providing spatial and temporal estimates of various oceanographic 

parameters.

2.3.1 Operational Background and Survey Design

CRED has used a diverse array of data collection methodologies to monitor and assess 

local oceanographic and water quality conditions, including in situ telemetered surface 

and subsurface moored instruments, shipboard and nearshore spatial hydrographic surveys 

performed during research cruises, and bioacoustic surveys. Oceanographic equipment 

and instrument specifications are detailed in Appendix I, Table I. ii. Shipboard surveys 

were conducted by the three different NOAA ships (discussed in Section 2.1: Operational 

Background), and nearshore surveys and instrument deployment/retrievals were accomplished 

by small boats deployed from these ships.

The monitoring sites were selected to characterize the prevailing climatic and oceanographic 

conditions by spatially and temporally quantifying key physical forcing mechanisms pertinent 

to biological processes (e.g., temperature, salinity, currents, wave energy, ultraviolet [UV] 

radiation, nutrients, chlorophyll, dissolved oxygen, and dissolved inorganic carbon) over 

seasonal, interannual, and decadal time scales. By so doing, CRED is generating a baseline 

for long-term observation of environmental conditions influencing reef ecosystems that are 

particularly important in aiding efforts to understand and predict the ecological impacts of 

climate change.

2.3.2 Shipboard Surveys

Shipboard deep-water (500 m) 

conductivity, temperature, and depth 

(CTD) casts with simultaneous 

water sample collection were 

conducted to determine prevailing 

water property profiles surrounding 

the islands and atolls of American 

Samoa. These deep-water casts 

provide high-resolution vertical 

profiles of conductivity (salinity), 

temperature, dissolved oxygen, 

and chlorophyll-a concentration 

versus depth. In addition, shipboard 

acoustic Doppler current profiler 

(ADCP) transects were conducted 

Figure 2.3.2a. Deep-water CTD (SBE 911plus) with rosette 

and Niskin water bottles being deployed from ship. (Photograph 

provided by NOAA PIFSC CRED)
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in the deep-water regions around each of the islands and atolls to examine the horizontal and 

vertical structure of the prevailing ocean currents (Lumpkin and Pazon, 2005).

Deep-water CTD Surveys

A Sea-Bird Electronics, Inc. (SBE) SBE 911plus CTD with a SBE 43 dissolved oxygen 

sensor and Wetlabs ECO FLNTU fluorescence and turbidity sensors was used to collect 

vertical profiles of water properties from the surface to 500 m deep in offshore environments 

around each island/atoll surveyed. In addition, a rosette with multiple 5-l Niskin bottles (Fig. 

2.3.2a) was used to collect water samples at selected depths for chlorophyll-a and nutrient 

analyses. Data from the deep-water CTD casts are presented in the archipelago chapter of 

this report (Chapter 8, Section 8.4.2: Seasonal Variation).

Shipboard ADCPs

Transects of ocean current velocity profiles were collected using shipboard ADCPs during 

ASRAMP cruises in 2002, 2004, and 2006. During the 2002 cruise aboard the Townsend 

Cromwell, the surveys were conducted using a hull-mounted 153-kHz RD Instruments (RDI) 

narrow beam ADCP, which collected current profiles in 8-m sampling bins over depths 

between 20 and approximately 250 m, averaged into over 5-min ensembles. During the 2004 

and 2006 cruises aboard the Oscar Elton Sette and Hi`ialakai, the surveys were conducted 

using hull-mounted 75 kHz RDI Ocean Surveyor instruments. These systems were configured 

with an 8-m pulse length which typically collects current profiles in 16-m depth bins between 

depths ranging from 25 to about 600 m averaged into 15-min ensembles. The actual depth 

range depended on the density and abundance of scattering material in the water column. In 

addition to dedicated ADCP transect grids around the islands data were generally collected 

continuously while the vessels were underway. Data from the shipboard ADCPs are not 

presented in this report.

2.3.3 Nearshore Spatial Surveys

Closely spaced nearshore CTD surveys were conducted 

throughout the shallow-water environments around each 

of the islands, atolls, and reefs surveyed during all of the 

ASRAMP cruises. The distance between adjacent casts 

ranged from 0.25 to 2.0 km, depending on the size of 

the area being sampled with each cast typically being 

conducted approximately 30 m deep. These surveys 

were conducted to characterize the spatial structure 

of the physical and chemical properties of the ocean 

environment influencing the living coral reef resources 

observed during REA and towed-diver surveys. Water 

samples were collected at a subset of the shallow-water 

CTD sites to examine nearshore water quality.

Shallow-water CTD Surveys

The shallow-water CTD surveys provided vertical 

profiles of conductivity and temperature versus depth 

using an SBE 19plus CTD. Beam transmission data were 

Figure 2.3.3a. SBE 19plus shallowwater CTD used for nearshore 

profiling of salinity, temperature and 

pressure-based depth. (Photograph 

provided by NOAA PIFSC CRED)
METHODS

39

collected concurrently using a Wetlabs C-Star Trans­missometer. The CTD profiles were 

collected by hand-lowering the CTD profiler (Fig. 2.3.3a) from a small boat at a descent 

rate of approximately 0.5 to 0.75 m s-1 to a 30-m max­imum depth. The shallow-water CTD 

observations around each island/atoll are presented as vertical cross-section plots generated 

using Ocean Data View software (http://odv.awi.de). Subsets of the data representing the 

same oceanographic parameters at a 20-m depth are presented to further illustrate their spatial 

structure around each of the islands and atolls of American Samoa.

Seawater Laboratory Analyses

Water samples were collected at a subset of the shallow- and deep-water CTD sites. During 

the shallow-water CTD surveys, a daisy chain of 1.75- and 5-l Niskin bottles were lowered 

to collect water samples at various depths (1, 10, 20, and 30 m) by triggering the bottles to 

close shut using a trip weight (messenger) sent down the line. These water samples were 

preserved for laboratory analyses of water quality including levels of: chlorophyll-a, nitrates, 

nitrites, phosphates, silicates, total nitrogen, partial pressure of carbon dioxide (pCO2), and/or 

alkalinity. Chlorophyll-a water samples were processed by Dr. Paul Bienfang of Analytical 

Services, Inc., Honolulu, Hawaii. Nutrients, pCO2, and alkalinity were processed at the 

NOAA Pacific Marine Environmental Laboratory in the nutrient laboratory of Dr. Calvin 

Mordy and in the carbon chemistry laboratory of Dr. Richard Feely.

2.3.4 Surface Moorings

As a key component of CREIOS, buoys were moored in shallow-water environments at 

many U.S.-affiliated Pacific Islands. These buoys provide near real-time observations of 

key oceanographic conditions influencing coral reef ecosystem processes to managers, 

stakeholders, and the public. These surface observations were transmitted via satellite for 

daily dissemination at the CRED website http://www.pifsc.noaa.gov/cred/.

Coral Reef Early Warning System (CREWS) Buoys

CREWS buoys are sea surface moorings that telemeter in situ 

observations of atmospheric and oceanographic parameters 

influencing reef conditions (Fig. 2.3.4a). CREWS buoys 

have been providing near real-time observations of highresolution SST and surface conductivity (or salinity) at 

a 1-m depth, air temperature, barometric pressure, and 

wind velocity. Enhanced versions additionally provide 

photosynthetically available radiation (PAR) and UV 

radiation. All data were sampled at 30-min intervals and 

internally recorded. Subsets of data have been transmitted 

daily via satellite telemetry to provide near real-time 

updates of changing environmental conditions. The sensors 

used to collect and record the data include an SBE 37 

MicroCAT conductivity and temperature recorder, an RM 

Young WS425 air temperature sensor, a Heise Instruments 

DXD barometric pressure sensor and a Vaisala Instruments 

acoustic wind velocity sensor. Enhanced versions of the 

CREWS buoys also include Biospherical Instrument’s 

Figure 2.3.4a. CREWS buoys relay 

oceanographic and meteorological 

data via satellite telemetry.

(Photograph provided by NOAA 

PIFSC CRED)
METHODS

40

PAR and UV radiation sensors. Data from the 

CREWS buoy at Rose are presented in Chapter 

6, Section 6.3.2: Habitat Characterization.

SST Buoys

SST buoys are sea surface moorings that 

telemeter in situ observations of high-resolution 

SST in near real-time. Data are recorded 

internally and transmitted, via satellite, at 1-hour 

intervals. The two types of buoys, an Ocean 

Trek Research (OTR) SB200 solar rechargeable 

buoy and the battery-powered Sound Ocean 

Systems, Inc. (SOSI) Model SST-001 use a SBE 

39 temperature recorder for SST measurements. 

Images of the two types of SST buoys can be seen in Figures 

2.3.4b and 2.3.4c. Data from the SST buoys are presented in 

the respective island/atoll chapters of this report.

2.3.5 Subsurface Moorings

Ocean data platforms (ODPs), wave and tide recorders (WTRs), 

subsurface temperature recorders (STRs), and Aanderaa 

current meters are subsurface moorings deployed at selected 

locations and configured to continuously record important 

oceanographic parameters that influence reef conditions. 

These moorings were recovered on a periodic basis and 

replaced with refurbished units to maintain a continuous time 

series of data at each location. ODPs record observations of 

ocean current profiles, wave energy, temperature, and salinity; 

WTRs record observations of sea level height, wave energy, and temperature; STRs record 

observations of subsurface temperature; and Aanderaa current meters record observations of 

ocean current velocity (at a fixed 

depth) and temperature.

ODPs

ODPs recorded directional 

current profiles and wave spectra 

using a Sontek 1000-kHz ADCP, 

and high-resolution ocean 

temperature and salinity using a 

SBE 37 MicroCAT conductivity 

and temperature recorder (Fig. 

2.3.5a).

Sample intervals for current 

and wave data varied depending 

on duration of deployment; 

Figure 2.3.4b. OTR SB200 SST buoy. 

(Photograph provided by NOAA PIFSC CRED)

Figure 2.3.5a. ODP mooring. (Photograph provided by NOAA 

PIFSC CRED)

Figure 2.3.4c. SOSI Model SST001 SST buoy. (Photograph 

provided by NOAA PIFSC 

CRED)
METHODS

41

temperature and salinity were sampled at 30-min intervals. Deployment depths typically 

ranged from 15 to 35 m. Data were internally recorded and retrieved from platforms during 

subsequent ASRAMP cruises. Data from the ODPs are not presented in this report.

WTRs

WTRs are subsurface moored instruments consisting of an SBE 26plus SEAGAUGE WTR 

that records observations of high-resolution pressure (wave height and tides) and temperature. 

Data were internally recorded with sample intervals determined by duration of deployment. 

Deployment depths typically ranged from 10 to 25 m.

STRs

STRs are subsurface moored instruments consisting of SBE 39 temperature recorders, 

which are physically attached to reef structures to record observations of high-resolution 

temperature influencing the corals and other benthic biota. Unlike CREWS buoys, SST buoys, 

and satellite observations of SST, STRs record the actual temperatures at the depth of the 

corals living near their point of deployment. These observations are particularly important 

during calm conditions conducive to coral bleaching. At these times, the water column is 

often well-stratified, meaning that many of the corals may not be subjected to the warmer 

temperatures at the surface, thereby potentially lessening the likelihood of bleaching. STRs 

have been deployed in a variety of locations and habitats throughout the coral reef ecosystems 

of American Samoa, particularly those considered most prone to coral bleaching.

Aanderaa RCM 9 Recording Current Meter (RCM)

The Aanderaa RCM 9 current meter is an autonomous subsurface mooring used to record 

observations of the speed and direction of ocean currents at a specific depth. Data were 

internally recorded with sample intervals determined by duration of the deployment.

Ecological Acoustic Recorders (EARs)

EARs (Fig. 2.3.9a) are passive acoustic recording devices developed specifically for 

monitoring fish, invertebrates, and human activity in marine habitats (Lammers et al., in 

press). The EAR is a digital, low-power system based on a Persistor CF2 microprocessor 

and a 16-bit analog-to-digital converter that records ambient sounds up to 30 kHz on a 

programmable schedule for up to 1 to 2 years. The EAR also responds to transient acoustic 

events that meet specific criteria, such as cetaceans or motorized vessels passing nearby. A 

total of eight EARs were deployed in American Samoa during ASRAMP 2006. Deployment 

depths typically ranged from 10 to 25 m. Four EARs were retrieved and their data (only for 

Tutuila) are presented in this report.

2.3.6 Oceanographic Equipment Deployment

Oceanographic instrumentation has been deployed across the American Samoa Archipelago 

since 2002. These deployments, accompanied by successive retrievals for specific devices, 

are summarized in Table 2.3.6a. At each island and atoll in the archipelago, important 

oceanographic features were evaluated and specific management concerns were addressed 

by selecting pertinent monitoring locations and using appropriate instrumentation. These 

instruments and the data they have collected are described in the oceanography and water 

quality sections of each island/atoll chapter.
METHODS

42

Table 2.3.6a. Number of oceanographic instruments deployed (Dep) and retrieved (Ret) by year in the American 

Samoa region. Instrument Types: CREWS buoy, EAR, ODP, RCM, STR, SST buoy, and WTR.

Instrument 

Type

2002 2004 2005 2006 Lost CURRENT Dep Ret Dep Ret Dep Ret Dep Ret

CREWS 1 0 1 1 0 0 1 1 0 1

EAR 0 0 0 0 0 0 4 0 0 4

ODP 1 0 0 1 0 0 0 0 0 0

RCM 2 0 0 2 0 0 0 0 0 0

STR 0 0 17 1 4 0 27 17 3 27

SST 8 4 5 5 3 2 5 3 2 5

WTR 0 0 2 0 1 1 2 2 0 2

TOTAL 12 4 25 10 8 3 39 23 5 39

2.3.7 Satellite Remote Sensing and Ocean Modeling

Satellite Remote Sensing

All satellite-derived data products presented in this report are produced and distributed 

publicly by various government and private organizations. Brief summaries of data providers 

and any further analyses performed by CRED are outlined below.

1. NOAA AVHRR Pathfinder 5.0 SST (Casey, 2006)

http://www.nodc.noaa.gov/sog/pathfinder4km/

Infrared Radiometer SST from NOAA polar orbiter satellites

4-km resolution grid

Climatology: Produced by National Oceanographic Data Center (NODC) using data 

from 1985 to 2001

Time series plots: Pathfinder 5.0 weekly data and climatology time series plots are 

based on data extracted from 1° × 1° latitude-longitude boxes surrounding the area 

of interest

2. National Aeronautics and Space Administration (NASA) Quikscat Scatterometer Winds

http://winds.jpl.nasa.gov/missions/quikscat/index.cfm

Microwave scatterometer that measures near-surface wind speed and direction

0.25-degree resolution grid

Climatology: Produced by CRED and NODC for OceanEye project using data from 

2000 to 2003

3. NASA SeaWiFS imager

http://oceancolor.gsfc.nasa.gov/SeaWiFS/

Measures bio-optical properties of the ocean, including a calculation of chlorophyll-a 

levels

9-km resolution grid

Climatology: Produced by CRED and NODC for OceanEye project using data from 

1998 to 2003

Ocean Modeling: Bleaching Threshold

As early as 1997, the NOAA National Environmental Satellite, Data, and Information Service 

began producing near real-time, web accessible, satellite-derived SST products to monitor 

•

•

•

•

•

•

•

•

•

•

•

•

•
METHODS

43

conditions conductive to coral bleaching from thermal stress around the globe. This activity 

evolved into a crucial part of CRW in 2000 (http://coralreefwatch.noaa.gov/satellite/index.

html).

The Bleaching Threshold, developed by CRW (http://www.coralreefwatch.noaa.gov), serves 

as a general indicator for coral bleaching and is defined by 1°C above the maximum monthly 

climatological SST value for a particular geographic area.

CRED generated SST and wave height time series around the islands and atolls of American 

Samoa between January 2002 and April 2006. Remotely sensed data (SST Climatology and 

weekly Pathfinder-derived SST) and modeled significant wave height derived from Wave 

Watch III were overlaid with CRED in situ observations from various locations around each 

island and atoll in the archipelago, with indicators for each region’s bleaching threshold and 

ASRAMP cruise dates. In situ and telemetered data were used to produce the time series 

record for each island or atoll, as shown in the respective oceanography and water quality 

sections of each island/atoll chapter.

Ocean Modeling: Wave Watch III

Wave Watch III is a third-generation full spectral ocean wind-wave model which provides 

historical and near real-time open-ocean, deep-water modeled spectral wave data (height, 

period, and direction). Three hourly forecasts of wave conditions, up to 144 hours (6 days) in 

advance, are generated twice daily.

Wave Watch III solves the spectral action density balance equation for the wave numberdirection spectra. The implicit assumption of this equation is that properties of medium 

(water depth and current) as well as the wave field itself vary on time and space scales that 

are much larger than the variation scales of a single wave. A further constraint is that the 

parameterizations of physical processes included in the model do not address conditions 

where the waves are strongly depth-limited. These two basic assumptions imply that the 

model can generally be applied on spatial scales (grid increments) larger than 1 to 10 km, 

and outside the surf zone (http://polar.ncep.noaa.gov/waves/wavewatch/wavewatch.html). 

Additional information can be referenced in Tolman (1999; 2002).

2.3.8 Surface Drifters

Satellite-tracked Lagrangian surface drifting buoys, commonly called drifters, measure 

SST and mixed layer currents in the upper ocean. As part of the World Ocean Circulation 

Experiment’s (WOCE) Surface Velocity Program (SVP), drifters are designed with a surface 

buoy attached by a thin tether to a subsurface holey-sock drogue or sea anchor, centered at 

15 m beneath the sea surface. Twenty-five SVP-compliant drifters (Lumpkin and Pazos, 

2005) have been deployed in the American Samoa region during ASRAMP research cruises 

since 2002 (Table 2.3.8a). Two drifter models have been used: the ClearSat-15 with on-board 

global positioning system (GPS) navigation manufactured by Clearwater Instrumentation and 

the WOCE SVP drifting buoys with on-board GPS navigation manufactured by Technocean. 

GPS data (including date, time [accurate to ± 1.0 sec] and location [accurate to ± 0.0001°]), 

SST, drogue presence and battery level are transmitted daily via satellite telemetry to the 

satellite-based Argos data collection system and delivered to CRED periodically by e-mail.
METHODS

44

Table 2.3.8a. Number of WOCE SVP drifter buoys deployed by year and location in the American Samoa 

Archipelago (Lumpkin and Pazos, 2005).

Deployment

Year

Drifter

Manufacturer

Drifter

Model Tutuila Manu`aIslands Rose Swains

2002 Technocean GPS, drogue 

at 15 m 4 1 1 1

2003 Clearwater ClearSat-15 

GPS 3 1 0 1

2004 Clearwater ClearSat-GPSHP 3 1 1 1

2006 Clearwater ClearSat-GPSHP 3 1 2 0

2.3.9 Bioacoustic Surveys

Understanding the biological 

interactions in coral reef 

ecosystems requires longterm observations of inter- and 

intraspecies relationships and 

their environments. While 

existing monitoring instruments 

are capable of measuring longterm physical environmental 

trends, they currently lack the 

ability to observe most biological 

processes. The sounds present in 

marine habitats can be an effective 

indicator of many biological 

processes such as spawning 

events, courtship behavior, 

feeding, and competition among 

many species of fish, invertebrates, and aquatic mammals. Acoustic monitoring of marine 

habitats is a promising means of tracking biological activity and detecting ecological responses 

to changing environmental conditions. In addition to tracking biological activity, acoustic 

monitoring can also be an effective tool for detecting human activities in the marine habitat, 

such as vessel traffic and fishing using explosives. This application is of particular use in 

areas where traditional monitoring methods are difficult or impossible to implement, such as 

remote islands and atolls. Long-term acoustic monitoring can provide a cost-effective means 

of logging the human presence at a particular location and thus help gauge the effectiveness 

of management practices.

CRED explored the benefits of bioacoustic surveys by collaboratively developing and 

deploying EARs with Drs. Marc Lammers and Whitlow Au of UH’s Hawaii Institute of 

Marine Biology. Refer to Section 2.3.5: Subsurface Moorings for additional information.

Figure 2.3.9a. An EAR secured to a concrete anchor ready for 

deployment. (Photograph provided by NOAA PIFSC CRED)
METHODS

45

2.4 Reef Benthic (Coral, Algae, Macroinvertebrate) and Fish Surveys

Information on the condition, abundance, diversity, and distribution of biological communities 

is vital to the effective management of coral reef resources. To provide resource managers 

with such information, CRED has supported two biological assessment teams focused on 

collecting reef fish and benthic community datasets. An REA team conducted fine-scale 

assessments at specific reef sites (~ 300 m2), while a team of towed divers conducted broadscale surveys (~ 15 000–25 000 m2

 per survey) around the islands and atolls of American 

Samoa. The two assessment teams collected complementary data relating to four ecological 

disciplines: coral, algae, other macroinvertebrates, and reef fish (Table 2.4a). An overview 

of each assessment team and its sampling design, operational description, and methods is 

presented in the following sections.

Table 2.4a. Overview of the biological data collected by the REA and towed-diver assessment teams presented 

in this report.

Survey Results Presented in Report

Discipline REA Towed-diver

Coral

Coral community 

composition and generic 

richness

Percent live coral cover

Coral density (# colonies 

m-2)

Scleractinian (stony) coral 

size class distribution

Coral disease distribution 

and prevalence

•

•

•

•

•

Percent live 

scleractinian (stony) 

coral cover

Percent dead/stressed 

coral cover

•

•

Algae

Algae percent occurrence 

by genera/functional group

Coralline algae disease 

distribution and density

•

•

Percent fleshy/

macroalgae cover

Percent coralline 

algae cover

•

•

Other 

Macroinvertebrate

Macroinvertebrate species 

presence

Macroinvertebrate species 

richness

•

•

Crown-of-thorns 

seastar (COTS), giant 

clam, sea cucumber, 

and sea urchin 

distribution and 

abundance

•

Reef Fish

Reef fish community 

composition and species 

richness

Reef fish biomass

•

•

Large fish (> 50 cm) 

biomass

Large fish species 

composition

•

•
METHODS

46

Within this report, summary statistics are presented as either standard deviation of the mean 

(SD) or the estimated standard deviation of the error (SE), depending on the variable being 

analyzed. SD quantifies how much values vary from one another. SE quantifies precision 

within the true mean of the population, factoring in both sample size and SD. Results from 

both REA and towed-diver surveys primarily include SE summary statistics because of 

the variations in the number and location of sites visited within and between years caused 

by environmental conditions (e.g., higher number of REA surveys along leeward versus 

windward sides). Data analyzed within ArcGIS from towed-diver surveys (e.g., depth data) 

include SD summary statistics primarily because of the inability of the software to directly 

calculate SE at the time of this report.

2.4.1 REA Surveys

REA surveys are investigations that provide a high degree of taxonomic resolution for coral, 

algae, other macroinvertebrate, and reef fish communities. The surveys were conducted 

using a combination of dive teams which generally included a two- to three-person fish team, 

a two-person coral/coral disease team, and a combined team of two algae biologists and a 

single macroinvertebrate biologist. The majority of REA surveys were conducted along the 

forereef slopes of individual islands at depths between 10 and 20 m. However, additional 

surveyed habitats included lagoonal patch reefs at Rose and a shallow offshore oceanic bank 

near Tutuila.

Selection of Sampling Sites and Transect Locations

The selection of REA sites in 2002 was not made randomly in close consultation with Dr. Andy 

Cornish, the coral reef monitoring coordinator for American Samoa’s Coral Reef Advisory 

Group (CRAG). Factors considered during REA site selection included: (1) ensuring a range 

of sample sites representative of the benthic and reef fish habitats around each island; (2) 

selecting a mixture of sites within and outside of marine protected areas; (3) selecting a 

mixture of both ‘impacted’ and ‘least impacted’ sites; (4) selecting some sites adjacent to 

local villages, and (5) selecting a number of sites that could be compared to and complement 

previous assessment and monitoring work done by Drs. Alison Green, Charles Birkeland, 

and Peter Craig, as well as future coral reef monitoring proposed by CRAG. It is important 

to note that access to REA sites can be limited by wave exposure, weather conditions, and 

other environmental factors such as currents, which can affect the ability to resurvey sites 

between years.

The nonrandom nature of site selection places limits on the degree to which biotic metrics 

such as percent cover, density, diversity, and coral/coralline algal disease prevalence can be 

extrapolated through statistic inference to the larger population constituted by each island/

atoll. It nonetheless remains statistically appropriate to examine differences among the same 

sites sampled over different years, which is the priority of CRED’s long-term monitoring 

efforts.

An additional caveat in tracking temporal changes in relatively immobile resources (e.g., coral, 

algae) versus mobile resources (e.g., schools of fish) is that benthic spatial plots may accrue 

cumulative, temporally non-independent impacts over a succession of surveys depending 

on the type of impact (e.g., successive years of bleaching versus singular hurricane events), 

whereas mobile schools of fish would be re-randomizing themselves in space when surveys 
METHODS

47

are conducted over time in the same sites. 

At each site, transects were deployed by the fish REA survey team, whose members were 

the first to enter the water. Transect placement was guided by: (1) a focus on hard-bottom 

communities; (2) deploying lines along an isobath to the extent possible at each site, and 

(3) laying the transect lines into the prevailing current. The latter was an important safety 

consideration to facilitate divers working against the current at the start of each dive but 

swimming with the current towards the end of each dive when they were more fatigued. The 

placement of transects by the fish team, rather than the benthic team, also helped reduce bias 

in the selection of specific benthic habitat that might otherwise be inadvertently introduced. 

Each benthic sub-discipline (e.g., corals, coral disease, algae, other macroinvertebrates) 

used survey protocols driven by: (1) accepted methods within the sub-discipline, and (2) the 

number of divers available and the need to choreograph each dive so as to stay within NOAA 

safety guidelines (e.g., proximity to a buddy). All sub-disciplines used the two transect lines 

as the geographical reference by which their selection of point, area, or quadrat placement 

was guided. Both random numbers and fixed intervals, which were used by the algal and 

macroinvertebrate researchers for quadrat placement, are commonly used sampling methods; 

both methods reduce observer bias by forcing scientists to sample pre-set areas.

Operational Description

During REA surveys, biological assessment teams follow highly structured protocols that 

are repeated at each REA site. Upon arrival at an REA site, three teams of divers enter the 

water over spaced time intervals. The first team to enter the water is the fish team, which 

consists of two to three investigators. The fish team deploys a 25-m transect line and two of 

the divers begin to survey along that transect while the remaining fish diver begins stationary 

point count assessments in the general vicinity. After approximately 20 min, the two-person 

coral team enters the water and begins to work along the first transect line. By this time the 

fish team has deployed and begun surveys along a second 25-m transect. About 10 min later, 

the algal/invertebrate team, consisting of two to three investigators, enters the water and 

begins surveying the first transect. In total, the fish team surveys three transects at each site 

(transects 1, 2, and 3), and the coral and algal/invertebrate teams survey transects 1 and 2 

(Fig. 2.4.1a). The sampling effort takes between 60 and 80 min to complete.

REA Disciplines and Methods

The biological assessment teams used specific methodologies targeting their respective 

biological communities. These methodologies overlapped and complemented each other to 

ensure that collected data were representative of the biological state at each REA site. A 

timeline of methods development for each discipline is displayed in Tables 2.4.1a and 2.4.1b, 

and the methods used by each assessment team are discussed in the following paragraphs.
METHODS

48

Table 2.4.1a. Timeline of methods development for each of the REA disciplines. Each REA discipline is 

separated by the various measured parameters.

REA Disciplines

Coral and Coral Disease Algae

Year

Generic 

richness/ 

composition

Percent 

live 

cover

Colony 

density (# 

colonies 

m-2)

Size 

class

Disease 

prevalence

Percent 

occurrence 

(Genera)

Species 

presence

2002 MD — — — — MD —

2004 BLT VE BLT BLT — QS, PQS VS

2006 BLT LPI BLT BLT BLT QS, PQS VS

Method Acronyms: BLT = Belt Transect, LPI = Line Point Intercept, MD = Methods Development, PQS = Photoquadrat 

Survey, QS = Quadrat Survey, VE = Visual Estimate, VS = Voucher Specimen.

Figure 2.4.1a. Schematic of REA site layout. The reef fish assessment team surveys transects 1, 2, and 3 and 

conducts four stationary point count surveys. The coral/coral disease and algae/macroinvertebrate teams each 

survey transects 1 and 2. (Photograph provided by NOAA PIFSC CRED; J. Kenyon, JIMAR)
METHODS

49

Table 2.4.1b. Timeline of methods development for each of the REA disciplines. Each REA discipline is 

separated by the various measured parameters.

REA Disciplines

Macroinvertebrates Reef Fish

Year Species

presence

Species

richness

Total fish 

biomass (all 

sizes)

Fish biomass

(> 25 cm) Species richness

2002 MD — — — BLT, RDS

2004 BLT, RDS BLT, RDS BLT, RDS SPC BLT, RDS

2006 BLT, QS — BLT, RDS SPC BLT, RDS

Method Acronyms: BLT = Belt Transect, MD = Methods Development, QS = Quadrat Survey, RDS = Roving-diver Survey, SPC = Stationary Point Count.

2.4.1.1 Coral and Coral Disease

The coral community at each REA site was assessed to quantify the diversity, abundance, 

density, and size class distribution of the anthozoan and hydrozoan corals. The methods 

employed by the coral assessment team in American Samoa were different in all survey 

years. These methods included several complementary and noninvasive underwater survey 

techniques, e.g., visual estimate, line point intercept, and belt-transect; all of which provide 

viable and complementary datasets for quantitative and descriptive analyses (Kenyon 

et al., 2006a). Details on each method are discussed below including a description of the 

development of coral methods during 2002 REA surveys (Coral Methods Development). 

The temporal variation of coral sampling methodologies is summarized in Table 2.4.1a. A 

common name index of American Samoan coral species can be found in Appendix I, Table 

I. iii.

Coral Methods Development

The REA coral surveys during ASRAMP 2002 were the first surveys conducted in American 

Samoa by CRED. As such, the methods employed varied between sites and were mostly 

qualitative and exploratory in nature. Tested methods included: (1) relative abundance 

estimates of coral by species or genus using a semiquantitative DACOR (dominant, abundant, 

common, occasional, and rare) protocol (Maragos et al., 2004); (2) visual estimates of the 

percent coral cover at each REA site; (3) belt transects consisting of a coral biologist swimming 

along as many transect lines as bottom time permitted identifying coral species (or genus, 

when species identification in the field was ambiguous) occurring within approximately 0.5 

m of each side of the transect lines; each colony was assigned to one of seven size classes 

(≤ 5, 6–10, 11–20, 21–40, 41–80, 81–160 or > 160 cm) based on a visual estimate of the 

maximum colony diameter; (4) wide-angle photo-documentation of the benthos using a Nikon 

RS camera with a 13-mm lens, and (5) video documentation of the three 25-m transects using 

a Sony PC digital PC100 camcorder in a Gates underwater housing while slowly swimming 

about 1 m above the seafloor along the length of each transect.

Anthozoan = Any of the Cnidarian class Anthozoa, such as the corals and sea anemones, that have radial segments and 

grow singly or in colonies. Hydrozoan = Any of the Cnidarian class Hydrozoa, such as the colonial hydrocorals, that 

secrete a calcium carbonate skeleton.
METHODS

50

Visual Estimates

Percent live coral cover was recorded at REA sites in 2004 using visual estimates. Estimation 

of coral cover was a subjective, qualitative assessment in which the coral biologist estimated 

(by eye) the percentage of benthic substrate that was covered by live coral in the general area 

traversed by the transect lines.

Line Point Intercepts

The line point intercept technique was used to quantitatively assess average percent live 

coral cover and other benthic substrates at REA sites during ASRAMP 2006 (Hill and 

Wilkinson, 2004). A coral biologist swam along two 25-m transect lines recording all benthic 

elements falling directly underneath the transect line at 50-cm intervals. Benthic elements 

were recorded as one of nine benthic categories: live coral, dead coral, carbonate pavement, 

coralline algae, macroalgae, coral rubble, sand, rock, and other benthic sessile invertebrates. 

Living benthic elements (e.g., coral, algae, and other invertebrates) were identified to the 

lowest taxonomic level possible.

Belt Transects

Colony density and size classes of each coral colony were quantitatively assessed using 

belt-transect surveys (Fig. 2.4.1.1a). At the beginning of each dive, subjective perceived 

colony density dictated the belt width: 1-m width was used in high density areas, while 

2-m width was used in low density areas. The coral biologist surveyed two 25-m transect 

lines, recording the maximum diameter of all coral colonies whose centers fell within 0.5 

to 1 m (depending on density) on either side of the transect line. Colonies were recorded to 

the genus level and assigned, by visual estimation, to one of seven size classes: ≤ 5, 6–10, 

11–20, 21–40, 41–80, 81–160, and > 160 cm (binning of coral colony size classes based 

on Mundy [1996]). Estimation of individual coral colony boundaries in the field can be 

complicated especially for species with life history strategies involving clonal propagation 

(e.g., Acropora formosa) or fissioning (e.g., Porites lobata). When estimating coral colony 

boundaries, consideration was given to tissue color, interfaces (e.g., skeletal ridges) with 

neighboring colonies of the same species, and variations in growth form. If determinations 

of individual colony boundaries could not be made on these criteria alone, conspecific areas 

of live tissue separated by more than 10 cm were considered to be separate colonies.

Results from 2004 and 2006 coral surveys were used to calculate generic richness, percent live 

coral cover, coral density (# colonies m-2), and size class distributions of scleractinian corals 

for each REA site. Generic richness was computed as the maximum number of coral genera 

recorded within belt transects at a site. Coral community composition values were calculated 

from the relative percentages of coral genera observed during belt-transect surveys. Percent 

live coral was calculated from the raw site estimates of coral cover during ASRAMP 2004 

and the average of the line point intercept results from each 25-m transect during ASRAMP 

2006. Coral size class histograms were created by calculating the relative frequencies of all 

scleractinian corals in each of the seven size classes recorded during belt-transect surveys.

Coral and coralline algal diseases and predation scars were quantified at each REA site to 

assess the health and viability of the coral reef populations in the nearshore waters. Coral 

and coralline algal diseases and predation were first surveyed during ASRAMP 2006 using 

belt transects.
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Coral disease and 

predation assessments 

were conducted along two 

25-m belt transects during 

which each affected coral 

colony was identified 

to the lowest taxonomic 

level possible. The width 

of belt transects varied 

depending on diver’s 

bottom time, but was 

generally conducted within 

3 to 5 m perpendicular 

to each transect line (~ 

300–400 m2 per site). For 

each affected coral the 

following information 

was recorded: colony size, 

type of affliction, area affected, percent live/dead, and severity of the affliction (mild = 1–

10%, moderate = 11–25%, marked = 26–50%, severe = 51–75%, acute = 76–100%). Coral 

afflictions were classified into one of six general categories (following Willis et al., 2004) 

including: bleaching, tissue loss, black band disease, skeletal growth anomaly, predation, 

and other lesions. This latter category included algal overgrowth, as well as unidentified 

syndromes causing deterioration of scleractinian corals. Afflictions to coralline algae were 

also enumerated based on the high incidence of lesions found in American Samoa. Coralline 

algae afflictions were classified into three general categories: coralline lethal orange disease 

(CLOD), coralline fungal disease, and unidentified coralline discoloration. Photographic 

records and tissue samples of select diseased colonies were also collected for future laboratory 

analysis. Descriptions of coral and coralline algae disease states are listed below.

Bleaching

Coral bleaching was characterized by a reduction in intensity or the complete absence of 

coloration within living coral as a result of loss of pigmentation and/or expulsion of the 

endosymbiotic zooxanthellae. The tissue of bleached corals can be transparent, making the 

coral appear white because of the skeleton of the coral (Fig. 2.4.1.1b[a]). However, coral 

tissue of corals can also appear pale, pinkish or bluish when bleaching occurs. Patterns of 

bleaching can vary, with only the upper surface or lower surface of the colony being affected 

and can also appear patchy or mottled or as a circular blotch, ring or wedge.

Tissue Loss

Losses of coral tissue were characterized by coral lesions of sharp, clean bands appearing 

where tissue was completely removed from the skeleton. The clean band of exposed skeleton 

is sometimes coupled with a region of filamentous and turf algae (Fig. 2.4.1.1b[b]). Tissue 

loss is sometimes also referred to as white syndrome and is distinguished from feeding scars 

by the narrow width of the zone of recently exposed white skeleton and the relatively regular 

appearance of the tissue front. These features contrast with the wide zone of white skeleton 

commonly exposed following COTS (Acanthaster planci) predation or the scalloped or 

Figure 2.4.1.1a. A coral assessment diver conducting a belt-transect survey. 

(Photograph provided by NOAA PIFSC CRED; J. Kenyon, JIMAR)
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irregular tissue front produced by the thaidinae gastropod Drupella (Willis et al., 2004).

Black Band Disease

Black band disease was characterized by a black mat, about 0.5 to 4 cm wide, moving 

across the living coral tissue and leaving behind bare white skeleton, while unaffected coral 

tissue remains normal in color and morphology (Fig. 2.4.1.1b[c]). The major component 

of the black mat is Phormidium corallyticum, a photosynthesizing cyanobacterium. Other 

microorganisms, including marine fungi, heterotrophic bacteria, sulfur-oxidizing bacteria 

(Beggiatoa), and sulfate-reducing bacteria (Desulfovibrio), are present in the black mat and 

also contribute to the loss of coral tissue (Ducklow and Mitchell, 1997; Richardson, 1996).

Skeletal Growth Anomaly

Skeletal growth anomalies were characterized by changes in the shape or form of coral 

skeletons resulting in unusual lumps and protuberances associated with an abnormal 

deposition of calcium carbonate (Fig. 2.4.1.1b[d]). Skeletal growth anomalies are caused 

by changes in the coral cells that deposit the carbonate skeleton. The two most common 

types of skeletal growth anomalies are hyperplasia, a process that leads to an increase in the 

number of cells in a tissue or organ, thereby increasing the bulk of the tissue or the organ, and 

neoplasia, a pathologic process that results in the formation and growth of an undifferentiated 

mass of cells.

Other Lesions and Pigmentation Response

Some reef corals, such as Porites, Montipora, and Astreopora, appear to respond to a variety 

of allopathic and parasitic interactions by producing a hyperpigmentation of polyps in contact 

with or adjacent to areas of interaction. These interactions sometimes result in impairment 

or inhibition of normal coral function (e.g., growth, calcification, and reproduction) and may 

take on the character of a disease (Willis et al., 2004). Pigmentation responses are often 

launched by the coral along adherent edges involved in interactions with algae, but also 

with cyanobacteria, polychaetes, molluscs, trematodes, etc. The range of pigmentation 

responses vary for each coral genera ranging from pink to light blue in Astreopora, from 

pink to purple but also blue to brown in Montipora (Fig. 2.4.1.1b[e]), and from pink to purple 

but also accompanied by swelling or enlargement of the affected polyps in Porites. These 

pigmentation responses, together with other unidentified cases of disease, were grouped 

under “other lesions” during coral disease surveys.

Predation

Coral predators often leave scars devoid of tissue which may lead to decreased health status 

and increased susceptibility to algal overgrowth, invasion by other pathogens or lower 

reproductive output. The pattern of tissue loss from predation often differs from tissue loss 

patterns stemming from other causes. Predation scars were characterized by wide zones 

of exposed coral skeleton commonly seen following predation by the COTS, Acanthaster

planci (Fig. 2.4.1.1b[f]) or by scalloped or irregular tissue fronts that are often produced by 

the thaidinae gastropod, Drupella (Willis et al., 2004).

CLOD

CLOD was characterized by a band of bright orange slimy material spreading across the 

algal surface, leaving behind the bare skeletal carbonate remains of the coralline algae (Fig. 

2.4.1.1c[a]). When this material reaches the margin of the algal thallus, it forms upright 
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53

Figure 2.4.1.1b. Coral Diseases. Underwater photographs illustrating the field appearance of lesions 

affecting scleractinian corals in the American Samoa Archipelago during ASRAMP 2006. (a) bleaching 

on Gardineroseris planulata; (b) tissue loss on Acropora cytherea; (c) black band disease on Porites; 

(d) skeletal growth anomalies on Acropora abrontanoides; (e) pigmentation response on Montipora sp. 

(Note blue pigmentation surrounding areas of allopathic interaction); (f) predation lesions on Pocillopora, 

probably caused by the corallivorous snail Drupella; also, note algal overgrowth on old dead colony surfaces. 

(Photographs by NOAA PIFSC CRED; B. Vargas-Angel, JIMAR)

a b

c

e f

d
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54

filaments and globules, similar to those formed by terrestrial slime molds. The globules can 

be caught by waves and easily spread to nearby corallines. Microscopic examination of the 

orange material revealed motile gliding rods of a colonial bacterium in a mucilaginous matrix. 

The orange globules can be experimentally transferred to other coralline algae and cause the 

same disease and loss of algal tissue. Additional studies of this bacterium associated with 

CLOD are underway (Littler and Littler, 1998).

Coralline Fungal Disease

This disease is characterized by a 1 to 5 cm black mat, moving across the surface of the 

coralline algae and leaving behind bare white carbonate skeleton (Fig. 2.4.1.1c[b]). 

Coralline fungal disease was discovered in 1996 by Diane and Mark Littler who observed 

abundant populations of this undescribed fungal disease in both calm and exposed coral reef 

environments in American Samoa (Littler and Littler, 2003).

a b

c d

Figure 2.4.1.1c. Underwater photographs illustrating the field appearance of diseases affecting crustose 

coralline algae in the American Samoa Archipelago, 2006. (a) CLOD; (b) coralline fungal disease; (c) and

(d) unidentified coralline discoloration. (Photographs provided by NOAA PIFSC CRED; B. Vargas-Angel, 

JIMAR)
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Unidentified Coralline Discoloration

Discolored (light yellow, green or white) bands, measuring 0.5 to 3 cm in width, which 

spread across the algal surface leaving behind the bare skeletal carbonate remains of the 

coralline algae were characterized as unidentified coralline discoloration (Figs. 2.4.1.1c [c] 

and 2.4.1.1c[d]). In some cases discolorations appeared as concentric, annular or horseshoe shaped bands radiating from a focal point (Littler and Littler, 2003). In other cases, 

discoloration appeared as wide, irregular, white bands along adherent edges.

Results of coral and coralline algae surveys were used to calculate prevalence values for 

coral disease and density values for coralline algae disease. Coral disease prevalence was 

computed as the percentage of diseased colonies (counts) out of the total estimated number 

of colonies within the survey area. The estimated number of colonies within the survey area 

was calculated by multiplying the coral density (# colonies m-2) value obtained from the 

coral belt transect by the total area covered in the disease survey at each site (Prevalence = 

[No. cases within the area surveyed for disease × 100] ÷ [colony density × area surveyed 

for presence of disease]). The relative abundance of coralline algal diseases per site was 

calculated by adding the total number of cases over the two transects and dividing by the 

total area surveyed for each site. Coral disease results are presented within the coral section 

of each island while coralline algae disease results are discussed within the algae section.

2.4.1.2 Algae

Algal populations were surveyed to assess the relative abundance and species diversity of 

algae in the American Samoa Archipelago. Algal survey methods in 2002 differed from 

methods employed in 2004 and 2006. Underwater survey methods included quadrat surveys, 

photoquadrat surveys, and voucher specimen surveys. Details on each method are discussed 

below including a description of the development of algal methods during 2002 REA surveys 

(Algal Methods Development). Temporal sampling variation is detailed in Table 2.4.1a.

Algal Methods Development

REA algae surveys in 2002 were the first surveys conducted in American Samoa by CRED. 

As such, the methods employed were mostly qualitative and exploratory in nature. Methods 

included collecting samples of algae and qualitative observations of the algal populations at 

each REA site.

Quadrat Surveys

Quadrat surveys were employed to document the relative abundance of macroalgal genera 

in the field. At each REA site, 12 sample 0.18-m2 quadrats were surveyed along two 25-m 

transects. Six quadrats were located at randomly selected points along each transect (three 

per transect), and six other quadrats were located at points 3 m perpendicular from each 

random point in the direction of shallower water (Preskitt et al., 2004; Vroom et al., 2005a). 

Macroalgae were identified to genus level in the field, whereas crustose-coralline red algae, 

branched coralline red algae, turf algae and cyanophytes were lumped into functional group 

categories. In addition, each genus or functional group found in each quadrat was assigned a 

rank based on its relative abundance in the quadrat (1 being the most abundant, 2 being the 

next most abundant, etc.). All ranked data for a given survey year were collected by the same 

individual, minimizing the effects of observer bias.
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56

Photoquadrat Surveys

During quadrat surveys, photographic documentation of each 0.18-m2 quadrat assessed was 

recorded to provide a quantitative dataset for further in-depth, algae species-level percent cover 

analyses. Twelve photos were taken at each site using either a Sony DSC P-9 or an Olympus 

C-4040 digital still camera and an Ikelite substrobe DS-50 (Fig. 2.4.1.2a). Photographs are 

being analyzed using Coral Point Count with Excel extensions (Kohler and Gill, 2006) to 

determine percent cover of benthic organisms at the species level (when possible).

Voucher Specimen Surveys

Algal voucher specimens were collected from a 2-m swath on either side of the same two 25-

m transects surveyed during the quadrat surveys. Samples were brought back to the laboratory 

for qualitative species identification at the microscopic level to assemble comprehensive 

species lists for each site. Voucher specimen surveys were conducted at all sites, even when 

environmental conditions (e.g., strong currents or surge) did not allow for the quantitative 

photoquadrat protocol to be completed.

Algae diver observation results from quadrat surveys were used to calculate percent 

occurrence of algae genera/functional groups for each REA site. Percent occurrence values 

were calculated by summing the number of quadrats in which each algal genus/functional 

group was observed and dividing by the total number of quadrats surveyed at the site (12). 

Percent occurrence results were then used to create distributional maps of algal abundance 

for each island/atoll. In addition, algal composition results by island/atoll were calculated 

Figure 2.4.1.2a. The algal assessment team conducting photoquadrat surveys. (Photograph provided by NOAA 

PIFSC CRED; J. Kenyon, JIMAR)
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57

by summing the percent occurrence values for each algal genus/functional group and then 

dividing the respective occurrence values by the sum.

2.4.1.3 Other Macroinvertebrates

Macroinvertebrate surveys were focused on quantifying the noncoral invertebrates that are 

common to the reef habitats of American Samoa. Several different survey techniques were 

used in each of the survey years to quantify the diverse communities. These methods included 

belt-transect, roving-diver, and quadrat surveys. The development of REA macroinvertebrate 

survey methods and the details of each are described below (Macroinvertebrate Methods

Development). Temporal sampling variation is detailed in Table 2.4.1b. 

It should be noted that in situ methods record invertebrate species that are generally noncryptic 

(i.e., visible) and easily enumerated during the course of a single scuba dive. Therefore, the 

marine invertebrate species recorded and identified during the course of these observations 

only represent the noncryptic fauna of the reef habitat and should not be considered the 

only species present at each site. It should also be noted that many invertebrate species are 

nocturnal and therefore unlikely to be observed during the daylight surveys conducted during 

Pacific RAMP.

Macroinvertebrate Methods Development

REA macroinvertebrate surveys in 2002 were the first surveys conducted in American Samoa 

by CRED. As such, the methods employed were mostly qualitative and exploratory in nature, 

aimed at collecting baseline data that would be used to refine methodologies for subsequent 

surveys. Two separate 50-m transect lines were surveyed using a zigzag search pattern that 

extended roughly 2 m on either side of each transect line. In addition, a roving-swim survey 

was conducted to survey a larger area and account for macroinvertebrate species not found 

in the transect area. During both surveys, species of macroinvertebrates were recorded and 

assigned a qualitative abundance ranking using the DACOR method (Maragos et al., 2004).

Belt-transect Surveys

Quantitative invertebrate counts were recorded along two 25-m belt transects in 2004 

and 2006. Highly detailed invertebrate observations (the target species list is presented in 

Appendix III) were recorded within 2 m on either side of each transect (total area = 100 m2) 

in 2004. During ASRAMP 2006, the target list of macroinvertebrates (Appendix IV) became 

more general, although the quantitative count methodology remained the same.

Roving-swim Surveys

In 2004 and 2006, a 500-m (10 × 50 m) roving-swim survey was conducted with the goal 

of quantifying larger invertebrates such as COTS and Tritons Trumpet molluscs which may 

not be seen during belt-transect surveys. The roving swim was accomplished by swimming 

a zigzag pattern extending 5 m to either side of both 25-m transect lines.

Quadrat Surveys

In 2006 quadrat surveys were used to quantify the smaller, more cryptic macroinvertebrates 

which were sometimes overlooked or too numerous to count during belt-transect surveys. 

Ten 0.25-m2 quadrats were laid out at 2-m intervals along two of the 25-m transects (total 
METHODS

58

area = 5 m2). For each quadrat the percent cover of sponges, octocorals (e.g., Sarcophyton, 

Lobophytum, Sinularia or Cladiella) and zoanthids was recorded, as well as all of the 

Echinostrephus spp. and Echinometra spp. urchins, hermit crabs of the genus Calcinus, 

trapezid crabs, and coralliophilid snails.

Macroinvertebrate results were used to calculate presence/absence data for each REA site. 

Presence data are only presented for ASRAMP 2004 and 2006 surveys and results from 

all survey methods employed during a respective year were used to calculate presence 

data. In addition, results from the 2004 macroinvertebrate surveys were used to calculate 

species richness values. Species richness values are not presented for 2006 as a result of the 

abbreviated target species list.

2.4.1.4 Reef Fish

Three complementary methods were used to catalog the diversity (species richness) and 

abundance (numeric density [# fish 100 m-2] and biomass density [kg 100 m-2]) of diurnally 

active reef fish assemblages including belt-transect, stationary point count, and roving-diver 

surveys. The methods remained the same for all survey years with the exception of stationary 

point counts which were first used in 2004. For all methods, fish were identified at the species 

level, when possible, and assigned to a size bin ranging from 1 to 200 cm based on a visual 

estimate of total fish length. The temporal variation of reef fish sampling is detailed in Table 

2.4.2b. 

Belt-transect Surveys

The entire diurnal fish community (all size classes) was quantified using belt-transect 

surveys. At each site, three 25-m lines were surveyed. Two fish biologists swam side-by-side 

along a transect, each recording all fish larger than 20 cm observed within a 4-m wide belt 

perpendicular to their respective side of the transect (200 m2 area per line, 100 m2 per diver). 

Then the fish biologists made a second pass along each transect recording all fish less than 

20 cm observed within a 2-m wide belt (100 m2 area per line, 50 m2 per diver). The survey of 

large fish took approximately 5 min to complete while the survey of smaller fish took about 

10 min to complete. All reef-associated fish, including those in the water column (including 

planktivores), were counted. Any coastal pelagic species (e.g., clupeids [sardines], belonids 

[beakfish], antherinids [silversides]) seen near the surface were not recorded.

Stationary Point Count Surveys

Quantification of larger, more mobile reef fish species that can be missed on belt-transect 

surveys was performed using the stationary point count method (Bohnsack and Bannerot, 

1986). For each stationary point count survey, the fish biologist swam approximately 15 

m away from a transect line concurrently being surveyed by the other fish biologists. The 

stationary point count biologist then recorded all fish greater than 25 cm in length that passed 

within a visually estimated 20-m diameter cylinder centered on the diver’s fixed position 

(10-m radius, total area = 314 m2). The survey time for each stationary point count survey 

was 5 min and a total of four stationary point count surveys were conducted at each REA 

site. The method for counting fish was the same as the method used in belt-transect surveys 

as described above.
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Roving-diver Surveys

Following belt-transect and stationary point count surveys, and as diver bottom time 

permitted, the fish assessment team conducted random swim surveys throughout the REA 

site area, recording, to the species level or the lowest recognizable taxon, the presence of reef 

fish not encountered during previous methods.

Results from REA reef fish surveys were used to calculate biomass estimates. Fish counts 

from belt-transect surveys were converted to biomass estimates (kg 100 m-2) using published 

length-weight relationships for individual species (Kulbicki et al., 2005). Total fish biomass 

at each REA site was calculated by combining fish biomass from the 100-m2 belt transects 

(small fish) with the biomass from the 200-m2 belt transects (larger fish). Biomass estimates 

were summed by fish families and used to create biomass totals by site and year as well as 

fish family composition graphs, which represent the biomass percent breakdown by fish 

family. In addition to total fish biomass estimates, data collected from belt-transect surveys 

were used to calculate species richness (# species 100 m-2) values at each site. Stationary 

point count and roving-diver survey results are not presented in this report.

2.4.2 Towed-diver Surveys

Towed-diver surveys were used to characterize benthic habitats and to quantify the 

abundance and spatial distributions of ecologically and economically important fish, coral, 

and macroinvertebrate taxa over a much broader area than is possible using REA techniques. 

While typical REA surveys provided species level documentation of marine organisms 

over spatial areas of approximately 300 m2, towed-diver surveys documented patterns of 

habitat condition and distributions of larger marine organisms over areas ranging from 

15 000 to 25 000 m2. In addition, towed-diver surveys were able to access exposed coasts 

(e.g., windward-facing shores and high swell conditions) not surveyed by stationary REA 

surveys, which are fundamentally limited to survey areas with more favorable environmental 

conditions (e.g., lower currents or lower surge/wave action).

The broad-scale nature of towed-diver surveys has helped to increase the breadth of the 

ecological benthic data collected by CRED and to improve the program’s ability to investigate 

and quantify large-scale environmental stresses, such as bleaching events (Kenyon et al., 

2006c) and COTS outbreaks. Towed-diver surveys were likewise tasked with recording 

unusual or important sightings which included significant biological or habitat gradients, 

derelict fishing gear or other types of marine debris, shipwrecks, and unexploded ordinance 

located on the seafloor.

This method also allowed for “snapshot assessments” of larger fish (e.g., sharks, jacks, 

and barracudas), and schools of various species whose range and abundance may be 

underestimated during area-limited REA surveys. Finally, other “species of concern” (e.g., 

sea turtles, cetaceans, and pinnipeds) not normally observed or examined by REA scientists 

were also recorded during towed-diver surveys.

Sampling Design

Towed-diver surveys were typically completed along the outer reef slopes and forereefs of 

individual islands/atolls, with additional surveys completed along backreefs, lagoons, and/or 
METHODS

60

offshore banks. Towed-diver survey tracks were intended to cover as many habitat types 

(e.g., slope, forereef, backreef, lagoon, and bank) and as much of a complete revolution 

around each island or atoll as time allowed while surveying along a relatively constant isobath 

(typically targeted at 15 to 20 m).

Towed-diver surveys typically completed circumnavigations around each of the islands and 

atolls of American Samoa, with most individual surveys covering linear distances between 

1.5 and 2.5 km along relatively fixed isobaths (10–20 m). For the smaller islands and atolls, 

such as Swains and Rose, multiple circumnavigations were conducted targeting different 

isobath depths (e.g., 5, 15, and 25 m).

Operational Description

Towed-diver surveys were conducted by teams of four scientists who alternated between 

data gathering and boat handling responsibilities. Surveys consisted of towing two divers 

approximately 60 m behind a small boat with one diver tasked with benthic composition and 

macroinvertebrate data collection while the other collected data on fish species larger than 50 

cm total length (Fig. 2.4.2a). Each diver made observations over a 10-m swath (5 m to each 

side of their respective tow lines, which act as transect lines). The diver/observers attempted 

to maintain their position approximately 1 m above the seafloor, while being towed at an 

average speed of 0.5 to 1.3 m s-1 (1–2.5 kn). Each survey took approximately 50 min with 

four to six surveys completed each field day.

To geo-reference all data collected during a tow, a GPS receiver located on the towboat was 

programmed to record longitude and latitude coordinates every 5 sec. When the divers were 

ready to begin recording data, an acoustic signal from the fish towed diver was sent to the 

towboat coxswain via telegraph. The coxswain would mark a waypoint indicating the start 

point of the towed-diver survey. The coxswain followed along a predetermined depth contour 

using a bathymetric chart, a singlebeam echosounder, and shoreline features (when present) 

as a guide while maintaining speed. Additional “o.k.” signals were sent to the towboat every 

5 min to inform the coxswain of the diver’s status, while “mark” signals were sent to record 

any sites of interest (natural or anthropogenic). At the end of the survey, prior to beginning 

an ascent to the safety stop, another coded signal was sent to the towboat to record the endposition of the survey.

In the years following the initial toweddiver surveys in 2002, specific routes 

were pre-programmed into the GPS prior 

to initiating field activities. This was 

done to: (1) transition from assessment to 

monitoring, and obtain as much track and 

area overlap with previous years as possible, 

and (2) coincide with logistical challenges 

associated with operating remote field 

operations involving several disciplines 

(REA, mapping, oceanography).

A byproduct of repeating previous towedFigure 2.4.2a. Towed divers conducting a survey in 

American Samoa. (Photograph provided by NOAA 

PIFSC CRED)
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diver survey tracks is that in certain areas it results in an inherent sampling bias assigned 

to nonrandomized route selection and the subsequent survey analyses including biological 

estimates generated. Some locations (e.g., Tutuila) have considerable portions of coastline 

that cannot be surveyed repeatedly due to operational, logistical, budgetary, and/or 

environmental constraints. The consequence is that certain abiotic and biotic metrics (e.g., 

concatenated habitat complexity from GIS IDW analyses) have to be inferred based on the 

results from surrounding survey areas. In addition, biological estimates of other metrics (e.g., 

macroinvertebrate populations) remain unknown for areas not surveyed. This is in contrast to 

smaller islands/atolls (e.g., Swains), where the entire island can be easily circumnavigated.

Following each day of field operations, GPS waypoints (survey start and stop points), trackline 

files, and SBE 39 depth and temperature data (recorded every 5 sec) were downloaded for 

each towed-diver survey of the day. All geo-referenced tracklines had associated, inherent 

positioning errors created by the difference between the location of the GPS unit aboard the 

towboat and the underwater position of the towed divers. To reduce this source of error, a 

custom-designed ArcView script was written based on a “layback” model created during 

the development of towed-diver survey methods (Kenyon et al., 2006a). The layback model 

was applied to all downloaded tow tracks within ArcView, which used SBE 39 depth and 

temperature data merged with GPS track information to calculate more accurate diver 

positions. Data were then uploaded into ArcGIS for further analysis with towed-diver data.

Data Collection

Data from towed-diver surveys were collected through direct diver observations and electronic instrumentation attached to the towboards. Observations were recorded by both the 

benthic and fish diver/observer every 5 min (~ 200 m survey length), summarizing the benthic habitat and biological organisms encountered throughout the segment. A total of 10 

observations were made over a typical 50 min survey, although the actual time and length of 

surveys varied depending on environmental conditions, diver air supply, bottom time, etc.

Temperature and depth data for each towed diver were recorded every 5 sec using an attached 

SBE 39 temperature and pressure recorder, while image data were collected using a forwardfacing video and a downward-facing video or digital still camera. Details on diver observations and accessory instrument data collection techniques are discussed below.

Diver Observations

Benthic

Benthic towed-diver methods changed among the field surveys completed in 2002, 2004, and 

2006 with the hope of fine-tuning data resolution and reducing the underwater task loading 

of the diver/observer. Methodological changes were generally limited to two aspects of the 

protocols: classification of benthic substrate categories and estimation of benthic substrate 

percent cover. Details on the interannual variations of towed-diver survey methods are 

outlined in Table 2.4.2a.

At 5-min intervals, the benthic diver/observer recorded a suite of information including: the 

predominant reef zone (forereef, backreef, lagoon, bank, bank escarpment, and channel), 

estimates of average habitat complexity, estimates of average percent cover for benthic 

substrate types (live and stressed hard coral, fleshy/macroalgae, coralline algae, sand, and 
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rubble), and counts of macroinvertebrates (COTS, sea urchin, sea cucumber, and giant clam) 

encountered within a 10-m tow swath (5 m on either side of the tow line).

Table 2.4.2a. Benthic cover composition categories (Kenyon et al., 2006a). 

Benthic 

Category Description Year

Live Hard 

Coral

All live hard coral species observed in the tow path. This included both stressed 

(see below), and unstressed corals. It did not include soft corals or dead coral. 

Live hard corals were characterized by colonies or portions of colonies covered 

with living tissue. Living tissue usually appeared colored (e.g., olive green, 

brown or bluish lavender) because of the presence of pigments in coral tissue 

and/or their symbiotic zooxanthellae; however, stressed coral tissue can also 

appear pale or completely white. 

2002 

2004 

2006

Stressed 

Coral

Live hard coral that appeared to be stressed or bleached as a result of loss of 

zooxanthellae and/or their pigments. Signs of stress included pale to white 

coloration caused by bleaching, COTS predation, disease or recent coral death. 

Recently dead corals were characterized by a heavily bleached white coloration 

representing exposed coral skeleton. In some cases it might be hard to differentiate 

between recently dead and severely bleached corals; for this reason, they were 

both classified as stressed.

2004 

2006

Dead Coral

Bare white colonies (or portions of) that had lost living tissue and had not been 

visibly encrusted by macroalgae or epiphytes were classified as dead coral. 

Lack of encrustation suggested tissue death was recent relative to encrusted 

portions of dead colonies. Dead coral with macroalgae growth, epiphytes or 

other forms of substrate cover were considered part of the fleshy/macroalgae or 

other category. 

2002

Soft Coral All soft corals observed in the tow swath. 2006

Fleshy 

Algae

Fleshy or frondose algaes (e.g., Sargassum or Padina), heavily calcified (e.g., 

Halimeda) species and turf algaes. 

2002 

2004

Macroalgae

Macroalgae were characterized by the fleshy or frondose algae (e.g., Sargassum

or Padina) and heavily calcified (e.g., Halimeda) species. This did not include 

turf algae.

2006

Coralline 

Algae

Encrusting calcareous algal species observed within the tow swath. These 

encrusting algae deposit calcium carbonate as part of their structure, often giving 

a pinkish or lavender appearance to the encrusted substrate. In some areas these 

algae can also form three-dimensional spires.

2002 

2004 

2006

Sand

Sand was characterized by unconsolidated sediment, ranging in texture and 

size from fine to coarse and including both inorganic (eroded rock) and organic 

(eroded fragments of calcareous organisms) sediments.

2002 

2004 

2006

Rubble

Unconsolidated fragments of coral skeleton or reef rock whose sizes are larger 

than sand. May be visibly encrusted by macroalgae, calcareous algae or corals.

2002 

2004

Rubble

Unconsolidated fragments of coral skeleton or reef rock whose sizes are larger 

than sand. Only rubble that was not visibly encrusted by macroalgae, calcareous 

algae or corals was included.

2006

Carbonate 

Pavement

Consolidated substrate, typically composed of calcareous and/or basaltic 

elements, which have become cemented together by biogenic and physical 

processes.

2002 

2004
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Estimates of habitat complexity were subjective assessments of topographical diversity and 

complexity of the benthic habitat and were classified according to one of six categories: low, 

medium-low, medium, medium-high, high, and very high (Fig. 2.4.2b). As examples, low 

habitat complexity is often associated with flat sand plains or rubble habitats; medium habitat 

complexity is often associated with small to moderate spur and groove, coral or boulder 

habitats; and high or very high habitat complexity are often observed as high or extreme 

vertical relief associated with steep spur-and-groove canyons, pinnacles, and walls.

Estimates of average benthic substrate cover were recorded as direct percents during 

ASRAMP 2002 and 2004 and then as percentage bins ranging from 1 to 10 during ASRAMP 

2006. Descriptions of benthic substrate categories and the percentage bins used in 2006 

are described in Tables 2.2.3c and 2.2.3d, respectively. Noncoral macroinvertebrates, 

Low Complexity Medium-low Complexity Medium Complexity

Medium-high Complexity High Complexity Very High Complexity

Figure 2.4.2b. Examples of low, medium-low, medium, medium-high, high, and very high complexity habitats. 

Note that towed divers calculate average complexity during each 5-min sampling period as they regularly 

encounter multiple habitat types. (Photographs provided by NOAA PIFSC CRED)
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except COTS, were counted singly up to 25 and then binned as follows: 26–50, 51–100, 

101–250, 251–500, 501–1000, and > 1000 organisms. COTS were counted singly up to 100 

organisms.

Results from benthic towed-diver observations were used to create: (1) habitat characterization 

maps for habitat complexity, sand, rubble, hard substrate/carbonate pavement, and live 

coral (discussed in Section 2.2.3: Optical Validation Surveys); (2) percent cover for live 

coral, stressed/dead coral, fleshy/macroalgae, and coralline algae, and (3) macroinvertebrate 

densities and distribution maps.

Diver observations for each 5-min tow segment were graphically projected onto ArcGIS 

maps using the midpoint for each tow segment (tow segment length = ~ 200 m, midpoint = ~ 

100 m). For benthic cover estimates, midpoint values in 2002 and 2004 were projected as the 

direct percents recorded by towed divers, while in 2006 the midpoint values were projected 

as the midpoint of the binned observations (midpoints of percent cover bins are listed in 

Table 2.4.2b). Macroinvertebrate values were projected as the total number of organisms 

observed per tow segment or as the midpoint of their binned range. Densities were calculated 

as the total number of macroinvertebrates observed during a tow divided by the area covered 

during the tow (10-m tow swath multiplied by tow length and presented in hectares).

Table 2.4.2b. Benthic cover binning categories used during ASRAMP 2006 towed-diver surveys.

Bin Benthic Cover (%) Midpoint

1 0.1–1 0.5

2 1.1–5 2.5

3 5.1–10 7.5

4 10.1–20 15.0

5 20.1–30 25.0

6 30.1–40 35.0

7 40.1–50 45.0

8 50.1–62.5 56.25

9 62.6–75 68.75

10 75.1–100 87.5

Fish

During each 5-min tow segment, the fish towed diver conducted a 360-degree scan during the 

first minute of the survey, recording all fish ≥ 50 cm total length within the range of visibility. 

During the remaining 4 min of each 5-min segment, all large fish ≥ 50 cm in total length that 

appeared within a 10-m survey swath (5 m to either side of the towline and 10 m in front were 

recorded). Species of particular concern observed outside the survey swath were classified 

as presence/absence data and recorded separately from the quantitative towed-diver survey 

data.

Results from towed-diver fish observations were used to calculate large-fish biomass figures 

for each tow and ultimately for each island. The length of each individual was determined 

visually with each individual being assigned to predetermined size classes. Large-fish biomass 

was calculated for each towed-diver survey by applying the midpoint length for each size 

class to published length-weight relationships (w = a × Lb) for individual species (Kulbicki 
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65

et al., 2005). When species-specific length-weight formulas were not available, formulas for 

the next higher class (genera, body type, etc.) were used. Large-fish sightings were summed 

for each tow segment and used to calculate total biomass estimates per tow as well as the 

biomass by fish family.

Accessory Instrumentation

Forward-facing Video Camera

A forward-facing digital video camera was attached to the fish towboard and used to collect 

streaming video images on Mini DV. Video footage from the forward-facing camera was 

archived as a durable record of the fish towed-diver survey track and can be used to quantify 

habitat composition and complexity, as well as abundance and distribution of ecologically and 

economically important fish taxa. No results derived from fish video imagery are presented 

in this report.

Downward-facing Video Camera and High-resolution Still Camera

A downward-facing digital video camera in a Gates underwater housing was mounted on 

the benthic towboard and used to record the benthos along each tow track during ASRAMP 

2002. During ASRAMP 2004 and 2006, the benthos was documented using a downwardfacing, high-resolution, digital still camera (Canon EOS-10D) in a customized underwater 

housing with dual Ikelite strobes. The camera was programmed to automatically photograph 

the benthos every 15 sec. In all survey years, the diver/observer attempted to maintain the 

downward-looking video/high-resolution still camera 1 to 2 m above the bottom.

Figure 2.4.2c. SBE 39 temperature and pressure units and other towed-diver instrumentation. (Photograph 

provided by NOAA PIFSC CRED)
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Results from towed-diver benthic videos/photographs are archived as durable records of 

the benthos at the various islands and atolls. Some of these data have been analyzed by 

researchers who subsampled frame grabs/photos for more detailed benthic composition 

analyses (Kenyon et al., 2006a). These results are not presented in this report.

Temperature and Pressure Recorders

SBE 39 temperature and pressure recorders were mounted on both benthic and fish towboards 

to accurately determine the temperature and depth of each diver and camera during toweddiver benthic and fish surveys. Data from both SBE 39 recorders were downloaded at the 

end of the day and merged with GPS tracklines to obtain accurate diver positions using the 

layback model described above. An image of a towboard with a subsurface temperature 

and pressure recorder and additional instrumentation (e.g., dive bottom timers/backup depth 

gauge, survey timers, and telegraph) is shown in Figure 2.4.2c.

Only depth data from SBE 39 temperature and pressure recorders are presented in this report. 

Mean depths for each tow segment were calculated and used to create depth distribution 

maps for each survey year.
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67

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