Survey Methods

Updated 4/01/2016

Benthic Monitoring

Rapid Ecological Assessment Methods (REA)

Line-point-intercept (LPI) for Benthic Cover (2008-Present)

The current line-point-intercept (LPI) method identifies hard corals, octocorals, macroalgae, crustose coralline algae, turf algae, cyanobacteria, and sessile macroinvertebrates to the highest possible taxonomic resolution and records, along with sand cover, at 20-cm intervals along two 25-m transect lines set in a single file row (and separated by a 5-m intertransect space). These surveys generate 125 points per transect (250 points per site) that are used to determine percentage of cover of benthic organisms and sand at each REA site (prior to 2008, this method was implemented at 50-cm intervals along the two transects). In concert with LPI surveys, photographs are taken to record the benthos at intervals of 2 m and 5 m along the same two transect lines with a high-resolution digital camera mounted on a pole. This work generates 32 photographs per site that are later analyzed by benthic specialists at CRED, using the computer program Coral Point Count with Excel extensions (CPCe), to determine the benthic composition at the genus, functional or morphological group level for each REA site (similar photographs of the benthos taken at REA sites surveyed by the fish team also will be analyzed).

Roving-diver surveys may also be conducted at an REA site: a swath of 3-5 m on either side of the transect lines is surveyed to record algal species richness. If an algal species encountered during LPI or roving-diver surveys was not identifiable in the field, a sample is collected as a voucher specimen and subsequently cataloged and critically analyzed to ensure positive species identification. Provisions are made to ensure appropriate preservation and curation of each algal specimen. These voucher specimens along with the benthic photographs form permanent historical records, the former of algal diversity and the latter of the composition of benthic communities at each REA site.

Photoquadrat (2000-2008)

Benthic team members performing photoquadrat survey to quantitatively measure algal percent cover at Kure Atoll, NWHI.
Benthic team members performing photoquadrat survey to quantitatively measure algal percent cover at Kure Atoll, NWHI.
Illustration of a PVC frame used in photoquadrat surveys to frame the survey area and to hold an Olympus C3040Z camera in Olympus 
        PT-010 housing. Designed by Linda Preskitt.
Illustration of a PVC frame used in photoquadrat surveys to frame the survey area and to hold an Olympus C3040Z camera in Olympus PT-010 housing. Designed by Linda Preskitt.

The goal of photoquadrat surveys was to quantitatively describe the algal community and generate a comprehensive species list for each REA site. This method minimized time in the water but yielded the greatest amount of data possible. This method relied on a high-resolution digital camera mounted on a 0.18-m2 photoquadrat. Working at depths of 3-16 m, two trained observers moved along two transect lines with one observer placing the photoquadrat frame at predetermined, randomly selected points and operating the camera, while the other diver recorded the name and rank abundance of each algal species found in the photoquadrat at each point. A representative sample of each algal species in the first photoquadrat was also collected for later identification in the laboratory and to form historical voucher collections for each site. Once data were recorded, the photoquadrat was moved to the next random point and this procedure repeated. To prevent redundancy, at subsequent photoquadrats, samples were collected only of algal species not found in the first photoquadrat. This method was published in Preskitt et al. (2004).

Photographs were analyzed for percent cover implementing PhotoGrid or CPCe, software programs. Field-collected specimens were critically analyzed in the laboratory to ensure positive species identification, cataloged, and subsequently accessioned in research institution collections.

Belt Transect for Coral Size Class (2002-2007)

The surveyor listed all coral species occurring within 0.5 m2 of each side of the two, 25-m transect lines and the size class to which the maximum diameter of the colony belonged (5 cm; 5-10 cm; 10-20 cm; 20-40cm; 40-80 cm; 80-160 cm; or 160 cm). In geographic regions such as the Northwestern Hawaiian Islands where coral richness and abundance are reduced relative to lower latitude regions with higher species richness, the protocol was amended to include all corals occurring within 1m of each side of the transect lines. Coral bleaching and disease surveys were conducted by a second diver who documented all cases occurring within 2-4 m on each side of the transect lines. Random swims were also conducted in the vicinity of the transect lines within an area of about 5,000m2 in which all coral species were listed and assigned a DACOR abundance code based on visual estimation (dominant, abundant, common, occasional, and rare). These surveys were routinely conducted between 2002 and 2004 only.

Belt Transect for Coral Demographics and Condition (2007-Present)

The REA belt transect method provides information on coral demographics and condition. The coral divers gather data along five evenly spaced segments (each 2.5 x 1 m; 0-2.5 m; 5.0-7.5 m; 10-12.5 m; 15-17.5 m; 20-22.5 m) along each of the same two 25-m transect lines implemented in the LPI survey. This strategy was designed to maximize time for capturing spatial heterogeneity per transect. Within each 2.5-m2 transect section, all coral colonies whose center falls within 0.5 m on either side of each transect line are identified and 2 planar measurements recorded (maximum diameter and the diameter perpendicular to the maximum diameter). For each coral colony identified the extent of mortality is estimated, dedicating special attention to any evidence of disease. Percentage of colony affected as well as lesion severity and levels of coral predation were also recorded.

Field characterization of coral diseases focuses on provision of a general description of lesions instead of attempts to establish a subjective interpretation of causality. Lesions are classified into general, unambiguous categories, including but not limited to: bleaching, acute tissue loss or white syndrome, subacute tissue loss, skeletal growth anomalies, pigmentation responses, discolorations other than bleaching, algal infections, cyanobacterial infections, fungal infections, other unidentified diseases and syndromes, and predation by crown-of-thorns seastars (Acanthaster planci), fish, and snails (primarily from the genus Drupella). Divers also make an effort to assess the incidence of coralline algal diseases with the following scheme: coralline lethal orange disease, coralline fungal disease, coralline lethal disease, and coralline ring disease.

Benthic Towed-diver Survey Method (2002-Present)

Visual representation of benthic towed-diver categories used to assess percent cover of functional groups.
Visual representation of benthic towed-diver categories used to assess percent cover of functional groups.

A pair of scuba divers (one collecting fish data, the other collecting benthic data) is towed about 1 m above the reef roughly 60 m behind a small boat at a constant speed of about 1.5 kt. Each diver maneuvers a towboard platform, which is connected to the boat by a bridle and towline and outfitted with a communications telegraph and various survey equipment, including a downward-facing digital SLR camera (Canon EOS 50D, Canon Inc., Tokyo). The benthic towed diver records general habitat complexity and type (e.g., spur and groove, pavement), percent cover by functional-group (hard corals, stressed corals, soft corals, macroalgae, crustose coralline algae, sand, and rubble) and for macroinvertebrates (crown-of-thorns seastars, sea cucumbers, free and boring urchins, and giant clams).

Towed-diver surveys are typically 50 min long and cover about 2-3 km of habitat. Each survey is divided into 5-min segments, with data recorded separately per segment to allow for later location of observations within the ~ 200-300 m length of each segment. Throughout each survey, latitude and longitude of the survey track are recorded on the small boat using a GPS; and after the survey, diver tracks are generated with the GPS data and a layback algorithm that accounts for position of the diver relative to the boat.

Diagram of one of two divers conducting a towed-diver survey.
Diagram of one of two divers conducting a towed-diver survey.
Diagram of the layout of a benthic towboard used in towed-diver surveys.
Diagram of the layout of a benthic towboard used in towed-diver surveys.

Autonomous Reef Monitoring Structures (ARMS) (2008-Present)

Each ARMS is composed of nine gray, type 1 PVC plates (23 x 23 cm) stacked in an alternating series of open and obstructed formats and attached to a base plate (35 x 45 cm). The entire structure is affixed to the sea floor with four stainless steel stakes, weights, and/or zip ties. ARMS typically are deployed on mid-depth (12 - 17 m) forereef habitats in replicate sets of three ARMS at three sites (3 x 3) per island or location. They remain on the bottom for 3 years during which time they become colonized with marine organisms.

An ARMS is retrieved from the sea floor by encapsulating it with a mesh-lined container to prevent the escape of motile organisms. It is then brought to a small boat and transported to shore or a NOAA ship for processing. Each ARMS is disassembled plate by plate, with both sides photodocumented. After the plates are photographed, they are scraped with a spatula and preserved in ethanol, 20% DMSO, or RNA later. Sea water sieved for motile organisms using 2-mm, 500-µm, and 100-µm geologic sieves to create three size fractions. Organisms from te 2-mm size fraction are sorted to morphospecies and the 500-µm and 100-µm size fractions are preserved in ethanol for future genetic analyses. See ARMS Deployment, ARMS Recovery, and ARMS Processing for more detail.

Deployed ARMS. Recovery of an ARMS. Recovered ARMS transported via small boat to a NOAA ship.
Photos (left to right): Deployed ARMS; recovery of an ARMS; rRecovered ARMS transported via small boat to a NOAA ship.
Photographing an ARMS plate. Looking for crabs. Scraping an ARMS plate.
Photos (left to right): Photographing an ARMS plate; looking for crabs; scraping an ARMS plate.

For more information on the ARMS project, contact the Benthic Program.

Fish Surveys

The fish team uses several complementary, noninvasive, underwater surveys are used to enumerate the diverse components of diurnally active shallow-water reef fish assemblages. We conduct diver surveys and use technology for remote observations. For diver surveys, we use two types: 1) Rapid Ecological Assessments (REA), which are comprehensive, small-scale, site-specific surveys that record the number, size, and species of fishes present at a survey site on a reef and are conducted with a new stationary point count (nSPC) method and 2) towed-diver surveys (TDS), which are designed to quantify relatively large-bodied (>50 cm total length, TL), wide-ranging fishes over a broad spatial scale. Each of these two survey types is replicated at locations within or among the various habitat types present around each island or bank. TL is estimated to the nearest centimeter for all quantified fishes, allowing for generation of biomass densities and size distributions by taxa.

In previous years (~2000-2009), REA surveys were conducted with a belt-transect (BLT) method and a different variation of a SPC method. Beginning in 2007, CRED began to incorporate the use of an improved nSPC method to quantify fish populations; this nSPC method completely replaced the BLT and old SPC methods by late 2009.

CRED also partners with other agencies and research institutions to use stereo-camera systems to assess bottomfishes (e.g., the BotCam system) and baited remote underwater video stations (BRUVS) for remote assessments of coral reef fishes.

Rapid Ecological Assessment Methods (REA)

new Stationary Point Count (nSPC) Method (2007-Present)

Diagram of one of two divers conducting an SPC survey at an REA site.
Diagram of one of two divers conducting an SPC survey at an REA site.
Diver counting coral reef fishes at Pearl and Hermes Reef using the SPC method. NOAA photo by Paula Ayotte.
Diver counting coral reef fishes at Pearl and Hermes Reef using the SPC method. NOAA photo by Paula Ayotte.

For the current CRED nSPC method, pairs of divers record the number, size, and species of all fishes observed within visually estimated cylinders 15 m in diameter. At the start of a survey dive, a pair of divers first lay down a 30-m transect line along a predetermined depth contour, and then the two divers move to the 7.5- and 22.5-m marks on that line; these marks serve as the centers of two adjacent nSPC cylinders. During the first 5 min of a survey, the divers create a list of the fish species observed in or passing through their cylinder. After the first 5 min, divers systematically proceed down their species lists, counting and estimating the size (TL) of each fish present to the nearest centimeter. Species seen after the 5 min or outside of the survey area are recorded as present.

Belt Transect (BLT) Method (2000-2009)

At each site, three 25-m lines were surveyed. Two fish biologists swam side-by-side along a transect, each recording all fishes > 20 cm TL observed within a belt that was 4 m wide, 4 m high and perpendicular to their respective side of the transect. Then, these fish divers made a second pass along each transect, recording all fishes <20 cm TL that were observed within belt that was 2m wide and 4 m high. The survey of large fishes took ~5 min to complete, and the survey of smaller fishes took ~10 min to complete.

Stationary Point Count (SPC) Method (2000-2007)

For each survey conducted with the old SPC method, a fish diver swam ~15 m from the transect lines concurrently being surveyed with the BLT method by the other fish biologists. The SPC biologist then recorded all fishes longer than 25 cm TL that passed within a visually estimated cylinder 20 m in diameter and centered on the diver's fixed position. The survey time for each SPC survey was 5 min and four SPC surveys were conducted at each REA site.

Towed-diver survey method (2000-Present)

Diagram of one of two divers conducting a towed-diver survey.
Diagram of one of two divers conducting a towed-diver survey.
Diver counting coral reef fishes using the towboard method. NOAA photo by Jason Helyer.
Diver counting coral reef fishes using the towboard method. NOAA photo by Jason Helyer.

A pair of scuba divers is towed about 1 m above the reef roughly 60 m behind a small boat at a constant speed of about 1.5 kn. One diver quantifies fish populations, and the other diver quantifies the benthos. Each diver maneuvers their own towboard. Towboards are connected to the small boat by a bridle and towline and outfitted with various survey equipment, including a video camera on the fish towboard. The fish diver records the number, size, and species of all large fishes (>50 cm TL) observed within a belt that is 10 m wide and centered on the diver. Observations and species tallies are recorded on preprinted data sheets attached to each towboard. The digital video camera on the fish towboard faces forward and takes a permanent record of fishes encountered in a standard field of view.

A towed survey is typically 50 min long and covers about 2 km of habitat. Each survey is divided into 5-min segments, with data recorded separately per segment to allow for georeferencing of observations within the ~200 m covered during each segment. Throughout a survey, the latitude and longitude of its survey track are recorded at 5-s intervals on the small boat with a global positioning system (GPS). Following a survey, diver tracks are generated using this GPS data and a layback algorithm to account for position of the diver relative to the small boat.

Bottomfish Stock Assessment and Remote Assessment

BotCam (2005-Present)

Although we conduct most of our reef fish surveys in nearshore areas (0-30 m), many commercially exploited fishes can be found beyond the range of scuba divers in habitats as deep as 400 m as well as in shallower coral reef environments. To survey these deeper populations at depths of 100-300 m, the NOAA Pacific Islands Fisheries Science Center, the University of Hawaiʻi, the State of Hawaiʻi, the Hawaiʻi Undersea Research Lab, and other partners collaborated to develop and implement a nonextractive sampling method that uses an autonomous camera system. The Bottom Camera Bait Station (BotCam) uses two ultra-low-light cameras to collect stereo-video images of fishes and their habitats in ambient light. These data allow for precise and accurate species identification and size and range information. This system was specifically designed to study Hawaiʻi's commercially fished bottomfish complex, which is often referred to as the "Deep 7" and includes six snappers and the endemic Hawaiian grouper (Hyporthodus quernus). Click here to learn more about the BotCam.

Baited Remote Underwater Video Station (BRUVS) (2010-Present)

Another type of remote video system used by CRED is the baited remote underwater video station (BRUVS). The BRUVS was developed and several of them have been used widely by Euan Harvey, PhD, and his colleagues at the University of Western Australia and Australia Institute of Marine Science. BRUVS are similar to the existing BotCam technology but are more suitable for deployment on coral reef systems because they are smaller, lighter, and can be deployed closer to a substrate. CRED uses BRUVS for reef surveys to depths of ~100 m.

Each BRUVS uses high-definition video cameras mounted 0.7 m apart on a base bar that is inwardly converged at 8°. This stereo-video system allows us to identify fish species and to accurately and precisely determine fish sizes and their distances from the camera when the video images from these cameras are subsequently analyzed. The use of bait attracts a wide diversity of fish species into the field of view of the cameras, but CRED is also experimenting with unbaited deployments.

Habitat Mapping

Mapping Instruments and Equipment

Towed-camera and Sonar Systems (2001-Present)

The Coral Reef Ecosystem Division (CRED) procured a bottom classification system based on single-beam bathymetry and a towed optical assessment device (TOAD) in 2001. Since their introduction, these instruments have been upgraded/reconfigured several times and are still used on numerous NOAA research cruises and ships.

A towed optical assessment device (TOAD). Control console used to monitor the position of the TOAD sled relative to the seafloor.
Important tools used by CRED for mapping and characterization of benthic habitats: (left) a towed optical assessment device (TOAD) and (right) control console used to monitor the position of the TOAD sled relative to the seafloor.

NOAA R/V AHI (2003-Present)

The NOAA R/V AHI is designed for seabed mapping surveys.
The NOAA R/V AHI is designed for seabed mapping surveys.

The NOAA Research Vessel Acoustic Habitat Investigator (AHI) is an 8-m (25-ft) aluminum-hulled vessel designed for seabed mapping surveys in the U.S. Pacific islands. The R/V AHI can either work in conjunction with a mother ship, such as a NOAA research vessel or operate independently from a small-boat harbor at inhabited islands. The AHI is equipped for high-resolution surveying of a seabed at depths of 10-200 m. This vessel was commissioned in 2003.

Autonomous Underwater Vehicle (2009-Present)

The CRED AUV has been used in a variety of missions from shallow coral habitat investigation, optical mapping of known underwater 
        archaeological sites, to newly discovered deep sea sponge reefs.
The CRED AUV has been used in a variety of missions from shallow coral habitat investigation, optical mapping of known underwater archaeological sites, to newly discovered deep sea sponge reefs.

Our autonomous underwater vehicle (AUV) is an untethered underwater robot that requires no real-time commands to operate. AUVs are designed to carry out a variety of missions, including deep-sea sonar surveys, oceanographic sampling, and mine detection. The Seabed-class AUV was originally designed by Hanumant Singh at Woods Hole Oceanographic Institute (WHOI) to be a cost effective low speed survey platform preforming optical and acoustic surveys below diver depths(>50m). The PIFSC's CRED and Northwest Fisheries Science Center's (NWFSC) Fishery Resource Analysis and Monitoring Division (FRAM) are collaborating with WHOI to develop and operate the SeaBED autonomous underwater vehicle (AUV) to collect fisheries-independent data and habitat mapping to depths less than 2000m.

Operational History Overview

Mapping in Depths > 20 m

In 2001, CRED began a program to systematically map coral reefs of the U.S. Pacific islands that occur in depths > 20 m. In these water depths, satellite-based imagery cannot be used routinely for mapping, and vessel-based acoustic systems must be employed instead. Acoustic mapping systems provide high-resolution depth information, and acoustic responses can be analyzed to extract information about a seabed's character (e.g., roughness or hardness). The regional variation in acoustic characteristics can be used to delineate changes in the seabed and identify regions of similar characteristics. Acoustics alone cannot identify specific habitats; therefore, CRED makes direct optical observations and uses them to identify specific habitats and correlate them with the acoustic regions. The tools required to perform deepwater benthic habitat mapping include mapping sonars and optical observing systems, such as towed optical assessment devices (TOAD), remotely operated vehicles (ROVs), manned submersibles, and, at depths of 20-30 m, direct diver observations, still photography, and videos. The optical observing systems already used by CRED include TOAD and diver observations. In the near future, an ROV also CRED is developing an ROV and plans to use it in the near future. Because of the time required to plan, procure, test, and field such systems, we implemented our deepwater mapping capability in three phases:

Phase 1: Mapping from Vessels of Opportunity

Photo of corals on a bank near the island of Tutuila in American Samoa taken by the underwater Towed Optical Assessment Device (TOAD).
Photo of corals on a bank near the island of Tutuila in American Samoa taken by the underwater Towed Optical Assessment Device (TOAD).
Acoustic variability values displayed over single-beam bathymetry around Tutuila, American Samoa. Values of a U.S. Geological Survey 
        10-m digital elevation model are shown in green.
Acoustic variability values displayed over single-beam bathymetry around Tutuila, American Samoa. Values of a U.S. Geological Survey 10-m digital elevation model are shown in green.

A bottom classification system based on single-beam bathymetry and TOAD device were procured by CRED in 2001; these instruments were used on numerous cruises aboard the NOAA Ship Townsend Cromwell. When the Cromwell was decommissioned in 2002, this equipment was transferred to the NOAA Ship Oscar Elton Sette. In 2002, our scientists also participated in a mapping cruise in the Northwestern Hawaiian Islands (NWHI) aboard the University of Hawaiʻi at Mānoa's R/V Kilo Moana during which more than 38,000 km2 of multibeam data at depths of 20-5000 m were collected.

On the Townsend Cromwell, acoustic mapping was conducted using a 50-kHz Simrad EQ 50* single-beam echosounder (Kongsberg Maritime AS, Horten, Norway) that was integrated with a QTC View data acquisition and bottom classification system (Quester Tangent Corp., Saanichton, British Columbia, Canada). When transferred to the Oscar Elton Sette, the QTC View was interfaced to one quadrant of the ship's 38-kHz split-beam transducer used in conjunction with a Simrad EK60 echosounder. Optical-validation data were collected using an underwater camera platform at depths of 20-100 m. Acoustic and underwater-camera data collection typically was done at night when other cruise operations, such as Rapid Ecological Assessment and towed-diver surveys and oceanographic instrument deployments, cannot be conducted. In 2001 and 2002, CRED collected more than 7500 linear km of single-beam and bottom classification data in the NWHI and 1600 linear km in the central Pacific. Thousands of photographs were taken with the TOAD, but only ~850 and 300 of the photographs taken in the NWHI and central Pacific, respectively, were of sufficient quality optically or georegistered well enough to use for benthic habitat identification.

The QTC View bottom classification system uses principal component analysis to process signals from an echosounder. QTC View data from the 2001 and 2002 Pacific Reef Assessment and Monitoring (Pacific RAMP) cruises were studied to determine if similar bottom characteristics could be detected throughout the NWHI, the Pacific Remote Island Areas, and American Samoa. This analysis showed promise, but one issue in particular limited its usefulness. The QTC system can be used with a variety of sonars and at different frequencies; however, data collected at different sonar frequencies or transmission characteristics cannot be combined for analysis. An example of this limitation occurred when the echosounder settings were changed on the bridge during the course of the Pacific RAMP cruise conducted in American Samoa in 2002. These problems led us to look at the spatial variability of the data classes rather than at the classes themselves. This avenue of research allowed us to use class variability as a predictor of bottom type when we returned to American Samoa in early 2004, thus, enabling us to target particular areas for optical surveys. To better determine the long-term value of collecting single-beam bottom classification data, we are planning to reassess the QTC data collected at Tutuila during the 2002 Pacific RAMP cruise and compare them with multibeam data collected in early 2004. The inability to combine data sets is of particular concern, because we are working on several different ships with different echosounders operating at different frequencies.

The original TOAD configuration used by CRED in 2001 to 2002 to collect optical data for the purposes of validating acoustic mapping 
        data and characterizing benthic habitats.
The original TOAD configuration used by CRED in 2001 to 2002 to collect optical data for the purposes of validating acoustic mapping data and characterizing benthic habitats.

Our initial TOAD integrated a digital still camera, an underwater video camera, lights, and laser pointers on a Guildline Instruments Ltd. (Smith Falls, Ontario, Canada) MiniBAT 8820 tow body. The MiniBAT design allowed limited control, by changing the angle of its wings, of the vehicle's position when it was being towed. This device was navigated with MiniBAT software in which the operator entered an estimated layback that was integrated with the ship's position to provide an estimated position of the tow body. Positional accuracies estimated with this method were on the order of 50 m. Various operational scenarios were tested, including towing of a towed sonar system at speeds of 1-3 kn and using it in a drifting mode. After several Pacific RAMP cruises, it was determined that the drift technique was most effective and presented the least risk towed sonar system and the operator's nerves in rugged, coral-rich areas. One of the drawbacks of this ship-based camera system is that when it is operated adjacent to islands with steeply sloping sides, areas of interest are often too close to a particular island for a ship to maneuver safely. One of the drawbacks of this ship-based camera system is that areas of interest are sometimes inaccessible: at islands with steeply sloping sides, a ship often cannot safely maneuver close enough for this camera system to be deployed at an area of interest.

CRED also participated in an extensive multibeam mapping cruise in the NWHI in October and November 2002 aboard the R/V Kilo Moana. A discussion of the mapping techniques used during this cruise is available, as are grids, the resulting bathymetric data.

Phase 2: Launch-based Mapping Systems

R/V AHI.
R/V AHI.

In 2001, CRED began planning for the deployment of a high-resolution, shallow-water mapping system that would be used at depths of 10-200m. The result was the R/V AHI, a survey launch that was commissioned in 2003. In 2004, we also upgraded our underwater camera systems by replacing the TOAD with two underwater towed camera sleds so that they could finally be deployed from small boats as well as from large ships.

The R/V AHI was designed by SAFE Boats International specifically to transport personnel and survey electronics for seabed mapping surveys in the U.S. Pacific islands. Outfitted for daytime operations, the AHI was built for high-resolution surveying of the seabed at depths of 10-250 m This vessel's hull and enclosed cabin house a 240-kHz Reson Seabat 8101 multibeam echosounder (Slangerup, Denmark), a POS/MV position and orientation sensor (with two GPS antennas and an inertial measurement unit), and a SAIC ISS-2000 data acquisition and survey control system (SAIC Inc., McLean, Va.). This boat typically is operated by a coxswain and a surveyor.

During its first year of operation in 2003, the AHI was transported to each work area by the NOAA Ship Oscar Elton Sette. Because the Oscar Elton Sette was not designed to deploy a boat of this size, the AHI was launched only in a calm harbor. The AHI in later years began working independently from a mother ship by launching directly from small boat facilities where available. During this first year, CRED used the AHI to survey more than 750 km2 of seafloor in the NWHI, Commonwealth of the Northern Mariana Islands (CNMI), Guam, and American Samoa.

In early 2009 our AUV was received in early and since then has conducted a verity of mission from shallow water coral habitat investigation, optical mapping of known underwater archaeological sites, to newly discovered deep sea sponge reefs. Successful collaborative mission have been run on Galvez Bank South of Guam and around the Chanel Islands National Marine Sanctuary, Santa Barbara, CA. The AUV continues to be used heavily today.

Phase 3: Ship-based Mapping Systems

In August 2004, the NOAA Ship Hiʻialakai arrived in Hawaiʻi. This ship is equipped with davits that allow the AHI to be deployed from it in moderate sea conditions, extending AHI's mapping range to isolated islands and banks. The Hiʻialakai had two multibeam echosounders installed in late 2004i—a 30-kHz Simrad EM 300 sonar for mapping at depths of 100-4000 m and a 300-kHz Simrad EM 3000 sonar for mapping at depths of 20-160 m. When working together, the Hiʻialakai and AHI cover up to 40 km2/day of shallow banktop regions that are typical in the NWHI. They also are able to effectively map in areas, such as the northern islands of the Mariana Archipelago or the U.S. Line Islands, where the Hiʻialakai can quickly survey offshore areas while the AHI surveys inshore areas that would be dangerous for a large ship to navigate.

The Hiʻialakai is equipped with an ROV and underwater positioning system that allows for collection of optical validation data that is much more efficient and precisely located than the data collection that was previously possible from either the Townsend Cromwell or Oscar Elton Sette.

Data Processing

Data from bottom characterization based on single-beam sonar are processed using QTC IMPACT software. First, spikes and outliers are removed from the data manually, and then a principal components analysis is used to analyze the shape of the electronic signal and separate the data into QTC "classes". The number of classes, the optimal groupings, and the spatial and depth limits are determined by the operator. Bottom classes are displayed in conjunction with linked optical samples in ArcView 10 software (ESRI, Redlands, Calif.), and the combined data are examined for groupings and relationships between the two data types. A depth model also is generated with the single-beam depths and multibeam data where available, and the QTC class data are displayed in 3D draped over the topographic model. As described previously, because of operational problems, an analysis was done of the variability among the QTC classes. This analysis avenue shows potential, and further analysis of the QTC data in relationship to recently acquired multibeam bathymetry and backscatter data in selected test areas has been done.

Multibeam data are acquired with an SAIC ISS-2000 system, which records the data and provides survey control and underway quality control displays. SAIC's SABER processing software is used to process the raw soundings, analyze the results, manually edit the sounding data to remove outliers, and derive average gridded data values. The data are corrected for predicted tides during field operations; if necessary, the data are later updated with observed tides after the fact. GMT is used to reformat SABER grids into final form. The Quality Positioning Systems (QPS) Fledermaus (Quality Positioning Systems, Portsmouth, N.H.) software and ESRI ArcGIS programs are used for viewing results and creating browse objects.

Oceanography

Details of the field methods used by the Ocean and Climate Change Team for data collection are outlined in this paper (Hoeke et al. 2009 (0.4 MB PDF)) on in situ oceanographic.

Ecological Acoustic Recorder (EAR)

Acoustic data is collected as .bin files via passive acoustics using an Ecological Acoustic Recorder (EAR). The EAR is a microprocessor-based autonomous recorder that samples the ambient sound field on a programmable duty cycle. EARs are generally programmed to record for periods of 30 s every 15 min at a sampling rate of 25-40 kHz, although these settings are at times different depending on the site and target sounds. An event detector allows for loud sounds that fall within certain parameters to turn on the recorder during duty periods to capture a 15-s recording.

Data obtained from each EAR are aurally and visually examined with the program Cool Edit (Adobe Systems, Inc., San Jose, Calif.) and processed with custom Matlab scripts (The MathWorks, Inc., Natick, Mass.) or Triton, a Matlab-based package developed by the Scripps Institution of Oceanography, University of California San Diego.

*Mention of trade names or commercial companies is for identification purposes only and does not imply endorsement by the National Marine Fisheries Service, NOAA.