Expanded Description of the Protocol for Habitat Characterization

1. Initial classification of features from existing maps and charts

Prior to selecting target sites, we examined and classified major geomorphic features (topography) of the continental shelf from available maps, including charts, side-scan, or multibeam images of the study area. If such maps did not exist fathometer runs were conducted prior to diving, and the information was transferred by hand to nautical charts. Target sites could then be selected, and a preliminary classification was made, as follows:

(a) Classification of geomorphology as first tier (major) categories for dominant features:

Geomorphology categories include:

  • sea mounts
  • mounds
  • pinnacles
  • ridges (e.g. paleo-shorelines)
  • drowned patch reefs
  • low relief hard bottom
  • rock outcrops
  • hard bottom with a veneer of sand
  • sand waves
  • pits

(b) Next, we subdivided first tier into second tier categories, as practical. As an example, paleo-shorelines can be subdivided into:

  • upper ridge
  • escarpment
  • rubble bottom
  • other

2. Preliminary reconnaissance to assess the variety and boundaries of habitats within target areas

Dives began with a brief reconnaissance of the defined geomorphic feature to identify the variety of feature types contained within the area, and to delimit the boundaries of the habitat. Also noted were subcategories of features and discontinuities in habitat characteristics. During this “recon” portion of the dive, pilots made video records with verbal comments, including the following:

  • an initial record of date, time, dive number, pilot, location and mission
  • frequent reference to depth and time
  • descriptions of observations of topography
  • descriptions of substrate types among various geomorphic features
    • clay (very fine)
    • silt (fine)
    • sand (coarse)
    • rubble/cobble

3. Fish community survey

Where fish community assessments were made, a 30-minute survey was made in the habitat selected for characterization. Pilots used either the Roving Diver Method and the Reef Environmental Education Foundation (REEF) survey forms (which record all species seen), or they surveyed only those species listed on the Dive Information Form. Video records were made for unidentified species, but the time required to make the records was not considered part of the survey. Following either 30-minute survey, relative abundances were assigned to each species as follows:

A=Abundant (>100)

M=Many (11-100; comparable to “Frequent” or “Common” of others)

F=Few (2-10; comparable to ”Occasional” of some others)

S=Single (1; comparable to “Rare” used by some others)

4. Benthic video transects, supplemented by pilot verbal descriptions

To evaluate benthic communities, quantitative strip (belt) transects were run within defined geomorphological features using videography and visual observations from the sub. Similar work can be accomplished using an ROV. All surveys recorded accurate latitude and longitude (or track) of the sub or ROV so that observational and video information could be referred to charts or other images.


Documentation: Digital video and audio and written were used to record habitat features and the fish community.

Number of transects: Five (5) transects within each defined feature generally provided an adequate sample size.

Length of transects: The target length for transects was 25 m. Longer transects are often made in habitats with low abundances.

Sub or ROV speed: The speed at which transects are made must be slow enough to ensure clear images on the down-looking video. The best speeds are around 0.1 to 0.2 m/s or less, comparable to a very slow walk. (Faster speeds produce blurred images in the down-looking video.) This means that each transect takes between 2 and 4 minutes to complete.

Videography: The preferred way to run transects is with two video systems in place, one downward-looking camera with a wide-angle lens, and one forward-looking (oblique) camera. Each video system should have laser metrics in the recorded image. The submersible and ROV should maintain an elevation of approximately 0.5 to 1.0 meter off the bottom for transect duration to ensure that the downward looking camera produces a clear image.

(i) Downward-looking video: two parallel-beam lasers a known distance apart, say 25 cm, can be used to judge quadrat size and organism size in the downward-looking video frames.

(ii) Forward-looking video: three lasers arranged horizontally in one plane projected at an oblique angle so that they reach the seafloor ahead of the path of the sub. The two outside lasers project parallel beams and the central laser (projecting from a position half way between these outside lasers) projects a beam that converges on one of the outside beams at a known distance from the sub, (e.g., 6 m, or ca. 20 ft). The parallel beam lasers give scale at a distance, and the central laser allows the determination of distance from the sub. For example, if the spot projected by the central laser coincides with the laser spot it converges on, then the object is about 20 ft away; if it is half way between center and one laser, the distance is 10 ft, and so on. The tilt of the forward-looking lasers should be under the control of the pilot.

5. Benthic video and audio reconnaissance and sampling

Following the censuses and transects, pilots conducted further characterization work. This could include exploration, video and audio documentation of habitat and creatures, and collection of samples. Good site descriptions consist of habitat descriptors, organism identification (either formal or informal, such as “red tube sponge”), a qualitative descriptor of relative frequency for each taxon, quantity (if appropriate; see Section 3. above), community descriptions (e.g. cover, distribution, vertical zonation, apparent ecological controls, habitat affinities of various species), and other comments, such as noteworthy behavior or evidence of human impacts.

6. Site-related descriptions

Any scientific pilot or observer must be familiar with terms that accurately convey habitat characteristics, and must use them as often as possible during a dive. Verbal comments should be nearly continuous, as video cameras do not perceive an environment as well as a live observer. It is also critical that there be very frequent reference to depth, as this is not always recorded by tapes or underwater tracking systems. Some frequently used terms that describe bottom morphology, substrate texture, and living elements of the habitat are given below.


  • Flat (0-5°)
  • Sloping (5-30°)
  • Steeply sloping (30-45°)
  • Vertical (45-90°)
  • Overhang (>90°)

Modifiers for bottom morphology

  • Regular
  • Irregular (continuous, non-uniform bottom, local relief 1-10 m)
  • Hummocky
  • Fractured/cracks
  • Outcrop
  • Bedding
  • Massive

Modifiers for deposition

  • Consolidation (unconsolidated, semi-consolidated, hard-packed)
  • Erodability (uniform, differential)
  • Sediment cover (land the sub and hit thrusters; dusting, thin, thick)

Modifiers for feature density

  • Occasional (random occurrence)
  • Scattered (covers 10-15% of area)
  • Contiguous (features nearly touching)
  • Pavement (features touching)

Modifiers for biological processes

  • Bioturbation (tracks, trails, burrows, excavation)
  • Cover of encrusting organisms (estimates for selected taxa)
  • Dominance (e.g., coralline algae-dominated)
  • Distribution (random, clumped, regular)
  • Behavior (courtship, spawning, aggression, attraction, avoidance, symbiosis)
  • Habitat affinities (site fidelity)
  • Suspected disease

Modifiers for ecological controls

  • Physically controlled (sediment burial, storm, currents)
  • Biologically controlled (space competition, predation)
  • Zonation (vertical, horizontal)

Modifiers for human impacts

  • Anchor damage
  • Trawl tracks/damage
  • Wrecks
  • Discarded fishing gear
  • Active fishing gear
  • Garbage
  • Excavations
  • Buoys/markers
  • Sedimentation
  • Spilled fuel
  • Cables
  • Oil or gas development

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