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Detailed Methods for Characterization and Monitoring of Coral Reef Ecosystems and Associated Biological Communities

diagram showing methodology

There are three complementary components to our field methodology. The first is a 25m long belt transect used to quantify fish species’ size and abundance. This component is particularly effective for sampling multiple habitat types such as mangroves where the diver is able to swim adjacent to the prop roots, or reefs, where it enables the diver to see what is on the distal side of structures. Additionally, high visibility is not as essential as with the second component, a point-count. The point-count methodology has historically been used in the Virgin Islands and Florida Keys for examination of reef fish communities. By continuing to make use of the same methodology it enables us to compare current data against historical record. Fish data collected from these two components can then be related back to large-scale habitat information to identify spatial patterns in community structure. Finally, the third component involves taking detailed habitat measurements along the belt transect. These measurements can later be correlated to the fish data in order to gain insight into small-scale fish-habitat relationships.

I. Belt Transect Fish Census

Once in the field, the boat captain navigates to previously selected sites using a handheld GPS unit. On-site, divers are deployed and maintain contact with each other throughout the entire census. One diver is responsible for collecting data on the fish communities utilizing the belt-transect visual census technique over an area of 100m2 (25m length X 4m width). The belt-transect diver obtains a random compass heading for the transect prior to entering the water and records the compass bearing (0-360°) on the data sheet. Visibility at each site must be sufficient to allow for identification of fish at a minimum of 2m away. Once reasonable visibility is ascertained, the diver attaches a tape measure to the substrate and allows it to roll out for 25m while they are collecting data.

Although the habitat should not be altered in any manner by lifting or moving structure, the observer should record fish seen in holes, under ledges and in the water column. To identify, enumerate, or locate new individuals, divers may move off the centerline of the transect as long as they stay within the 4m transect width and do not look back along area already covered. The diver is allowed to look forward toward the end of the transect for the distance remaining (i.e. if the diver is at meter 15, he can look 10 meters distant, but if he is at meter 23, he can only look 2 meters ahead).

On-site, no attempt to avoid structural features within a habitat such as a sand patch or an anchor should be made as these features affect fish communities and are "real" features of the habitats. The only two instance where the transect should deviate from the designated path is to stay above 110 ft or while surveying mangrove habitats. In mangrove areas the diver swims close to the prop roots and looks as far into the mangroves as possible, up to 2m and then out to the edge of the mangrove overhang such that the total area surveyed is still 100m2. In this case, some of the survey may necessarily fall on seagrass habitat. This is allowed as the mangrove habitat is defined as a transition zone habitat. The transect should take 15 minutes regardless of habitat type or number of animals present. This allows more mobile animals the opportunity to swim through the transect, and standardizes the samples collected to allow for comparisons.

dive photo

Data are collected on the following:

  1. Logistic information - diver name, dive buddy, date, time of survey, site code, transect bearing.
  2. Taxa presence - as the tape roles out at a relatively constant speed, the diver records all fish species to the lowest taxonomic level possible that come within 2m of either side of the transect. To decrease the total time spent writing, four letter codes are used that consist of the first two letters of the genus name followed by the first two letters of the species name. In the rare case that two species have the same four-letter code, letters are added to the species name until a difference occurs. If the fish can only be identified to the family or genus level then this is all that is recorded. If the fish cannot be identified to the family level then no entry is necessary.
  3. Abundance & size - the number of individuals per species is tallied in 5cm size class increments up to 35cm using visual estimation of fork length. If an individual is greater than 35cm, then an estimate of the actual fork length is recorded.
  4. Photos - individuals too difficult to identify or unique in some manner may be photographed for later clarification.

II. Point—count Fish Census: Bohnsack—Bannerot (1986)

The point-count diver records all fish species seen within a vertical cylinder of radius 7.5m that extends from the substrate to the surface of the water. Using a random number of fin kicks and a randomly chosen compass heading the center of the cylinder is positioned to the side or behind the tape rolled out by the belt-transect diver such that there is no overlap between the two surveys. The point-count diver also makes no attempt to avoid features within a habitat (see above). While staying at the center point of the cylinder the point-count diver slowly rotates in a circle. All species seen within the cylinder during a 5 minute period are recorded using the 4 letter codes described above. After the 5 minutes are up, the diver records the number and size (in 5cm size class increments) of individuals seen for each species identified. This is done during one full rotation per species in order from the bottom of the list to the top. Only schools of fishes unlikely to remain in the cylinder past the first 5 minutes are enumerated and measured during the initial time period. In the instance where species observed in the initial period are no longer seen in the area the count and measurement are done by memory. After completion of the point-count survey, the point-count diver and the belt transect diver conduct habitat rugosity measurements (see below).

III. Habitat Composition Census

Once on site, divers are deployed and maintain contact with each other throughout the entire census. One diver is responsible for collecting data on the benthic composition. The habitat diver follows the belt-transect diver and records data on small-scale benthic habitat composition and structure along the 25m transect. The habitat diver places a 1m2 quadrat divided into 100 (10 x 10cm) smaller squares (1 square equals 1 percent cover) at 5 separate positions. Each position is randomly chosen before entering the water such that there is one random point within every 5m interval along the transect. Percent cover is obtained as if looking at the quadrat in a two dimensional plane (i.e. a photograph) vs. three dimensions where percent cover could add up to greater than 100%.

Data are collected on the following:

  1. Logistic information — diver name, dive buddy, date, time of survey, site code, and meter numbers at which the quadrat is placed.
  2. Habitat structure — to characterize the benthic habitats of the dive site, the habitat diver first categorizes the habitat structure of the site: hard, soft or mangrove.
  3. Proximity of structure — on seagrass and sand sites, the habitat diver records the absence or presence of reef or hard structure within 3m of the belt transect. A score of zero (0) indicates that no reef or other hard structure is present; one (1) indicates that a reef or hard structure smaller than 4m2 is present; and (2) indicates that a reef or hard structure larger than 4m2 is present within 3m of the diver. The point-count diver also uses this scoring system to record the absence, presence, and proximity of reef or hard structures within their cylinder.
  4. Transect depth profile — the depth at each quadrat position. Depth is measured with a digital depth gauge to the nearest 1ft.
  5. Abiotic footprint — defined as the percent cover (to the nearest 1 percent) of sand, rubble, hard bottom, and fine sediments within a 1m2 quadrat. Rubble refers to rocks and coral fragments that are moveable; immovable rocks are considered hard bottom. The percent cover given as a part of the abiotic footprint should total 100 percent. In a seagrass area for example, despite the fact that seagrass may provide 50 percent cover the underlying substrate is 100 percent sand so this is what is recorded. To estimate percent cover, the habitat diver first positions the quadrat at the chosen meter mark along the transect tape. If the meter mark is an odd number, then the quadrat is placed on left side of the tape; if even, it is placed on the right. Next, the habitat diver lays the quadrat along the substrate (regardless of the slope) and estimates percent cover based on a two-dimensional (planar) view (e.g. if bottom is sloping, the quadrat is not held horizontally). Also, the diver should try to use the same planar view for all estimates of percent cover. The habitat diver then estimates, for each quadrat, the height (in centimeters) of the hardbottom from the substrate to get a sense of bottom relief. Note: Height is collected for all hardbottom substrates, excluding rubble; height is not collected for softbottom substrate.
  6. Biotic footprint — defined as the percent cover (to the nearest 0.1 percent) of algae, seagrass, live corals, sponges, gorgonians, and other biota (tunicates, anemones, zooanthids, and hydroids) within a 1m2 quadrat. The remaining cover is recorded as bare substrate to bring the total to 100 percent. Again, the diver must use a planar view to estimate percent cover of the biota. Seagrasses and gorgonians should not be stacked upright. For example, e.g., if a single seagrass blade crosses 10 squares, then total seagrass coverage should be the sum of the area taken up by that blade in all 10 squares instead of the area covered if the blade was held upright. Species covering less than 0.1 percent of the area are not recorded. Taxa are identified to the following levels: stony coral-species, algae-morphological group (macro, turf, crustose, rhodolith, filamentous, cyanobacteria), sponge-morphological group, and gorgonians-morphological group. When estimating percent cover, it is important to realize there is a balance between precision and time. For stony corals, the approximate area covered by living coral tissue is recorded. Coral skeleton (without living tissue) is usually categorized as turf algae or uncolonized substrate. Data on the condition of coral colonies are also recorded. When coral is noticeably bleached, the percentage of bleached coral is estimated to the nearest 0.1 percent. Diseased/dead coral refers to coral skeleton that has recently lost living tissue because of disease or damage that is still visible, and has not yet been colonized by turf algae. Turf algae include a mix of short (less than 1cm high) algae that colonize dead coral substrate.
  7. Maximum canopy height — for each soft biota type (e.g., gorgonians, seagrass, algae), structure is recorded to the nearest 10cm.
  8. Number of individuals — for sponges, gorgonians and "other" biota type (non-encrusting anemones and non-encrusting hydroids) the number of individuals at the quadrat level is recorded.
  9. Rugosity — measured by placing a 6-m chain at two randomly selected positions along the 25m belt transect. The chain is placed such that it follows the substrate's relief along the centerline of the belt transect. Two divers measure the straight-line horizontal distance covered by the chain. The chain is placed on top of any hard substrate encountered, but not on top of soft corals or sponges since we are measuring hard bottom rugosity. Data on rugosity are collected for reef sites only. Rugosity measurements typically are made by the point-count and belt-transect divers while awaiting the completion of other benthic habitat measurements by the habitat diver. Upon completion of the dive, the rugosity data are transferred from the fish data sheet to the habitat data sheet by the habitat diver.
  10. conch diagramAbundance and maturity of queen conchs (Strombus gigas) — a count of the total number of conch encountered within the 25m x 4m belt transect are enumerated. The maturity of each conch is determined by the presence or absence of a flared lip and labeled mature or immature, respectively.
    If conch abundance is counted by a fish diver, the data are then reported to habitat diver. The decision of who will collect conch data should be made prior to entering the water.
  11. Abundance of spiny lobsters (Panilaurus argus) — a count of the total number of lobsters encountered within the 25m x 4m belt transect. No measurements are taken. If lobster abundance is counted by a fish diver, the data are then reported to habitat diver. The decision of who will collect lobster data should be made prior to entering the water
  12. Abundance of long-spined urchin (Diadema antillarium) — a count of the total number of urchins encountered within the 25m x 4m belt transect. No measurements are taken. If urchin abundance is counted by a fish diver, the data are then reported to habitat diver. The decision of who will collect urchin data should be made prior to entering the water.
  13. Marine debris — type of marine debris within the transect is noted. The size of the marine debris and the area of habitat that it is affecting is also recorded along with a note identifying any flora or fauna that has colonized it.

NOTE: If rugosity, conch, lobster, or urchin data are collected by a fish diver, data must be transferred to the habitat data sheet. The habitat diver is responsible for transferring the data to their data sheet; however, the fish diver should assist the habitat diver with this task by reporting the data once the dive concludes.

IV. Rapid Habitat Assessment (RHA)

This habitat survey is modified from a detailed (microscale) habitat assessment used to characterize nearshore habitats and is utilized to characterize areas within and nearby the Virgin Islands Coral Reef National Monument (VICR) boundaries. The VICR consists of two geographic locations: the mid-shelf ridge and Coral Bay. Site selection begins by stratifying NOAA’s nearshore benthic habitat maps into predetermined habitat strata and monument boundaries. ArcGIS is then employed to randomly select sites within the hardbottom strata inside and outside the boundaries of the two VICR locations. Using a handheld GPS unit, the boat captain navigates to the previously selected sites. Once on site, two divers are deployed, a fish transect diver and a fish point-count/habitat diver. The habitat measurements are collected by the point-count diver for the area within his/her cylinder and those measurements are assumed representative of the habitat along the transect.

Data are collected on the following:

  1. Dive logistics — name of the diver, station ID, date, and the start time of the survey.
  2. Habitat structure — the dive site is categorized based on the hierarchical classification used to produce the benthic habitat maps.
  3. Depth — minimum and maximum depth of the survey area, to provide an estimate of bottom slope.
  4. Rugosity (low, medium, or high) — based on the height of the tallest hardbottom structure.
  5. Abiotic footprint — an estimate of % cover (within 5%) of hardbottom, sand, and rubble in the 15-m cylinder. The sum of % cover in the abiotic footprint must total 100%.
  6. Biotic footprint — an estimate of the % cover (within 1%) of live coral, gorgonians, sponges, macro algae, and uncolonized substrate in the 15-m cylinder. The sum of % cover (including uncolonized substrate) in the biotic footprint must total 100%.
Photography — the point count or habitat diver will take at least two photos in different directions at each stie to maintain an anecdotal and permanent visual description of the sites that were sampled. Proper care and maintance is neccessary for all camera and camera housings. It is important to maintain the cameras and housings before, after, and in between dives.

Figure 1. Table of measured variables sampled per biotic cover group.
= data collected; o = data not collected.

Biotic Cover Group Variable
% cover % height # individuals
Corals (live, diseased/ dead, & bleached) x o o
Macro algae x x o
Seagrass x x o
Gorgonians x x x
Sponges x x x
Anemones & Hydroids x o x
Tunicates & Zooanthids x o o
Lobster, conch, Diadema o o x

Changes in Data Collected for Benthic Composition Over Time