The basis for this work was the nearshore benthic habitats maps (less than 100 ft depth) created by NOAA's Biogeography Program in 2001 and NOS' bathymetry models. Using ArcView GIS software, the digitized habitat maps were stratified to select sampling stations. Sites were randomly selected within strata to ensure coverage of the entire study region. The habitat stratification was divided into three major habitat types: hardbottom which includes reef, pavement, etc. inside STEER; softbottom which consists of sand and seagrass, and mangrove. In addition, two harbottom areas outside STEER of interest to STEERs Core Team were included as a separate stratum. Using standardized protocols of NOAAs Coral Reef Ecosystem Monitoring Project, the fish and benthic habitat survey was conducted by two scientific divers. During each dive one diver quantified the species and size of fish within a 25 x 4 m transect while a second diver characterized the habitat and invertebrate community.
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 each quadrat position. 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 one side of the transect tape, alternating sides of the transect for subsequent quadrats. 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 cm) 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 each quadrat position. 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, 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 entire colony is considered affected and is recorded to the nearest 0.1 percent. Coral colonies are reported as entirely bleached if they contain any portion of white, blotchy, mottled, or pale tissue. This protocol assumes stress throughout the colony and estimates maximum bleaching impact. 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 1cm at the quadrat level.
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) Abundance and maturity of queen conchs (Eustrombus gigas) - a count of the total number of conch encountered within the 25 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 the habitat diver. The decision of who will collect conch data should be made prior to entering the water.
11) Abundance of spiny lobsters (Panulirus argus) - a count of the total number of lobsters encountered within the 25 x 4m belt transect. No measurements are taken. If lobster abundance is counted by a fish diver, the data are then reported to the 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 antillarum) - a count of the total number of urchins encountered within the 25 x 4m belt transect. No measurements are taken. If urchin abundance is counted by a fish diver, the data are then reported to the habitat diver. The decision of who will collect urchin data should be made prior to entering the water.
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.
13) Marine debris - type of marine debris within the transect is noted. The size of the marine debris and the area of affected habitat is also recorded along with a note identifying any flora or fauna that has colonized the debris.
14) Acropora presence - mark if A. palmata or A. cervicornis are seen along the transect or at the site.
15) Photography - the point count or habitat diver will take at least two photos in different directions at each site to maintain an anecdotal and permanent visual description of the sites that were sampled. Proper care and maintenance is necessary for all camera and camera housings. It is important to maintain the cameras and housings before, after and in between dives.
Data Caveats: Due to water quality concerns and low visibility, a portion of Mangrove Lagoon and Benner Bay were excluded from the study area. In addition, extra precautions were taken in the area where the ferries traverse.