Coral reef biota including stony corals, sponges, gorgonians, fish, benthic macroinvertebrates and foraminifera were surveyed in coastal waters near La Parguera, in southwestern Puerto Rico. The goal was to evaluate sensitivity of coral reef biological indicators to human disturbance. Proxies for human disturbance were measured as distance to town (DTT) and rankings of a low-level sediment contamination gradient analyzed from a previous study. Contaminant rank and DTT showed that percent mud, stony coral taxa richness, reef rugosity, and numbers of invertebrates and sponges were higher at sites closer to human disturbance, but a foraminiferal assemblage index was significantly lower at sites with higher proxies for human disturbance. Fish indicators showed no significant relationships with human activity, but associations between fish community measures and certain measures of stony corals, gorgonians and sponges were found. Contrasting responses between foraminifera and reef organisms may be due to greater exposure and sensitivity of foraminifera to sediment contaminants.

States may protect coral reefs using biological water quality standards outlined by the Clean Water Act. This requires biological assessments with indicators sensitive to human disturbance and regional, probability-based survey designs. Stony coral condition was characterized on a regional scale for the first time in the nearshore waters of the US Virgin Islands (USVI). Coral composition, abundance, size, and health were assessed at 66 stations in the St. Croix region in fall 2007 and at 63 stations in the St. Thomas and St. John region in winter 2009. Indicators were chosen for their sensitivity to human disturbance. Both surveys were probability-based (random) designs with station locations preselected from areas covered by hardbottom and coral reef substrate. Taxa richness was as high as 21 species but more than half the area of both regions exhibited taxa richness of <10 species in the 25 m2 transect area. Coral density was as high as 5 colonies m−2 but more than half the area of both regions had <2 colonies m−2. Both regions showed similar dominant species based on frequency of occurrence and relative abundance. Because of large colony sizes, Montastrea annularis provided more total surface area and live surface area than more abundant species. The surveys establish baseline regional conditions and provide a foundation for long-term regional monitoring envisioned by the USVI Department of Planning and Natural Resources. The probabilistic sampling design assures the data can be used in Clean Water Act reporting.

A rapid method to estimate the three-dimensional (3D) surface area (SA) of marine gorgonians and sponges from field measurements of colony height, diameter, and morphology was developed as an indicator of habitat availability for fish and invertebrates. Colony characteristics for sponges and gorgonians were compiled from field measurements, expert judgment, and taxonomic literature, and employed to generate 3D images using computer-aided design software. The images were used to test various statistical models and geometric surrogates that best estimated SA using only height and diameter measurements. A morphological classification system was devised using shapes and relative proportions of sponges and gorgonians which are commonly found in shallow waters (< 25 m depth) of the Central Western Atlantic Ocean. Regression models (linear, quadratic, or cubic) were found to be more robust than geometric surrogates, exhibiting greater accuracy at range extremes. Statistical models explained over 90% of the variation in SA and forecast errors of less than 20%. The best models for estimating SA are presented for eight sponge and nine gorgonian morphologies. Application of these methods with existing estimators for stony corals SA can be used as an indicator of structural habitat availability, which is an important ecosystem service of coral reefs.

Thalassia testudinum belowground biomass weights, leaf weights, leaf growth rates, areal shoot densities (m-2), and leaf C:N:P ratios were compared to a set of biogeochemical parameters to gain information on seagrass-sediment interactions that may influence seagrass growth. Data were compiled from three surveys conducted in Santa Rosa Sound, located in northwest Florida, at three different meadows in sequential years. Biomass measurements and leaf growth rates decreased between stations along transects from shallow to deeper water. Belowground biomass weights decreased and leaf C:P ratios increased with temperature reflecting a seasonal growth pattern. The T. testudinum parameters were highly correlated with each other. Sulfate reduction rates (at times exceeding 1000 nmol ml-1 day-1) were among the highest recorded for seagrass beds with temperature accounting for 79% of the variation. Even though sulfate reduction rates were high, total Fe:reduced S ratios indicated sufficient Fe to account for all reduced S as pyrite. Sediment Fe, C, N, and organic P concentrations increased with sediment depth, whereas inorganic P decreased with depth, suggesting burial of organic P and root uptake of inorganic P. Leaf C:N:P ratios indicated P-limited growth for two surveys. NH4 + was detected in water above the sediment surface during some surveys demonstrating T. testudinum meadows at times may serve as sources of inorganic N to the water column. Plant parameters correlated with concentrations of sediment organic C and N, Fe, S, and porewater NH4 +. These results highlight the importance of the organic matter and Fe contents of sediments to seagrass growth.

The decline of coral reefs in the Caribbean over the last 40 years has been attributed to multiple chronic stressors and episodic large-scale disturbances. This study assessed the resilience of coral communities in two different regions of the Florida Keys reef system between 1998 and 2002 following hurricane impacts and coral bleaching in 1998. Resilience was assessed from changes in coral abundance, diversity, disease, and bleaching prevalence in reefs near the remote off-shore islands of the Dry Tortugas compared to reefs near Key West, a center of high population density and anthropogenic influences. During the first assessment in spring 1998, Key West and Dry Tortugas coral communities had similar abundance, species diversity, and disease prevalence. Bleaching and disease significantly increased in all reef areas during the summer 1998 El Niño event, with Key West reefs exhibiting higher bleaching and disease prevalence and severity compared to Dry Tortugas. Acroporids and total coral abundance significantly declined in both regions during 1998 following mass-coral bleaching and hurricane impact, but remained reduced only on Key West reefs during the 5-year assessment. These results provide additional evidence that coral reef systems distant from anthropogenic influences may have greater resilience to large-scale disturbances.

Colonies of reef-building stony corals at 57 stations around St. Croix, US Virgin Islands were characterized by species, size and percentage of living tissue. Taxonomic, biological and physical indicators of coral condition were derived from these measurements and assessed for their response to gradients of human disturbance-a requirement for indicators used in regulatory assessments under authority of the Clean Water Act. At the most intensely disturbed location, five of eight primary indicators were highly correlated with distance from the source of disturbance: Coral taxa richness, average colony size, the coefficient of variation of colony size, total topographic coral surface area, and live coral surface area. An additional set of exploratory indicators related to rarity, reproductive and spawning mode and taxonomic identity were also screened. The primary indicators demonstrated sufficient precision to detect levels of change that would be applicable in a regional-scale regulatory program.

Coral reefs provide shoreline protection, biological diversity, fishery harvests, and tourism, all values that stem from the physically-complex coral infrastructure. Stony corals (scleractinians) construct and maintain the reef through deposition of calcium carbonate. Therefore, assessment of coral reefs requires at least some measurement endpoints that reflect the biological and physical condition of stony corals. Most monitoring programs portray coral quantity as live coral cover, which is the two-dimensional proportion of coral surface to sea floor viewed from above (planar view). The absence of the third dimension, however, limits our ability to characterize coral reef value, physiology, health and sustainability. A three-dimensional (3D) approach more realistically characterizes coral structure available as community habitat and, when combined with estimates of live coral tissue, quantifies the amount of living coral available for photosynthesis, growth and reproduction. A rapid coral survey procedure that coupled 3D coral quantification with more traditional survey measurements was developed and tested in the field. The survey procedure relied on only three underwater observations – species identification, colony size, and proportion of live tissue – made on each colony in the transect. These observations generated a variety of metrics, including several based on 3D colony surface area, that are relevant to reef management.

Fish were collected by otter trawl at 367 sites from 119 coastal water bodies in the northern Gulf of Mexico, ranging from north-central Florida to the Rio Grande, Texas, during the summer months of 1992-1994. The fish were identified and enumerated, and tissue contaminants (in fillets), and external abnormalities (body, buccal, branchial, and ocular) were determined. Results were compared for sites east and weft of the Mississippi River, within the Mississippi River, seven estuarine categories, and over 3 years. Approximately 31,000 individual fish were captured, representing 100 genera and 141 species. Thirteen species comprised 91 % of the total abundance; abundances of 128 species were 1% or less. Pinfish Lagodon rhomboides, Atlantic croaker Micropogonias undulatus, Gulf menhaden Brevoortia patronus, and bay anchovy Anchoa mitchilli were the more dominant species. Fourteen species were collected from at least 10% of the sites; 85 species were captured at no more than 1% of the sites. Atlantic croakers and hardhead catfish Ariopsis felis were collected more frequently (>50% of sites). Indices of community structure from the full data set ranged as follows: 2.8 for the Shannon-Wiener index, 0.90 for Simpson's index, and 0.56 for Pielou's evenness index. Chemical contaminants (predominantly total mercury and polychlorinated biphenyls [PCBs]) exceeded federal risk-based consumption guidelines in 2.7% of fillets from four species. External abnormalities occurred on 17 species and approximately 1% of the total number of fish examined. Community structural properties varied temporally across years and spatially over estuarine categories and between areas east and west of the Mississippi River. Four distinct assemblages were identified by cluster analysis of species abundance. Cluster membership was associated with salinity, depth, dissolved oxygen, water clarity, and geographic area.

Baseline information on the chemical and biological quality of sediments is provided for six coastal locations in the northern Gulf of Mexico, which were considered possible candidates for regional reference areas. Chemical quality, toxicity and benthic community composition were determined for sediments collected three times from each of 12 sites during an approximate one-year period. Potential contaminants in the usually sand-dominated sediments exceeded individual threshold effects level guidelines proposed for Florida coastal areas in approximately 31% of the samples collected from 8 of 12 sites. No probable effects level guidelines were exceeded. Acute toxicity occurred in 16% or less of the sediment samples and no significant chronic toxicity was observed to the infaunal amphipod, Leptocheirus plumulosus. Approximately, 11% and 17% of the sediments were classified as poor or marginal, based on low benthic taxa abundance and diversity index values, respectively. Sediment quality at many sites was less degraded than that for nearby coastal areas receiving point and non-point source contaminants, which suggests their suitability to serve as reference sediments although further confirmation is recommended. In a broader context, the results of this survey reflect the complexity infield verification of reference conditions for near-coastal sediments. This is attributable largely to the natural variability in their physical, biological, and chemical characteristics and to the lack of biocriteria for benthic macro and meiofauna.

Contaminant fate in coastal areas impacted by golf course runoff is not well understood. This report summarizes trace metal, pesticide and PCB residues for colonized periphyton, Ruppia maritima (widgeon grass), Callinectes sapidus Rathbun (blue crabs) and Crassostrea virginica Gemlin (Eastern oyster) collected from areas adjacent to a Florida golf course complex which receive runoff containing reclaimed municipal wastewater. Concentrations of 19 chlorinated pesticides and 18 PCB congeners were usually below detection in the biota. In contrast, 8 trace metals were commonly detected although concentrations were not usually significantly different for biota collected from reference and non-reference coastal areas. Residue concentrations in decreasing order were typically: zinc, arsenic, copper, chromium, lead, nickel, cadmium and mercury. Mean BCF values for the eight trace metals ranged between 160-57000 (periphyton), 79-11033 (R. maritima), 87-162625 (C. virginica) and 12-9800 (C. sapidus). Most trace metal residues in periphyton colonized adjacent to the golf complex, were either similar to or significantly less than those reported for periphyton colonized in nearby coastal areas impacted by urban stormwater runoff and treated municipal and industrial wastewater discharges. Consequently, the recreational complex does not appear to be a major source of bioavailable contaminants locally nor in the immediate watershed based on results for the selected biota.

A shading experiment was conducted over a growing season to measure the effects of light reduction on Vallisneria americana in Perdido Bay on the Florida–Alabama border and to determine the response of heterotrophic bacteria in the rhizosphere. Plants subjected to 92% light reduction showed the most pronounced effects in chlorophyll a concentration, above- and below-ground biomass, and leaf dimensions. These results further suggested that the V. americana life cycle, as exhibited in temperate waters, was impaired. Heterotrophic bacteria were enumerated and identified (i) from the roots and sediments of fully illuminated plants and from unvegetated sediments at three intervals and (ii) from the roots of plants that have been subjected to 92% light reduction for 3 months. Up to two orders of magnitude greater numbers of bacteria were enumerated from root samples than sediment samples on a dry weight basis. Bacteria enumerated from the roots of plants subjected to light reduction (1.3±1.1×108 CFU g−1) were significantly higher than numbers of bacteria enumerated from the roots of fully illuminated plants (4.8±1.8×107 g−1 in the summer) or sediment samples (1.4±0.03×106 g−1). This suggests the roots of seagrasses stressed by light reduction provided more nutrients for bacterial growth. Higher percentages of Gram-negative bacteria were isolated from roots (up to 85% in the fall) than sediments (0–15%). Examination of isolates for traits characteristic of rhizosphere bacteria (siderophore production, formation of the phytohormone indole-3-acetic acid, and antifungal activity) did not show a clear distinction between root-associated and sediment isolates. Taxonomic identifications of root-associated bacteria based on MIDI analysis of fatty acid methyl esters were consistent with bacteria known to be associated with other plants or found at oxic–anoxic interfaces. In addition, the bacterial identifications showed most species were associated with only roots or only sediments. These results support studies suggesting seagrass rhizospheres harbor distinct bacterial communities.

The objective of this study was to determine inorganic and organic contaminant concentrations in edible tissue of fish collected from eight coastal areas receiving wastewater discharges and from two reference locations. Trace metal residues were statistically similar regardless of the collection site. Zinc (100% detection in all samples), total mercury (100%), total arsenic (92%), copper (92%), and selenium (88%) were the more commonly detected trace metals. Mercury concentrations exceeded the Florida health-based standard of 0.5 μg/g for limited fish consumption in 30% of the total samples and averaged 0.40 (±1 S.D.=0.22, range≤0.08 to 0.85) μg/g wet weight. The average total PAH concentrations were 1.79 (±1.60) ng/g (reference areas) and 2.17 (±3.29) ng/g (wastewater-impacted areas). Pyrene was detected most frequently (63% of the total samples) and averaged 0.74 (±0.35) ng/g wet wt. The average total PCB concentrations were 4.8 (±7.1) ng/g (reference areas) and 31.6 (±31.3) ng/g (wastewater-impacted areas) Concentrations of dieldrin and cis-chlordane were approximately eight times greater, respectively, in fish collected from wastewater receiving waters, whereas total DDT and total pesticide concentrations were not elevated in the same areas. Concentrations of total PCBs and all chlorinated pesticides were below US health-based standards. The lack of a published reference data base for fish tissue quality in near-coastal areas of the Gulf of Mexico restricts an assessment of the environmental significance of results from this and similar studies investigating the fate of point source contaminants.

The objective of this study was to provide baseline information on the effects of a golf course complex on water quality, colonized periphyton, and seagrass meadows in adjacent freshwater, near-coastal, and wetland areas. The chemical and biological impacts of the recreational facility, which uses reclaimed municipal wastewater for irrigation, were limited usually to near-field areas and decreased seaward during the 2-year study. Concentrations of chromium, copper, and organochlorine pesticides were below detection in surface water, whereas mercury, lead, arsenic, and atrazine commonly occurred at all locations. Only mercury and lead exceeded water quality criteria. Concentrations of nutrients and chlorophyll a were greater in fairway ponds and some adjacent coastal areas relative to reference locations and Florida estuaries. Periphyton ash free dry weight and pigment concentrations statistically differed but not between reference and non-reference coastal areas. Biomass of Thalassia testudinum (turtle grass) was approximately 43% less in a meadow located adjacent to the golf complex (P < 0.05). The results of the study suggest that the effects of coastal golf courses on water quality may be primarily localized and limited to peripheral near-coastal areas. However, this preliminary conclusion needs additional supporting data.

Water and sediment quality in threetidal bayous located near Pensacola, Florida, wereassessed during 1993–1995. The primary objective wasto determine the environmental condition of therelatively small urban bayous by comparing thechemical quality of the sediments and surface waterwith published guidelines and criteria developed toprotect marine life. Surface water concentrations ofmost potential toxicants such as heavy metals,organochloride pesticides, PAHs and PCBs were usuallybelow method detection limits. The major exception tothis trend was for copper which consistently exceededFlorida and National acute and chronic water qualitycriteria. Nickel, cadmium and chromium intermittentlyexceeded these criteria. Sediment contamination wassite-specific and chemically diverse. Theconcentrations of as many as 17 compounds exceededproposed Florida sediment quality assessmentguidelines indicating the potential for adversebiological effects. Nutrient concentrations, with oneexception, were below average levels found in otherFlorida estuaries. Seasonal variation in contaminantconcentrations for sediment collected from the samesampling station was less than an order of magnitude. The differences in the concentrations of the sameanalytes as measured for the multiple samplingstations located within the same bayou varied 1 to 2orders of magnitude and over 2 orders of magnitude forthe 20 sampling stations located in the three bayous. A within-bayou sediment contaminant gradient wasevident; sediment quality generally improved seaward.

Periphyton colonization and sediment bioassessment were used ina survey to compare the relative environmental condition ofsampling sites located in Florida Bay and four peripheral sloughareas during the summer of 1995. Periphyton biomass, pigmentcontent, tissue quality and community composition weredetermined. In addition, benthic community composition and thetoxicities of whole sediments and associated pore waters weredetermined for two species of rooted macrophytes, an epibenthicinvertebrate and bioluminescent bacteria. Several locational differences were observed for the response parameters.Periphyton biomass was significantly greater in the Taylor Riverand the least in Shell Creek (P < 0.05). Most sediments were notacutely toxic to mysid shrimp nor phytotoxic. However, sedimentsfrom the Taylor River were more phytostimulatory than others (P< 0.05). Contaminant bioresidues were similar at most sites,however, mercury, chromium and nickel concentrations weregreater for periphyton colonized in the Taylor River and TroutCreek areas. Structural characteristics of the periphytic algalcommunity usually were statistically similar but a consistenttrend of lower density and diversity was evident for ShellCreek. The benthic community was the least diverse and dense inthe Canal C-111. The results of this study provide an initialindication of differences in the role of several slough areas aspossible sources of bioavailable contaminants to Florida Baywhich warrants additional investigation.

Recently, the distribution and changes in submerged aquatic vegetation (SAY) in the Escambia-Pensacola Bay System in northeastern Florida were monitored by two techniques. One technique used divers to measure changes in the deepwater margin of beds and provided horizontal growth measurements to the nearest centimeter, the other used a differential global positioning system (DGPS) on a small boat to map the perimeter of SAY beds in shallow water. Current distribution of SAY in Escambia Bay shows that most of the SAY losses that occurred during the 1950s to 1970s have been recovered. In Santa Rosa Sound and Pensacola Bay, SAY showed significant increased growth with horizontal growth rates of some beds averaging more than 50 em over the past year. In Big Lagoon, however, SAY has declined an average of 10 em in horizontal coverage along the deepwater edge. Water quality and photosynthetically active radiation light measurements from the Escambia-Pensacola Bay System suggest that increased light availability was associated with the increased seagrass coverage in Santa Rosa Sound and Pensacola Bay, and elevated nutrient concentrations were associated with the seagrass declines in Big Lagoon.