Effects of terrigenous sedimentation are considered a serious threat to Puerto Rico's coral reefs. This study assesses: 1) the composition of sediments accumulating at reef sites on the southwestern shelf of Puerto Rico; 2) the spatial extent to which terrigenous materials are reaching these reefs; and 3) the spatial and temporal variability of sediment composition, grain size and trap collection rates. Sediment traps were deployed at 9 sites from inner shelf to shelf edge. Analyses of total sediment weight (April 2006 – April 2007) show a similar temporal pattern at all sites with June and August having the highest accumulation rates. In general, there is a decrease in trap accumulation rate with depth. Carbon composition analyses indicate that samples consist primarily of calcium carbonate with lesser amounts of terrigenous and organic material, and a slightly higher percentage of terrigenous material in the <63 µm fraction. At a given site, the percentage of terrigenous material is fairly constant regardless of trap collection rate, suggesting that observed changes in accumulation rates are due to resuspension of existing material rather than an influx of new terrigenous material. These results, illustrate that in some reef systems, resuspension of existing bottom sediments is as important as the influx of new terrigenous material.

Mixed siliciclastic-carbonate systems are globally distributed throughout the tropics, but have received limited research attention on active sedimentation. A detailed examination of sedimentation near La Parguera, Puerto Rico has been conducted to better understand this mixed system on the border of the Caribbean Sea, along the southwest coast of the island. This study includes an assessment of the sediment composition and texture of material accumulating on the La Parguera seabed, as well as an examination of excess ²¹⁰Pb-activity profiles and accumulation rates. Variations in grain-size distribution and carbonate and loss-on-ignition (LOI) percentages are examined on the shelf. More specifically, an increase in carbonate percentage and a decrease in the LOI fraction in the seaward direction are evident. Excess ²¹⁰Pb-activity profiles display steady-state and non-steady-state profiles. Steady-state profiles are most common and display a range of thicknesses in surface-mixed layers (3 - >20 cm). Non-steady-state profiles are observed in some nearshore settings, reflecting episodic deposition or human influence. Greatest sediment accumulation rates are generally found close to shore, where maximum rates approach 0.5 cm y^-1. Sediment accumulation rates in more seaward reef areas are approximately 0.2 cm y^-1. Mass accumulation rates calculated from the composition and accumulation rate data indicate there is a seaward decrease in terrestrial (non-carbonate and LOI-free) sediment flux to the seabed. Fluxes of terrestrial sediment in nearshore areas are typically several times higher (>0.05 vs. 0.01 g cm^-2 y^-1). These trends in composition and mass accumulation reflect sediment supply and dispersal from terrestrial and marine sources along with the reduced wave climate from reef sheltering. A preliminary sediment budget suggests the majority (61%) of terrestrial sediment supplied to the shelf is stored locally. Sediment accumulating on the shelf is principally carbonate (85%) and is assumed to be marinederived. Terrestrial (12%) and LOI (3%) material represent considerably smaller, but significant constituents of the sediment stored. Collectively, data suggest terrestrial sedimentation is a lesser, but increasing sedimentary component of the La Parguera mixed siliciclastic-carbonate setting.

Baseline information on the water quality status of coral reefs and associated habitats of La Parguera, southwestern PR, is presented. Measurements of temperature, salinity, chlorophyll a, turbidity, fluorescence of dissolved organic matter, bacterial abundance and productivity, bacteriophytoplankton, sedimentation and stable isotopes of particulate organic matter were made at various stations within the area from 2003 through 2005. Significant daily fluctuations were observed at all stations and seasonal changes indicate inputs of materials from terrestrial sources even at the shelf edge. The δ¹³C data indicates low inputs from terrestrial particles (min = -18 ‰ vs. PDB) while variations of dissolved organic matter fluorescence suggest periodic inputs of terrestrially derived matter and nutrients throughout the shelf, though most notable towards the coast. Chlorophyll a (mostly > 0.5µg.l^-1), bacteria (ca. 1 ×10⁶ cells.ml^-1) and bacteriophytoplankton (72-122 ×10³ cell.ml^-1) indicate the presence of significant nutrient inputs while particle δ¹⁵N shows minimum to moderate enrichment from anthropogenic sources (max = 3.5 ‰ vs. air). Sedimentation rates were mostly <100 g.m^-2.d^-1, being higher during stormy conditions. Significant co-variation between turbidity and sedimentation was observed to be useful for modeling sedimentation patterns. Higher levels of the different water quality indictors were observed closer to the coast.

A survey was conducted to investigate possible presence of an inshore to shelf edge gradient in % nitrogen (%N) and stable nitrogen isotope ratio (δ¹⁵N; ‰ vs. air) in tissues of the rhodophyte Acanthophora spicifera and the ocrophytes Lobophora variegata and Dictyota bartayresiana in coastal waters of La Parguera, southwest Puerto Rico. Average %N (1.26 ± 0.08 SD to 3.25 ± 0.10) and δ¹⁵N (2.06 ± 0.04 to 8.16 ± 0.14‰) in Acanthophora spicifera was highly variable along the shoreline. The highest inshore values of δ¹⁵N occurred at two stations influenced by secondary sewage input and a bird rookery and lower values (0.81 ± 0.06‰) were observed at mid-shelf locations. Dictyota bartayresiana and L. variegata did not display clear trends in %N across the insular shelf; however, δ¹⁵N for Dictyota bartayresiana was significantly higher inshore (3.48 ± 0.09‰) versus mid-shelf and shelf edge (0.00 ± 0.08‰) and δ¹⁵N for L. variegata was significantly higher at mid-shelf (2.13 ± 0.25‰) versus shelf edge locations (0.34 ± 0.24‰). These results indicate that anthropogenic effects on tissue nutrients are spatially distributed across the shelf, being higher near shore and not evident at the shelf edge.

Coral (Porites astreoides) from eight sites in southwest Puerto Rico were analyzed for approximately 150 chemical contaminants, to provide a preliminary characterization of environmental contamination in the corals, and assess the relationships between chemical contamination in corals and adjacent sediments. Overall, the concentration of PAHs (polycyclic aromatic hydrocarbons) and PCBs (polychlorinated biphenyls) detected in the limited number of coral samples collected were comparable to concentrations found in sediments. However, the concentration of a chemical contaminant (e.g., PAHs) in the corals at a site was often different from what was found in adjacent sediments. The level of PCBs and DDT (dichlorodiphenyltrichloroethane) in the corals appeared higher just outside of Guanica Bay, and there was some evidence of a downstream concentration gradient for these two contaminant classes. The trace elements copper and zinc were frequently detected in Porites astreoides, and the concentrations were usually comparable to those found in adjacent sediments. Chromium was an exception in that it was not detected in any of the coral samples analyzed, although it was detected in all of the sediment samples.

In the summer/fall of 2005, extensive coral bleaching on reefs in the US Virgin Islands (USVI) was associated with sea water temperatures exceeding 30°C. Almost all coral species bleached, including Acropora palmata, which bleached for the first time on record in the USVI. As water temperatures cooled, corals began to regain their normal coloration. However, a severe disease outbreak then occurred on deeper, non-acroporid reefs. The disease demonstrated signs consistent with white plague. Monitoring of coral cover along previously established long-term transects on several reefs in St. John and St. Croix was intensified. Data on bleaching and disease were collected before, during and after this bleaching/disease episode. Average coral cover declined by over 50%, from 21.4% to 10.3% at the long-term study sites, within one year of the onset of bleaching, declining further to 8.3% after two years. This loss of coral cover was greater than from all other stressors affecting the USVI reefs in preceding years, and no significant recovery is evident. Disease prevalence increased on bleached A. palmata colonies that were being monitored as well as on the colonies of other species on the deeper reefs. Bleached A. palmata colonies had more disease (primarily white pox and other un-described diseases) than unbleached colonies. The non-acroporid corals that bleached most severely suffered the highest mortality from disease. Although the research summarized in this paper is not conclusive, the results suggest that high water temperatures lead to bleaching, which weakens corals and makes them more vulnerable to diseases.

Temporal and spatial variability of prevalence of the fungal disease aspergillosis (ASP) affecting Gorgonia ventalina colonies was assessed at several reef sites in La Parguera, southwest Puerto Rico. During 2005 and 2006, all G. ventalina colonies were checked for signs of ASP twice a year, within permanent 20 m² (10×2m) band transects at each of six sites located in three reef zones. Overall, there was high variability in disease prevalence in both space and time (0–28%). The average prevalence of ASP increased significantly from 5.1 ± 9.5% in March 2005 to 14.4 ± 16.0% in September 2006. There was no consistent temporal trend in ASP prevalence affecting all reefs, but shelf-edge reefs had significantly lower prevalence than inner and/or mid-shelf reefs in all sampling periods. Higher disease prevalence found in shallower areas may be related to higher water temperatures in these habitats, and unseasonably high temperatures during the winter and spring of 2006 associated with the extensive bleaching event of 2005.

Most coral reefs in the wider Caribbean have been showing alarming signs of decline in recent years. Coral diseases and bleaching were monitored seasonally from 2003 to 2007 using the modified CARICOMP protocol with a stratified design to assess spatial and temporal variability in community level coral disease prevalence (proportion of affected colonies) at six reefs along an inshore-offshore gradient in La Parguera, southwest coast of Puerto Rico. Temperature loggers were deployed in each reef to assess co-variation between disease prevalence and virulence, and temperature. Virulence was assessed in Montastraea faveolata by tagging colonies, marking diseased edges, photographing and following them through time. Overall, all major reef-building species and other common reef groups were variously affected by disease and bleaching. Eleven diseases affected up to 42 species of scleractinian corals, 5 octocorals, 2 hydrocorals, 3 zoanthids, 2 sponges and 2 crustose coralline algae. Bleaching affected 52 species of corals, 22 octocorals, 3 hydrocorals, 2 zoanthids and 3 sponges. The prevalence of the diseases compromised coral health and varied significantly between seasons within years as well as among reefs within years and across years for each reef. White plague, yellow band and bleaching were the most prevalent and damaging diseases. Three white plague, two yellow band outbreaks and three bleaching events of different intensities were observed during the five years of study. Yellow band disease increased in prevalence (from 4 % to 30%) and virulence (0.8 ± 0.2 to 3.9 ± 1.4 cm/month) over 6 years, becoming one of the most important agents of coral mortality. Higher disease prevalence was consistently found at the mid-shelf and shelf-edge reefs than in reefs closest to the shoreline. The combination of white plague disease outbreaks, the intensive bleaching of 2005 and the chronic yellow band caused an average 53 % of live coral tissue loss in four years, the highest coral mortalities ever recorded in southwest Puerto Rico.

Examining the relationship between habitat characteristics and utilization patterns by herbivorous fishes on coral reefs will add to our understanding of the factors that influence the abundance and distribution of this important group. The abundances of parrotfishes (Scaridae) and surgeonfishes (Acanthuridae) on fore-reef habitats were sampled along an inshore-offshore gradient to provide for within reef and cross-shelf comparisons in relation to the environmental parameters of depth and topographic relief. Temporally replicated visual surveys were conducted along permanent belt transects (100m²) at three depth intervals (3, 10, 15 m) to obtain data on fish species density and lengths, which were used to calculate biomass. The roving herbivorous fish assemblage was dominated by three species of parrotfishes (Scarus iseri, Sparisoma aurofrenatum and S. viride) and three surgeonfishes (Acanthurus bahianus, A. chirurgus and A. coerulus). Overall the biomass of both families was highest at 3m compared to 10 or 15m (p<0.05). However, the relative decrease in biomass across depths for both families was greatest at inshore reefs where water transparency is lowest. The mean biomass for both families differed between inner and mid-shelf reefs at 10 and 15 m (p<0.05) but not at 3m. Fish biomass was correlated to reef topographic relief at 3m for parrotfishes (p<0.05) and at all three depth intervals for surgeonfishes (p<0.05). Overall patterns of herbivore biomass across the shelf reflect differences in light penetration, suggesting that fish may be responding to algal productivity. Thus, within fore-reef habitats along a cross-shelf gradient water transparency and topographic relief may interact to structure biomass patterns.

The objective of this study was to provide evidence supporting the contention that sediment transport (bedload) is a major environmental factor controlling the distribution of shallow-water gorgonian species. Gorgonians were surveyed annually from 2003–2008 in 3 replicated sets of transects at 2 shelf edge, 3 midshelf and 3 nearshore reefs on the southwest coast of Puerto Rico. Except for the shelf edge reefs, the transects were located in the fore reef terrace, break and base zones. A Reciprocal Averaging (RA) ordination analysis was used to identify the environmental factor underlying the distribution of gorgonian species. Substratum slope was used as a proxy of bedload levels to assess the overall RA results among and within reefs. Within reef RA scores decreased monotonically from the reef terrace to the slope to the base in all applicable cases. This pattern is consistent with sediment transport because increases in substratum slope from the terrace to the base of reefs should result in decreasing levels of bedload within reefs. RA scores were highly related to substratum slope (r²=0.79, p<0.01) supporting the premise that sediment transport controls the distribution of gorgonian species.

Percentage cover of coral reef associated algae increased significantly from 2003 to 2007 at two shelf edge sites in southwest Puerto Rico (42.8 % to 75.3% at Weinberg Reef and 67.4% to 81.8% at El Hoyo). While the increase was driven largely by increase in cover of Lobophora variegata, percent cover of the individual spatially dominant algal species was highly variable temporally. The variability was apparent even at the subquadrat level (0.0625m²) for which adjacent subquadrats demonstrated little concordance in species cover over subsequent sampling periods.

Juvenile coral survivorship (the proportion of juvenile colonies surviving from t₁ to t₂) was assessed by counting, photographing and mapping all juveniles found in 2003 within random permanent 0.25m² quadrats at four depth intervals at each of four inshore and mid-shelf reefs and at deeper habitats (>18m) in two shelf-edge reefs (N=96/reef) in La Parguera, southwest coast of Puerto Rico. Quadrats were resurveyed and photographed in 2005 to evaluate surviving juveniles, mortality and new recruits. Total number of juveniles dropped from 718 in 31 scleractinian species in 2003 to 396 in 28 species in 2005, an average juvenile survivorship of 54.8%. Mean juvenile density decreased from 1.2 (± 0.06) colonies/0.25 m² in 2003 to 0.7 (± 0.05) colonies/0.25 m² in 2005. Juvenile coral composition, relative abundances, survivorship and recruitment varied significantly across depth intervals within reefs and among reefs. Some species with high relative abundances in 2003 showed high survivorship in 2005 [Siderastrea siderea (28.3% and 65% respectively), Porites astreoides (15.1% and 55.6%), and Diploria strigosa (7.5% and 45.2%)]. Other taxa had relative low abundances but high survivorship [Montastraea cavernosa (4.6% and 66.7%) and Stephanocoenia intersepta (4.6% and 48.3%)]. Survivorship was significantly higher in deeper habitats at three of the four fringing reefs. Furthermore, the semi-exposed inshore, highly sedimented reefs, showed higher juvenile survivorship than the mid-shelf and shelf-edge reefs. There was no clear relationship between survivorship and reproductive mode (brooding vs. broadcast spawning) of sexual reproduction. Overall, only 78 new recruits were found in 2005.

Few studies have quantified the extent of nocturnal cross-habitat movements for fish, or the influence of habitat adjacencies on nutrient flows and trophodynamics. To investigate the patterns of nocturnal cross-boundary movements of fish and quantify trophic connectivity, fish were sampled at night with gillnets set along the boundaries between dominant habitat types (coral reef/seagrass and mangrove/ seagrass) in southwestern Puerto Rico. Fish movement across adjacent boundary patches were equivalent at both coral reefs and mangroves. Prey biomass transfer was greater from seagrass to coral reefs (0.016 kg/km) and from mangroves to seagrass (0.006 kg/km) but not statistically significant, indicating a balance of flow between adjacent habitats. Pelagic species (jacks, sharks, rays) accounted for 37% of prey biomass transport at coral reef/seagrass and 46% at mangrove/seagrass while grunts and snappers accounted for 7% and 15%, respectively. This study indicated that coral reefs and mangroves serve as a feeding area for a wide range of multi-habitat fish species. Crabs were the most frequent prey item in fish leaving coral reefs while molluscs were observed slightly more frequently than crabs in fish entering coral reefs. For most prey types, biomass exported from mangroves was greater than biomass imported. The information on direction of fish movement together with analysis of prey data provided strong evidence of ecological linkages between distinct adjacent habitat types and highlighted the need for greater inclusion of a mosaic of multiple habitats when attempting to understand ecosystem function including the spatial transfer of energy across the seascape.

Reef fish movements over short and long time frames have important consequences for identifying essential fish habitat, quantifying ecological flows across the seascape and designing marine reserves. We use grunts (Haemulidae) as a representative model group for quantifying movement in terms of distances, time scales, temporal patterns, habitat associations and controls. Here, we provide a review based on recent studies and our own experience. The ritualized, twilight feeding migrations of grunts represent an important mechanism for transferring nutrients and organic matter across habitat boundaries, with movements on the order of 100–300 m. Both compass orientation and vision are used for navigation during feeding migrations. Feeding movements of adults are less ritualized in both space and time and typically occur on the same scale of distance as juveniles, although longer excursions have been documented. Ontogenetic migrations occur over years and take the form of discrete habitat shifts, with most individuals moving progressively offshore. Distances and pathways followed by fish will depend on the exact width of the shelf and distribution of suitable habitats. Transplant experiments suggest there are significant barriers to fish migration, and migration corridors, especially reef margins, seem to be important in determining the direction of ontogenetic habitat shifts, but these may be disrupted by environmental perturbations. Theoretical considerations relative to barrier perception and growth-survival trade-offs appear to explain normal movements of grunts and their responses to environmental perturbations, but lack of information on how fish may sense new locations at distance prevents the full use of theory to generate rules of migration covering timing, distance and direction.

La Parguera, Puerto Rico, a well-studied Caribbean reef system, is showing signs of overfishing and thus, is a good candidate to evaluate fishery policy scenarios using ecosystem modeling. The first steps taken to build a plausible ecosystem model of the La Parguera reef system using Ecopath with Ecosim software included synthesizing fisheries and ecological data then balancing and analyzing trophic relationships for the year 2000. The model is centered around species of commercial and ecological importance in the ecosystem, grouped by habitat preferences. Model construction identified gaps in available data (e.g., diet compositions, metrics of fishing effort, incomplete landings) and balancing raised interesting ecological questions. Some groups, such as parrotfish are so underutilized as prey that the accuracy of biomass estimates and our understanding of predator-prey relationships are questioned. Apparent shortcomings in estimates of primary production relative to consumer biomass generated questions of whether estimates are inaccurate or whether the system is highly subsidized by importation from outside ecosystem boundaries. Although details are not directly comparable because of different structures, a similar Carribean model built for the 1970–1980s estimated total biomass 5.6 times higher than the present model. Changes of this magnitude, if found to be accurate, point out the need for further study of the roles fishing and environmental change have played in reshaping this system over the last 30–40 years. This modeling effort defined future data needs, generated hypotheses for further coral reef research, and provided a starting point towards evaluation of fishery management scenarios in an ecosystem context.

The primary objective of this study was to assess the efficacy of the Virgin Islands Coral Reef National Monument (VICR), a marine protected area in St John, US Virgin Islands. Surveys of habitat and fishes inside and outside of VICR were conducted in 2003–2008. Areas outside the VICR had significantly more scleractinian corals, greater habitat complexity, and greater species richness and density of reef fishes than areas inside., Areas inside and outside the VICR exhibited significant decreases in percent scleractinian coral coverage over the study period. A contrasting trend of increasing macroalgal cover was also observed. No clear effect of the severe 2005 coral bleaching event was observed suggesting other causal factors. No obvious trends in the fish community were observed across the study period. The significant decline in habitat condition, coupled with the initial incorporation of some of the more degraded reefs into the marine protected area may result in a longer time period necessary to detect positive changes in the St. John coral reef ecosystem and associated reef fish abundance and community structure.

No-take marine fishery reserves have been established worldwide to reduce the impact of overfishing in marine ecosystems and to restore depleted fishery stocks. In this study we used capture-markrecapture methodology to evaluate the effectiveness of a small no-take marine fishery reserve in enhancing local abundance, size structure, survival and growth of the red hind grouper, Epinephelus guttatus. The benthic and fish communities were also characterized to discern between the effects of reserve protection from those of habitat variability. A total of 342 red hinds were captured at three localities inside and three outside (200 inside, 142 outside), with a recapture rate of 21.9%. All recaptures were made at the site of initial capture. Density of red hind groupers significantly differed among localities; however, no effect of the reserve was evident. The highest red hind grouper densities were found in hard ground habitats irrespective of management (i.e. inside vs. outside no-take marine fishery reserve). Survival and growth rates did not vary significantly among localities or between management treatments. However, red hind groupers inside the reserve were significantly larger than those outside. Significant differences in benthic community structure were found among localities, but not between management treatments. Variation in red hind grouper population parameters among sites did not correlate with benthic community variables, except for relief, that correlated negatively with red hind grouper density. The overriding factor accounting for differences in red hind grouper density among sites appears to be habitat choice, not the protection from fishing conferred by the reserve.

For generations, fishermen have constructed, shared, and refined knowledge (Traditional Ecological Knowledge) from their perceptions of habitats and species. Following our earlier work in La Parguera, Southwest Puerto Rico, we argue that fishers have a wealth of information on coastal ecosystem ecology, fish behavior, temporal patterns and spatial distribution. Recent work shows that fishers in other areas of Puerto Rico developed schemas that serve as cognitive models associating fishes, groups of fishes and habitats. This article explores the fishers' mental schema of habitats and the habitat-species coupling using the specific example of mutton snapper or sama (Lutjanus analis). Traditional ecological knowledge can be an important component of information used in Ecosystem Based Management. Furthermore, TEK can provide unique knowledge and perspectives on local ecology and the health of fishery resources.