Depth drive shifts in the fish and benthic assemblages of the South American Reef System

The low-latitude habitats of the South American reef system have a high endemism and represent important stepping-stones due to the connectivity with Amazon and Caribbean reefs. We provide the first seabed mapping, and analyze the benthic cover and fish assemblages of these extreme reefs. Fleshy macroalgae (2-66% of cover), algal turfs (0-47%), and sponges (3-25%) are the dominant benthic groups. The main reef builders are crustose coralline algae (2-23%) and only four coral species (0 to 18%), mainly the weedy Siderastrea stellata. Cluster analysis distinguished two groups. The first group includes the shallowest reefs (~ 17 m deep) where fleshy macroalgae are abundant together with higher siltation on the reefs (~ 31% covered by sediments). The second group, by contrast, includes the deeper reefs (22.5-27 m), which have much higher algal turf cover, and the lowest sediment cover (4%). The deeper reefs also have the highest cover of corals (18%) and sponges (25%). We recorded a total of 63 fish species, with the deep reefs being the richest. Analysis indicated that the composition of the benthos was considerably more homogeneous across the study area than the composition of fish assemblages, which had a higher turnover of species among reefs. Moreover, we identified the depth of the reef as a variable structuring the benthic assemblages. The fish assemblage is influenced, in turn, by the benthos. Overall, the seabed mapping revealed the existence of a single reef system with high spatial heterogeneity. Our results provide new insights into the structure of these extreme reefs that have evolved under the influence of sediment resuspension, moderate turbidity, and are warmer than other West Atlantic reefs located at middle- and high-latitudes.

Gambierdiscus species diversity and community structure in St. Thomas, USVI and the Florida Keys, USA

Ciguatera Poisoning (CP) is a widespread and complex poisoning syndrome caused by the consumption of fish or invertebrates contaminated with a suite of potent neurotoxins collectively known as ciguatoxins (CTXs), which are produced by certain benthic dinoflagellates species in the genera Gambierdiscus and Fukuyoa. Due to the complex nature of this HAB problem, along with a poor understanding of toxin production and entry in the coral reef food web, the development of monitoring, management, and forecasting approaches for CP has lagged behind those available for other HAB syndromes. Over the past two decades, renewed research on the taxonomy, physiology, and toxicology of CP-causing dinoflagellates has advanced our understanding of the species diversity that exists within these genera, including identification of highly toxic species (so called "superbugs") that likely contribute disproportionately to ciguatoxins entering coral reef food webs. The recent development of approaches for molecular analysis of field samples now provide the means to investigate in situ community composition, enabling characterization of spatio-temporal species dynamics, linkages between toxic species abundance and toxin flux, and the risk of ciguatoxin prevalence in fish. In this study we used species-specific fluorescent in situ hybridization (FISH) probes to investigate Gambierdiscus species composition and dynamics in St. Thomas (USVI) and the Florida Keys (USA) over multiple years (2018-2020). Within each location, samples were collected seasonally from several sites comprising varying depths, habitats, and algal substrates to characterize community structure over small spatial scales and across different host macrophytes. This approach enabled the quantitative determination of communities over spatiotemporal gradients, as well as the selective enumeration of species known to exhibit high toxicity, such as Gambierdiscus silvae. The investigation found differing community structure between St. Thomas and Florida Keys sites, driven in part by differences in the distribution of toxin-producing species G. silvae and G. belizeanus, which were present throughout sampling sites in St. Thomas but scarce or absent in the Florida Keys. This finding is significant given the high toxicity of G. silvae, and may help explain differences in fish toxicity and CP incidence between St. Thomas and Florida. Intrasite comparisons along a depth gradient found higher concentrations of Gambierdiscus spp. at deeper locations. Among the macrophytes sampled, Dictyota may be a likely vector for toxin transfer based on their widespread distribution, apparent colonization by G. silvae, and palatability to at least some herbivore grazers. Given its ubiquity throughout both study regions and sites, this taxa may also serve as a refuge, accumulating high concentrations of Gambierdiscus and other benthic dinoflagellates, which in turn can serve as source populations for highly palatable and ephemeral habitats nearby, such as turf algae. These studies further demonstrate the successful application of FISH probes in examining biogeographic structuring of Gambierdiscus communities, targeting individual toxin-producing species, and characterizing species-level dynamics that are needed to describe and model ecological drivers of species abundance and toxicity.

CiguaMOD I: A conceptual model of ciguatoxin loading in the Greater Caribbean Region

Ciguatera poisoning (CP) is the most common form of phycotoxin-borne seafood poisoning globally, affecting thousands of people on an annual basis. It most commonly occurs in residential fish of coral reefs, which consume toxin-laden algae, detritus, and reef animals. The class of toxins that cause CP, ciguatoxins (CTXs), originate in benthic, epiphytic dinoflagellates of the genera, Gambierdiscus and Fukuyoa, which are consumed by herbivores and detritivores that facilitate food web transfer. A number of factors have hindered adequate environmental monitoring and seafood surveillance for ciguatera including the low concentrations in which the toxins are found in seafood causing illness (sub-ppb), a lack of knowledge on the toxicity equivalence of other CTXs and contribution of other benthic algal toxins to the disease, and the limited availability of quantified toxin standards and reference materials. While progress has been made on the identification of the dinoflagellate taxa and toxins responsible for CP, more effort is needed to better understand the dynamics of toxin transfer into reef food webs in order to implement a practical monitoring program for CP. Here, we present a conceptual model that utilizes empirical field data (temperature, Gambierdiscus cell densities, macrophyte cover) in concert with other published studies (grazing rates and preference) to produce modeling outputs that suggest approaches that may be beneficial to developing monitoring programs: 1) targeting specific macrophytes for Gambierdiscus and toxin measurements to monitor toxin levels at the base of the food web (i.e., toxin loading); and 2) adjusting these targets across sites and over seasons. Coupling this approach with other methodologies being incorporated into monitoring programs (artificial substrates; FISH probes; toxin screening) may provide an "early warning" system to develop strategic responses to potential CP flare ups in the future.

Does Predation Exacerbate the Risk of Endosymbiont Loss in Heat Stressed Hermatypic Corals? Molecular Cues Provide Insights Into Species-Specific Health Outcomes in a Multi-Stressor Ocean

Ocean warming has been a major driver of coral reef bleaching and mass mortality. Coupled to other biotic pressures, corals’ ability for acclimatization and adaptation may become compromised. Here, we tested the combined effects of warming scenarios (26, 30, and 32°C) and predation (wound vs. no wound) in coral health condition (paleness, bleaching, and mortality), cellular stress responses (heat shock protein 70 kDa Hsp70, total ubiquitin Ub, and total antioxidant capacity TAC), and physiological state (integrated biomarker response index, IBR) of seven Scleractinian coral species, after being exposed for 60 days. Results show that although temperature was the main factor driving coral health condition, thermotolerant species (Galaxea fascicularis, Psammocora contigua, and Turbinaria reniformis) displayed increased paleness, bleaching, and mortality in predation treatments at high temperature, whereas thermosensitive species (Acropora tenuis, Echinopora lamellosa, and Montipora capricornis brown and green morphotypes) all died at 32°C, regardless of predation condition. At the molecular level, results show that there were significant main and interactive effects of species, temperature, and predation in the biomarkers assessed. Temperature affected Hsp70, Ub, and TAC, evidencing the role of protein folding and turnover, as well as reactive oxygen species scavenging in heat stress management. Predation increased Hsp70 and Ub, suggesting the activation of the pro-phenoloxidase system and cytokine activity, whereas the combination of both stressors mainly affected TAC during moderate stress and Ub under severe stress, suggesting that redox balance and defense of homeostasis are crucial in tissue repair at high temperature. IBR levels showed an increasing trend at 32°C in predated coral fragments (although non-significant). We conclude that coral responses to the combination of high temperature and predation pressure display high inter-species variability, but these stressors may pose a higher risk of endosymbiont loss, depending on species physiology and stress intensity.

Adaptive Variation in Homolog Number Within Transcript Families Promotes Expression Divergence in Reef-Building Coral

Gene expression, especially in multi-species experiments, is used to gain insight into the genetic basis of how organisms adapt and respond to changing environments. However, evolutionary processes which can influence gene expression patterns between species such as the presence of paralogs which arise from gene duplication events are rarely accounted for. Paralogous transcripts can alter the transcriptional output of a gene and thus exclusion of these transcripts can obscure important biological differences between species. To address this issue, we investigated how differences in transcript family size is associated with divergent gene expression patterns in five species of Caribbean reef-building corals. We demonstrate that transcript families that are rapidly evolving in terms of size have increased levels of expression divergence. Additionally, these rapidly evolving transcript families are enriched for multiple biological processes, with genes involved in the coral innate immune system demonstrating pronounced variation in homolog number between species. Overall, this investigation demonstrates the importance of incorporating paralogous transcripts when comparing gene expression across species by influencing both transcriptional output and the number of transcripts within biological processes. As this investigation was based on transcriptome assemblies, additional insights into the relationship between gene duplications and expression patterns will likely emergence once more genome assemblies are available for study.

Asynchrony of Gambierdiscus spp. Abundance and Toxicity in the U.S. Virgin Islands: Implications for Monitoring and Management of Ciguatera

Ciguatera poisoning (CP) poses a significant threat to ecosystem services and fishery resources in coastal communities. The CP-causative ciguatoxins (CTXs) are produced by benthic dinoflagellates including Gambierdiscus and Fukuyoa spp., and enter reef food webs via grazing on macroalgal substrates. In this study, we report on a 3-year monthly time series in St. Thomas, US Virgin Islands where Gambierdiscus spp. abundance and Caribbean-CTX toxicity in benthic samples were compared to key environmental factors, including temperature, salinity, nutrients, benthic cover, and physical data. We found that peak Gambierdiscus abundance occurred in summer while CTX-specific toxicity peaked in cooler months (February-May) when the mean water temperatures were approximately 26-28 °C. These trends were most evident at deeper offshore sites where macroalgal cover was highest year-round. Other environmental parameters were not correlated with the CTX variability observed over time. The asynchrony between Gambierdiscus spp. abundance and toxicity reflects potential differences in toxin cell quotas among Gambierdiscus species with concomitant variability in their abundances throughout the year. These results have significant implications for monitoring and management of benthic harmful algal blooms and highlights potential seasonal and highly-localized pulses in reef toxin loads that may be transferred to higher trophic levels.

Microbial dysbiosis reflects disease resistance in diverse coral species

Disease outbreaks have caused significant declines of keystone coral species. While forecasting disease outbreaks based on environmental factors has progressed, we still lack a comparative understanding of susceptibility among coral species that would help predict disease impacts on coral communities. The present study compared the phenotypic and microbial responses of seven Caribbean coral species with diverse life-history strategies after exposure to white plague disease. Disease incidence and lesion progression rates were evaluated over a seven-day exposure. Coral microbiomes were sampled after lesion appearance or at the end of the experiment if no disease signs appeared. A spectrum of disease susceptibility was observed among the coral species that corresponded to microbial dysbiosis. This dysbiosis promotes greater disease susceptiblity in coral perhaps through different tolerant thresholds for change in the microbiome. The different disease susceptibility can affect coral’s ecological function and ultimately shape reef ecosystems.

MacKnight et al. compared the phenotypic and microbial responses of seven Caribbean coral species with diverse life-history strategies after exposure to white plague disease. The different species exhibited a spectrum of disease susceptibility and associated mortality that corresponded with their tolerances to microbial change, indicating that coral disease and microbial dysbiosis may ultimately shape reef ecosystems.

Spatial benthic community analysis of shallow coral reefs to support coastal management in Culebra Island, Puerto Rico

Caribbean coral reefs provide essential ecosystem services to society, including fisheries, tourism and shoreline protection from coastal erosion. However, these reefs are also exhibiting major declining trends, leading to the evolution of novel ecosystems dominated by non-reef building taxa, with potentially altered ecological functions. In the search for effective management strategies, this study characterized coral reefs in front of a touristic beach which provides economic benefits to the surrounding coastal communities yet faces increasing anthropogenic pressures and conservation challenges. Haphazard photo-transects were used to address spatial variation patterns in the reef’s benthic community structure in eight locations. Statistically significant differences were found with increasing distance from the shoreline, reef rugosity, Diadema antillarum density, among reef locations, and as a function of recreational use. Nearshore reefs reflected higher percent macroalgal cover, likely due to increased exposure from both recreational activities and nearby unsustainable land-use practices. However, nearshore reefs still support a high abundance of the endangered reef-building coral Orbicella annularis, highlighting the need to conserve these natural shoreline protectors. There is an opportunity for local stakeholders and regulatory institutions to collaboratively implement sea-urchin propagation, restoration of endangered Acroporid coral populations, and zoning of recreational densities across reefs. Our results illustrate vulnerable reef hotspots where these management interventions are needed and recommend guidelines to address them.

The timing and causality of ecological shifts on Caribbean reefs

Caribbean reefs have experienced unprecedented changes in the past four decades. Of great concern is the perceived widespread shift from coral to macroalgal dominance and the question of whether it represents a new, stable equilibrium for coral-reef communities. The primary causes of the shift-grazing pressure (top-down), nutrient loading (bottom-up) or direct coral mortality (side-in)-still remain somewhat controversial in the coral-reef literature. We have attempted to tease out the relative importance of each of these causes. Four insights emerge from our analysis of an early regional dataset of information on the benthic composition of Caribbean reefs spanning the years 1977-2001. First, although three-quarters of reef sites have experienced coral declines concomitant with macroalgal increases, fewer than 10% of the more than 200 sites studied were dominated by macroalgae in 2001, by even the most conservative definition of dominance. Using relative dominance as the threshold, a total of 49 coral-to-macroalgae shifts were detected. This total represents ~35% of all sites that were dominated by coral at the start of their monitoring periods. Four shifts (8.2%) occurred because of coral loss with no change in macroalgal cover, 15 (30.6%) occurred because of macroalgal gain without coral loss, and 30 (61.2%) occurred owing to concomitant coral decline and macroalgal increase. Second, the timing of shifts at the regional scale is most consistent with the side-in model of reef degradation, which invokes coral mortality as a precursor to macroalgal takeover, because more shifts occurred after regional coral-mortality events than expected by chance. Third, instantaneous observations taken at the start and end of the time-series for individual sites showed these reefs existed along a continuum of coral and macroalgal cover. The continuous, broadly negative relationship between coral and macroalgal cover suggests that in some cases coral-to-macroalgae phase shifts may be reversed by removing sources of perturbation or restoring critical components such as the herbivorous sea urchin Diadema antillarum to the system. The five instances in which macroalgal dominance was reversed corroborate the conclusion that macroalgal dominance is not a stable, alternative community state as has been commonly assumed. Fourth, the fact that the loss in regional coral cover and concomitant changes to the benthic community are related to punctuated, discrete events with known causes (i.e. coral disease and bleaching), lends credence to the hypothesis that coral reefs of the Caribbean have been under assault from climate-change-related maladies since the 1970s.

Effect of Louisiana sweet crude oil on a Pacific coral, Pocillopora damicornis

Recent oil spill responses such as the Deepwater Horizon event have underscored the need for crude oil ecotoxicological threshold data for shallow water corals to assist in natural resource damage assessments. We determined the toxicity of a mechanically agitated oil-seawater mixture (high-energy water-accommodated fraction, HEWAF) of a sweet crude oil on a branched stony coral, Pocillopora damicornis. We report the results of two experiments: a 96 h static renewal exposure experiment and a "pulse-chase" experiment of three short-term exposure durations followed by a recovery period in artificial seawater. Five endpoints were used to determine ecotoxicological values: 1) algal symbiont chlorophyll fluorescence, 2) a tissue regeneration assay and a visual health metric with three endpoints: 3) tissue integrity, 4) tissue color, and 5) polyp behavior. The sum of 50 entrained polycyclic aromatic hydrocarbons (tPAH50) was used as a proxy for oil exposure. For the 96 h exposure dose response experiment, dark-adapted maximum quantum yield (Fv/Fm) of the dinoflagellate symbionts was least affected by crude oil (EC₅₀ = 913 μg/L tPAH50); light-adapted effective quantum yield (EQY) was more sensitive (EC₅₀ =  428 μg/L tPAH50). In the health assessment, polyp behavior (EC₅₀ = 27 μg/L tPAH50) was more sensitive than tissue integrity (EC₅₀ = 806 μg/L tPAH50) or tissue color (EC₅₀ = 926 μg/L tPAH50). Tissue regeneration proved to be a particularly sensitive measurement for toxicity effects (EC₅₀ = 10 μg/L tPAH50). Short duration (6-24 h) exposures using 503 μg/L tPAH50 (average concentration) resulted in negative impacts to P. damicornis and its symbionts. Recovery of chlorophyll a fluorescence levels for 6-24 h oil exposures was observed in a few hours (Fv/Fm) to several days (EQY) following recovery in fresh seawater. The coral health assessments for tissue integrity and tissue color were not affected following short-term oil exposure durations, but the 96 h treatment duration resulted in significant decreases for both. A reduction in polyp behavior (extension) was observed for all treatment durations, with recovery observed for the short-term (6-24 h) exposures within 1-2 days following placement in fresh seawater. Wounded and intact fragments exposed to oil treatments were particularly sensitive, with significant delays observed in tissue regeneration. Estimating ecotoxicological values for P. damicornis exposed to crude oil HEWAFs provides a basis for natural resource damage assessments for oil spills in reef ecosystems. These data, when combined with ecotoxicological values for other coral reef species, will contribute to the development of species sensitivity models.

Recovery ability of lowshore sessile assemblages in a highly contaminated post-industrial area

The inheritance of environmental contamination left by abandoned industrial plants is widespread globally. Here we compared the patterns of recovery of lowshore algal and invertebrate assemblages between the post-industrial site of Bagnoli-Coroglio and four reference sites distributed along the coast in the Gulf of Naples, southern Tyrrhenian Sea. The structure of whole assemblages, richness of taxa and abundance of individual taxa were followed during one year since an event of experimental disturbance consisting in the removal of all erect organisms from the rocky substrate. Our main findings suggest that the examined benthic assemblages recovered effectively and quickly after a pulse disturbance and, contrarily to initial expectations, that this ability was comparable between the post-industrial site and the reference sites. This result is discussed in terms of several plausible processes and mechanisms, including the general capability of intertidal organisms to recover from physical disturbance, the potential high level of environmental stress affecting the reference sites too, the chance that the most intense impacts of contamination remained restricted to the sediments of the post-industrial site without propagating to adjacent rocky habitats, and the large natural variability of reference sites that may have masked weak effects of the historical contamination. Irrespective of the actual causes, we emphasize the need for including natural variability of the examined system in any future restoration interventions, to guarantee representation of the range of variation of target organisms and of their underlying processes, and to avoid confounding the intended post-industrial impact with the effects of other natural and anthropogenic processes.

Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic

Active coral restoration typically involves two interventions: crossing gametes to facilitate sexual larval propagation; and fragmenting, growing, and outplanting adult colonies to enhance asexual propagation. From an evolutionary perspective, the goal of these efforts is to establish self-sustaining, sexually reproducing coral populations that have sufficient genetic and phenotypic variation to adapt to changing environments. Here, we provide concrete guidelines to help restoration practitioners meet this goal for most Caribbean species of interest. To enable the persistence of coral populations exposed to severe selection pressure from many stressors, a mixed provenance strategy is suggested: genetically unique colonies (genets) should be sourced both locally as well as from more distant, environmentally distinct sites. Sourcing three to four genets per reef along environmental gradients should be sufficient to capture a majority of intraspecies genetic diversity. It is best for practitioners to propagate genets with one or more phenotypic traits that are predicted to be valuable in the future, such as low partial mortality, high wound healing rate, high skeletal growth rate, bleaching resilience, infectious disease resilience, and high sexual reproductive output. Some effort should also be reserved for underperforming genets because colonies that grow poorly in nurseries sometimes thrive once returned to the reef and may harbor genetic variants with as yet unrecognized value. Outplants should be clustered in groups of four to six genets to enable successful fertilization upon maturation. Current evidence indicates that translocating genets among distant reefs is unlikely to be problematic from a population genetic perspective but will likely provide substantial adaptive benefits. Similarly, inbreeding depression is not a concern given that current practices only raise first-generation offspring. Thus, proceeding with the proposed management strategies even in the absence of a detailed population genetic analysis of the focal species at sites targeted for restoration is the best course of action. These basic guidelines should help maximize the adaptive potential of reef-building corals facing a rapidly changing environment.

Regional coral disease outbreak overwhelms impacts from a local dredge project

A repeated-measures coral monitoring program established as part of the PortMiami expansion program provided an unparalleled opportunity to quantify the levels of coral mortality that resulted from both local dredging stress and as a result of climate-related bleaching stress and the subsequent outbreak of a white-plague-like disease (WPD) epizootic. By comparing measured rates of coral mortality at 30 sites throughout Miami-Dade County to predicted mortality levels from three different coral mortality scenarios, we were able to evaluate the most likely source of coral mortality at both the local and regional levels during the 2014-2016 coral bleaching and WPD event. These include scenarios that assume (1) local dredging increases coral disease mortality, (2) regional climate-related stress is the proximal driver of coral disease mortality, and (3) local and regional stressors are both responsible for coral disease mortality. Our results show that species-specific susceptibility to disease is the determining factor in 93.3% of coral mortality evaluated throughout Miami-Dade County, whereas local dredging stress only accurately predicted coral mortality levels 6.7% of the time. None of the monitoring locations adjacent to the PortMiami expansion had levels of coral mortality that exceeded predictions when coral community composition was taken into account. The novel result of this analysis is that climate-mediated coral disease mortality was more than an order of magnitude (14x) more deadly than even the largest marine construction project performed in the USA, and that until climate change is addressed, it is likely that local attempts to manage coral resilience will continue to fail.

Effects of moderate thermal anomalies on Acropora corals around Sesoko Island, Okinawa

Over the past several decades, coral reef ecosystems have experienced recurring bleaching events. These events were predominantly caused by thermal anomalies, which vary widely in terms of severity and spatio-temporal distribution. Acropora corals, highly prominent contributors to the structural complexity of Pacific coral reefs, are sensitive to thermal stress. Response of Acropora corals to extremely high temperature has been well documented. However, studies on the effects of moderately high temperature on Acropora corals are limited. In the summer of 2016, a moderate coral bleaching event due to moderately high temperature was observed around Sesoko Island, Okinawa, Japan. The objective of this study was to examine thermal tolerance patterns of Acropora corals, across reefs with low to moderate thermal exposure (degree heating weeks ~2-5°C week). Field surveys on permanent plots were conducted from October 2015 to April 2017 to compare the population dynamics of adult Acropora corals 6 months before and after the bleaching events around Sesoko Island. Variability in thermal stress response was driven primarily by the degree of thermal stress. Wave action and turbidity may have mediated the thermal stress. Tabular and digitate coral morphologies were the most tolerant and susceptible to thermal stress, respectively. Growth inhibition after bleaching was more pronounced in the larger digitate and corymbose coral morphologies. This study indicates that Acropora populations around Sesoko Island can tolerate short-term, moderate thermal challenges.

IDENTIFYING AND STRUCTURING OBJECTIVES FOR A CORAL REEF PROTECTION PLAN AT THE U.S. ENVIRONMENTAL PROTECTION AGENCY

Region 2 of the U.S. Environmental Protection Agency initiated a Coral Reef Protection Plan (CRPP) in 2014 to reduce anthropogenic stress on Caribbean coral reefs. The CRPP is intended to foster institutional practices that improve reef condition and focus regulatory and nonregulatory decision making on minimizing pollutant release to coastal systems. A framework incorporating two sets of objectives was constructed to examine the short- and long-term costs and benefits of tasks. The first set of objectives was derived from existing tasks in the CRPP and was intended to support an update of the CRPP for 2015. Fundamental objectives were constructed to communicate the end objectives across tasks and means objectives were constructed to communicate the means for achieving them. The second set of objectives was created to reflect costs and benefits of the CRPP beyond 2015. These objectives contained fundamental objectives comprising broad social, economic, learning and governance topics. The means objectives included tasks such as building capacity, providing regulatory oversight, and learning and reducing uncertainties. The second set of objectives also included strategic objectives that identify long-range benefits such as coral reef integrity and reef ecosystem services. The process of defining objectives helped to ascertain and better elucidate the important consequences for the CRPP. Understanding objectives not only provides a roadmap for coral reef protection but can help Region 2 communicate internally and externally with other agencies, industry, and the public.

Assessing land use, sedimentation, and water quality stressors as predictors of coral reef condition in St. Thomas, U.S. Virgin Islands

Coral reef condition on the south shore of St. Thomas, U.S. Virgin Islands, was assessed at various distances from Charlotte Amalie, the most densely populated city on the island. Human influence in the area includes industrial activity, wastewater discharge, cruise ship docks, and impervious surfaces throughout the watershed. Anthropogenic activity was characterized using a landscape development intensity (LDI) index, sedimentation threat (ST) estimates, and water quality (WQ) impairments in the near-coastal zone. Total three-dimensional coral cover, reef rugosity, and coral diversity had significant negative coefficients for LDI index, as did densities of dominant species Orbicella annularis, Orbicella franksi, Montastraea cavernosa, Orbicella faveolata, and Porites porites. However, overall stony coral colony density was not significantly correlated with stressors. Positive relationships between reef rugosity and ST, between coral diversity and ST, and between coral diversity and WQ were unexpected because these stressors are generally thought to negatively influence coral growth and health. Sponge density was greater with higher disturbance indicators (ST and WQ), consistent with reports of greater resistance by sponges to degraded water quality compared to stony corals. The highest FoRAM (Foraminifera in Reef Assessment and Monitoring) indices indicating good water quality were found offshore from the main island and outside the harbor. Negative associations between stony coral metrics and LDI index have been reported elsewhere in the Caribbean and highlight LDI index potential as a spatial tool to characterize land-based anthropogenic stressor gradients relevant to coral reefs. Fewer relationships were found with an integrated stressor index but with similar trends in response direction.

Bleaching events regulate shifts from corals to excavating sponges in algae-dominated reefs

Changes in coral-sponge interactions can alter reef accretion/erosion balance and are important to predict trends on current algal-dominated Caribbean reefs. Although sponge abundance is increasing on some coral reefs, we lack information on how shifts from corals to bioeroding sponges occur, and how environmental factors such as anomalous seawater temperatures and consequent coral bleaching and mortality influence these shifts. A state transition model (Markov chain) was developed to evaluate the response of coral-excavating sponges (Cliona delitrix Pang 1973) after coral bleaching events. To understand possible outcomes of the sponge-coral interaction and build the descriptive model, sponge-corals were monitored in San Andres Island, Colombia (2004-2011) and Fort Lauderdale, Florida (2012-2013). To run the model and determine possible shifts from corals to excavating sponges, 217 coral colonies were monitored over 10 years (2000-2010) in Fort Lauderdale, Florida, and validated with data from 2011 to 2015. To compare and test its scalability, the model was also run with 271 coral colonies monitored in St. Croix, US Virgin Islands over 7 years (2004-2011), and validated with data from 2012 to 2015. Projections and sensitivity analyses confirmed coral recruitment to be key for coral persistence. Excavating sponge abundance increased in both Fort Lauderdale and St. Croix reefs after a regional mass bleaching event in 2005. The increase was more drastic in St. Croix than in Fort Lauderdale, where 25% of the healthy corals that deteriorated were overtaken by excavating sponges. Projections over 100 years suggested successive events of coral bleaching could shift algae-coral dominated reefs into algae-sponge dominated. The success of excavating sponges depended on the intensity of coral bleaching and consequent coral mortality. Thus, the proportion of C. delitrix excavating sponges is a sensitive indicator for the intensity and frequency of recent disturbance on Caribbean coral reefs.

Abundance of commercially important reef fish indicates different levels of over-exploitation across shelves of the U.S. Virgin Islands

The United States Virgin Islands are comprised of two separate insular platforms separated by the deep water Anegada Passage. Although managed by the same regulations, as one fishery, several physical and spatial differences exist between the two northern shelf islands, St. Thomas and St. John, and isolated St. Croix. Based on two long-term fisheries independent datasets, collected by the U.S. Virgin Islands Territorial Coral Reef Monitoring Program and the National Oceanographic and Atmospheric Administration Center for Coastal Monitoring and Assessment, there were significant differences between the northern USVI and St. Croix in both the occurrence and size of several species of large and commercially important reef fishes. These fishes are primarily apex piscivores and generally the first species over-exploited in small-scale fisheries. The disparities between the fish communities on the two island shelves cannot be explained solely by differences in habitat (coral cover, rugosity) or fisheries management, such as relative amount of marine protected area in local waters. They are instead probably caused by a combination of several other interrelated factors including water depth, fishing methodology, fishable area, and the presence or absence of viable fish spawning areas. This study considers those aspects, and illustrates the need for management of island artisanal fisheries that is tailored to the physical and spatial constraints imposed by insular platforms.

Intraspecific variation in growth rate is a poor predictor of fitness for reef corals

Genetic variation underlying differences in organism performance is subject to natural selection, and organisms with high values of genetically determined phenotypic measures of fitness should perform better than those that do not. Using small scleractinian corals (i.e., ≤40-mm diameter), this principle was tested with 20 yr of census data from St. John, US Virgin Islands. Using growth rate (change in diameter) as a measure of fitness, growth in one year was tested for association with growth and survivorship in the following two years, and this process was repeated over 20 yr using a 3-yr sliding window. Virtually all variation in growth was independent of colony size, and growth among pairs of years was highly variable, with corals that grew fast in one year rarely growing fast in the next 2 yr. While growth in some pairs of years was positively correlated, ≤4% of the growth variance was explained by growth in the preceding 2 yr. Survivorship was related positively to growth in the preceding year, but the association was weak, it did not extend over 3 yr, and was inconsistent over the study. These results demonstrate the importance of the environment in translating phenotypic measures of fitness into future performance, and for small Caribbean corals, they suggest that environmental conditions may preempt genotype in determining short-term success.

Coral reef health response to chronic and acute changes in water quality in St. Thomas, United States Virgin Islands

It is suspected that land cover alteration on the southern coast of St. Thomas, USVI has increased runoff, degrading nearshore water quality and coral reef health. Chronic and acute changes in water quality, sediment deposition, and coral health metrics were assessed in three zones based upon perceived degree of human influence. Chlorophyll (p<0.0001) and turbidity (p=0.0113) were significantly higher in nearshore zones and in the high impact zone during heavy precipitation. Net sediment deposition and terrigenous content increased in nearshore zones during periods of greater precipitation and port activity. Macroalgae overgrowth significantly increased along a gradient of decreasing water quality (p<0.0001). Coral bleaching in all zones peaked in November with a regional thermal stress event (p<0.0001). However, mean bleaching prevalence was significantly greater in the most impacted zone compared to the offshore zone (p=0.0396), suggesting a link between declining water quality and bleaching severity.

Unprecedented Disease-Related Coral Mortality in Southeastern Florida

Anomalously high water temperatures, associated with climate change, are increasing the global prevalence of coral bleaching, coral diseases, and coral-mortality events. Coral bleaching and disease outbreaks are often inter-related phenomena, since many coral diseases are a consequence of opportunistic pathogens that further compromise thermally stressed colonies. Yet, most coral diseases have low prevalence (<5%), and are not considered contagious. By contrast, we document the impact of an extremely high-prevalence outbreak (61%) of white-plague disease at 14 sites off southeastern Florida. White-plague disease was observed near Virginia Key, Florida, in September 2014, and after 12 months had spread 100 km north and 30 km south. The disease outbreak directly followed a high temperature coral-bleaching event and affected at least 13 coral species. Eusmilia fastigiata, Meandrina meandrites, and Dichocoenia stokesi were the most heavily impacted coral species, and were reduced to <3% of their initial population densities. A number of other coral species, including Colpophyllia natans, Pseudodiploria strigosa, Diploria labyrinthiformis, and Orbicella annularis were reduced to <25% of their initial densities. The high prevalence of disease, the number of susceptible species, and the high mortality of corals affected suggests this disease outbreak is arguably one of the most lethal ever recorded on a contemporary coral reef.

Caribbean mesophotic coral ecosystems are unlikely climate change refugia

Deeper coral reefs experience reduced temperatures and light and are often shielded from localized anthropogenic stressors such as pollution and fishing. The deep reef refugia hypothesis posits that light-dependent stony coral species at deeper depths are buffered from thermal stress and will avoid bleaching-related mass mortalities caused by increasing sea surface temperatures under climate change. This hypothesis has not been tested because data collection on deeper coral reefs is difficult. Here we show that deeper (mesophotic) reefs, 30-75 m depth, in the Caribbean are not refugia because they have lower bleaching threshold temperatures than shallow reefs. Over two thermal stress events, mesophotic reef bleaching was driven by a bleaching threshold that declines 0.26 °C every +10 m depth. Thus, the main premise of the deep reef refugia hypothesis that cooler environments are protective is incorrect; any increase in temperatures above the local mean warmest conditions can lead to thermal stress and bleaching. Thus, relatively cooler temperatures can no longer be considered a de facto refugium for corals and it is likely that many deeper coral reefs are as vulnerable to climate change as shallow water reefs.

Depth-Independent Reproduction in the Reef Coral Porites astreoides from Shallow to Mesophotic Zones

Mesophotic coral ecosystems between 30–150 m may be important refugia habitat for coral reefs and associated benthic communities from climate change and coastal development. However, reduced light at mesophotic depths may present an energetic challenge to the successful reproduction of light-dependent coral organisms, and limit this refugia potential. Here, the relationship of depth and fecundity was investigated in a brooding depth-generalist scleractinian coral, Porites astreoides from 5–37 m in the U.S. Virgin Islands (USVI) using paraffin tissue histology. Despite a trend of increasing planulae production with depth, no significant differences were found in mean peak planulae density between shallow, mid-depth and mesophotic sites. Differential planulae production over depth is thus controlled by P. astreoides coral cover, which peaks at 10 m and ~35 m in the USVI. These results suggest that mesophotic ecosystems are reproductive refuge for P. astreoides in the USVI, and may behave as refugia for P. astreoides metapopulations providing that vertical larval exchanges are viable.

Fertile fathoms: Deep reproductive refugia for threatened shallow corals

The persistence of natural metapopulations may depend on subpopulations that exist at the edges of species ranges, removed from anthropogenic stress. Mesophotic coral ecosystems (30–150 m) are buffered from disturbance by depth and distance, and are potentially massive reservoirs of coral diversity and fecundity; yet we know little about the reproductive capabilities of their constituent species and the potential for these marginal environments to influence patterns of coral reef persistence. We investigated the reproductive performance of the threatened depth-generalist coral Orbicella faveolata over the extent of its vertical range to assess mesophotic contributions to regional larval pools. Over equal habitat area, mesophotic coral populations were found to produce over an order of magnitude more eggs than nearby shallow populations. Positive changes with depth in both population abundance and polyp fecundity contributed to this discrepancy. Relative larval pool contributions of deeper living corals will likely increase as shallow habitats further degrade due to climate change and local habitat degradation. This is a compelling example of the potential for marginal habitat to be critical to metapopulation persistence as reproductive refugia.

Environmental conditions influence tissue regeneration rates in scleractinian corals

Natural and anthropogenic factors may influence corals' ability to recover from partial mortality. To examine how environmental conditions affect lesion healing, we assessed several water quality parameters and tissue regeneration rates in corals at six reefs around St. Thomas, US Virgin Islands. We hypothesized that sites closer to developed areas would have poor water quality due to proximity to anthropogenic stresses, which would impede tissue regeneration. We found that water flow and turbidity most strongly influenced lesion recovery rates. The most impacted site, with high turbidity and low flow, recovered almost three times slower than the least impacted site, with low turbidity, high flow, and low levels of anthropogenic disturbance. Our results illustrate that in addition to lesion-specific factors known to affect tissue regeneration, environmental conditions can also control corals' healing rates. Resource managers can use this information to protect low-flow, turbid nearshore reefs by minimizing sources of anthropogenic stress.

Synergistic impacts of global warming on the resilience of coral reefs

Recent epizootics have removed important functional species from Caribbean coral reefs and left communities vulnerable to alternative attractors. Global warming will impact reefs further through two mechanisms. A chronic mechanism reduces coral calcification, which can result in depressed somatic growth. An acute mechanism, coral bleaching, causes extreme mortality when sea temperatures become anomalously high. We ask how these two mechanisms interact in driving future reef state (coral cover) and resilience (the probability of a reef remaining within a coral attractor). We find that acute mechanisms have the greatest impact overall, but the nature of the interaction with chronic stress depends on the metric considered. Chronic and acute stress act additively on reef state but form a strong synergy when influencing resilience by intensifying a regime shift. Chronic stress increases the size of the algal basin of attraction (at the expense of the coral basin), whereas coral bleaching pushes the system closer to the algal attractor. Resilience can change faster—and earlier—than a change in reef state. Therefore, we caution against basing management solely on measures of reef state because a loss of resilience can go unnoticed for many years and then become disproportionately more difficult to restore.

The cumulative impact of annual coral bleaching can turn some coral species winners into losers

Mass coral bleaching events caused by elevated seawater temperatures result in extensive coral loss throughout the tropics, and are projected to increase in frequency and severity. If bleaching becomes an annual event later in this century, more than 90% of coral reefs worldwide may be at risk of long-term degradation. While corals can recover from single isolated bleaching and can acclimate to recurring bleaching events that are separated by multiple years, it is currently unknown if and how they will survive and possibly acclimatize to annual coral bleaching. Here, we demonstrate for the first time that annual coral bleaching can dramatically alter thermal tolerance in Caribbean corals. We found that high coral energy reserves and changes in the dominant algal endosymbiont type (Symbiodinium spp.) facilitated rapid acclimation in Porites divaricata, whereas low energy reserves and a lack of algal phenotypic plasticity significantly increased susceptibility in Porites astreoides to bleaching the following year. Phenotypic plasticity in the dominant endosymbiont type of Orbicella faveolata did not prevent repeat bleaching, but may have facilitated rapid recovery. Thus, coral holobiont response to an isolated single bleaching event is not an accurate predictor of its response to bleaching the following year. Rather, the cumulative impact of annual coral bleaching can turn some coral species 'winners' into 'losers', and can also facilitate acclimation and turn some coral species 'losers' into 'winners'. Overall, these findings indicate that cumulative impact of annual coral bleaching could result in some species becoming increasingly susceptible to bleaching and face a long-term decline, while phenotypically plastic coral species will acclimatize and persist. Thus, annual coral bleaching and recovery could contribute to the selective loss of coral diversity as well as the overall decline of coral reefs in the Caribbean.

Regional status assessment of stony corals in the US Virgin Islands

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 m(2) 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.