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Genotype-by-environment interactions (GxE) indicate that variation in organismal traits cannot be explained by fixed effects of genetics or site-specific plastic responses alone. For tropical coral reefs experiencing dramatic environmental change, identifying the contributions of genotype, environment, and GxE on coral performance will be vital for both predicting persistence and developing restoration strategies. We quantified the impacts of G, E, and GxE on the morphology and survival of the endangered coral, Acropora cervicornis , through an in situ transplant experiment exposing common garden (nursery)-raised clones of ten genotypes to nine reef sites in the Florida Keys. By fate-tracking outplants over one year with colony-level 3D photogrammetry, we uncovered significant GxE on coral size, shape, and survivorship, indicating that no universal winner exists in terms of colony performance. Rather than differences in mean trait values, we found that individual-level morphological plasticity is adaptive in that the most plastic individuals also exhibited the fastest growth and highest survival. This indicates that adaptive morphological plasticity may continue to evolve, influencing the success of A. cervicornis and resulting reef communities in a changing climate. As focal reefs are active restoration sites, the knowledge that variation in phenotype is an important predictor of performance can be directly applied to restoration planning. Taken together, these results establish A. cervicornis as a system for studying the ecoevolutionary dynamics of phenotypic plasticity that also can inform genetic- and environment-based strategies for coral restoration.

Reef restoration programs in Florida, US, focused initially on Acropora, but there is now a need to include other species that have also experienced declines. An outplanting experiment using Acropora cervicornis, Montastraea cavernosa, and Orbicella faveolata was conducted to compare performance among species and evaluate the impacts of contact interactions with macroalgae and the zoanthid Palythoa caribaeorum. Montastraea cavernosa and O. faveolata showed high survivorship (78% and 92%, respectively) over 18 mo. However, surviving colonies had limited growth and lost tissue due to factors like predation and disease. In contrast, A. cervicornis showed exponential growth. Colonies in contact with macroalgae showed the lowest survivorship. Removing macroalgae provided no long-term benefits in growth and a slight improvement in colony survivorship. Acropora cervicornis in contact with Palythoa grew 45% less than controls. Our study showed that: (1) coral taxa with massive morphologies (40–130 cm2) can be transplanted with low colony mortality but that their slow growth is not enough to balance partial tissue mortality caused by multiple chronic stressors; (2) removal of macroalgae at the time of outplanting improves colony survivorship; (3) periodic removal of macroalgae does not enhance growth; and (4) contact with Palythoa should be avoided. The impacts of contact competition were variable among species with different colony morphologies, with A. cervicornis showing the highest susceptibility to competition from algae and Palythoa. While restoration can rapidly increase coral abundance, long-term success will require a multifaceted approach to reduce the impacts of chronic reef stressors on wild and outplanted corals alike.

Genotype-by-environment interactions (GxE) indicate that variation in organismal traits cannot be explained by fixed effects of genetics or site-specific plastic responses alone. For tropical coral reefs experiencing dramatic environmental change, identifying the contributions of genotype, environment, and GxE on coral performance will be vital for both predicting persistence and developing restoration strategies. We quantified the impacts of G, E, and GxE on the morphology and survival of the endangered coral,A. cervicornis, through an in situ transplant experiment exposing common garden (nursery) raised clones of ten genotypes to nine reef sites in the Florida Keys. By fate-tracking outplants over one year with colony-level 3D photogrammetry, we uncovered significant GxE on coral size and survivorship indicating that no universal winner exists in terms of colony performance. Moreover, the presence of GxE also implies the existence of intraspecific variation in phenotypic plasticity. Rather than differences in mean trait values, we find that individual-level morphological plasticity is adaptive in that the most plastic individuals also exhibited the fastest growth and highest survival. This indicates that adaptive morphological plasticity may continue to evolve, influencing the success ofA. cervicornisand resulting reef communities in a changing climate. As focal reefs are active restoration sites, the knowledge that variation in phenotype is an important predictor of performance can be directly applied to restoration planning. Taken together, these results establishA. cervicornisas a system for studying the eco-evolutionary dynamics of phenotypic plasticity that also can inform genetic- and environment-based strategies for coral restoration.

The rapid loss of reef-building corals owing to ocean warming is driving the development of interventions such as coral propagation and restoration, selective breeding and assisted gene flow. Many of these interventions target naturally heat-tolerant individuals to boost climate resilience, but the challenges of quickly and reliably quantifying heat tolerance and identifying thermotolerant individuals have hampered implementation. Here, we used coral bleaching automated stress systems to perform rapid, standardized heat tolerance assays on 229 colonies of Acropora cervicornis across six coral nurseries spanning Florida's Coral Reef, USA. Analysis of heat stress dose–response curves for each colony revealed a broad range in thermal tolerance among individuals (approx. 2.5°C range in F v /F m ED50), with highly reproducible rankings across independent tests ( r = 0.76). Most phenotypic variation occurred within nurseries rather than between them, pointing to a potentially dominant role of fixed genetic effects in setting thermal tolerance and widespread distribution of tolerant individuals throughout the population. The identification of tolerant individuals provides immediately actionable information to optimize nursery and restoration programmes for Florida's threatened staghorn corals. This work further provides a blueprint for future efforts to identify and source thermally tolerant corals for conservation interventions worldwide.

Knowledge of multi-stressor interactions and the potential for tradeoffs among tolerance traits is essential for developing intervention strategies for the conservation and restoration of reef ecosystems in a changing climate. Thermal extremes and acidification are two major co-occurring stresses predicted to limit the recovery of vital Caribbean reef-building corals. Here, we conducted an aquarium-based experiment to quantify the effects of increased water temperatures and pCO2 individually and in concert on 12 genotypes of the endangered branching coral Acropora cervicornis, currently being reared and outplanted for large-scale coral restoration. Quantification of 12 host, symbiont and holobiont traits throughout the two-month-long experiment showed several synergistic negative effects, where the combined stress treatment often caused a greater reduction in physiological function than the individual stressors alone. However, we found significant genetic variation for most traits and positive trait correlations among treatments indicating an apparent lack of tradeoffs, suggesting that adaptive evolution will not be constrained. Our results suggest that it may be possible to incorporate climate-resistant coral genotypes into restoration and selective breeding programmes, potentially accelerating adaptation.

Knowledge of multi-stressor interactions and the potential for tradeoffs among tolerance traits is essential for developing intervention strategies for the conservation and restoration of reef ecosystems in a changing climate. Thermal extremes and acidification are two major co-occurring stresses predicted to limit the recovery of vital Caribbean reef-building corals. Here, we conducted an aquarium-based experiment to quantify the effects of increased water temperatures andpCO2individually and in concert on 12 genotypes of the endangered branching coralAcropora cervicornis,currently being reared and outplanted for large-scale coral restoration. Quantification of 12 host, symbiont and holobiont traits throughout the two-month-long experiment showed several synergistic negative effects, where the combined stress treatment often caused a greater reduction in physiological function than the individual stressors alone. However, we found significant genetic variation for most traits and positive trait correlations among treatments indicating an apparent lack of tradeoffs, suggesting that adaptive evolution will not be constrained. Our results suggest that it may be possible to incorporate climate-resistant coral genotypes into restoration and selective breeding programmes, potentially accelerating adaptation.

Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont-the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals' health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy

Summary There are a few baseline reef‐systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected ‘crown jewel’ offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundant Prochlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta‐diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria.

Microbiome studies across taxa have established the influence of host genotype on microbial recruitment and maintenance. However, research exploring host-specific epibionts in scleractinian corals is scant and the influence of intraspecific differences across environments remains unclear. Here, we studied the epibiome of ten Acropora cervicornis genotypes to investigate the relative roles of host genotype and environment in structuring the epibiome. Coral mucus was sampled in a common garden nursery from replicate ramets of distinct genotypes (T0). Coral fragment replicates (n=3) of each genotype were then transplanted to nine different field sites in the Lower Florida Keys and mucus was again sampled one year later from surviving ramets (T12). 16S rRNA amplicon sequencing was used to assess microbial composition, richness, and beta-diversity. The most abundant and consistent amplicon sequencing variants (ASVs) in all samples belonged to Fokiniaceae (MD3-55 genus) and Cyanobacteria (Synechococccus). The abundances of these bacterial taxa varied consistently between genotypes whereas neither the composition nor taxonomic abundance were significantly different among field sites. Interestingly, several high MD3-55 hosting genotypes showed rapid diversification and an increase in MD3-55 following transplantation. Overall, our results indicate healthy A. cervicornis genotypes retain distinct epibiome signatures through time, suggesting a strong host component. Lastly, our results show that differences in MD3-55 abundances can be consistently detected in the epibiome of distinct host-genotypes of A. cervicornis. As this organism (sensu Aquarickettsia rohweri) has been implicated as a marker of disease resistance, this finding reinforces the potential use of microbial indicators in reef restoration efforts via non-invasive surface/mucus sampling.

The ability to quantify changes in the structural complexity of reefs and individual coral colonies that build them is vital to understanding, managing, and restoring the function of these ecosystems. However, traditional methods for quantifying coral growth in situ fail to accurately quantify the diversity of morphologies observed both among and within species that contribute to topographical complexity. Three-dimensional (3D) photogrammetry has emerged as a powerful tool for the quantification of reefscape complexity but has yet to be broadly adopted for quantifying the growth and morphology of individual coral colonies. Here we debut a high-throughput method for colony-level 3D photogrammetry and apply this technique to explore the relationship between linear extension and other growth metrics in Acropora cervicornis. We fate-tracked 156 individual coral transplants to test whether initial growth can be used to predict subsequent patterns of growth. We generated photographic series of fragments in a restoration nursery immediately before transplanting to natural reef sites and re-photographed coral at 6 months and 1 year post-transplantation. Photosets were used to build 3D models with Agisoft Metashape, which was automated to run on a high-performance computing system using a custom script to serially process models without the need for additional user input. Coral models were phenotyped in MeshLab to obtain measures of total linear extension (TLE), surface area, volume, and volume of interstitial space (i.e., the space between branches). 3D-model based measures of TLE were highly similar to by-hand measurements made in the field (r = 0.98), demonstrating that this method is compatible with established techniques without additional in water effort. However, we identified an allometric relationship between the change in TLE and the volume of interstitial space, indicating that growth in higher order traits is not necessarily a linear function of growth in branch length. Additionally, relationships among growth measures weakened when comparisons were made across time points, implying that the use of early growth to predict future performance is limited. Taken together, results show that 3D photogrammetry is an information rich method for quantifying colony-level growth and its application can help address contemporary questions in coral biology.

In the Caribbean, corals are commonly cultured in ocean-based nurseries and outplanted back to reefs for population enhancement. Intraspecific diversity in host and symbiont is an important consideration for nursery and resource managers. We built upon a previous study that quantified Acropora cervicornis growth phenotypes in a nursery by outplanting the same genets across two reef sites and tracking their performance for 1 yr. Further, we identified the Symbiodinium ‘fitti’ strains present in each of the A. cervicornis genets during the restoration process from the initial wild collection as early as 2008 to 24 months post-outplant in 2017. Survival to 1 yr post-outplant was consistent with regional averages and did not differ significantly among A. cervicornis genets or between outplant sites. Outplant site and host genet had significant effects on coral growth. However, genet growth response did not depend on outplant site, providing no evidence for site-genet matching. Conversely, growth rates measured for each genet in the nursery were not predictive of performance following outplanting. Instead, A. cervicornis genets appear to exhibit differences in relative growth through the restoration process. Despite this variability, relative differences in growth among genets were consistent within a given timeframe, even across varying environments. Most colonies sampled were infected by one of five unique strains of S. ‘fitti’. Host-symbiont specificity varied among coral genets, but four out of five genets exhibited spatial and/or temporal differences in symbiont strain composition throughout the restoration process. The ability for A. cervicornis to associate with more than one S. ‘fitti’ strain and the lack of correlation between nursery and outplant growth performance contribute to a growing understanding of the A. cervicornis population enhancement process.

As climate changes, sea surface temperature anomalies that negatively impact coral reef organisms continue to increase in frequency and intensity. Yet, despite widespread coral mortality, genetic diversity remains high even in those coral species listed as threatened. While this is good news in many ways, it presents a challenge for the development of biomarkers that can identify resilient or vulnerable genotypes. Taking advantage of three coral restoration nurseries in Florida that serve as long-term common garden experiments, we exposed over 30 genetically distinct Acropora cervicornis colonies to hot and cold temperature shocks seasonally and measured pooled gene expression responses using RNAseq. Targeting a subset of 20 genes, we designed a high-throughput qPCR array to quantify expression in all individuals separately under each treatment with the goal of identifying predictive and/or diagnostic thermal stress biomarkers. We observed extensive transcriptional variation in the population, suggesting abundant raw material is available for adaptation via natural selection. However, this high variation made it difficult to correlate gene expression changes with colony performance metrics such as growth, mortality and bleaching susceptibility. Nevertheless, we identified several promising diagnostic biomarkers for acute thermal stress that may improve coral restoration and climate change mitigation efforts in the future.

Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis, across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis, including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

Coral gardening plays an important role in the recovery of depleted populations of threatened Acropora cervicornis in the Caribbean. Over the past decade, high survival coupled with fast growth of in situ nursery corals have allowed practitioners to create healthy and genotypically diverse nursery stocks. Currently, thousands of corals are propagated and outplanted onto degraded reefs on a yearly basis, representing a substantial increase in the abundance, biomass, and overall footprint of A. cervicornis. Here, we combined an extensive dataset collected by restoration practitioners to document early (1–2 yr) restoration success metrics in Florida and Puerto Rico, USA. By reporting region-specific data on the impacts of fragment collection on donor colonies, survivorship and productivity of nursery corals, and survivorship and productivity of outplanted corals during normal conditions, we provide the basis for a stop-light indicator framework for new or existing restoration programs to evaluate their performance. We show that current restoration methods are very effective, that no excess damage is caused to donor colonies, and that once outplanted, corals behave just as wild colonies. We also provide science-based benchmarks that can be used by programs to evaluate successes and challenges of their efforts, and to make modifications where needed. We propose that up to 10% of the biomass can be collected from healthy, large A. cervicornis donor colonies for nursery propagation. We also propose the following benchmarks for the first year of activities for A. cervicornis restoration: (1) >75% live tissue cover on donor colonies; (2) >80% survivorship of nursery corals; and (3) >70% survivorship of outplanted corals. Finally, we report productivity means of 4.4 cm yr−1 for nursery corals and 4.8 cm yr−1 for outplants as a frame of reference for ranking performance within programs. Such benchmarks, and potential subsequent adaptive actions, are needed to fully assess the long-term success of coral restoration and species recovery programs.

Staghorn coral, Acropora cervicornis, is a threatened species and the primary focus of western Atlantic reef restoration efforts to date. We compared linear extension, calcification rate, and skeletal density of nursery-raised A. cervicornis branches reared for 6 months either on blocks attached to substratum or hanging from PVC trees in the water column. We demonstrate that branches grown on the substratum had significantly higher skeletal density, measured using computerized tomography, and lower linear extension rates compared to water-column fragments. Calcification rates determined with buoyant weighing were not statistically different between the two grow-out methods, but did vary among coral genotypes. Whereas skeletal density and extension rates were plastic traits that depended on grow-out method, calcification rate was conserved. Our results show that the two rearing methods generate the same amount of calcium carbonate skeleton but produce colonies with different skeletal characteristics and suggest that there is genetically based variability in coral calcification performance.

Staghorn coral Acropora cervicornis is an important framework-building species that has declined severely throughout the Caribbean since the early 1980s. This species is now widely cultured in ocean-based nurseries to restore degraded populations. A variety of techniques have been adopted to grow A. cervicornis for restoration purposes, however the effect of each of these methods on nursery-reared corals is not well-understood. In particular, systematic evaluation of nursery-reared A. cervicornis between water column-suspended and benthic-attached culture methods is lacking. To better understand the effect of these techniques, a one-year A. cervicornis propagation experiment in the Florida Keys was conducted to compare growth, condition, and survivorship between common suspended (i.e. tree) and benthic-attached (i.e. block) grow-out methods. The effect of coral genotype on growth was also considered. Colonies were measured and monitored monthly from December 2014 until November 2015, when only three colonies had survived an extreme bleaching event. Colonies on trees grew up to three times faster than those on blocks and the location of colonies on trees did not affect growth. Genotype had a significant effect on colony growth, which was consistent across grow-out methods. Interestingly, colonies grown on blocks bleached sooner but survived longer than those on trees. These findings contribute to a growing understanding of A. cervicornis nursery culture, and could aid in the selection of culture methods and genotypes for coral nurseries throughout the wider Caribbean.

As coral restoration efforts increase globally, there is a growing need to not only increase post-restoration monitoring, but also advance reef restoration monitoring methods. Utilizing autonomous technology to compliment manual, SCUBA-based monitoring will diversify the types of data available to coral restoration practitioners and aid in determining the efficacy of restoration efforts. This study sought to investigate how existing reef monitoring technologies can be applied to coral restoration to improve monitoring resolution and assess restoration progress. The Benthic Ecosystem and Acidification Measurement System, which uses the gradient flux approach to measure benthic community metabolism, was used to monitor two arrays of nursery grown Acropora cervicornis within an offshore coral nursery in the Florida Keys. The first deployment monitored corals arranged in a density mimicking pre-restoration coral cover, while the second deployment monitored corals arranged in a density mimicking a reef site recently restored with nursery-grown A. cervicornis. The post-restoration density demonstrated a 36% increase in the observed ratio of net community calcification to net community production as compared to the pre-restoration density. Additionally, the post-restoration density demonstrated net accretion throughout the observation period (20 mmol CaCO3 m−2d−1) as compared to the pre-restoration density which experienced net dissolution (−5.0 mmol CaCO3 m−2d−1). Overall, the results of this study are promising indicators that metabolic monitoring could one day be widely utilized within the coral restoration field to remotely monitor benthic composition changes associated with coral restoration progress over time, providing valuable information to restoration practitioners, stakeholders, and resource managers.

The staghorn coral was once prevalent throughout the Florida Reef Tract. However, the last few decades have seen a substantial reduction in the coral population because of disease outbreaks and increasing ocean temperatures. The staghorn coral shows no evidence of natural recovery, and so has been the focus of restoration efforts throughout much of the Florida region. Why put the time and effort into growing corals that are unlikely to survive within environmental conditions that continue to deteriorate? One reason is that the genetic make-up – the genotype – of some corals makes them more resilient to certain threats. However, there could be tradeoffs associated with these resilient traits. For example, a coral may be able to tolerate heat, but may easily succumb to disease. Previous studies have identified some staghorn coral genotypes that are resistant to an infection called white-band disease. The influence of high water temperatures on the ability of the coral to resist this disease was not known. There also remained the possibility that more varieties of coral might show similar disease resistance. To investigate Muller et al. conducted two experiments exposing staghorn coral genotypes to white-band diseased tissue before and during a coral bleaching event. Approximately 25% of the population of staghorn tested was resistant to white-band disease before the bleaching event. When the corals were exposed to white-band disease during bleaching, twice as much of the coral died. Two out of the 15, or 13%, of the coral genotypes tested were resistant to the disease even while bleached. Additionally, the level of bleaching within the coral genotypes was not related to how easily they developed white-band disease, suggesting that there are no direct tradeoffs between heat tolerance and disease resistance. These results suggest that there are very hardy corals, created by nature, already in existence. Incorporating these traits thoughtfully into coral restoration plans may increase the likelihood of population-based recovery. The Florida Reef Tract is estimated to be worth over six billion dollars to the state economy, providing over 70,000 jobs and attracting millions of tourists into Florida each year. However, much of these ecosystem services will be lost if living coral is not restored within the reef tract. The results presented by Muller et al. emphasize the need for maintaining high genetic diversity while increasing resiliency when restoring coral. They also emphasize that disease resistant corals, even when bleached, already exist and may be an integral part of the recovery of Florida’s reef tract.

As climate changes, sea surface temperature anomalies that negatively impact coral reef organisms continue to increase in frequency and intensity. Yet, despite widespread coral mortality, genetic diversity remains high even in those coral species listed as threatened. While this is good news in many ways it presents a challenge for the development of biomarkers that can identify resilient or vulnerable genotypes. Taking advantage of three coral restoration nurseries in Florida that serve as long-term common garden experiments, we exposed over thirty genetically distinct Acropora cervicornis colonies to hot and cold temperature shocks seasonally and measured pooled gene expression responses using RNAseq. Targeting a subset of twenty genes, we designed a high-throughput qPCR array to quantify expression in all individuals separately under each treatment with the goal of identifying thermal stress biomarkers. We observed extensive transcriptional variation in the population, suggesting abundant raw material is available for adaptation via natural selection. However, this high variation made it difficult to correlate gene expression changes with colony performance metrics such as growth, mortality, and bleaching susceptibility. Nevertheless, we identified several promising biomarkers for acute thermal stress that may improve coral restoration and climate change mitigation efforts in the future.

Threatened Caribbean coral communities can benefit from high‐resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis, across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis, including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

Background Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species’ ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions. To evaluate active restoration strategies for the staghorn coral, the genetic diversity of A. cervicornis within and among populations was assessed in 77 individuals collected from 68 locations along the Florida Reef Tract (FRT) and in the Dominican Republic. Results Genotyping by Sequencing (GBS) identified 4,764 single nucleotide polymorphisms (SNPs). Pairwise nucleotide differences (π) within a population are large (~37 %) and similar to π across all individuals. This high level of genetic diversity along the FRT is similar to the diversity within a small, isolated reef. Much of the genetic diversity (>90 %) exists within a population, yet GBS analysis shows significant variation along the FRT, including 300 SNPs with significant FST values and significant divergence relative to distance. There are also significant differences in SNP allele frequencies over small spatial scales, exemplified by the large FST values among corals collected within Miami-Dade county. Conclusions Large standing diversity was found within each population even after recent declines in abundance, including significant, potentially adaptive divergence over short distances. The data here inform conservation and management actions by uncovering population structure and high levels of diversity maintained within coral collections among sites previously shown to have little genetic divergence. More broadly, this approach demonstrates the power of GBS to resolve differences among individuals and identify subtle genetic structure, informing conservation goals with evolutionary implications.

During an unusual cold-water event in January 2010, reefs along the Florida Reef Tract suffered extensive coral mortality, especially in shallow reef habitats in close proximity to shore and with connections to coastal bays. The threatened staghorn coral, Acropora cervicornis ,i s the focus of propagation and restoration activities in Florida and one of the species that exhibited high susceptibility to low temperatures. Complete mortality of wild staghorn colonies was documented at 42.9% of donor sites surveyed after the cold event. Remarkably, 72.7% of sites with complete A. cervicornis mortality had fragments surviving within in situ coral nurseries. Thus, coral nurseries served as repositories for genetic material that would have otherwise been completely lost from donor sites. The location of the coral nurseries at deeper habitats and distanced from shallow nearshore habitats that experienced extreme temperature conditions buffered the impacts of the cold-water event and preserved essential local genotypes for future Acropora restoration activities.

We examined the photoreactivity of chromophoric dissolved organic matter (CDOM) derived from Rhizophora mangle (red mangrove) leaf litter and floating Sargassum colonies as these marine plants can be important contributors to coastal and open ocean CDOM pools, respectively. Mangrove and Sargassum CDOM readily degraded when exposed to simulated solar irradiance (CPS SunTest solar simulator exposures). CDOM produced from brown mangrove leaves (representative of substantial senescence) exhibited shorter photobleaching half-lives (a305 t1/2

Chromophoric dissolved organic matter (CDOM) strongly absorbs solar radiation in the blue-green and serves as the primary attenuator of water column ultraviolet radiation (UV-R). CDOM interferes with remote sensing of ocean chlorophyll and can control UV-R-induced damage to light-sensitive organisms including corals. We used laboratory incubations to evaluate CDOM production from senescing Rhizophora mangle (red mangrove) leaf litter (yellow, orange, and brown) and floating Sargassum colonies. Mangroves exist at the land–ocean interface near coral reefs in sub-tropical and tropical regions while floating Sargassum colonies tend to congregate in sub-tropical ocean gyres. CDOM production (∼ 48 h) from mangrove leaves collected during a dry period in June 2004 (0.17 ± 0.11 m − 1 g − 1 l h − 1 ) was lower than production from leaves collected during a wet period in September 2003 (0.57 ± 0.42 m − 1 g − 1 l h − 1 ) suggesting that CDOM production from leaf litter fluctuates in response to environmental factors. CDOM production was greatest for the mid-senescence orange leaves and lowest for the severely senesced brown leaves in both experiments. Along the sub-tropical Florida Keys coral reef ecosystem, the primary source of CDOM is discharge from the shallow seagrass-dominated Florida Bay as evidenced by a strong correlation between field CDOM measurements and previously reported Florida Bay discharge volumes. However, field observations provide evidence that large expanses of red mangroves throughout the Keys could be important CDOM sources to the region's coral reefs during periods of reduced Florida Bay discharge. Floating Sargassum colonies also readily produced CDOM in laboratory incubations, but at much more variable rates than mangrove leaves. However, our calculations indicate that large mats of floating Sargassum could provide important CDOM quantities to oligotrophic oceanic waters including the Gulf of Mexico and North Atlantic.

Solar ultraviolet (UV) radiation can have deleterious effects on coral assemblages in tropical and subtropical marine environments, but little information is available on UV penetration into ocean waters surrounding corals. Here we provide an extensive data set of optical properties in the UV domain (280[en]400 nm) that were obtained during 1998-2005 at sites located in the Lower and Middle Keys and the Dry Tortugas. Absorption coefficients of the colored component of the dissolved organic carbon (DOC; colored dissolved organic matter [CDOM]) were 6x to 25 X larger than particulate absorption coefficients in the UV region, indicating that CDOM controls UV penetration in the inshore coastal waters and reef tract. CDOM absorption coefficients (a CDOM ) and DOC were highly correlated to diffuse attenuation coefficients (K d ) in the UV spectral region. Measurements using moored sensors showed that UV penetration at the reef tract in the Lower Keys varies significantly from day to day and diurnally. The diurnal variations were linked to tidal currents that transport CDOM over the reef tract. Summertime stratification of Case 1 bluewaters near the reef tract during periods of low wind resulted in higher temperatures and UV penetration than that observed during well-mixed conditions. This result suggests that higher UV exposure accompanying ocean warming during low-wind doldrums conditions significantly contributes to coral bleaching. Modeling results indicate that changes in underwater sunlight attenuation over the coral reefs can affect UV-induced deoxyribonucleic acid (DNA) damage and inhibition of coral photosynthesis much more strongly than changes in the stratospheric ozone layer.

Seagrasses play a variety of important ecological roles in coastal ecosystems. Here we present evidence that seagrass detritus from the widespread species Thalassia testudinum is an important source of ocean color and a UV-protective substance in a low latitude coastal shelf region of the United States. The production and light-induced degradation of chromophoric (sunlight- absorbing) dissolved organic matter (CDOM) from T. testudinum was examined under field and con- trolled laboratory conditions to obtain data that could be used to estimate the contribution of sea- grass-derived CDOM to the coastal pool. The laboratory studies measured the temperature depen- dence and photodegradation of the spectral (UV-visible, fluorescence) and molecular mass properties of CDOM produced during the degradation of T. testudinum detritus. The rate of CDOM production is temperature-dependent with rates doubling when temperature increases from 21.4 to 32.6°C. The magnitude of this increase is close to the widely observed Q10 factor for microbial decomposition, indicating that the CDOM production was likely microbially mediated. The absorption coefficients and fluorescence of CDOM from T. testudinum decreased on exposure to solar UV radiation (UVR) and the wavelength dependence was determined for this photobleaching process.

Studying the mechanisms that enable coral populations to inhabit spatially varying thermal environments can help evaluate how they will respond in time to the effects of global climate change and elucidate the evolutionary forces that enable or constrain adaptation. Inshore reefs in the Florida Keys experience higher temperatures than offshore reefs for prolonged periods during the summer. We conducted a common garden experiment with heat stress as our selective agent to test for local thermal adaptation in corals from inshore and offshore reefs. We show that inshore corals are more tolerant of a 6-week temperature stress than offshore corals. Compared with inshore corals, offshore corals in the 31 °C treatment showed significantly elevated bleaching levels concomitant with a tendency towards reduced growth. In addition, dinoflagellate symbionts (Symbiodinium sp.) of offshore corals exhibited reduced photosynthetic efficiency. We did not detect differences in the frequencies of major (>5%) haplotypes comprising Symbiodinium communities hosted by inshore and offshore corals, nor did we observe frequency shifts (‘shuffling’) in response to thermal stress. Instead, coral host populations showed significant genetic divergence between inshore and offshore reefs, suggesting that in Porites astreoides, the coral host might play a prominent role in holobiont thermotolerance. Our results demonstrate that coral populations inhabiting reefs

SUMMARY Disease epizootics are increasing with climatic shifts, yet within each system only a subset of species are identified as the most vulnerable. Understanding ecological immunology patterns as well as environmental influences on immune defenses will provide insight into the persistence of a functional system through adverse conditions. Amongst the most threatened ecosystems are coral reefs, with coral disease epizootics and thermal stress jeopardizing their survival. Immune defenses were investigated within three Caribbean corals, Montastraea faveolata, Stephanocoenia intersepta and Porites astreoides, which represent a range of disease and bleaching susceptibilities. Levels of several immune parameters were measured in response to elevated water temperature and the presence of a commercial pathogen-associated molecular pattern (PAMP) – lipopolysaccharide (LPS) – as an elicitor of the innate immune response. Immune parameters included prophenoloxidase (PPO) activity, melanin concentration, bactericidal activity, the antioxidants peroxidase and catalase, and fluorescent protein (FP) concentration. LPS induced an immune response in all three corals, although each species responded differently to the experimental treatments. For example, M. faveolata, a disease-susceptible species, experienced significant decreases in bactericidal activity and melanin concentration after exposure to LPS and elevated temperature alone. Porites astreoides, a disease-resistant species, showed increased levels of enzymatic antioxidants upon exposure to LPS independently and increased PPO activity in response to the combination of LPS and elevated water temperature. This study demonstrates the ability of reef-building corals to induce immune responses in the presence of PAMPs, indicating activation of PAMP receptors and the transduction of appropriate signals leading to immune effector responses. Furthermore, these data address the emerging field of ecological immunology by highlighting interspecific differences in immunity and immunocompetences among Caribbean corals, which are reflected in their life-history characteristics, disease susceptibilities and bleaching-induced mortality.

Background Coral reefs are facing increasing pressure from natural and anthropogenic stressors that have already caused significant worldwide declines. In January 2010, coral reefs of Florida, United States, were impacted by an extreme cold-water anomaly that exposed corals to temperatures well below their reported thresholds (16°C), causing rapid coral mortality unprecedented in spatial extent and severity. Methodology/Principal Findings Reef surveys were conducted from Martin County to the Lower Florida Keys within weeks of the anomaly. The impacts recorded were catastrophic and exceeded those of any previous disturbances in the region. Coral mortality patterns were directly correlated to in-situ and satellite-derived cold-temperature metrics. These impacts rival, in spatial extent and intensity, the impacts of the well-publicized warm-water bleaching events around the globe. The mean percent coral mortality recorded for all species and subregions was 11.5% in the 2010 winter, compared to 0.5% recorded in the previous five summers, including years like 2005 where warm-water bleaching was prevalent. Highest mean mortality (15%–39%) was documented for inshore habitats where temperatures were

Background:The rising temperature of the world’s oceans has become a major threat to coral reefs globally as the severityand frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropicalAtlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin.Methodology/Principal Findings:Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers’ field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles.Conclusions/Significance:Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA CoralReef Watch’s Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality willundoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate NOAA Coral Reef Conservation Program Article Nr: e13969