The degradation of coral reefs has resulted in the expansion of coral reef restoration projects worldwide. In the tropical western Atlantic, most restoration efforts focus on outplanting Acropora cervicornis, once a dominant reef‐building branching coral, now found predominantly in spatially isolated populations. Hundreds of thousands of A. cervicornis colonies are outplanted onto degraded reefs every year; however, long‐term growth and survival data of outplanted corals is limited. In this study, we assessed the long‐term restoration of A. cervicornis by determining the relationship between surviving outplant populations and restoration effort. We surveyed coral populations at 11 sites in the upper Florida Keys that represented a gradient of restoration effort, defined by the total number of outplants, number of outplanting years, and time since last outplanting. We found a negative relationship between the amount of A. cervicornis live tissue and time since last outplanting, suggesting that outplants are not surviving longer than 2 years. In addition to restoration effort, we investigated how past and present benthic community metrics such as coral density and diversity may influence long‐term outplant survival. We found a positive relationship between the amount of live A. cervicornis tissue and pre‐restoration coral density, suggesting that areas that previously supported dense populations of corals may facilitate restoration success. Ultimately, this study finds that restored A. cervicornis populations decline over time, and continued outplanting effort is needed for the persistence of the species in certain areas. This study also highlights the need for more long‐term monitoring to inform adaptive management and restoration strategies.

Outbreaks of coral disease have been a dominant force shaping western Atlantic coral-reef assemblages since the late 1970s. Stony coral tissue loss disease (SCTLD) is nonetheless having an unprecedented impact in the region. Whereas numerous studies over the last decade have worked to characterize this novel pathogen and its impacts on coral populations, few have quantified its functional effects on reef ecosystems. Of particular importance is how SCTLD may be impacting the essential reef-accretion process and the myriad ecosystem services it supports. Here, we evaluated the impact of SCTLD on reef-accretion potential by estimating carbonate budgets and taxon-level carbonate production at 43 sites throughout the Florida Keys from 2016−2022. Average regional reef-accretion potential declined from an already low, but positive rate of 0.30 ± 0.16 mm y -1 (mean ± standard error) in 2016 before the disease was first observed, to a state of accretionary stasis (0.08 ± 0.12 mm y -1 ) by 2022. This 70% relative decline in reef-accretion potential was driven by the loss of reef-building corals, with significant decreases in carbonate production by massive taxa including Colpophyllia natans , Montastraea cavernosa , Pseudodiploria strigosa , Orbicella spp., and Siderastrea siderea , and increasing contributions from less susceptible, weedy taxa including Millepora spp., Agaricia spp., and Porites astreoides . In general, changes in taxon-level carbonate production following the SCTLD outbreak mirror long-term shifts in reef assemblages in response to previous stressors. One striking exception, however, is S. siderea , which had become increasingly dominant in recent decades, but declined significantly in response to SCTLD. Overall, by further decimating the already depauperate reef-building coral populations in the Florida Keys, SCTLD has caused a functionally significant shift in the composition of Florida’s coral-reef assemblages and accelerated the loss of regional reef-building capacity. The dire impacts of the disease in south Florida may serve as an early warning that the persistence of the invaluable ecological and socioeconomic functions coral reefs provide will be increasingly threatened throughout the western Atlantic in the aftermath of SCTLD.

Scleractinian coral populations are in global decline, and successful recruitment is fundamental to community persistence and recovery, but recruitment may vary by coral reproductive mode. Using settlement tiles, we assessed coral recruitment over 3 consecutive years across 4 regions (~300 km) of the Florida Reef Tract (FRT) to determine whether spatio-temporal variation differs between brooding and broadcast spawning corals and whether coral recruit distributions correlate with adult coral live tissue area, site temperature, or depth. We deployed 32 tiles to each of 30 sites with depths ranging from 2 to 18 m; tiles were retrieved and replaced annually. From 2016-2018, we counted 11633 scleractinian coral recruits, most of which belonged to the Siderastreidae, Agariciidae, Poritidae, and Faviidae families. Faviid recruits were rare (<1%). While recruitment of brooding agariciids and poritids was relatively stable across the 3 yr, recruitment of broadcast spawning siderastreids increased an unprecedented 70.7-fold from 2017 to 2018, in a boom that spanned 19 sites across the FRT. Elevated temperature during the preceding reproductive season was a significant predictor of low recruitment for all groups except siderastreids and faviids, and recruitment of brooding taxa was positively linked to adult confamilial live tissue area. For siderastreids, adult live tissue area was also related to recruitment, but the direction of the relationship differed by year and region. The unprecedented high recruitment of siderastreids in Florida, preceded by 2 yr of comparatively low recruitment, demonstrates that broadcast-spawning scleractinians are among the marine taxa capable of employing boom-and-bust recruitment cycles over geographically widespread areas.

The epizootic disease outbreak known as stony coral tissue loss disease (SCTLD) is arguably the most devastating coral disease in recorded history. SCTLD emerged off the coast of South Florida in 2014 and has since moved into the Caribbean, resulting in coral mortality rates that have changed reef structure and function. Currently, the cause of SCTLD is unknown, but there is evidence from 16S rRNA gene sequencing and bacterial culture studies that the microbial community plays a role in the progression of SCTLD lesions. In this study, we applied shotgun metagenomics to characterize the potential function of bacteria, as well as the composition of the micro-eukaryotic community, associated with SCTLD lesions. We re-examined samples that were previously analyzed using 16S rRNA gene high-throughput sequencing from four coral species: Stephanocoenia intersepta, Diploria labyrinthiformis, Dichocoenia stokesii, and Meandrina meandrites. For each species, tissue from apparently healthy (AH) corals, and unaffected tissue (DU) and lesion tissue (DL) on diseased corals, were collected from sites within the epidemic zone of SCTLD in the Florida Keys. Within the micro-eukaryotic community, the taxa most prominently enriched in DL compared to AH and DU tissue were members of Ciliophora. We also found that DL samples were relatively more abundant in less energy-efficient pathways like the pentose phosphate pathways. While less energy-efficient processes were identified, there were also relatively higher abundances of nucleotide biosynthesis and peptidoglycan maturation pathways in diseased corals compared to AH, which suggests there was more bacteria growth in diseased colonies. In addition, we generated 16 metagenome-assembled genomes (MAGs) belonging to the orders Pseudomonadales, Beggiatoales, Rhodobacterales, Rhizobiales, Rs-D84, Flavobacteriales, and Campylobacterales, and all MAGs were enriched in DL samples compared to AH samples. Across all MAGs there were antibiotic resistance genes that may have implications for the treatment of SCTLD with antibiotics. We also identified genes and pathways linked to virulence, such as nucleotide biosynthesis, succinate dehydrogenase, ureases, nickel/iron transporters, Type-1 secretion system, and metalloproteases. Some of these enzymes/pathways have been previously targeted in the treatment of other bacterial diseases and they may be of interest to mitigate SCTLD lesion progression.

Acute disturbances and chronic pressures have an important and increasing influence on the structure of coral reef communities. For the viability of benthic taxa such as stony corals, a balance between loss following disturbance and recovery is vital. Coral populations on reefs with lower exposure to chronic pressures are often presumed to have increased resilience, enabling them to recover quickly following disturbance, but decades of anthropogenic stress and degradation may undermine the systematic recovery and reassembly of benthic communities. This study explored spatiotemporal changes in benthic community structure over a 15 yr period at three distinct coral reef regions with a gradient of chronic pressures in Florida, USA, (southeast Florida, the Florida Keys and the Dry Tortugas). We specifically assessed the spatial scale, potential drivers of change and resilience in stony coral, octocoral, sponge and macroalgae cover. Spatiotemporal changes were assessed at four different scales: among regions, habitats, sub-regions, and habitat types within regions. Cover of stony corals remained very low or declined in every region from 2004 to 2018, with corresponding increases in macroalgae cover. Stony coral recovery was limited regardless of regional differences in chronic pressure. Octocorals exhibited greater resilience due to increased recovery following disturbance and generally had higher cover than stony corals on Florida's Coral Reef, while sponge cover was very stable over the study period. Acute disturbances, which affected sites on average once every 3 yr, negatively impacted stony coral and/or octocoral cover in every region and habitat, contributing to the regionwide proliferation of macroalgae. This study determined that high disturbance frequency and chronic anthropogenic pressures on Florida's Coral Reef have led to sustained declines in stony corals and corresponding proliferation of macroalgae. Stony corals were expected to recover during inter-disturbance periods, but in Florida, even in locations with lower chronic pressure, recovery is severely limited.

Quantifying recruitment of corals is important for evaluating their capacity to recover after disturbances through natural processes, yet measuring recruitment rates in situ is challenging due to the minute size of the study organism and the complexity of benthic communities. Settlement tiles are widely used in studies of coral recruitment because they can be viewed under a microscope to enhance accuracy, but methodological choices such as the rugosity of tiles used and when and how to scan tiles for recruits post-collection may cause inconsistencies in measured recruitment rates. We deployed 2,880 tiles with matching rugosity on top and bottom surfaces to 30 sites along the Florida Reef Tract for year-long saturations during a three year study. We scanned the top and bottom surfaces of the same tiles for scleractinian recruits before (live scans) and after treating tiles with sodium hypochlorite (corallite scans). Recruit counts were higher in corallite than live scans, indicating that scleractinian recruitment rates should not be directly compared between studies using live scans and those scanning tiles which have been processed to remove fouling material. Recruit counts also were higher on tile tops in general, but the proportion of settlement to the top and bottom surfaces varied significantly by scleractinian family. Thus, biases may be introduced in recruitment datasets by differences in tile rugosity or by only scanning a subset of tile surfaces. Finally, we quantified octocoral recruitment during live scans and found they preferentially settled to tile tops. We recommend that recruitment tile studies include corallite scans for scleractinian skeletons, deploy tiles with matching rugosity on top and bottom surfaces, and scan all tile surfaces.

Quantifying recruitment of corals is important for evaluating their capacity to recover after disturbances through natural processes, yet measuring recruitment rates in situ is challenging due to the minute size of the study organism and the complexity of benthic communities.Settlement tiles are widely used in studies of coral recruitment because they can be viewed under a microscope to enhance accuracy, but methodological choices such as the rugosity of tiles used and when and how to scan tiles for recruits post-collection may cause inconsistencies in measured recruitment rates.We deployed 2880 tiles with matching rugosity on top and bottom surfaces to 30 sites along the Florida Reef Tract for year-long saturations during a three year study.We scanned the top and bottom surfaces of the same tiles for scleractinian recruits before (live scans) and after treating tiles with sodium hypochlorite (corallite scans).Recruit counts were higher in corallite than live scans, indicating that scleractinian recruitment rates should not be directly compared between studies using live scans and those scanning tiles, which have been processed to remove fouling material.Recruit counts also were higher on tile tops in general, but the proportion of settlement to the top and bottom surfaces varied significantly by scleractinian family.Thus, biases may be introduced in recruitment datasets by differences in tile rugosity or by only scanning a subset of tile surfaces.Finally, we quantified octocoral recruitment during live scans and found they preferentially settled to tile tops.We recommend that recruitment tile studies include corallite scans for scleractinian skeletons, deploy tiles with matching rugosity on top and bottom surfaces, and scan all tile surfaces.

In 2014, Stony Coral Tissue Loss Disease (SCTLD) was first detected off the coast of Miami, FL, United States, and continues to persist and spread along the Florida Reef Tractr (FRT) and into the Caribbean. SCTLD can have up to a 61% prevalence in reefs and has affected at least 23 species of scleractinian corals. This has contributed to the regional near-extinction of at least one coral species, Dendrogyra cylindrus. Initial studies of SCTLD indicate microbial community shifts and cessation of lesion progression in response to antibiotics on some colonies. However, the etiology and abiotic sources of SCTLD transmission are unknown. To characterize SCTLD microbial signatures, we collected tissue samples from four affected coral species: Stephanocoenia intersepta, Diploria labyrinthiformis, Dichocoenia stokesii, and Meandrina meandrites. Tissue samples were from apparently healthy (AH) corals, and unaffected tissue (DU) and lesion tissue (DL) on diseased corals. Samples were collected in June 2018 from three zones: (1) vulnerable (ahead of the SCTLD disease boundary in the Lower Florida Keys), (2) endemic (post-outbreak in the Upper Florida Keys), and (3) epidemic (SCTLD was active and prevalent in the Middle Florida Keys). From each zone, sediment and water samples were also collected to identify whether they may serve as potential sources of transmission for SCTLD-associated microbes. We used 16S rRNA gene amplicon high-throughput sequencing methods to characterize the microbiomes of the coral, water, and sediment samples. We identified a relatively higher abundance of the bacteria orders Rhodobacterales and Rhizobiales in DL tissue compared to AH and DU tissue. Also, our results showed relatively higher abundances of Rhodobacterales in water from the endemic and epidemic zones compared to the vulnerable zone. Rhodobacterales and Rhizobiales identified at higher relative abundances in DL samples were also detected in sediment samples, but not in water samples. Our data indicate that Rhodobacterales and Rhizobiales may play a role in SCTLD and that sediment may be a source of transmission for Rhodobacterales and Rhizobiales associated with SCTLD lesions.

As coral cover has declined throughout the Caribbean, interest in determining the potential for reef recovery via natural recruitment processes has increased. Studies investigating recruitment have been hampered by the difficulty of identifying early stage corals that often lack distinguishing morphological characters. In this study, the utility of targeting the noncoding ribosomal internal transcribed spacer (ITS) regions with a single-step nested multiplex (SSNM) PCR assay to identify common Caribbean coral species was investigated. To design this assay, a database of ITS sequences for 17 common Caribbean coral species was developed. Phylogenies based on the ITS region were generally consistent with current published coral taxonomy and indicated that the ITS regions provided sufficient variability to be useful for distinguishing corals to at least the genus level. Ultimately, we developed ITS-targeted single-step nested multiplex PCR assays capable of differentiating six corals to the species level, two to the genus level, and a pair of coral species that were recently separated at the genus level. This assay was used to classify coral recruits previously identified based on morphological characters. Agreement between these two approaches was low and highlighted the ability of the SSNM-PCR assay to increase the certainty and accuracy of coral recruit identifications. The coral SSNM assay shows promise as an effective method of identifying early stage corals to the genus or species level, and as a valuable tool in studies investigating reef recovery.

In January 2010, reefs in the Upper and Middle Florida Keys experienced prolonged exposure to extremely cold water temperatures, below lethal thresholds for many reef organisms including corals. We examined post-disturbance juvenile assemblages of stony corals and octocorals on eight patch reefs, four of which were categorized as high impact and four as low impact, based on declines in stony-coral cover following disturbance. We established permanent quadrats to conduct field surveys in spring and fall of 2012 and 2013. Overall, juvenile abundances of both stony corals and octocorals were greater on low-impact sites, suggesting that those sites had higher recruitment and juvenile survival than high-impact sites. Juvenile assemblages also showed a regional pattern, with more stony corals on Middle Keys sites and more octocorals on Upper Keys sites. The stony-coral juvenile assemblage was dominated by Siderastrea siderea (46%) and Porites astreoides (19%), whereas previously abundant species such as Orbicella annularis were nearly absent (<3%). Octocoral juveniles were dominated by Antillogorgia spp. (25%), Gorgonia spp. (21%), Eunicea spp. (19%) and Erythropodium caribaeorum (14%). Overall, post-disturbance juvenile assemblages displayed a wide range of octocoral genera, but only a few select stony-coral species, which exhibited either opportunistic or hardy life-history characteristics.

AbstractOrganismal and community‐wide responses of reef‐building corals are documented before and after a severe cold‐water thermal anomaly that occurred in 2010 in the Florida Keys, USA. In January 2010 seawater temperatures dropped far below the normal minima (to <11°C), resulting in the largest documented coral mass mortality event ever recorded in the Florida Keys. Physiological measurements demonstrated species‐specific thermal sensitivities to this environmental perturbation. Four common corals with narrow thermal tolerance, Acropora cervicornis, Orbicella annularis, O. faveolata, and Porites astreoides, sustained high mortality (>80%) on inshore reefs. In contrast, another common coral with a wide thermal tolerance, Siderastrea siderea, was not affected by this cold anomaly. We measured biomass, symbiotic algal densities (genus: Symbiodinium), chlorophyll a content, and maximum quantum efficiency of photosystem II for reef‐building corals on a seasonal basis before and after the 2010 cold anomaly. Our data document a clear correspondence between physiological response, biomass levels, and survivorship among these five scleractinian coral species. These physiological findings are mirrored by in‐shore benthic community monitoring data, which show the dramatic loss of the three cold‐sensitive species and continued survival of the cold‐tolerant species. Finally, we document recruitment and survival rates of newly settled reef‐building corals on four inshore reefs, which experienced high coral mortality during the 2010 cold‐kill. Interestingly, both a cold‐tolerant species, S. siderea, and a cold‐intolerant species, P. astreoides, were the most abundant species recruiting to these postdisturbance reefs.

The increase in anthropogenic carbon dioxide in seawater, termed ocean acidification (OA), depresses calcification rates of coral and algae, and may contribute toward reef ecosystem degradation. To test how future OA conditions will influence biologically-mediated dissolution (bioerosion) of coral by the common Caribbean boring sponge Pione lampa (de Laubenfels, 1950), we conducted a series of carefully controlled incubations and used changes in total alkalinity (TA) to calculate calcium carbonate dissolution. We present data showing a positive relationship between seawater pCO(2) and chemical bioerosion that predict a 99% increase in chemical erosion before the end of the century, more than double the expected decline in coral calcification rate. To examine how OA-enhanced erosion will influence reef ecosystem persistence, we incorporated these and other data into a carbonate budget model of 37 reefs along the Florida Reef Tract (FRT). Our model showed that all FRT reefs had a positive CaCO3 budget [mean = 8.257 (SE 0.8077) kg m(-2) yr(-1)] in preindustrial times, whereas approximately 89% of reefs presently exhibit net erosion. Present-day reef-specific calcification would need to increase by 29.4% to compensate for projected end of the century OA-enhancement of total bioerosion. These findings show that OA may accelerate Caribbean and Atlantic coral reef degradation more rapidly than previously predicted.

Recent increases in both the frequency and severity of coral bleaching events have spurred numerous surveys to quantify the immediate impacts and monitor the subsequent community response. Most of these efforts utilize conventional diver-based methods, which are inherently time-consuming, expensive, and limited in spatial scope unless they deploy large teams of scientifically-trained divers. In this study, we evaluated the effectiveness of the Along-Track Reef Imaging System (ATRIS), an automated image-acquisition technology, for assessing a moderate bleaching event that occurred in the summer of 2011 in the Florida Keys. More than 100,000 images were collected over 2.7km of transects spanning four patch reefs in a 3-h period. In contrast, divers completed 18, 10-m long transects at nine patch reefs over a 5-day period. Corals were assigned to one of four categories: not bleached, pale, partially bleached, and bleached. The prevalence of bleaching estimated by ATRIS was comparable to the results obtained by divers, but only for corals >41cm in size. The coral size-threshold computed for ATRIS in this study was constrained by prevailing environmental conditions (turbidity and sea state) and, consequently, needs to be determined on a study-by-study basis. Both ATRIS and diver-based methods have innate strengths and weaknesses that must be weighed with respect to project goals.

Annual surveys conducted by the Coral Reef Evaluation and Monitoring Project (CREMP) reported that average benthic cover of stony corals in the Florida Keys National Marine Sanctuary, USA declined from similar to 13% in 1996 to 8% in 2009. Keys-wide, mean species richness (SR) declined by similar to 2.3 species per station. Stress due to temperature extremes is suspected to be a major driver of this trend. We tested the potential for sea surface temperature (SST) variability and acute warm-temperature events (assessed with Degree Heating Weeks) to affect stony coral diversity in the Florida Keys. Benthic cover of 43 stony coral species was examined with respect to SST variability and habitat type (patch, offshore shallow, and offshore deep reefs). For each CREMP site, SST annual variance was classified as low (<7.0 degrees C-2), intermediate (7.0 to 10.9 degrees C-2), or high (>= 11.0 degrees C-2). Nonparametric MANOVA analyses showed that in the Upper, Middle, and Lower Keys regions, massive-type stony coral species (e.g. Siderastrea siderea, Pseudodiploria strigosa, Orbicella annularis complex, Montastraea cavernosa, and Colpophyllia natans) were prevalent in the patch reef habitats exposed to intermediate to high SST variability. Intermediate SST variability was also correlated with higher Shannon diversity means in patch reefs in the Upper Keys and higher SR means in the Middle Keys, indicating either that the stony coral species in these habitats are adapted to an intermediate temperature range or that individual colonies have acclimatized to that range. No significant relationships were found between stony coral diversity and SST variability in the Dry Tortugas region.

Disturbances that result in the mass mortality of reef-building corals are changing the appearance of reefs worldwide. Many reefs are transitioning away from scleractinian-coral- dominated assemblages to benthic communities composed primarily of non-scleractinian taxa. This study evaluated recovery patterns of reef communities in the Florida Keys following the mortality associated with the 1997/1998 El Nino. We examined temporal trends among the 5 most spatially abundant reef taxa and stony coral species from 1999 to 2009 at 3 spatial scales, and applied a Principal Coordinate Analysis (PCoA) to determine whether changes in their cover resulted in a shift in community structure. Trends of decreasing stony coral cover were not identi- fied Keys-wide between 1999 and 2009, but 2 of the 3 habitats examined—shallow and deep for- ereefs—did show a significant decline in cover. Concomitantly, octocoral cover significantly increased Keys-wide and in all 3 habitats. The transition to octocorals was most evident on shallow forereefs, where octocoral cover significantly increased at 9 of 12 reefs and overwhelmingly influ- enced the PCoA. On deep forereefs, octocoral and sponge cover did significantly increase, but did not impart a clearly defined shift in community structure like that observed on shallow forereefs. Community composition at patch reefs was relatively consistent during the study, but the increase in octocoral cover may accelerate further following a cold-water mortality event in 2010. These results demonstrate that octocorals are emerging as the predominant benthic taxa in the Florida Keys. Although the transition to octocorals may have started long ago, their apparent resilience to present-day stressors will likely allow this shift to continue into the foreseeable future.

Climate change scenarios predict stronger and more frequent hurricanes. We studied survival patterns of Acropora palmata during the hyper-active 2005 Atlantic Hurricane Season [AHS] to assess future effects of routinely elevated storm seasons. Before the start of the 2005 AHS, 105 colonies on three survey reefs in the EPA/NOAA Coral Reef Monitoring Project were marked and tracked through 2007. Only 13 of the original 105 marked colonies survived the 2005 AHS (12%). When grouped into classes based on a combination of size, morphology, and position, results show a highly significant interaction between these classes and survivorship (Chi Sq. = 23.61; d.f. = 1; ρ < 0.0001). None of the large, 3-D exposed corals, and few of the medium, 3-D exposed corals survived. By contrast, highest survivorship occurred among small, 2-D protected corals. Medium-sized, 2-D protected corals had intermediate survival rates. None of the corals that were loose on the bottom survived. By asexual reproduction mechanisms such as breakage and fission, the socalled ‘Sorcerer’s Apprentice Effects,’ these 13 original colonies were represented on the post-hurricane reef by 33 distinct propagules (9 pieces by breakage and 24 by fission). None of the colonies formed by breakage and only 3 of the colonies formed by fission remained by 2007. No putative sexual recruitment was observed in the two years following the 2005 AHS. As a matter of public policy, we should undertake colony cementation and snail removal as perhaps the only way to promote Acropora palmata regrowth and recolonization following catastrophic disturbances.