Stony coral tissue loss disease decimated Caribbean coral populations and reshaped reef functionality

Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea

Coral populations worldwide are declining rapidly due to elevated ocean temperatures and other human impacts. The Caribbean harbors a high number of threatened, endangered, and critically endangered coral species compared with reefs of the larger Indo-Pacific. The reef corals of the Caribbean are also long diverged from their Pacific counterparts and may have evolved different survival strategies. Most genomic resources have been developed for Pacific coral species which may impede our ability to study the changes in genetic composition of Caribbean reef communities in response to global change. To help fill the gap in genomic resources, we used PacBio HiFi sequencing to generate the first genome assemblies for 3 Caribbean reef-building corals, Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea. We also explore the genomic novelties that shape scleractinian genomes. Notably, we find abundant gene duplications of all classes (e.g. tandem and segmental), especially in S. siderea. This species has one of the largest genomes of any scleractinian coral (822 Mb) which seems to be driven by repetitive content and gene family expansion and diversification. As the genome size of S. siderea was double the size expected of stony corals, we also evaluated the possibility of an ancient whole-genome duplication using Ks tests and found no evidence of such an event in the species. By presenting these genome assemblies, we hope to develop a better understanding of coral evolution as a whole and to enable researchers to further investigate the population genetics and diversity of these 3 species.

Cryptic coral community composition across environmental gradients

Cryptic genetic variation is increasingly being identified in numerous coral species, with prior research indicating that different cryptic genetic lineages can exhibit varied responses to environmental changes. This suggests a potential link between cryptic coral lineages and local environmental conditions. In this study, we investigate how communities of cryptic coral lineages vary along environmental gradients. We began by identifying cryptic genetic lineages within six coral species sampled around St. Croix, USVI based on 2b-RAD sequencing data. We then analyzed associations between the distributions of cryptic lineages across the six coral species (i.e., "cryptic coral community composition") and ecoregions, or geographically distinct environmental conditions. Our findings show that depth is a more significant predictor of community composition than ecoregions and is the most influential factor among the 40 abiotic variables that characterize ecoregions. These results imply that cryptic coral communities are influenced by both depth and local environmental conditions, although the exact environmental factors driving these patterns remain unknown. Understanding community turnover across a seascape is important to consider when outplanting corals to restore a reef, as locally-adapted lineages may have differential fitness in different environmental conditions.

The differential physiological responses to heat stress in the scleractinian coral Pocillopora damicornis are affected by its energy reserve

The scleractinian corals conduct various responses upon heat stress such as bleaching and tissue loss, and colonies from the same coral species can conduct differential physiological activities with the biochemical basis unknown. In the present study, factors that influence the heat stress responses in coral Pocillopora damicornis were investigated. It was observed that P. damicornis conducted three differential physiological responses under heat treatment including tissue loss, bleaching, and polyp bailout. During heat response process, coral colonies conducting tissue loss had significantly higher total antioxidant capacity (T-AOC) level, while the bleached coral colonies exhibited higher caspase-3 activation level. Moreover, the stress response varied based on the energy reserve status. Colonies with higher lipid and sugar reserves were more likely to bleach, while those with lower reserves tended to undergo polyp bailout. We demonstrate that energy reserves influence the heat response patterns of P. damicornis. Colonies with higher lipid and sugar reserves may survive longer under heat stress, suggesting that these energy reserves contribute to their heat resistance. This study suggests that colonies with higher energy reserves prior to thermal stress may have greater thermal resistance, indicating that long-term environmental stressors that deplete energy reserves could increase susceptibility to thermal stress.

Tracking over 30 years of coral reef infrastructure degradation in Barbados

Coral reefs face escalating threats from global and local stressors, and these challenges are exacerbated in the Caribbean. This study focuses on coral reef structure in Barbados, where a previous study documented reef degradation in the 1990s. As 30 years have passed, we examined the rate of change of reef structure and quantified associated substrate presence along the western reefs of Barbados. Using satellite and geotagged imagery, we analyzed 19 reef structures over the interval 2013 to 2023 along the west coast of Barbados, comparing them to the previous study's findings in 1950 and 1991. We ground-truthed five sites previously categorized as highly degraded reefs to confirm their structural integrity and substrate-type. Results confirmed ongoing reef structural loss, averaging ~ 137.68 m1 annually across all sites. We identified four primary substrate types: coral, algae-covered substrate, rubble, and sand, with algae-covered substrate predominating and projected to persist. Our results underscore the urgency of monitoring reef health and highlight the potential limitations of satellite assessment. This research enhances understanding of reef dynamics and offers a framework for identifying vulnerable areas, which are crucial for effective conservation efforts.

Coral Disease: Direct and Indirect Agents, Mechanisms of Disease, and Innovations for Increasing Resistance and Resilience

As climate change drives health declines of tropical reef species, diseases are further eroding ecosystem function and habitat resilience. Coral disease impacts many areas around the world, removing some foundation species to recorded low levels and thwarting worldwide efforts to restore reefs. What we know about coral disease processes remains insufficient to overcome many current challenges in reef conservation, yet cumulative research and management practices are revealing new disease agents (including bacteria, viruses, and eukaryotes), genetic host disease resistance factors, and innovative methods to prevent and mitigate epizootic events (probiotics, antibiotics, and disease resistance breeding programs). The recent outbreak of stony coral tissue loss disease across the Caribbean has reenergized and mobilized the research community to think bigger and do more. This review therefore focuses largely on novel emerging insights into the causes and mechanisms of coral disease and their applications to coral restoration and conservation.

Structural and Evolutionary Relationships of Melanin Cascade Proteins in Cnidarian Innate Immunity

Melanin is an essential product that plays an important role in innate immunity in a variety of organisms across the animal kingdom. Melanin synthesis is performed by many organisms using the tyrosine metabolism pathway, a general pathway that utilizes a type-three copper oxidase protein, called PO-candidates (phenoloxidase candidates). While melanin synthesis is well-characterized in organisms like arthropods and humans, it is not as well-understood in non-model organisms such as cnidarians. With the rising anthropomorphic climate change influence on marine ecosystems, cnidarians, specifically corals, are under an increased threat of bleaching and disease. Understanding innate immune pathways, such as melanin synthesis, is vital for gaining insights into how corals may be able to fight these threats. In this study, we use comparative bioinformatic approaches to provide a comprehensive analysis of genes involved in tyrosine-mediated melanin synthesis in cnidarians. Eighteen PO-candidates representing five phyla were studied to identify their evolutionary relationship. Cnidarian species were most similar to chordates due to domain presents in the amino acid sequences. From there, functionally conserved domains in coral proteins were identified in a coral disease dataset. Five stony corals exposed to stony coral tissue loss disease were leveraged to identify 18 putative tyrosine metabolism genes, genes with functionally conserved domains to their Homo sapiens counterpart. To put this pathway in the context of coral health, putative genes were correlated to melanin concentration from tissues of stony coral species in the disease exposure dataset. In this study, tyrosinase was identified in stony corals as correlated to melanin concentrations and likely plays a key role in immunity as a resistance trait. In addition, stony coral genes were assigned to all modules within the tyrosine metabolism pathway, indicating an evolutionary conservation of this pathway across phyla. Overall, this study provides a comprehensive analysis of the genes involved in tyrosine-mediated melanin synthesis in cnidarians.

Half of Atlantic reef-building corals at elevated risk of extinction due to climate change and other threats

Atlantic reef-building corals and coral reefs continue to experience extensive decline due to increased stressors related to climate change, disease, pollution, and numerous anthropogenic threats. To understand the impact of ocean warming and reef loss on the estimated extinction risk of shallow water Atlantic reef-building scleractinians and milleporids, all 85 valid species were reassessed under the IUCN Red List Categories and Criteria, updating the previous Red List assessment of Atlantic corals published in 2008. For the present assessment, individual species declines were estimated based on the modeled coral cover loss (1989-2019) and projected onset of annual severe bleaching events (2020-2050) across the Atlantic. Species traits were used to scale species' relative vulnerability to the modeled cover declines and forecasted bleaching events. The updated assessments place 45.88%-54.12% of Atlantic shallow water corals at an elevated extinction risk compared to the previous assessments conducted in 2008 (15.19%-40.51%). However, coral cover loss estimates indicate an improvement in reef coverage compared to the historic time-series used for the 2008 assessments. Based on this, we infer that, although remaining dangerously high, the rate of Atlantic reef coral cover decline has surprisingly slowed in recent decades. However, based on modeled projections of sea-surface temperature that predict the onset of annual severe bleaching events within the next 30 years, we listed 26 (out of 85) species as Critically Endangered in the IUCN Red List. Each of these species had previously been listed under a lower threatened category and this result alone highlights the severe threat future bleaching events pose to coral survival and the reef ecosystems they support.

Acclimation and size influence predation, growth, and survival of sexually produced Diploria labyrinthiformis used in restoration

Stony coral tissue loss disease (SCTLD) has swept through Florida reefs and caused mass mortality of numerous coral species. In the wake of these losses, efforts are underway to propagate coral species impacted by SCTLD and promote population recovery. However, numerous knowledge gaps must be addressed to effectively grow, outplant, and restore populations of the slower growing, massive species that were lost. Here, we used sexual recruits of Diploria labyrinthiformis spawned in captivity to understand how conditioning, coral size, and nutritional status at outplanting affect coral survivorship, growth, and susceptibility to predation. We found that ex situ conditioning with supplemental feeding increased coral growth rates, resulting in larger sized corals at the time of outplanting. In turn, these corals had higher growth rates in the field and a lower probability of being removed by predators than outplants that were conditioned in in situ nurseries. Additionally, we found that coral size was an important predictor of survivorship, suggesting that hastening the speed at which young corals grow and outplanting larger juveniles can improve restoration outcomes. Taken together, our results suggest that providing supplemental food to corals at ex situ facilities confers benefits that could help restore populations of massive coral species impacted by SCTLD.

Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning

Coral diseases contribute to the rapid decline in coral reefs worldwide, and yet coral bacterial pathogens have proved difficult to identify because 16S rRNA gene surveys typically identify tens to hundreds of disease-associate bacteria as putative pathogens. An example is white band disease (WBD), which has killed up to 95% of the now-endangered Caribbean Acropora corals since 1979, yet the pathogen is still unknown. The 16S rRNA gene surveys have identified hundreds of WBD-associated bacterial amplicon sequencing variants (ASVs) from at least nine bacterial families with little consensus across studies. We conducted a multi-year, multi-site 16S rRNA gene sequencing comparison of 269 healthy and 143 WBD-infected Acropora cervicornis and used machine learning modelling to accurately predict disease outcomes and identify the top ASVs contributing to disease. Our ensemble ML models accurately predicted disease with greater than 97% accuracy and identified 19 disease-associated ASVs and five healthy-associated ASVs that were consistently differentially abundant across sampling periods. Using a tank-based transmission experiment, we tested whether the 19 disease-associated ASVs met the assumption of a pathogen and identified two pathogenic candidate ASVs-ASV25 Cysteiniphilum litorale and ASV8 Vibrio sp. to target for future isolation, cultivation, and confirmation of Henle-Koch's postulate via transmission assays.

Habitat quality effects on the abundance of a coral-dwelling fish across spatial scales

Microhabitat associated fishes are expected to be negatively affected by coral reef degradation, given that many species are coral dwellers. However, the factors underlying this negative impact and the spatial scale(s) at which it occurs are poorly understood. We explored how habitat quality metrics and host preferences influence fish abundance across multiple spatial scales, using the functionally important cleaner fish Elacatinus evelynae as a study species. We surveyed fish at 10 sites in Curaçao that varied in coral cover and health. At the microhabitat scale, we found that E. evelynae group size increases on large, healthy corals and on some coral host species, namely Montastraea cavernosa. We also found that, although E. evelynae can occupy at least 10 coral host species, it selectively inhabits just three corals: M. cavernosa, Colpophyllia natans, and Diploria labrynthiformis. Scaling up to explore goby abundance along 30-m transects, we did not find a clear relationship between live coral cover and goby abundance. However, goby abundance was substantially higher at one location with elevated coral cover and a high relative abundance of E. evelynae host species. Collectively, these results confirm that E. evelynae abundance is impacted by reef health. They also indicate that the species' long-term persistence may depend on both the maintenance of healthy coral hosts and the gobies' plasticity in host preferences on changing reefscapes. Cryptobenthic fishes such as E. evelynae play a vital role in the ecosystem and understanding drivers of their abundance is important as reefs face increased degradation.

Microbiomes of three coral species in the Mexican Caribbean and their shifts associated with the Stony Coral Tissue Loss Disease

Stony Coral Tissue Loss Disease (SCTLD) has caused widespread coral mortality in the Caribbean Region. However, how the disease presence alters the microbiome community, their structure, composition, and metabolic functionality is still poorly understood. In this study, we characterized the microbial communities of the tissues of apparently healthy and diseased SCTLD colonies of the species Siderastrea siderea, Orbicella faveolata, and Montastraea cavernosa to explore putative changes related to the presence of SCTLD. Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia were the best represented classes in the healthy tissues of all coral species, and alpha diversity did not show significant differences among the species. The microbial community structure between coral species was significantly different (PERMANOVA: F = 3.46, p = 0.001), and enriched genera were detected for each species: Vibrio and Photobacterium in S. siderea, Spirochaeta2 and Marivivens in O. faveolata and SAR202_clade and Nitrospira in M. cavernosa. Evidence of SCTLD in the microbial communities was more substantial in S. siderea, where differences in alpha diversity, beta diversity, and functional profiles were observed. In O. faveolata, differences were detected only in the community structure, while M. cavernosa samples showed no significant difference. Several microbial groups were found to have enriched abundances in tissue from SCTLD lesions from S. siderea and O. faveolata, but no dominant bacterial group was detected. Our results contribute to understanding microbial diversity associated with three scleractinian coral species and the shifts in their microbiomes associated with SCTLD in the Mexican Caribbean.

Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea

Corals populations worldwide are declining rapidly due to elevated ocean temperatures and other human impacts. The Caribbean harbors a high number of threatened, endangered, and critically endangered coral species compared to reefs of the larger Indo-Pacific. The reef corals of the Caribbean are also long diverged from their Pacific counterparts and may have evolved different survival strategies. Most genomic resources have been developed for Pacific coral species which may impede our ability to study the changes in genetic composition of Caribbean reef communities in response to global change. To help fill the gap in genomic resources, we used PacBio HiFi sequencing to generate the first genome assemblies for three Caribbean, reef-building corals, Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea. We also explore the genomic novelties that shape scleractinian genomes. Notably, we find abundant gene duplications of all classes (e.g., tandem and segmental), especially in S. siderea. This species has one of the largest genomes of any scleractinian coral (822Mb) which seems to be driven by repetitive content and gene family expansion and diversification. As the genome size of S. siderea was double the size expected of stony corals, we also evaluated the possibility of an ancient whole genome duplication using Ks tests and found no evidence of such an event in the species. By presenting these genome assemblies, we hope to develop a better understanding of coral evolution as a whole and to enable researchers to further investigate the population genetics and diversity of these three species.

Novel metagenomics analysis of stony coral tissue loss disease

Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from 4 stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared with a prior metagenome analysis of the same dataset.

Novel metagenomics analysis of stony coral tissue loss disease

Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from four stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared to a prior metagenome analysis of the same dataset.

Stony coral tissue loss disease indirectly alters reef communities

Many Caribbean coral reefs are near collapse due to various threats. An emerging threat, stony coral tissue loss disease (SCTLD), is spreading across the Western Atlantic and Caribbean. Data from the U.S. Virgin Islands reveal how SCTLD spread has reduced the abundance of susceptible coral and crustose coralline algae and increased cyanobacteria, fire coral, and macroalgae. A Caribbean-wide structural equation model demonstrates versatility in reef fish and associations with rugosity independent of live coral. Model projections suggest that some reef fishes will decline due to SCTLD, with the largest changes on reefs that lose the most susceptible corals and rugosity. Mapping these projected declines in space indicates how the indirect effects of SCTLD range from undetectable to devastating.

Microorganisms uniquely capture and predict stony coral tissue loss disease and hurricane disturbance impacts on US Virgin Island reefs

Coral reef ecosystems are now commonly affected by major climate and disease disturbances. Disturbance impacts are typically recorded using reef benthic cover, but this may be less reflective of other ecosystem processes. To explore the potential for reef water-based disturbance indicators, we conducted a 7-year time series on US Virgin Island reefs where we examined benthic cover and reef water nutrients and microorganisms from 2016 to 2022, which included two major disturbances: hurricanes Irma and Maria in 2017 and the stony coral tissue loss disease outbreak starting in 2020. The disease outbreak coincided with the largest changes in the benthic habitat, with increases in the percent cover of turf algae and Ramicrusta, an invasive alga. While sampling timepoint contributed most to changes in reef water nutrient composition and microbial community beta diversity, both disturbances led to increases in ammonium concentration, a mechanism likely contributing to observed microbial community shifts. We identified 10 microbial taxa that were sensitive and predictive of increasing ammonium concentration. This included the decline of the oligotrophic and photoautotrophic Prochlorococcus and the enrichment of heterotrophic taxa. As disturbances impact reefs, the changing nutrient and microbial regimes may foster a type of microbialization, a process that hastens reef degradation.

Ammonia removal mitigates white plague type II in the coral Pocillopora damicornis

White Plague Type II (WPL II) is a disease increasingly affecting scleractinian coral species and progresses rapidly. However, the etiological pathogen and remedy remain elusive. In this study, transmission experiments demonstrated that Aureimonas altamirensis and Aurantimonas coralicida, representing the WPL II pathogens, could infect Pocillopora damicorni. The infection produced selected pathological symptoms, including bleaching, tissue loss, and decolorization. Furthermore, ammonia degradation significantly reduced the severity of infection by these pathogens, indicating that ammonia may be a virulence factor for WPL II. Coral microbiome analysis suggested that ammonia degradation mediates the anti-white plague effect by maintaining the density of Symbiodiniaceae and stabilizing the core and symbiotic bacteria. Aureimonas altamirensis and Aurantimonas coralicida have been shown to cause diseases of P. damicornis, with ammonia acting as a virulence factor, and ammoniac degradation may be a promising and innovative approach to mitigate coral mortality suffering from increasing diseases.

Effects of surface geometry on light exposure, photoacclimation and photosynthetic energy acquisition in zooxanthellate corals

Symbiotic corals display a great array of morphologies, each of which has unique effects on light interception and the photosynthetic performance of in hospite zooxanthellae. Changes in light availability elicit photoacclimation responses to optimize the energy balances in primary producers, extensively documented for corals exposed to contrasting light regimes along depth gradients. Yet, response variation driven by coral colony geometry and its energetic implications on colonies with contrasting morphologies remain largely unknown. In this study, we assessed the effect of the inclination angle of coral surface on light availability, short- and long-term photoacclimation responses, and potential photosynthetic usable energy. Increasing surface inclination angle resulted in an order of magnitude reduction of light availability, following a linear relationship explained by the cosine law and relative changes in the direct and diffuse components of irradiance. The light gradient induced by surface geometry triggered photoacclimation responses comparable to those observed along depth gradients: changes in the quantum yield of photosystem II, photosynthetic parameters, and optical properties and pigmentation of the coral tissue. Differences in light availability and photoacclimation driven by surface inclination led to contrasting energetic performance. Horizontally and vertically oriented coral surfaces experienced the largest reductions in photosynthetic usable energy as a result of excessive irradiance and light-limiting conditions, respectively. This pattern is predicted to change with depth or local water optical properties. Our study concludes that colony geometry plays an essential role in shaping the energy balance and determining the light niche of zooxanthellate corals.

Characterization of trade-offs between immunity and reproduction in the coral species Astrangia poculata

Background

Living organisms face ubiquitous pathogenic threats and have consequently evolved immune systems to protect against potential invaders. However, many components of the immune system are physiologically costly to maintain and engage, often drawing resources away from other organismal processes such as growth and reproduction. Evidence from a diversity of systems has demonstrated that organisms use complex resource allocation mechanisms to manage competing needs and optimize fitness. However, understanding of resource allocation patterns is limited across taxa. Cnidarians, which include ecologically important organisms like hard corals, have been historically understudied in the context of resource allocations. Improving understanding of resource allocation-associated trade-offs in cnidarians is critical for understanding future ecological dynamics in the face of rapid environmental change.

Methods

Here, we characterize trade-offs between constitutive immunity and reproduction in the facultatively symbiotic coral Astrangia poculata. Male colonies underwent ex situ spawning and sperm density was quantified. We then examined the effects of variable symbiont density and energetic budget on physiological traits, including immune activity and reproductive investment. Furthermore, we tested for potential trade-offs between immune activity and reproductive investment.

Results

We found limited associations between energetic budget and immune metrics; melanin production was significantly positively associated with carbohydrate concentration. However, we failed to document any associations between immunity and reproductive output which would be indicative of trade-offs, possibly due to experimental limitations. Our results provide a preliminary framework for future studies investigating immune trade-offs in cnidarians.

Filamentous virus-like particles are present in coral dinoflagellates across genera and ocean basins

Filamentous viruses are hypothesized to play a role in stony coral tissue loss disease (SCTLD) through infection of the endosymbiotic dinoflagellates (Family Symbiodiniaceae) of corals. To evaluate this hypothesis, it is critical to understand the global distribution of filamentous virus infections across the genetic diversity of Symbiodiniaceae hosts. Using transmission electron microscopy, we demonstrate that filamentous virus-like particles (VLPs) are present in over 60% of Symbiodiniaceae cells (genus Cladocopium) within Pacific corals (Acropora hyacinthus, Porites c.f. lobata); these VLPs are more prevalent in Symbiodiniaceae of in situ colonies experiencing heat stress. Symbiodiniaceae expelled from A. hyacinthus also contain filamentous VLPs, and these cells are more degraded than their in hospite counterparts. Similar to VLPs reported from SCTLD-affected Caribbean reefs, VLPs range from ~150 to 1500 nm in length and 16-37 nm in diameter and appear to constitute various stages in a replication cycle. Finally, we demonstrate that SCTLD-affected corals containing filamentous VLPs are dominated by diverse Symbiodiniaceae lineages from the genera Breviolum, Cladocopium, and Durusdinium. Although this study cannot definitively confirm or refute the role of filamentous VLPs in SCTLD, it demonstrates that filamentous VLPs are not solely observed in SCTLD-affected corals or reef regions, nor are they solely associated with corals dominated by members of a particular Symbiodiniaceae genus. We hypothesize that filamentous viruses are a widespread, common group that infects Symbiodiniaceae. Genomic characterization of these viruses and empirical tests of the impacts of filamentous virus infection on Symbiodiniaceae and coral colonies should be prioritized.

Genomic signatures of disease resistance in endangered staghorn corals

White band disease (WBD) has caused unprecedented declines in the Caribbean Acropora corals, which are now listed as critically endangered species. Highly disease-resistant Acropora cervicornis genotypes exist, but the genetic underpinnings of disease resistance are not understood. Using transmission experiments, a newly assembled genome, and whole-genome resequencing of 76 A. cervicornis genotypes from Florida and Panama, we identified 10 genomic regions and 73 single-nucleotide polymorphisms that are associated with disease resistance and that include functional protein-coding changes in four genes involved in coral immunity and pathogen detection. Polygenic scores calculated from 10 genomic loci indicate that genetic screens can detect disease resistance in wild and nursery stocks of A. cervicornis across the Caribbean.

Newly deceased Caribbean reef-building corals experience rapid carbonate loss and colonization by endolithic organisms

Coral mortality triggers the loss of carbonates fixed within coral skeletons, compromising the reef matrix. Here, we estimate rates of carbonate loss in newly deceased colonies of four Caribbean reef-building corals. We use samples from living and recently deceased colonies following a stony coral tissue loss disease (SCTLD) outbreak. Optical densitometry and porosity analyses reveal a loss of up to 40% of the calcium carbonate (CaCO3) content in dead colonies. The metabolic activity of the endolithic organisms colonizing the dead skeletons is likely partially responsible for the observed dissolution. To test for the consequences of mass mortality events over larger spatial scales, we integrate our estimates of carbonate loss with field data of the composition and size structure of coral communities. The dissolution rate depends on the relative abundance of coral species and the structural properties of their skeletons, yet we estimate an average reduction of 1.33 kg CaCO3 m-2, nearly 7% of the total amount of CaCO3 sequestered in the entire system. Our findings highlight the importance of including biological and chemical processes of CaCO3 dissolution in reef carbonate budgets, particularly as the impacts of global warming, ocean acidification, and disease likely enhance dissolution processes.

Coral affected by stony coral tissue loss disease can produce viable offspring

Stony coral tissue loss disease (SCTLD) has caused high mortality of at least 25 coral species across the Caribbean, with Pseudodiploria strigosa being the second most affected species in the Mexican Caribbean. The resulting decreased abundance and colony density reduces the fertilization potential of SCTLD-susceptible species. Therefore, larval-based restoration could be of great benefit, though precautionary concerns about disease transmission may foster reluctance to implement this approach with SCTLD-susceptible species. We evaluated the performance of offspring obtained by crossing gametes of a healthy P. strigosa colony (100% apparently healthy tissue) with that of a colony affected by SCTLD (>50% tissue loss) and compared these with prior crosses between healthy parents. Fertilization and settlement were as high as prior crosses among healthy parents, and post-settlement survivorship over a year in outdoor tanks was 7.8%. After thirteen months, the diseased-parent recruits were outplanted to a degraded reef. Their survivorship was ∼44% and their growth rate was 0.365 mm ± 1.29 SD per month. This study shows that even diseased parent colonies can be effective in assisted sexual reproduction for the restoration of species affected by SCTLD.

Environmental degradation of the Mexican Caribbean reef lagoons

Insufficient attention to the large volumes of wastewater produced by expansive tourism and urban development in the north of the Mexican Caribbean has increased concerns on the ecological and economic sustainability of this important tourist destination, which is currently threatened by massive arrivals of pelagic Sargassum. Comparing environmental descriptions for sites exposed to contrasting anthropogenic pressure and before and during massive Sargassum tides, uncovered significant shifts in the environmental conditions in the last 20 years, from oligotrophic to mesotrophic-eutrophic conditions. The most significant changes were observed in the north, for habitats exposed to high anthropogenic pressure. Accordingly, the severe threat that massive Sargassum beaching currently represents for the survival of Caribbean coral reefs cannot be considered the only driver of reef eutrophication in the Mexican Caribbean, as the habitat degradation documented here has an important contribution from anthropogenic fertilization.

A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in unaffected and lesion tissue in diseased colonies

Stony coral tissue loss disease (SCTLD) has been causing significant whole colony mortality on reefs in Florida and the Caribbean. The cause of SCTLD remains unknown, with the limited concurrence of SCTLD-associated bacteria among studies. We conducted a meta-analysis of 16S ribosomal RNA gene datasets generated by 16 field and laboratory SCTLD studies to find consistent bacteria associated with SCTLD across disease zones (vulnerable, endemic, and epidemic), coral species, coral compartments (mucus, tissue, and skeleton), and colony health states (apparently healthy colony tissue (AH), and unaffected (DU) and lesion (DL) tissue from diseased colonies). We also evaluated bacteria in seawater and sediment, which may be sources of SCTLD transmission. Although AH colonies in endemic and epidemic zones harbor bacteria associated with SCTLD lesions, and aquaria and field samples had distinct microbial compositions, there were still clear differences in the microbial composition among AH, DU, and DL in the combined dataset. Alpha-diversity between AH and DL was not different; however, DU showed increased alpha-diversity compared to AH, indicating that, prior to lesion formation, corals may undergo a disturbance to the microbiome. This disturbance may be driven by Flavobacteriales, which were especially enriched in DU. In DL, Rhodobacterales and Peptostreptococcales-Tissierellales were prominent in structuring microbial interactions. We also predict an enrichment of an alpha-toxin in DL samples which is typically found in Clostridia. We provide a consensus of SCTLD-associated bacteria prior to and during lesion formation and identify how these taxa vary across studies, coral species, coral compartments, seawater, and sediment.

Upwelling, climate change, and the shifting geography of coral reef development

The eastern tropical Pacific is oceanographically unfavorable for coral-reef development. Nevertheless, reefs have persisted there for the last 7000 years. Rates of vertical accretion during the Holocene have been similar in the strong-upwelling Gulf of Panamá (GoP) and the adjacent, weak-upwelling Gulf of Chiriquí (GoC); however, seasonal upwelling in the GoP exacerbated a climate-driven hiatus in reef development in the late Holocene. The situation is now reversed and seasonal upwelling in the GoP currently buffers thermal stress, creating a refuge for coral growth. We developed carbonate budget models to project the capacity of reefs in both gulfs to keep up with future sea-level rise. On average, the GoP had significantly higher net carbonate production rates than the GoC. With an estimated contemporary reef-accretion potential (RAP) of 5.5 mm year^-1, reefs in the GoP are projected to be able to keep up with sea-level rise if CO₂ emissions are reduced, but not under current emissions trajectories. With an estimated RAP of just 0.3 mm year^-1, reefs in the GoC are likely already unable to keep up with contemporary sea-level rise in Panamá (1.4 mm year^-1). Whereas the GoP has the potential to support functional reefs in the near-term, our study indicates that their long-term persistence will depend on reduction of greenhouse gases.

First report of yellow-banded tissue loss disease on coral reefs outside the Arabian/Persian Gulf

Coral disease is a major cause of coral reef degradation, yet many diseases remain understudied. Yellow-banded tissue loss disease (YBTLD) has a distinct gross lesion morphology and to date has only been reported from the Arabian/Persian Gulf; little else is known about the ecology of the disease. We report on the first occurrence of YBTLD outside of the Arabian/Persian Gulf at 2 sites (Laku Point, Narara Reef) within the Gulf of Kachchh (GoK) located on the northwest coast of India. At Narara Reef, YBTLD was observed at 12 out of 24 transects with an average prevalence of 4.7 ± 1.3%. At Laku Point, YBTLD was observed at 19 out of 24 transects with an average prevalence of 5.4 ± 1%. Four out of 15 coral genera within transects had signs of YBTLD and included Goniopora, Dipsastraea, Lobophyllia, and Turbinaria. Lobophyllia and Turbinaria had the highest susceptibility to the disease, with prevalence significantly higher than expected based on their abundance on the reefs. The distribution and prevalence of YBTLD in the GoK was higher than in coral reefs in the Arabian/Persian Gulf. The GoK is an extreme environment for coral reefs with both natural stressors (high salinities, strong, seasonal storm activities, and extreme tides) and anthropogenic pollutants from industrial, mining, agricultural, and domestic activities. These poor environmental conditions may help explain the high occurrence of YBTLD on GoK reefs.

Photosynthetic usable energy explains vertical patterns of biodiversity in zooxanthellate corals

The biodiversity in coral reef ecosystems is distributed heterogeneously across spatial and temporal scales, being commonly influenced by biogeographic factors, habitat area and disturbance frequency. A potential association between gradients of usable energy and biodiversity patterns has received little empirical support in these ecosystems. Here, we analyzed the productivity and biodiversity variation over depth gradients in symbiotic coral communities, whose members rely on the energy translocated by photosynthetic algal symbionts (zooxanthellae). Using a mechanistic model we explored the association between the depth-dependent variation in photosynthetic usable energy to corals and gradients of species diversity, comparing reefs with contrasting water clarity and biodiversity patterns across global hotspots of marine biodiversity. The productivity-biodiversity model explained between 64 and 95% of the depth-related variation in coral species richness, indicating that much of the variation in species richness with depth is driven by changes in the fractional contribution of photosynthetically fixed energy by the zooxanthellae. These results suggest a fundamental role of solar energy availability and photosynthetic production in explaining global-scale patterns of coral biodiversity and community structure along depth gradients. Accordingly, the maintenance of water optical quality in coral reefs is fundamental to protect coral biodiversity and prevent reef degradation.

Structure-from-motion photogrammetry demonstrates variability in coral growth within colonies and across habitats

Coral growth is an important metric of coral health and underpins reef-scale functional attributes such as structural complexity and calcium carbonate production. There persists, however, a paucity of growth data for most reef-building regions, especially for coral species whose skeletal architecture prevents the use of traditional methods such as coring and Alizarin staining. We used structure-from-motion photogrammetry to quantify a range of colony-scale growth metrics for six coral species in the Mexican Caribbean and present a newly developed workflow to measure colony volume change over time. Our results provide the first growth metrics for two species that are now major space occupiers on Caribbean reefs, Agaricia agaricites and Agaricia tenuifolia. We also document higher linear extension, volume increase and calcification rates within back reef compared to fore reef environments for four other common species: Orbicella faveolata, Porites astreoides, Siderastrea siderea and Pseudodiploria strigosa. Linear extension rates in our study were lower than those obtained via computed tomography (CT) scans of coral cores from the same sites, as the photogrammetry method averages growth in all dimensions, while the CT method depicts growth only along the main growth axis (upwards). The comparison of direct volume change versus potential volume increase calculated from linear extension emphasizes the importance of assessing whole colony growth to improve calcification estimates. The method presented here provides an approach that can generate accurate calcification estimates alongside a range of other whole-colony growth metrics in a non-invasive way.

Mixtures of genotypes increase disease resistance in a coral nursery

Marine infectious diseases are a leading cause of population declines globally due, in large part, to challenges in diagnosis and limited treatment options. Mitigating disease spread is particularly important for species targeted for conservation. In some systems, strategic arrangement of organisms in space can constrain disease outbreaks, however, this approach has not been used in marine restoration. Reef building corals have been particularly devastated by disease and continue to experience catastrophic population declines. We show that mixtures of genotypes (i.e., diversity) increased disease resistance in the critically endangered Acropora cervicornis, a species that is frequently targeted for restoration of degraded reefs in the broader Caribbean region. This finding suggests a more generalized relationship between diversity and disease and offers a viable strategy for mitigating the spread of infectious diseases in corals that likely applies to other foundation species targeted for restoration.