Coral Tissue Loss Research Articles

Metabolomic profiles of stony coral species from the Dry Tortugas National Park display inter- and intraspecies variation.

Previous research profiling gene expression, proteins, and metabolites produced during thermal stress have reported the importance of endosymbiont-derived pathways in coral bleaching resistance. However, our understanding of interspecies variation in these pathways among healthy corals and their role in diseases is limited. We surveyed the metabolomes of four species of healthy corals with differing susceptibilities to the devastating stony coral tissue loss disease and applied advanced annotation approaches in untargeted metabolomics to determine the interspecies variation in host and endosymbiont-derived pathways. Using this approach, we propose the survey of immune markers such as vitamin E family compounds, acylcarnitines, and other metabolites to infer their role in resilience to coral diseases. As time-resolved multi-omics datasets are generated for disease-impacted corals, our approach and findings will be valuable in providing insight into the mechanisms of disease resistance.

Pathology of lesions in corals from the US Virgin Islands after emergence of stony coral tissue loss disease

Pathology of lesions in corals from the US Virgin Islands after emergence of stony coral tissue loss disease

The effects of disease lesions and amoxicillin treatment on the physiology of SCTLD-affected corals

Metrics of coral physiology can be used to identify changes in coral health due to environmental stressors or management actions. One of the most unprecedented stressors to Caribbean corals is the spread of stony coral tissue loss disease (SCTLD), which also resulted in the novel management action of in-water amoxicillin treatments on active disease lesions. Though highly effective at halting lesions and preventing coral mortality, possible unintended consequences of topical application of amoxicillin to coral tissue were unknown. We used in-water instrumentation to measure and compare photosynthesis (P), respiration (R), P/R ratios, and calcification of corals that were visually healthy, actively diseased, and diseased but treated with amoxicillin paste. Measurements occurred across three time points and two species – Orbicella faveolata and Montastraea cavernosa. Across all metrics, treatment type did not cause significant differences, indicating that neither SCTLD lesions nor amoxicillin treatments impacted the physiology of adjacent tissues. There were significant variations among time points, which may have resulted from changes to coral health across the reef, variations due to environmental variables, or other unknown factors. We suggest that physiological metrics could be an interesting way to fate track coral health across short- and long-term timeframes. We also conclude that amoxicillin treatments as a tool to halt SCTLD are not detrimental to respiration, photosynthesis, or calcification rates of adult corals.

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.

Assessment of nutrient amendments on stony coral tissue loss disease in Southeast Florida

Assessment of nutrient amendments on stony coral tissue loss disease in Southeast Florida

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.

Investigating the link between the Port of Miami dredging and the onset of the stony coral tissue loss disease epidemics

Since 2014, the stony coral tissue loss disease (SCTLD) has been decimating corals in the Caribbean. Although the trigger of this outbreak remains elusive, evidence suggests waterborne sediment-mediated disease transmission. The outbreak reportedly initiated in September 2014 at a reef site off Virginia Key (VKR), during extensive dredging operations at the Port of Miami. Here we use a high-resolution ocean model to identify the potential driver of the outbreak by simulating the dispersal of dredged sediments, wastewater plumes and disease agents. Our results suggest that VKR could have been impacted by fine sediments produced by dredging operations, especially those involving non-conventional rock-chopping techniques. Wastewater contamination was unlikely. Additionally, our connectivity analysis indicates potential disease transmission from other affected reefs to VKR. Our results therefore suggest that dredging operations might be responsible for the onset of the epidemics. This underscores the need for stricter operational guidelines in future dredging projects.

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.

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.

Coral restoration: a mapping review through a scientometric analysis

Reef restoration has gained attention as it has strategic actions and powerful means in sustaining and maintaining coastal ecosystem services. This scientometric study systematically analyzes the current trends and research hotspot in coral restoration across the last five decades (1971–2022). The metadata (12,667 articles with 652,860 cited references) were obtained from the Clarivate Web of Science platform through the Core Collection database, associated with the CiteSpace and R‐software for further analysis. The results indicated that the trend of coral restoration is increasing in paper/year, with the United States, Australia, and China as major contributors to the related research. Furthermore, James Cook University, Australia had the largest number of articles, and the Consortium of Research Libraries of the United Kingdom was the most influential institution on coral restoration. The highly cited keywords are “Great Barrier Reef,” “climate change,” and “coral reef,” while the most influential keywords are “coral,” “model,” and “Atlantic.” A total of 23 clusters in the field with “coral reef,” “phase shift,” “bacterial communities,” “coral restoration,” “symbiotic dinoflagellate,” “stony coral tissue loss disease,” “bleaching event,” “ocean acidification,” “oyster reef,” and “quantitative reconstruction” are among the top cluster size labeled. Early‐stage researcher may use both keywords and cluster analysis to find topics attractive to their future research projects. In addition, this study contributes toward evaluating recent scientific productivity about coral restoration as well as informing researchers and policymakers regarding funding, future strategic planning, and potential collaboration opportunities.

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 to 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 eighteen putative tyrosine metabolism genes, genes with functionally conserved domains to their Homo sapiens counterpart. To put this pathway 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.

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.

Hurricanes enhance coral connectivity but also superspread coral diseases.

Climate change poses an existential threat to coral reefs. A warmer and more acidic ocean weakens coral ecosystems and increases the intensity of hurricanes. The wind-wave-current interactions during a hurricane deeply change the ocean circulation patterns and hence potentially affect the dispersal of coral larvae and coral disease agents. Here, we modeled the impact of major hurricane Irma (September 2017) on coral larval and stony coral tissue loss disease (SCTLD) connectivity in Florida's Coral Reef. We coupled high-resolution coastal ocean circulation and wave models to simulate the dispersal of virtual coral larvae and disease agents between thousands of reefs. While being a brief event, our results suggest the passage of hurricane Irma strongly increased the probability of long-distance exchanges while reducing larval supply. It created new connections that could promote coral resilience but also probably accelerated the spread of SCTLD by about a month. As they become more intense, hurricanes' double-edged effect will become increasingly pronounced, contributing to increased variability in transport patterns and an accelerated rate of change within coral reef ecosystems.

Spatial differences in recruit density, survival, and size structure prevent population growth of stony coral assemblages in southeast Florida

The size structure of stony coral populations can reveal underlying demographic barriers to population growth or recovery. Recent declines in coral cover from acute disturbances are well documented, but few studies have assessed size structure and the demographic processes that determine population growth. Vital rates, such as recruitment and survival, vary spatially and temporally in response to environmental conditions, in turn influencing assemblage composition. The Southeast Florida Coral Reef Ecosystem Conservation Area (Coral ECA) is a high-latitude reef system offshore of a heavily urbanized coastline. Consecutive heat stress events, stony coral tissue loss disease (SCTLD), and Hurricane Irma caused significant declines in stony coral cover and density from 2014 to 2018. The recovery potential of stony coral assemblages is influenced by their composition, the size structure of the remnant populations, and population growth during inter-disturbance periods. To assess the viability of the remaining stony coral assemblages in the Coral ECA, we quantified variation in stony coral recruit density, abundance, size structure, and assemblage composition across depth and latitude at permanent sites over 3 years (2019–2022) when no disturbances occurred. We found spatial decoupling in recruit density, adult colony density, and cover that maintains a preponderance of small colonies and skewed size structure. At sites close to shore where recruit density was higher, there was limited evidence of survival and growth of recruits, while at sites where large colonies were sampled or cover was relatively high, there was limited recruitment. The majority (>75%) of recruits sampled were Siderastrea siderea, but size frequency distributions were positively skewed and the coefficient of variation was high, suggesting high recruit/juvenile colony mortality and little growth into larger size classes. Porites astreoides size structure was generally lognormal and mesokurtic, particularly closer to shore, suggesting a transition between size classes. Skewness decreased moving offshore in Montastraea cavernosa and S. siderea, suggesting a transition between size classes. Recruit and adult diversity also increased moving offshore, but recruits of most species were uncommon throughout the study area. We suggest that low recruitment and high mortality, particularly in small colonies and inshore, even during inter-disturbance periods, limit the population growth of stony coral assemblages in southeast Florida.

Southeast Florida large Orbicella faveolata are highly fecund without evident disease intervention effects

The recent widespread mortality and tissue loss in Florida from stony coral tissue loss disease (SCTLD) has propelled the need for assisted reproduction to restore reefs, especially for the ESA listed species Orbicella faveolata. In situ gamete collection can be challenging due to the weather and resources (boats and divers) required during the expected spawning window. In the northern portion of the Florida coral reef tract, coral spawn collection has been even more difficult due to historical inconsistency in annual spawning times and the potential for “zombie” corals, i.e. large but reproductively senescent individuals. Therefore, we examined the current reproductive potential of seven large (>2 m diameter) O. faveolata colonies from this region, quantified their fecundity, and estimated the spawning timeframe using histology. Additionally, we explored whether previous SCTLD lesion amoxycillin treatments affected reproductive metrics. Understanding the reproductive capacity and spawning timing of these large corals, given their history of disease and disease treatment, is critical to evaluate potential impacts of SCTLD treatments and the success of assisted reproduction efforts. The histological analysis coupled with in-water observations indicated a probable split-spawn in these individuals in 2020, although the dates of spawning may not be consistent with predictions for the wider Caribbean or with other colonies in Miami and the Florida Keys. All seven large O. faveolata colonies were found to contain abundant oocytes, with no obvious impact of SCTLD treatments on gamete development or fecundity.

Measuring multi-year changes in the Symbiodiniaceae algae in Caribbean corals on coral-depleted reefs.

Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from nine species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019). While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together, these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.

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.

Impacts of stony coral tissue loss disease on the persistence of Caribbean cleaner gobies

Because they serve as the main architects of coral reefs, the distribution and abundance of stony coral species have major impacts on other associated community members. Thus, coral diseases can have significant cascading effects throughout the ecosystem. Stony coral tissue loss disease (SCTLD) is the most recent of many diseases documented to impact Caribbean stony corals. SCTLD is known to impact over 20 species of reef-building corals and can cause complete colony mortality of large corals in only one month. Among the coral species impacted are those occupied as cleaning stations by Caribbean cleaner gobies. This study examined the persistence of these gobies on living coral cleaning stations where SCTLD was most recently or not yet affected (emergent), recently established (epidemic), and well-established (endemic),. Timed surveys were conducted at nine reefs in the U.S. Virgin Islands between October 2019 and March 2021. Study sites were surveyed both before and after the outbreak/establishment of SCTLD where possible. Monitoring sites were established at six reefs by tagging 25 live coral cleaning stations at each of two endemic and two epidemic sites and 50 cleaning stations at each of two emergent sites. Goby abundance at each site was monitored at least five times from March 2020 to April 2021. Timed surveys found cleaner goby abundance was 50% lower in the endemic zone compared to epidemic and emergent zones. Overall, goby abundance declined on tagged cleaning stations throughout the course of this study at all sites. However, overall goby density within monitored areas remained stable across most sites from the beginning to the end of the study. One emergent site experienced a two-fold increase in goby density and one epidemic site experienced a decline in goby density. This suggests that gobies are remaining at the site but may be abandoning live coral cleaning stations as the individual colonies are affected by SCTLD. Given the benefit cleaner gobies have on local coral reef fishes, changes in cleaning activity associated with coral disease have the potential to negatively impact Caribbean reef fish communities.

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.

A quantitative assessment of the status of benthic communities on US Atlantic coral reefs using a novel standardized approach

As coral reefs decline globally, the need for an objective approach to quantify the status and trends of corals has become increasingly important. Empirical data on predisturbance conditions are rare, and integrating data from multiple and disparate survey designs and methods can be analytically challenging. Our goal was to conduct a holistic, data-driven evaluation of the status of corals and benthic communities in US Atlantic coral reef jurisdictions: Florida, Flower Garden Banks, Puerto Rico, and the US Virgin Islands. A quantitative approach based upon standardized data was used to compare the change in multiple indicators of coral condition (hard coral, macroalgae, and crustose coralline algae cover, coral density, and old mortality) from historic to current conditions in each geographic region. For each indicator, historic, reference baseline conditions from long-term monitoring data or literature data were first identified, reviewed, and classified on a categorical scale from Very Good to Critical by regional experts to account for condition changes that pre-dated current monitoring data. A reference-centering approach then allowed for categorization of statistical changes from historic to current conditions on the same scale to produce results that could be communicated to a broad audience. Our findings show continued declines for multiple indicators in all regions except Flower Garden Banks, illustrate particularly dire declines from regions that had been impacted by Stony Coral Tissue Loss Disease at the most recent monitoring included in this study, and demonstrate the increasingly critical need for effective coral reef conservation.