Stony Coral Tissue Loss Disease Research Articles

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.

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.

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.

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.

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.

Stony coral tissue loss disease (SCTLD) induced mass mortality at Arecibo, Puerto Rico

Stony coral tissue loss disease (SCTLD) induced mass mortality at Arecibo, Puerto Rico

Algal symbiont genera but not coral host genotypes correlate to stony coral tissue loss disease susceptibility among Orbicella faveolata colonies in South Florida

Stony coral tissue loss disease (SCTLD) has spread throughout the entirety of Florida’s Coral Reef (FCR) and across the Caribbean, impacting at least 30 coral species. The threatened hermatypic coral, Orbicella faveolata, demonstrates intraspecific variation in SCTLD affectedness with some colonies experiencing chronic disease lesions, while other nearby O. faveolata colonies appear unaffected with no disease signs over long monitoring periods. This study evaluated potential genotypic underpinnings of variable disease responses to SCTLD by monitoring and sampling 90 O. faveolata colonies from southeast Florida and the lower Florida Keys. High resolution analyses of >11,000 single nucleotide polymorphisms (SNPs) generated from 2bRAD sequencing indicated there were no SNP loci or genetic lineages significantly associated with O. faveolata SCTLD affectedness. Genotypic differences may still contribute to SCTLD susceptibility; however, these differences were not captured using this reduced representation sequencing approach. Algal symbiont community structure characterized from 2bRAD data revealed that the presence of Durusdinium spp. corresponded with SCTLD-affected colonies as compared to unaffected colonies, suggesting that algal symbiont community make-up may play some role in SCTLD resistance. Data generated by this study will be combined with complementary molecular and physiological approaches to further investigate the complex drivers of intraspecific SCTLD susceptibility and resilience.

Stony coral tissue loss disease: a review of emergence, impacts, etiology, diagnostics, and intervention

Stony coral tissue loss disease (SCTLD) is destructive and poses a significant threat to Caribbean coral reef ecosystems. Characterized by the acute loss of coral tissue, SCTLD has impacted over 22 stony coral species across the Caribbean region, leading to visible declines in reef health. Based on the duration, lethality, host range, and spread of this disease, SCTLD is considered the most devastating coral disease outbreak ever recorded. Researchers are actively investigating the cause and transmission of SCTLD, but the exact mechanisms, triggers, and etiological agent(s) remain elusive. If left unchecked, SCTLD could have profound implications for the health and resilience of coral reefs worldwide. To summarize what is known about this disease and identify potential knowledge gaps, this review provides a holistic overview of SCTLD research, including species susceptibility, disease transmission, ecological impacts, etiology, diagnostic tools, host defense mechanisms, and treatments. Additionally, future research avenues are highlighted, which are also relevant for other coral diseases. As SCTLD continues to spread, collaborative efforts are necessary to develop effective strategies for mitigating its impacts on critical coral reef ecosystems. These collaborative efforts need to include researchers from diverse backgrounds and underrepresented groups to provide additional perspectives for a disease that requires creative and urgent solutions.

Broadscale coral disease interventions elicit efficiencies in endemic disease response

The presence and abundance of reef-building corals are crucial to the long-term existence of Caribbean coral reef ecosystems, providing both direct and indirect, local and global, ecological, economic, and social benefits. In 2014, stony coral tissue loss disease (SCTLD) was first identified in southeast Florida and remains endemic to the region, while continuing to spread throughout the Caribbean. Effective in situ intervention treatments using antibiotic paste can halt lesion progression on Montastraea cavernosa up to 90% of the time. This study investigated intervention activities over a three-year period to identify efficiencies in disease response. Since May 2019, 1,037 corals, >85% of which were M. cavernosa, were treated during disease intervention dives in southeast Florida. Treated coral density, the number of treated corals per meter along a dive track, was significantly higher in the first year compared to subsequent years and displayed annual peaks in late summer each year. Season significantly influenced treatment density, leading to higher values in the wet season across all years, 2019 to 2022. Areas of highest treatment density were identified between Haulover Inlet and Government Cut near Miami and Hillsboro Inlet in northern Broward County. Areas with the highest treatment density were only identified in the first year, suggesting that broadscale interventions may have decreased disease prevalence in subsequent years. Results indicate that in endemic areas with sporadic and dynamic disease prevalence, intervention efforts should be weighted proportionally across space and time to maximize intervention efficiency. This study provides optimistic results for the potential of interventions reducing disease prevalence and supports that disease interventions are an effective coral restoration tool that can decrease the increasing burden on post hoc coral restoration.

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.

Stony coral tissue loss disease accelerated shifts in coral composition and declines in reef accretion potential in the Florida Keys

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.

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.

Stony coral tissue loss disease intervention with amoxicillin leads to a reversal of disease-modulated gene expression pathways.

Stony coral tissue loss disease (SCTLD) remains an unprecedented disease outbreak due to its high mortality rate and rapid spread throughout Florida's Coral Reef and wider Caribbean. A collaborative effort is underway to evaluate strategies that mitigate the spread of SCTLD across coral colonies and reefs, including restoration of disease-resistant genotypes, genetic rescue, and disease intervention with therapeutics. We conducted an in-situ experiment in Southeast Florida to assess molecular responses among SCTLD-affected Montastraea cavernosa pre- and post-application of the most widely used intervention method, CoreRx Base 2B with amoxicillin. Through Tag-Seq gene expression profiling of apparently healthy, diseased, and treated corals, we identified modulation of metabolomic and immune gene pathways following antibiotic treatment. In a complementary ex-situ disease challenge experiment, we exposed nursery-cultured M. cavernosa and Orbicella faveolata fragments to SCTLD-affected donor corals to compare transcriptomic profiles among clonal individuals from unexposed controls, those exposed and displaying disease signs, and corals exposed and not displaying disease signs. Suppression of metabolic functional groups and activation of stress gene pathways as a result of SCTLD exposure were apparent in both species. Amoxicillin treatment led to a 'reversal' of the majority of gene pathways implicated in disease response, suggesting potential recovery of corals following antibiotic application. In addition to increasing our understanding of molecular responses to SCTLD, we provide resource managers with transcriptomic evidence that disease intervention with antibiotics appears to be successful and may help to modulate coral immune responses to SCTLD. These results contribute to feasibility assessments of intervention efforts following disease outbreaks and improved predictions of coral reef health across the wider Caribbean.

Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD).

Effective treatment and prevention of any disease necessitates knowledge of the causative agent, yet the causative agents of most coral diseases remain unknown, in part due to the difficulty of distinguishing the pathogenic microbe(s) among the complex microbial backdrop of coral hosts. Stony coral tissue loss disease (SCTLD) is a particularly destructive disease of unknown etiology, capable of transmitting through the water column and killing entire colonies within a matter of weeks. Here we used a previously described method to (i) isolate diseased and apparently healthy coral colonies within individual mesocosms containing filtered seawater with low microbial background levels; (ii) incubate for several days to enrich the water with coral-shed microbes; (iii) use tangential-flow filtration to concentrate the microbial community in the mesocosm water; and then (iv) filter the resulting concentrate through a sequential series of different pore-sized filters. To investigate the size class of microorganism(s) associated with SCTLD transmission, we used 0.8 µm pore size filters to capture microeukaryotes and expelled zooxanthellae, 0.22 µm pore size filters to capture bacteria and large viruses, and 0.025 µm pore size filters to capture smaller viruses. In an attempt to further refine which size fraction(s) contained the transmissible element of SCTLD, we then applied these filters to healthy "receiver" coral fragments and monitored them for the onset of SCTLD signs over three separate experimental runs. However, several factors outside of our control confounded the transmission results, rendering them inconclusive. As the bulk of prior studies of SCTLD in coral tissues have primarily investigated the associated bacterial community, we chose to characterize the prokaryotic community associated with all mesocosm 0.22 µm pore size filters using Illumina sequencing of the V4 region of the 16S rRNA gene. We identified overlaps with prior SCTLD studies, including the presence of numerous previously identified SCTLD bioindicators within our mesocosms. The identification in our mesocosms of specific bacterial amplicon sequence variants that also appear across prior studies spanning different collection years, geographic regions, source material, and coral species, suggests that bacteria may play some role in the disease.