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ABSTRACT Marine disturbance events are often influenced by the environment, making it difficult to parse abiotic and biotic drivers. This is particularly true of disease infection and spread in coral reef environments, where pathogens are challenging to isolate and transmission may occur through the movement of water masses. Here we assess mesoscale conditions related to coral community disturbance from 2001 to 2023 on isolated reefs, using the Flower Garden Banks (FGB) as a case study. During the study period, relative to other western Atlantic reefs, this high latitude coral reef system experienced relatively few disturbance events (2 disease events, 1 hypoxia event, and 6 thermal stress events) and lower coral mortality, allowing it to maintain remarkably high coral cover. We explore mesoscale oceanographic features during the study period, predominantly the northwest extension of the Loop Current (LC), to understand its connection to disturbance events at FGB. LC position was linked to disease and hypoxia events, but not consistently to thermal stress events. Low LC extension, as seen in 2016, may have facilitated the transport of freshwater river output across the GoM resulting in a hypoxia event at FGB. To examine the influence of circulation and upstream connectivity to disease at FGB, we used a biophysical Lagrangian particle tracking model to backtrack virtual disease agents from FGB over 23 years of hydrodynamic forcing. Our results highlight a link between observed coral disease incidence at FGB, seasonality, and a 30‐day connectivity window to reefs of the Mesoamerican Reef. Operational biophysical and oceanographic models can provide a valuable tool for reef disturbance prediction and monitoring. These models are likely to become increasingly relevant as climate change alters the behavior of ocean circulation, with implications for reef connectivity, disease dispersal, freshwater inputs, and the management of these and other isolated coral reefs. 

Abstract Anthropogenic climate change has had devastating effects on the Florida and Caribbean reef systems, in part due to increased disease outbreaks. Climate change exacerbates marine diseases by expanding pathogen ranges and heightening host susceptibility through environmental stress. Specifically, there has been a stark rise in marine disease events outbreaks targeting multiple coral species, resulting in high mortality rates and declining reef biodiversity. Although many of these diseases present similar visual symptoms, they exhibit varying mortality rates and require distinct treatment protocols. Advances in coral transcriptomics research have enhanced our understanding of coral responses to various diseases, but more sophisticated methods are required to classify diseases that appear visually similar. This study provides the first machine learning (ML) model that can classify two common coral diseases: stony coral tissue loss disease (SCTLD) and white plague (WP). Using various algorithms, 463 gene expression biomarkers were identified, with 275 unique to SCTLD and 167 unique to WP, revealing distinct immune responses between the two diseases. The final ML model was built with partial least squares discriminant analysis (PLS-DA) and the identified biomarkers were tested and validated with samples collected in situ. It achieved high predictive performance, with an Area Under the Receiver Operating Characteristic (ROC) Curve (AUC) of 0.9895, an average overall error rate of 0.0754, and an average balanced error rate (BER) of 0.0799. This study provides a preliminary disease classification model that reliably distinguishes between SCTLD and WP and offers valuable insights into their underlying cellular responses. Additionally, the identified biomarkers provide a foundation for the development of rapid diagnostic tools to identify and mitigate future coral disease outbreaks. 

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. 

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. 

Abstract Stony coral tissue loss disease (SCTLD), one of the most pervasive and virulent coral diseases on record, affects over 22 species of reef-building coral and is decimating reefs throughout the Caribbean. To understand how different coral species and their algal symbionts (family Symbiodiniaceae) respond to this disease, we examine the gene expression profiles of colonies of five species of coral from a SCTLD transmission experiment. The included species vary in their purported susceptibilities to SCTLD, and we use this to inform gene expression analyses of both the coral animal and their Symbiodiniaceae. We identify orthologous coral genes exhibiting lineage-specific differences in expression that correlate to disease susceptibility, as well as genes that are differentially expressed in all coral species in response to SCTLD infection. We find that SCTLD infection induces increased expression of rab7 , an established marker of in situ degradation of dysfunctional Symbiodiniaceae, in all coral species accompanied by genus-level shifts in Symbiodiniaceae photosystem and metabolism gene expression. Overall, our results indicate that SCTLD infection induces symbiophagy across coral species and that the severity of disease is influenced by Symbiodiniaceae identity. 

Abstract Half of the marine virosphere is hypothesized to be RNA viruses (kingdom Orthornavirae ) that infect abundant micro-eukaryotic hosts (e.g. protists). To test this, quantitative approaches that broadly track infections in situ are needed. Here, we describe a technique—dsRNA-Immunofluorescence (dsRIF)—that uses a double-stranded RNA (dsRNA) targeting monoclonal antibody to assess host infection status based on the presence of dsRNA, a replicative intermediate of all Orthornavirae infections. We show that the dinoflagellate Heterocapsa circularisquama produces dsRIF signal ~ 1000 times above background autofluorescence when infected by the + ssRNA virus HcRNAV. dsRNA-positive virocells were detected across > 50% of the 48-h infection cycle and accumulated to represent at least 63% of the population. Photosynthetic and chromosomal integrity remained intact during peak replication, indicating HcRNAV infection does not interrupt these processes. This work validates the use of dsRIF on marine RNA viruses and their hosts, setting the stage for quantitative environmental applications that will accelerate understanding of virus-driven ecosystem impacts. 

East and West Flower Garden Bank (FGB) are part of Flower Garden Banks National Marine Sanctuary (FGBNMS) in the northwest Gulf of Mexico. This geographically-isolated reef system contains extensive coral communities with the highest coral cover (>50%) in the continental United States due, in part, to their remoteness and depth, and have historically exhibited low incidence of coral disease and bleaching despite ocean warming. Yet in late August 2022, disease-like lesions on seven coral species were reported during routine monitoring surveys on East and West FGB (2.1–2.6% prevalence). A series of rapid response cruises were conducted in September and October 2022 focused on 1) characterizing signs and epidemiological aspects of the disease across FGB and within long-term monitoring sites, 2) treating affected coral colonies with Base 2B plus amoxicillin, and 3) collecting baseline images through photostations and photomosaics. Marginal and/or multi-focal lesions and tissue loss were observed, often associated with substantial fish and invertebrate predation, affecting the dominant coral species Pseudodiploria strigosa (7–8% lesion prevalence), Colpophyllia natans (11–18%), and Orbicella spp. (1%). Characterizing this disease event during its early epidemic phase at East and West FGB provides a critical opportunity to observe how coral disease functions in a relatively healthy coral ecosystem versus on reefs chronically affected by various stressors (e.g., Caribbean reefs adjacent to urban centers). Insights into the etiology, spread, and impacts of the disease can ultimately inform efforts to mitigate its effects on coral communities. 

Abstract Stony coral tissue loss disease (SCTLD) remains an unprecedented epizootic disease, representing a substantial threat to the persistence and health of coral reef ecosystems in the Tropical Western Atlantic since its first observation near Miami, Florida in 2014. In addition to transport between adjacent reefs indicative of waterborne pathogen(s) dispersing on ocean currents, it has spread throughout the Caribbean to geographically- and oceanographically-isolated reefs, in a manner suggestive of ship and ballast water transmission. Here we evaluate the potential for waterborne transmission of SCTLD including via simulated ballast water, and test the efficacy of commonly-used UV radiation treatment of ballast water. Two species of reef-building corals ( Orbicella faveolata and Pseudodiploria strigosa ) were subjected to (1) disease-exposed or UV-treated disease-exposed water, and (2) a ballast hold time series of disease-exposed water in two carefully-controlled experiments to evaluate transmission. Our experiments demonstrated transmission of SCTLD through water, rather than direct contact between diseased and healthy corals. While UV treatment of disease-exposed water led to a 50% reduction in the number of corals exhibiting disease signs in both species, the statistical risk of transmission and volume of water needed to elicit SCTLD lesions remained similar to untreated disease-exposed water. The ballast hold time (24 h vs. 120 h) did not have a significant effect on the onset of visible disease signs for either species, though there appeared to be some evidence of a concentration effect for P. strigosa as lesions were only observed after the 120 h ballast hold time. Results from both experiments suggest that the SCTLD pathogens can persist in both untreated and UV-treated ballast water and remain pathogenic. Ballast water may indeed pose a threat to the continued spread and persistence of SCTLD, warranting further investigation of additional ballast water treatments and pathogen detection methods.