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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. 

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 Mass mortality of Diadematidae urchins, caused by theDiadema antillarumscuticociliatosis Philaster clade (DScPc),affected the Caribbean in spring 2022 and subsequently spread to the eastern Mediterranean, Red Sea, and western Indian Ocean. A key question around Diadematidae scuticociliatosis (DSc), the disease caused by the scuticociliate, is whether the urchin microbiome varies between scuticociliatosis-affected and grossly normal urchins. Tissue samples from both grossly normal and abnormalDiadema antillarumwere collected in the field during the initial assessment of the DSc causative agent and from an experimental challenge of DScPc culture on aquaculturedD. antillarum. Specimens were analyzed using 16S rRNA gene amplicon sequencing. Additional abnormal urchin samples were collected from the most recent outbreak site in the western Indian Ocean (Réunion Island). At reference (i.e., unaffected by DSc) sites,Kistimonasspp., Propionigeniumspp., andEndozoicomonasspp. were highly represented in amplicon libraries. DSc-affected urchin amplicon libraries had lower taxonomic richness and a greater representation of taxa related toFangia hongkongensisandPsychrobiumspp. Amplicon libraries of urchins experimentally challenged with the DSc pathogen had some shifts in microbial composition, butF. hongkongensiswas not a part of the core bacteria in DSc-challenged specimens. DSc-affectedEchinothrix diademafrom Réunion Island showed a similar high representation ofF. hongkongensisas that seen on CaribbeanD. antillarum. Our results suggest that DSc altersDiadematidaemicrobiomes and thatF. hongkongensismay be a candidate bacterial biomarker for DSc in environmental samples. The mechanism driving microbiome variation in host–pathogen interactions remains to be explored.IMPORTANCEThe mass mortality of Diadematidae urchins due toDiadema antillarumscuticociliatosis (DSc) has had significant ecological impacts, spreading from the Caribbean to the eastern Mediterranean, Red Sea, and western Indian Ocean. This study investigates whether the microbiome of urchins varies between those affected by DSc and those that are not. Using 16S rRNA gene amplicon sequencing, researchers found that DSc-affected urchins had lower taxonomic richness and a greater representation ofFangia hongkongensisandPsychrobiumspp. The findings indicate thatF. hongkongensiscould serve as a bacterial biomarker for DSc in environmental samples, providing a potential tool for early detection and management of the disease. Understanding these microbiome changes is crucial for developing strategies to mitigate the spread and impact of DSc on marine ecosystems. 

BackgroundEchinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality. MethodsWe performed viral surveillance in two common coral reef echinoderms,Diadema antillarumandHolothuria floridana, using metagenomics. Urchin specimens were obtained during the 2022Diadema antillarumscuticociliatosis mass mortality event from the Caribbean and grossly normalH. floridanaspecimens from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2. ResultsD. antillarumwas devoid of viruses typically seen in echinoderms, butH. floridanayielded viral taxa similar to those found in other sea cucumbers, includingPisoniviricetes(Picornaviruses),Ellioviricetes(Bunyaviruses), andMagsaviricetes(Nodaviruses). The lack of viruses detected inD. antillarummay be due to the large amount of host DNA in viral metagenomes, or because viruses are less abundant inD. antillarumtissues when compared toH. floridanatissues. Our results also suggest that RNA amplification approach may influence viral representation in viral metagenomes. While our survey was successful in describing viruses associated with both echinoderms, our results indicate that viruses are less pronounced inD. antillarumthan in other echinoderms. These results are important in context of wider investigation on the association between viruses andD. antillarummass mortalities, since the conventional method used in this study was unsuccessful. 

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. 

Gene expression profiles are correlated to disease phenotypes in resistant and susceptible corals.