A holistic time-series analysis of stony coral tissue loss disease (Phase II)

Florida’s Coral Reef is currently experiencing a multi-year disease-related mortality event, that has resulted in massive die-offs in multiple coral species. Approximately 21 species of coral, including both Endangered Species Act-listed and the primary reef-building species, have displayed tissue loss lesions which often result in whole colony mortality. First observed near Virginia Key in late 2014, the disease has since spread to the northernmost extent of Florida’s Coral Reef, and southwest past the Marquesas in the Lower Florida Keys. The best available information indicates that the disease outbreak is continuing to spread west and throughout the Caribbean. Previous studies, including those by our research group, confirmed SCTLD to be an infectious disease (Aeby et al., 2019; Muller et al., 2020; Meiling et al., 2021). However, the exact etiological agent has yet to be identified. Several bacterial groups are associated with disease (Meyer et al., 2019; Rosales et al., 2020; Becker et al., 2021) while broad-spectrum antibiotics are mostly effective against disease lesions (Aeby et al., 2019; Neely et al., 2020; Shilling et al., 2021; Walker et al., 2021). Although, it is unclear if bacteria are initiating disease or are playing more of an opportunistic role. For example, the bacterial pathogen Vibrio coralliilyticus may be causing coinfections with SCTLD that exacerbate lesion progression, but pure cultures of this microbe are unable to consistently initiate disease (Ushijima et al., 2020). This was an important and concerning revelation that further complicates the situation, but it allowed researchers to rule out this pathogen as a primary agent, although it remains a threat to corals. A recent study had identified viral-like particles (VLPs) within coral tissue that were associated with the microalgae symbionts, which appeared to resemble filamentous RNA viruses (Work et al., 2021). The authors of that study suggested they belonged to the viral family Alphaflexiviridae based on morphology, but they did not have supporting sequencing data. Also, these VLPs were observed in both diseased and apparently healthy corals, so no connection between these VLPs and disease has yet to be established. There have been other described viruses associated with corals and their symbionts unrelated to SCTLD (Wilson et al., 2001; Lohr et al., 2007; Thurber et al., 2009). Viruses typically outnumber bacteria in a 10:1 ratio in marine systems, so their mere presence does not provide strong evidence for their role as a primary pathogen. The presence of these VLPs could be latent infections that manifest during host stress, which was observed in the previous viral studies (Wilson et al., 2001; Lohr et al., 2007; Thurber et al., 2009). Alternatively, they could also be an opportunistic infection that occurs after a primary agent infects, or SCTLD may be polymicrobial disease that requires infection with multiple pathogens. The latter two scenarios are observed with other coral diseases with the primary and secondary infections of Montipora white syndrome in Hawaii (Beurmann et al., 2017) and the polymicrobial black band disease (Cooney et al., 2002; Meyer et al., 2016), respectively. This project is building upon the current work of our research group, which is focusing on identifying the viruses and microbes associated with diseased corals, determining if they are specific to SCTLD lesions, and establishing if there are any associations between potential pathogens and the start of SCTLD lesions through time. This is a multi-phase project with Phase I focusing on sample collection and the beginning of sample processing. Phase II will focus on samples analysis. The goals of this project are to 1) create a comprehensive dataset from DNA, RNA, proteins, and metabolites extracted from SCTLD samples taken over time, and 2) document the cellular pathologies of SCTLD over time using histology and transmission electron microscopy (TEM). The data generated from this project will provide a comprehensive view of what is occurring during a SCTLD infection over time, as well as generate samples and data that can be used by other research groups for future analyses. The project proposed here is a multi-phase project; this is Phase I of the project (FY 2023 – 2024) that will only focus on sample collection and processing. Analysis of the samples will be conducted in Phase II of the project (FY 2024-2025). Histology slides are available upon request at the following link: https://myfwc.com/research/about/resources/eslide/