A holistic time-series analysis of stony coral tissue loss disease

As stony coral tissue loss disease (SCTLD) continues to spread throughout the Caribbean and continues to kill off corals in Florida, the causative agent responsible for this malady is still unidentified. Because the causative agent is still unknown, the development of more targeted treatments and feasible diagnostic tools is severely hampered. However, the various analyses conducted on a wide variety of sample sets have not positively identified a causative agent for SCTLD. This may be, in part, due to the variability between reefs and coral colonies over time and location as well as the potential complexity of this disease, which may involve multiple agents and environmental stressors. Therefore, the goal of this project was to take a holistic approach and begin processing a standardized set of SCTLD samples for a wide variety of analyses. The strength of this approach is that all the datasets generated from each sample can be directly compared to one another.

To reduce potential ‘background noise’ and environmental variables, this project uses closed, aquarium systems as well as the use of naïve healthy corals that were obtained from areas before SCTLD had arrived and subsequently kept in captivity. This ensured we could control any environmental variables such as temperature, nutrient input, and microbes entering the system. Further, the use of naïve corals reduced the possibility of SCTLD-associated microbes associated with healthy fragments before exposure to disease. Lastly, these naïve corals were infected in the laboratory using diseased corals, but samples were taken at various time points to try to capture the transition from a healthy to a disease state in our future analyses. Samples were taken at five timepoints: pre-experiment (T1), 48 h from the start of the experiment (T2), 7 days post-T2 or the first gross signs of disease (T3), 7-days post T3 or before full fragment mortality (T4), and 7-days post T4 or before full fragment mortality (T5). For every experimental tank, there was also a control tank with only naïve healthy corals under similar conditions except for a healthy fragment instead of a diseased fragment.

At each timepoint, a fragment in the experimental tank as well a control tank was split into five subsamples and preserved for multi-omics extractions, chemical extraction, histology, transmission electron microscopy (TEM), and extractions for immunological assays. This project (FY 2023-2024) focused on the processing of these >300 samples in preparation for the analyses that are planned for next phase (FY 2024-2025). All the samples have been processed and will be analyzed for this funding period and analysis will begin during the next funding period.