Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Instruments
• Project Information
• Funding

Methodology: 

Sampling and analytical procedures:

A SCTLD transmission experiment was carried out at the University of the Virgin Islands (UVI) in April of 2019 and is described in Meiling et al. (2021). One fragment from 6 species of stony coral was placed into a control mesocosm equidistant from a central healthy coral colony. Corresponding genet fragments were placed into an experimental mesocosm equidistant from a SCTLD-infected coral colony. This paired design was replicated for a total of 8 genets per species. Experimental coral fragments that developed lesions were removed and stored at -80ºC for RNA sequencing when 30% tissue loss was achieved. Corresponding control coral fragments were removed and stored at the same time. Tissue samples were harvested from the fragments and total RNA was extracted using the RNAqeous-4PCR total RNA isolation kit (Invitrogen, Life Technologies AM1914) as explained in Veglia et al. (2022). Tissues were lysed using a refrigerated Qiagen TissueLyser II micro centrifuge at 30 oscillations per second for 30 s. Contaminating DNA and chromatin were removed from the total RNA using the Ambion DNase I (RNase-free) kit (Invitrogen, Life Technologies AM2222). Samples were preprocessed by Novogene Co., Ltd. for mRNA enrichment using polyA tail capture; the mRNA libraries underwent 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 instrument using the NEBNext Ultra II RNA library prep kit.

Processing notes from researcher:

BBSplit was used to map quality-filtered (fast v0.20.1) reads to coral or Symbiodiniaceae transcriptome and generate three read files: (I) coral, (ii) Symbiodiniaceae, and (iii) noncoral/non-Symbiodiniaceae. Noncoral/non-Symbiodiniaceae reads were uploaded to NCBI.

BCO-DMO processing description:

• Converted dates to YYYY-MM-DD or YYYY-MM formats where appropriate
• Removed apostrophes (') from Dive_Site column
• Replaced spaces (" ") with underscores (_) in column headers
• Converted lat and long from degrees, hours, seconds to decimal degrees format (64˚55'33.5"W → -64.925972)

NSF Award Abstract:
Coral reef ecosystems provide substantial economic resources to the societies of the United States Virgin Islands (USVI) and other US locations in the forms of tourism, fishing and coastal protection. However, reefs are among the most threatened marine environments, and coral disease is having a devastating impact on these valued systems. In early 2019, a multi-species rapid tissue loss disease matching the description of stony coral tissue loss disease (SCTLD) was found severely affecting a reef off the southwest coast of St. Thomas in the US Virgin Islands (USVI). SCTLD has been devastating coral reef communities in southeast Florida for the last four years, and was very recently reported from disparate areas around the Caribbean, including Mexico, Jamaica, and St. Martin. Rapid surveys by the investigators at the University of the Virgin Islands believe that a 50 km2 area southwest of St. Thomas is the initial incidence area of the disease, but will likely spread across the USVI, British Virgin Islands, and Puerto Rico. This study performs experiments to understand how this disease affects coral species immune traits and compares the microbiology and physiology of disease samples in the USVI to samples from Florida. It also examines how changing the species composition of a coral community affects the spread and impact of the disease. The overall aim is to produce a model to predict the impact of multi-species disease spread on reefs based on coral species assemblages. The project contributes to the research training of at least 2 undergraduates, 2 M.S. students, and 3 Ph.D. students, who benefit from cross-investigator mentoring. The research team includes representatives to the Coral Disease Advisory Committees for the USVI and Florida, which ensures rapid communication of findings to management bodies in both regions.

Coral disease is a significant and increasing threat to Caribbean coral reef systems. Recent results demonstrate that coral species immune traits can predict disease resistance, and thus, forecast impacts to coral community structure, under multi-species coral disease. The onset of this epizootic in the USVI offers an unprecedented opportunity to test hypotheses about the impact of coral resistance, tolerance and immune traits on disease spread during the early stages of an outbreak that could profoundly change the diversity of Caribbean reefs. It is hypothesized that the abundance of highly susceptible species dictates 1) the onset of disease at reef sites downstream of the initial incidence area, and 2) the spread of disease within reef sites. Furthermore, 3) downstream reef sites where highly susceptible species are removed or treated show lower immune responses in all susceptible corals, later onset of disease, and slower within-site disease spread. To test these hypotheses, two experiments directly compare species responses to disease exposure and test the effect of species assemblage on coral immune function and disease spread. Results from these experiments aim to inform a generalizable model to predict the impact of multi-species disease spread on reefs based on coral species assemblages. Results of this project include direct comparison of the USVI disease to Florida SCTLD and a better understanding of how the abundance of highly susceptible host species impacts the spread of disease during the early onset of a multi-species panzootic.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.