Coral Reef Stony Coral Tissue Loss Disease Microbiomes in Coral Tissue and Near-Coral Seawater

Stony Coral Tissue Loss Disease (SCTLD) is a devastating coral disease. Since 2014, it has spread along the entire Florida Reef Tract, where it affects over one-third of Caribbean reef-building coral species, and has since spread throughout the greater Caribbean, presumably via a water-borne vector. In January 2019, it was first detected in St. Thomas, United States Virgin Islands (USVI). To more quickly identify and respond to this coral disease outbreak, we developed a rapid pipeline for microbiome characterization, which employed the portable, high-accuracy sequencing platform, the Illumina iSeq 100 System. By transforming a home rental in St. Thomas, USVI, to a molecular laboratory, we collected, processed, and sequenced 51 diseased or apparently healthy coral tissues from Colpophyllia natans, Montastrea cavernosa, Meandrina meandrites and Orbicella franksi and seawater surrounding each coral over a span of 10 days. Analysis of bacterial 16S ribosomal RNA (rRNA) gene amplicon sequences from microbial communities associated with diseased tissue revealed 25 SCTLD-enriched amplicon sequence variants (ASVs). Furthermore, these taxa were all detectable in near-coral seawater (within 5 cm of coral surface), a potential recruitment zone for pathogens. Phylogenetic analysis of disease-associated ASVs belonging to Vibrio, Arcobacter, Rhizobiaceae, and Rhodobacteraceae revealed representatives of previously identified coral disease-associated bacteria as well as undescribed lineages not previously associated with corals. Additionally, we identified four ASVs that were also represented in SCTLD-infected Floridian corals (Algicola, Cohaesibacter, Thalassobius and Vibrio). This work represents the first rapid coral disease sequencing effort and offers specific bacterial targets for SCTLD research, which could help slow or stop the spread of this unprecedented coral disease.