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Summary Stony Coral Tissue Loss Disease (SCTLD) is a devastating disease. Since 2014, it has spread along the entire Florida Reef Tract and into the greater Caribbean. It was first detected in the United States Virgin Islands in January 2019. To more quickly identify microbial bioindicators of disease, we developed a rapid pipeline for microbiome sequencing. Over a span of 10 days we collected, processed and sequenced coral and near‐coral seawater microbiomes from diseased and apparently healthyColpophyllia natans,Montastraea cavernosa,Meandrina meandritesandOrbicella franksi. Analysis of bacterial and archaeal 16S ribosomal RNA gene sequences revealed 25 bioindicator amplicon sequence variants (ASVs) enriched in diseased corals. These bioindicator ASVs were additionally recovered in near‐coral seawater (<5 cm of coral surface), a potential reservoir for pathogens. Phylogenetic analysis of microbial bioindicators with sequences from the Coral Microbiome Database revealed thatVibrio,Arcobacter, Rhizobiaceae and Rhodobacteraceae sequences were related to disease‐associated coral bacteria and lineages novel to corals. Additionally, four ASVs (Algicola,Cohaesibacter,ThalassobiusandVibrio) were matches to microbes previously associated with SCTLD that should be targets for future research. Overall, this work suggests that a rapid sequencing framework paired with specialized databases facilitates identification of microbial disease bioindicators.
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Coral microbiome database: Integration of sequences reveals high diversity and relatedness of coral‐associated microbes
Summary Coral‐associated microorganisms are thought to play a fundamental role in the health and ecology of corals, but understanding of specific coral–microbial interactions are lacking. In order to create a framework to examine coral–microbial specificity, we integrated and phylogenetically compared 21,100 SSU rRNA gene Sanger‐produced sequences from bacteria and archaea associated with corals from previous studies, and accompanying host, location and publication metadata, to produce the Coral Microbiome Database. From this database, we identified 39 described and candidate phyla of Bacteria and two Archaea phyla associated with corals, demonstrating that corals are one of the most phylogenetically diverse animal microbiomes. Secondly, this new phylogenetic resource shows that certain microorganisms are indeed specific to corals, including evolutionary distinct hosts. Specifically, we identified 2–37 putative monophyletic, coral‐specific sequence clusters within bacterial genera associated with the greatest number of coral species (Vibrio,EndozoicomonasandRuegeria) as well as functionally relevant microbial taxa (“CandidatusAmoebophilus”, “CandidatusNitrosopumilus” and under recognized cyanobacteria). This phylogenetic resource provides a framework for more targeted studies of corals and their specific microbial associates, which is timely given the escalated need to understand the role of the coral microbiome and its adaptability to changing ocean and reef conditions.
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- Award ID(s):
- 1736288
- PAR ID:
- 10075767
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Environmental Microbiology Reports
- Volume:
- 11
- Issue:
- 3
- ISSN:
- 1758-2229
- Format(s):
- Medium: X Size: p. 372-385
- Size(s):
- p. 372-385
- Sponsoring Org:
- National Science Foundation
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