Insights into the Cultured Bacterial Fraction of Corals

Michael Sweet, Helena Villela, Tina Keller-Costa, Rodrigo Costa, Stefano Romano, David G. Bourne, Anny Cárdenas, Megan J. Huggett, Allison H. Kerwin, Felicity Kuek, Mónica Medina, Julie L. Meyer, Moritz Müller, F. Joseph Pollock, Michael S. Rappé, Mathieu Sere, Koty H. Sharp, Christian R. Voolstra, Nathan Zaccardi, Maren ZieglerRaquel Peixoto

Research output: Contribution to journalArticlepeer-review

47 Scopus citations

Abstract

Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite their putative importance, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable bacteria isolated from corals originating from tropical, temperate, and cold-water habitats. A total of 3,055 isolates from 52 studies were considered by our metasurvey. Of these, 1,045 had full-length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterium-coral symbioses among the strains. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features—not previously described for coral-bacterium symbioses—potentially involved in host colonization and host-symbiont recognition, antiviral defense mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning and guide the selection of probiotic candidates to promote coral resilience and improve holistic and customized reef restoration and rehabilitation efforts.
Original languageEnglish (US)
JournalmSystems
DOIs
StatePublished - Jun 22 2021

Bibliographical note

KAUST Repository Item: Exported on 2021-06-24
Acknowledgements: Part of this research was carried out in association with the ongoing R&D project registered as ANP 21005-4, “PROBIO-DEEP - Survey of potential impacts caused by oil and gas exploration on deep-sea marine holobionts and selection of potential bioindicators and bioremediation processes for these ecosystems” (UFRJ/Shell Brasil/ANP), sponsored by Shell Brasil under the ANP R&D levy as “Compromisso de Investimentos com Pesquisa e Desenvolvimento.” This research project won the Great Barrier Reef Foundation’s Out of the Blue Box Reef Innovation Challenge People’s Choice Award supported by The Tiffany & Co. Foundation. The Institute of Bioengineering and Biosciences acknowledges funding provided by the Portuguese Foundation for Science and Technology (FCT) and the European Regional Development Fund (ERDF) through grant UIDB/04565/2020. Part of this work was supported by the research grant FA_05_2017_032 conceded to R.C. and T.K.-C. by the Portuguese Ministry of the Sea (Direção Geral de Política do Mar) under the program “Fundo Azul.” T.K.-C. is the recipient of a Research Scientist contract with FCT (CEECIND/00788/2017). N.Z. and K.H.S. were supported in part by the INBRE-NIGMS by NIH grant P20GM103430.
M.S. designed the initial study and led the collection, analysis, and write-up of the paper. H.V. conducted the majority of the analysis on the 16S data, and T.K.-C. and R.C. conducted the majority of the analysis of the genome data. S.R. assisted with the meta-analysis component of the project, and R.P. co-funded the project with M.S. All authors assisted with data collection, analysis, and writing/editing

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