Environmental DNA as a Tool for the Assessment of Coral (Anthozoa) Composition in the Chagos Archipelago

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Abstract
Human‐induced global warming has triggered a persistent decline in the health of marine ecosystems, particularly coral reefs, which are experiencing increasingly frequent and severe bleaching and mortality events. Refining cost‐effective and precise monitoring tools, such as environmental DNA (eDNA) metabarcoding, is essential to supplement future coral reef monitoring programs, with ongoing efforts focused on improving methods, validating results, and understanding limitations. Although eDNA has been widely used in aquatic ecosystem studies, its application to corals (Anthozoa) remains underexplored. Here, we investigate the use of eDNA metabarcoding with molecular markers targeting the ITS2 region of Anthozoa for monitoring coral communities in a remote and relatively undisturbed atoll system. We integrate three mainstream taxonomic assignment approaches (IDTAXA, BLAST Top Hits, and BLAST LCA), retaining only consensus identifications across methods for downstream analyses. This conservative strategy ensures highly robust and reliable taxonomic resolution, with over 90% of the sequences classified within Anthozoa, encompassing 18 genera and 15 genera of hard corals (Scleractinia). A considerable overlap in coral identification is observed between eDNA and traditional benthic transect surveys, giving support to the ability of eDNA to identify the community composition of Anthozoan taxa. Importantly, cryptic genera, such as Cycloseris , Cyphastrea , Merulina , Oxypora , and Turbinaria were identified by the eDNA approach but not the traditional surveys. Conversely, genera such as Alveopora , Astreopora , Caulastrea , Fungia , Galaxea , Halomitra , Herpolitha , Leptastrea , Platygyra , Plerogyra , and Stylophora were identified by the traditional surveys but not the eDNA approach, likely due to primer bias, taxonomic resolution or incomplete reference databases, supporting the complementary use of both methods. We also observe that the eDNA metabarcoding may capture differences in coral community structure between our lagoonal and seaward reef habitat types and point to potential characteristic taxa. This study underscores the utility of eDNA metabarcoding as a noninvasive, cost‐effective tool for coral biodiversity monitoring and provides insights into how to improve eDNA techniques for use as a coral biodiversity monitoring tool.
Funding Information
  • Natural Environment Research Council
  • University College London

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