Characterization of coral reefs of La Reunion using eDNA

The western Indian Ocean is a coral reef hotspot and home to Reunion Island, which hosts short stretches of narrow fringing reefs inhabited by hyperdiverse animal assemblages. Reunionese reefs are at risk from mounting external stressors and efforts to counteract reef degradation typically involve regular biodiversity surveys. Environmental DNA (eDNA) has emerged as a method to circumvent some limitations of visual surveys, which remain a prevailing approach for tracking the health of habitats, though the use of eDNA requires deliberate study design and optimization for each new application. The utility of eDNA for detecting metazoans was therefore examined within four lagoons of on Reunion Island, by developing a contemporary workflow that integrated specialized equipment to collect and preserve water samples. Teleost and invertebrate communities were characterized through metabarcoding fragments of the 12S ribosomal RNA, Cytochrome c Oxidase subunit 1 and small ribosomal subunit 18S genes. eDNA surveys detected high species richness that varied by site, and in a single collection period, recovered the presence of 60 teleost families, several conspicuous members of reef invertebrate communities including a multitude of annelid, mollusk and echinoderm families, as well as less studied phyla, such as nematodes, bryozoans and tardigrades. Further, eukaryotic communities were found to be distinct across sites, supporting the differing environmental characteristics of each sampled area. These results demonstrate the applicability and sensitivity of eDNA as a complementary method for generating comprehensive bio-inventories necessary for appraising the state of Reunionese reefs.