eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem

Environmental DNA (eDNA) metabarcoding, a technique for retrieving multi-species DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for efficient whole-ecosystem surveying approaches to baseline biodiversity, study assemblage changes and implement appropriate conservation protections. In this study, we investigated the utility of eDNA metabarcoding as a high-resolution, multi-trophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI) – a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seaw...