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 seawater samples collected from 42 sites within a 140 km2 area.
Our assays successfully detected a wide range of bony fish and
elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms
(7). Site composition varied significantly, reflecting habitat
partitioning across the island ecosystem and demonstrating the
localisation of eDNA signals despite extensive tidal and oceanic
movements. In addition, we document putative new occurrence records for 46
taxa and compare the efficiency of our eDNA approach to visual survey
techniques at CKI. Our study demonstrates the utility of a multi-marker
metabarcoding approach in capturing multi-trophic biodiversity across an
entire coral reef atoll and sets an important baseline for ongoing
monitoring and management.