DOI: 10.5061/dryad.4qrfj6q6h
title: eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem

description: 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.
description: Six one-litre seawater replicates were sampled from 42 sites in
 and around the main Cocos (Keeling) Island atoll, Australia, in April
 2017, totalling 252 samples across a 140 km<sup>2</sup> area.
 Each sample was individually filtered across Pall 0.2ml Supor® polyethersulfone
 membranes using a Pall Sentino® Microbiology pump
 (Pall Corporation, Port Washington, USA), within three hours of
 collection. DNA was extracted from the filter membranes, within two weeks
 of collection, using a DNeasy Blood and Tissue Kit (Qiagen; Venlo,
 Netherlands) with the following modifications: 540ml of ATL lysis buffer
 and 60ml of Proteinase K during the cell digestion phase. Previously
 published primers were sourced to amplify bony fish, elasmobranchs,
 crustaceans and other eukaryotes (including molluscs and echinoderms),
 respectively, from mixed environmental samples. We applied four PCR
 assays, herein referred to as 16S Fish, COI Elasmobranch, 16S Crustacean
 and 18S Universal; primer information can be sourced from Table 1 of the
 manuscript. Fusion-tagged amplicons were sequenced on either a 300 cycle (for
 unidirectional sequencing) or 500 cycle (for paired-end sequencing)
 MiSeq® V2 Standard Flow Cell on an
 Illumina MiSeq platform (Illumina, San Diego, USA), housed in the TrEnD
 Laboratory at Curtin University. Sequences were merged, demultiplexed and
 filtered using a combination of AdapterRemoval (v2;
 Schubert, Lindgreen, &
 Orlando, 2016),
 Geneious® (10.0.6;
 Kearse <i>et
 al.</i>, 2012), USEARCH
 (v9.0.2132; Edgar,
 2010) and OBITools (v1.2.9;
 Boyer, Mercier, Bonin,
 Taberlet, & Coissac, 2014); see supplementary information of
 manuscript for more details. We provide here the demultiplexed
 (unfiltered) data for each sample per assay and subsampled
 presence/absence matrices for each taxonomic group, i.e.
 fish/elasmobranchs, crustaceans, molluscs and
 echinoderms.