eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem
West, Katrina et al. (2020), eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem, Dryad, Dataset, https://doi.org/10.5061/dryad.4qrfj6q6h
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 km2 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 et al., 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.
Australian Research Council, Award: LP160100839