From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference

Adamowicz, Sarah J.; Chain, Frédéric J. J.; Clare, Elizabeth L.; Deiner, Kristy; Dincă, Vlad; Elías‐Gutiérrez, Manuel; Hausmann, Axel; Hogg, Ian D.; Kekkonen, Mari; Lijtmaer, Darío A; Naaum, Amanda M.; Steinke, Dirk; Valdéz-Moreno, Martha; Bank, Michelle van der; Wilson, John James; Xu, Jianping

doi:10.1139/gen-2016-0159

Cited by 4 publications

(1 citation statement)

References 25 publications

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“…Benthic collection methods (i.e. Autonomous Reef Monitoring Structures; ARMS) combined with metabarcoding using universal primer sets have also proven useful in surveying cryptobenthic biodiversity not revealed by visual techniques (Al-Rshaidat et al, 2016;Pearman et al, 2016;Pearman et al, 2018). ARMS and comparable methods, however, are not without their own taxonomic biases (Ransome et al, 2017), need to be deployed for months to years in order for sufficient animals to settle in the fibrous matrix, and often require taxonomic specialists to identify the larger fraction of organisms (Pearman et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient (v0.1)"

Pearman¹

2019

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Background. Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing (NGS) metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods. We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results. Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family-level) detected in sediments when compared across different depths ranging from 10 to 40 meters (p = 0.001). Significant depth zonation was observed across OTUs assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e. anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion. Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.

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