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Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder


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Suter, L, Polanowski, AM, Clarke, LJ ORCID: 0000-0002-0844-4453, Kitchener, LA and Deagle, BE 2020 , 'Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder' , Molecular Ecology , pp. 1-15 , doi: 10.1111/mec.15587.

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Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship‐based bulk plankton sampling and morphological identification. We assessed whether eDNA metabarcoding (2 L filtered seawater) could capture similar Southern Ocean zooplankton biodiversity as conventional CPR bulk sampling (~1,500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with (a) conventional morphological CPR sampling and (b) bulk DNA metabarcoding of CPR collected plankton (two transects for each comparison, 40 and 44 paired samples, respectively). A metazoan‐targeted cytochrome c oxidase I (COI) marker was used to characterize species‐level diversity. In the 2 L seawater eDNA samples, this marker amplified large amounts of non‐metazoan picoplanktonic algae, but eDNA metabarcoding still detected up to 1.6 times more zooplankton species than morphologically analysed bulk CPR samples. COI metabarcoding of bulk DNA samples mostly avoided nonmetazoan amplifications and recovered more zooplankton species than eDNA metabarcoding. However, eDNA metabarcoding detected roughly two thirds of metazoan species and identified similar taxa contributing to community differentiation across the subtropical front separating transects. We observed a diurnal pattern in eDNA data for copepods which perform diel vertical migrations, indicating a surprisingly short temporal eDNA signal. Compared to COI, a eukaryote‐targeted 18S ribosomal RNA marker detected a higher proportion, but lower diversity, of metazoans in eDNA. With refinement and standardization of methodology, eDNA metabarcoding could become an efficient tool for monitoring open ocean biodiversity.

Item Type: Article
Authors/Creators:Suter, L and Polanowski, AM and Clarke, LJ and Kitchener, LA and Deagle, BE
Keywords: biodiversity, biomonitoring, continuous plankton recorder, environmental DNA, metabarcoding, open ocean
Journal or Publication Title: Molecular Ecology
Publisher: Blackwell Publishing Ltd
ISSN: 0962-1083
DOI / ID Number: 10.1111/mec.15587
Copyright Information:

© 2020 John Wiley & Sons LtdThis is the peer reviewed version of the following article: Suter, L, Polanowski, AM, Clarke, LJ, Kitchener, JA, Deagle, BE. Capturing open ocean biodiversity: Comparing environmental DNA metabarcoding to the continuous plankton recorder. Mol Ecol. 2020; 00: 1– 18. E], which has been published in final form at This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.

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