Using low volume eDNA methods to sample pelagic marine animal assemblages

Dan, Michelle E.; Portner, Elan J.; Bowman, Jeff S.; Semmens, Brice X.; Owens, Sarah M.; Greenwald, Stephanie M.; Choy, C. Anela

doi:10.1371/journal.pone.0303263

Title: Using low volume eDNA methods to sample pelagic marine animal assemblages

Journal Article · 14 May 2024 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0303263 · OSTI ID:2482255

Dan, Michelle E. ^[1];

^[1]; Bowman, Jeff S. ^[1];

^[1]; Owens, Sarah M. ^[2]; Greenwald, Stephanie M. ^[2];

^[1]

Univ. of California, San Diego, CA (United States)
Argonne National Laboratory (ANL), Argonne, IL (United States)

Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380–1800 mL) collected at depths of 0–2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Science Foundation (NSF); US Department of the Navy, Office of Naval Research (ONR); USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 2482255

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 5 Vol. 19; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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