Fish community surveys in eelgrass beds using both eDNA metabarcoding and seining: implications for biodiversity monitoring in the coastal zone

Susan G. Heaslip,Kristen M. Westfall,Emily M. Rubidge,Xiaoping He,Lorraine C. Hamilton,Louise-Marie D. Roux,Nicholas W. Jeffery,Scott R. Gilmore,Royce Steeves,Ryan R.E. Stanley,Cathryn L. Abbott,Katie S.P. Gale

doi:10.1139/cjfas-2021-0215

Abstract

Marine Protected Areas (MPAs) have been adopted globally as a tool to combat biodiversity loss and restore marine ecosystems. Successful application of MPAs will be predicated on the ability to monitor biodiversity in a synoptic and noninvasive manner. Environmental DNA (eDNA) methods have important advantages over traditional biodiversity survey methods for monitoring conservation areas. To evaluate the efficacy of eDNA metabarcoding for fish biodiversity monitoring, we sampled 19 coastal eelgrass (Zostera marina) beds in Canada, as eelgrass beds are known for high biodiversity and significant conservation value. At each site, beach seines were used to survey fish and water samples were collected contemporaneously for eDNA metabarcoding. In total, beach seining caught 32 672 individuals across 59 fish taxa, and eDNA detected 129 fish taxa. eDNA captured site-level variation and detected higher species richness at both site and regional levels compared to seining. eDNA abundance had a positive association with capture abundance. Collectively these results highlight how eDNA metabarcoding offers an efficient approach for monitoring fish biodiversity in coastal eelgrass beds, thus providing a valuable and noninvasive tool for MPA planning and coastal monitoring.

Highlights

Awareness of the implications of global biodiversity loss has increased over the past two decades, as has acknowledgement that biodiversity conservation should be part of broader economic and political discussions at both national and international levels (Worm et al 2006; Cardinale et al 2012)
Summary of Environmental DNA (eDNA) metabarcoding data For the 12S marker, 6.44 million raw paired-end reads were generated for 87 samples
In the final 12S amplicon sequence variant (ASV) table, there were 331 ASVs from a total of 3.36 million reads across 56 samples (Supplementary Table S61). These ASVs were assigned to 80 fish species and 17 species groups, the latter representing identical sequences shared by multiple fish species, of which 13 contained species from the same genus and four contained species from different genera within a family (Supplementary Table S101)

Summary

Introduction

Awareness of the implications of global biodiversity loss has increased over the past two decades, as has acknowledgement that biodiversity conservation should be part of broader economic and political discussions at both national and international levels (Worm et al 2006; Cardinale et al 2012). Combating biodiversity loss has become a point of international cooperation, with the Convention on Biological Diversity setting various targets to combat and reduce loss (Thomas et al 2014; Meehan et al 2020). Marine Protected Areas (MPAs) have been adopted globally to conserve and restore marine ecosystems. Coastal zones are dynamic ecosystems characterized by relatively high fish diversity (Suchanek 1994). They are at the interface of the Received 4 August 2021.

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