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As a recipient of both land- and sea-based inputs, coastal ecosystems are areas of both high productivity and high human impact. Biodiversity within these ecosystems is impacted by a multitude of often synergistic stressors. Marine Protected Areas (MPAs) have been adopted globally as a tool to combat biodiversity loss and restore marine ecosystems. Central to the application of MPAs is the ability to monitor changes in biodiversity in a synoptic and preferably non-invasive manner. Environmental DNA (eDNA) methods offer relatively new approaches for measuring aquatic biodiversity that have important advantages over traditional marine survey methods. We test the application of eDNA metabarcoding for characterizing fish diversity in the coastal zone focusing on eelgrass beds, which are known for high biodiversity and are therefore of significant conservation value. We sampled 19 coastal sites in Atlantic and Pacific Canada; at each site, beach seines were used to survey fish in eelgrass beds and water samples were collected contemporaneously for eDNA metabarcoding to characterize fish biodiversity using two genetic markers (12S rRNA and 16S rRNA). Across all sample locations, beach seining caught 32,672 individuals from across 59 fish taxa, while eDNA detected 129 fish taxa. There were only three species caught by seining and not detected by eDNA, and for these species only one or two individuals were nettedcaught. eDNA clearly captured site-level variation and detected higher fish species richness at local and regional levels when compared to seining. We found eDNA abundance had a positive association with fish capture abundance. Collectively these results highlight how eDNA metabarcoding could offer a non-invasive and efficient approach for monitoring fish biodiversity in coastal eelgrass beds and could thus become a valuable tool to support MPA planning and coastal monitoring.

Xiaoping He¹, Ryan R.E. Stanley², Emily M. Rubidge³, Nicholas W. Jeffery², Lorraine C. Hamilton², Kristen M. Westfall¹, Scott R. Gilmore¹, Louise-Marie D. Roux¹, Katie S.P. Gale³, Susan G. Heaslip², Royce Steeves⁴, Cathryn L. Abbott¹*

*Corresponding author

1. Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
2. Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, Dartmouth, NS, B2Y 4A2, Canada
3. Institute of Ocean Sciences, Fisheries and Oceans Canada, 9860 W Saanich Rd, Sidney, BC V8L 5T5, Canada
4. Gulf Fisheries Centre, Fisheries and Oceans Canada, 343 Université Avenue, Moncton, NB, E1C 9B6, Canada

Figure 1 Map of the 19 coastal eelgrass beds sampled in the Pacific (a) and Atlantic (b) regions of Canada.

Figure 2 Venn diagrams compared the fish taxa detected by eDNA and seining at family and species levels. For the lower panel, only taxa identified to the species level were considered.