UC San Diego

The metazoan (i.e., multicellular animal) community of the Southern California Current Ecosystem (CCE) supports commercial fisheries and has been surveyed by the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program since 1951. However, understanding of metazoan diversity and variability remains limited by current sampling techniques, namely net-based methods. Environmental DNA (eDNA) methods have demonstrated promise in detecting pelagic metazoans and community biogeography in marine ecosystems. eDNA offers advantages over traditional small net trawls, like those deployed by CalCOFI, in identifying metazoans which are able to avoid nets, are too small or delicate for net capture, or inhabit deeper regions of the water column than the upper 200 or 500 meters where nets are typically deployed. Here, we apply eDNA tools opportunistically from low-volume seawater samples in combination with trawls to investigate differences between these sampling methods in detecting diverse taxonomic groups. We apply two primer sets, targeting vertebrate and invertebrate groups, and customize a metazoan-specific bioinformatics pipeline to assign taxonomy to eDNA sequences. We then assess how well eDNA methods perform with depth and across metazoan taxa, and whether eDNA analyses can reveal community biogeography in the CCE. Overall, eDNA and net-based sampling showed strong concordance, with large differences attributed to identification of coastal forage fishes and copepods. eDNA methods’ identification abilities declined with depth but were able to resolve taxonomic shifts in community structure over a large geographic area. We discuss hypotheses for discrepancies between sampling methods and highlight recommendations for improving eDNA applications in the midwater.