eDNA May Prove a Cost-Effective Alternative to Better Understanding Coastal Species Diversity

NOAA Fisheries researchers are looking to use of environmental DNA metabarcoding as a feasible, cost-effective alternative to traditional sampling for collecting species diversity data in coastal areas and identifying essential fish habitat.

Preliminary results of an e-DNA study released in late February by the Alaska Fisheries Science Center’s Auke Bay Laboratories said a pilot study using eDNA techniques in 2020 identified more than 40 species in nine sites around Juneau.

According to Wes Larson, program manager for the genetics lab at AFSC at Auke Bay, there are many ways eDNA can help them do their jobs better. Through water sampling, researchers are able to detect a fish after it has left an area, including cryptic fish, those that may not typically be sampled in traditional survey gear, or may be a rare or low-density organism that surveys miss. e-DNA sampling can also help identify pelagic fish like Pacific cod and Alaska Pollock that may be offshore and could avoid smaller nets, he said. To assess species diversity, researchers are using eDNA metabarcoding, a cutting-edge technique that allows for identification of numerous species from a single water sample.

Resource managers at NOAA Fisheries Alaska Regional Office, the North Pacific Fishery Management Council and the U.S. Army Corps of Engineers are all interested in this project also for its importance in identifying essential fish habitat (EFH), as well as the possibility of using eDNA as a cost-effective way to learn which fish and crab species are present at specific locations throughout Alaska.

State and federal fisheries managers, as well as the Corps of Engineers can use EFH information in numerous ways, from fisheries management to making decisions on permitting resource development projects. Larson also sees this work as an important complement to long term genetic studies, including estimating stock compositions of salon caught as bycatch in federal fisheries and understanding stock-specific impacts.

Other NOAA laboratories are already conducting eDNA research at Northwest and Northeast fisheries science centers.
Long term plans are to conduct eDNA sampling in many areas of Alaska, including nearshore habitats near Baranof Island, Kodiak, Prince William Sound, the Gulf of Alaska, Aleutian Islands, and the Bering, Chukchi and Beaufort seas.

Larson and Gretchen Harrington, with NOAA Fisheries Alaska Region Habitat Conservation Division, said they are also exploring use of eDNA to understand fish and crab habitat use and distribution in the nearshore and to detect marine invasive species, such as European green crab. “As budgets shrink, we are continuing to find innovative ways to do more with less,” they said. “We are particularly excited about pairing eDNA with un-crewed instrumentation such as remote autosamplers.”

Researchers are currently piloting the use of eDNA autosamplers that can collect samples in remote locations, in hope that these samplers will be able to provide high-resolution data on species presence and/or absence and abundance without requiring a boat, crew and infrastructure to set and retrieve nets.