Environmental DNA Generating Critical Data on Nearshore Fisheries, NOAA Says

Winter flounder
Winter flounder collected on a fish and water sampling survey of Sandy Hook Bay, NJ. Photo: Liza Baskin/Marine Academy of Science and Technology.

DNA technology is helping NOAA Fisheries use bottles of water collected from the ocean to determine critical data about the fish living in those waters.

A new NOAA Fisheries report says scientists have now demonstrated that environmental DNA (eDNA) metabarcoding can characterize nearshore fish communities in different marine habitats and tidal conditions in Southeast Alaska. 

Collaborators on the project include the Alaska Fisheries Science Center’s Auke Bay Laboratories, the University of Alaska Fairbanks College of Fisheries and Ocean Sciences and the Alaska regional office’s Habitat Conservation Division.

Wes Larson, manager of the science center’s genetics program, notes that “environmental or eDNA can revolutionize how we assess nearshore fish communities in Alaska.”

“Traditionally, the only way to sample nearshore fish communities is by using beach seines or similar gear types set from either shore or small boats,” he said. “Now we have another technique for generating similar data sets—analyzing a simple water sample with eDNA metabarcoding.”

Major goals of the study were to verify that the method could be used successfully across distinct habitats and to understand how the large tidal swings typical of many high-latitude marine environments might impact fish species detection.

eDNA is the genetic material shed by organisms into the surrounding environment. Some sources of eDNA include scales, skin cells, mucus, feces and gametes. This genetic material can be recovered from environmental samples and used to detect a fish’s presence even after it has moved through the area. 

After an environmental sample—in this case, a liter of water—is collected and filtered, the DNA is extracted and analyzed using eDNA metabarcoding.

eDNA metabarcoding is a method of species identification that compares short sections of DNA, also known as “sequences,” with a reference library of known sequences. It’s similar to how a supermarket scanner uses the familiar black stripes of the UPC barcode to identify an item in its stock against its reference database.

Marine Academy of Science and Technology
Collaborators on an environmental DNA project conduct a trawl survey in Sandy Hook Bay, NJ. File photo courtesy of Liza Baskin/Marine Academy of Science and Technology.

Metabarcoding provides a snapshot of entire communities across taxonomic groups from a single standardized sample. Larson and his colleagues sampled sandy beaches, eelgrass beds and rocky shorelines along the coast of Juneau, Alaska during high and low tides. They detected 21 unique groups of fish, including salmon, Pacific herring, flatfish, pricklebacks and gunnels, sculpin, cod, sablefish, smelt, rockfish and lingcod.

Species richness—indicating the number of species—and composition based on eDNA detections differed substantially across habitats, according to the data. Rocky habitats contained fewer species, different species and fewer positive detections for each species compared to sand and eelgrass habitats. 

Larson said he suspects that differences in fish communities across these habitats could be driven by physical characteristics such as shoreline slope and bottom depth. Those depths at sampling locations in rock habitats were often deeper, with slopes that descend rapidly from the collection location. In contrast, sand and eelgrass environments are characterized by more gradual slopes. 

“The lower detection rates for some fish species in rocky habitats could be a function of sampling farther from the seafloor in areas where water is not well mixed between the bottom and the surface,” Larson said.

In rocky habitats, the halocline—the border between layers of water that contain different amounts of salt—can act as a barrier to eDNA movement, effectively trapping surface and bottom sourced eDNA in their respective layers. The halocline may be especially pronounced in coastal southeast Alaska due to large freshwater inputs from rivers, glaciers and precipitation.

The study demonstrates how eDNA metabarcoding can be used to characterize nearshore fish communities in a high-latitude marine environment. These ecosystems are influenced by large tidal swings, strong currents and significant freshwater input from large rivers, rain and snowmelt.

The authors concluded that marine eDNA transport was minimal, with many of the eDNA detections coming from locally abundant species. They also noted that the majority of species in the fish community were detected with eDNA regardless of tidal stage.