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Crew on the R / V Sea Wolf count fish during a trawl survey. Environmental DNA could be a cost-effective way to improve these investigations.
Urban Coast Institute of Monmouth University
By Erik Stokstad
Estimating the number of fish in the sea is a wet, cold and inaccurate business. To gauge how populations are doing, a key part of fisheries management, researchers typically drag a large net behind a ship, counting and measuring what they catch. But these trawl surveys only provide a rough indication of fish populations and cost tens of thousands of dollars a day. Many researchers hope that sampling loose DNA fragments floating in seawater can improve surveys and extend them to places where trawl nets cannot go: sensitive habitats such as coral reefs, wind farms, and stretches of rocky seabed that are dangerous for heavy nets.
A large study published today raises confidence that environmental DNA (eDNA) could become a reliable indicator of fish abundance. “There is more and more evidence,” says Einar Nielsen, a geneticist at the Technical University of Denmark who was not involved in the work. But more research is needed before the technique can be put into practice, say he and other experts.
EDNA comes from cells that organisms leave behind when they shed tiny flakes of skin, shed mucus or saliva, defecate or die and decompose. Fragments of DNA persist in the water for days or more and can suggest to researchers the presence of a particular species. As the DNA fragments swirl and move in the water, a small sample can reveal which fish inhabit a lake, river, or marine environment. The technique can indicate whether an endangered species persists in a headwater stream, for example, or whether an invasive fish has reached a new lake.
But fisheries managers also want to know how many individuals of a species are present so they can set sustainable catch limits. And gleaning abundance from eDNA isn’t easy. “It’s just a really, really hard problem to solve,” says Jesse Ausubel, an environmental scientist at Rockefeller University who helped organize the new study. Questions abound: Does a certain amount of DNA indicate several small fish or one large one? Under conditions where the DNA degrades slowly, have the detected fish actually long since disappeared?
Recently, researchers have tried to address these questions by correlating DNA samples with trawl investigations. Their success was mixed. Last year, a team led by Ian Salter, a chemical oceanographer at the Faroe Marine Research Institute showed an 80% match between sites where eDNA and trawling indicated Atlantic cod was more abundant. . But another group working in the Baltic Sea found a much weaker correlation with the abundance of many other fish species.
The new work stems from a collaboration between Rockefeller University, Monmouth University and the Bureau of Marine Fisheries of New Jersey, which has been investigating fish species in coastal waters for over 30 years. The team, led by Rockefeller environmental geneticist Mark Stoeckle, analyzed the DNA of dozens of water samples collected from a research vessel that conducted trawl nets throughout 2019. “That’s an incredible amount of work,” says Ole Shelton, a fishery biologist at the National Oceanic and Atmospheric Administration, who was not involved. “This is a big step forward.”
Stoeckle knew that eDNA had the power to reveal tremendous diversity, but he was impressed with the results nonetheless. The team found 99 species of fish throughout the year; a single liter of sea water produced as many species as were netted by a trawl, which sampled 66 million liters.
Overall, the team found a 70% match between the species abundance recorded by eDNA and trawls, they report today in CIEM Journal of Marine Sciences. (The team was only able to evaluate species abundance relative to each other, not absolute abundance in the water. “You would have to do a lot more work to figure that out,” Stoeckle says.) The area of each species strengthened this correlation, Stoeckle says. Researchers speculated that a large fish lost less DNA than a group of smaller fish with the same combined mass.
“I was really blown away,” says Nielsen. “It is one of the strongest evidence that there is a good correlation” between trawls and eDNA.
Ausubel predicts that standard procedures for estimating eDNA abundance could be in place by the end of the decade or sooner if researchers can address key issues such as DNA degradation rate and variation by species. “The fishing community is ready to start adopting it, and I think you will see rapid absorption in the next few years,” he says. What is needed to build confidence in eDNA-based abundance measurements are more years of confronting trawl surveys, Shelton adds.
Stoeckle and his colleagues hope to get back on the water when the COVID-19 pandemic is over. Salter’s Atlantic cod project has the funds to complete a five-year comparison of eDNA and trawl surveys by 2022.
Since eDNA sampling costs much less than trawling, it can be done more frequently, offering more accurate maps of fish abundance as species move through the season. “If there is a good correlation between eDNA and fish abundance, you will be able to fill in a lot of gaps,” says Nielsen. Salter envisions weekly eDNA surveys to monitor how fish populations are changing.
But eDNA alone cannot provide information on the age, size and sex of fish, which biologists need to predict population changes. That means it won’t completely replace polls with trawl nets, at least not anytime soon.
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