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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 surveys.

Monmouth University Urban Coast Institute

Fisheries in a flask? Loose DNA in seawater offers a new measure of marine populations

Estimating the number of fish in the sea is a wet, cold, and inexact business. To gauge how populations are faring—a critical part of managing fisheries—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 they cost tens of thousands of dollars a day. Many researchers are hoping sampling loose bits of DNA that float in seawater can improve the surveys and extend them into places where trawls can’t go: sensitive habitats like coral reefs, wind farms, and stretches of rocky sea floor that are treacherous for heavy nets.

A large study published today boosts confidence that environmental DNA (eDNA) could become a reliable indicator of the abundance of fish. “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 additional research is needed before the technique can be put into practice, he and other experts say.

eDNA comes from cells that organisms leave behind when they lose tiny flakes of skin, shed mucus or saliva, defecate, or die and decompose. Fragments of DNA persist in water for days or longer, and they can tip researchers to the presence of a particular species. Because the bits of DNA swirl and drift in 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 is not straightforward. “It’s just a really, really hard problem to crack,” 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? In conditions where DNA degrades slowly, are the detected fish actually long gone?

Recently, some researchers have tried to tackle these questions by correlating DNA samples with trawl surveys. Their success has been mixed. Last year, a group led by Ian Salter, a chemical oceanographer at the Faroe Marine Research Institute showed about an 80% match between the sites where eDNA and trawling indicated that Atlantic cod were most abundant. But another group working in the Baltic Sea found a much weaker correlation with the abundance of several other fish species.

The new work comes from a collaboration of Rockefeller University, Monmouth University, and New Jersey’s Bureau of Marine Fisheries, which has surveyed fish species in coastal waters for more than 30 years. The team, led by Rockefeller environmental geneticist Mark Stoeckle, analyzed DNA from dozens of water samples collected by a research vessel that conducted trawls throughout 2019. “It’s an incredible amount of work,” says Ole Shelton, a fisheries biologist with the National Oceanic and Atmospheric Administration, who was not involved. “This is a nice step forward.”

Stoeckle knew eDNA had the power to reveal enormous diversity, but he was still impressed by the results. The team detected 99 fish species during the year; a single liter of seawater turned up just as many species as were netted by a trawl, which sampled 66 million liters.

Overall, the team found about a 70% match between species abundance recorded by eDNA and trawls, they report today in ICES Journal of Marine Science. (The team was only able to assess the abundance of species relative to each other, not the absolute abundance in the water. “You’d have to do a lot more work to understand that,” Stoeckle says.) Accounting for the average surface area of each species strengthened that correlation, Stoeckle says. The researchers assumed that one large fish shed less DNA than a group of smaller fish with the same combined mass.

“I was really astonished,” Nielsen says. “It’s among the strongest evidence that there’s a good correlation” between trawls and eDNA.

Ausubel expects standard procedures for estimating abundance from eDNA could be in place by the end of the decade or sooner, if researchers can tackle key questions such as DNA degradation rate and variation by species. “The fisheries community is poised to start adopting this, and I think you’ll see a lot of rapid uptake in the next few years,” he says. What’s needed to build confidence in eDNA-based abundance measurements is more years of comparison with trawl surveys, Shelton adds.

Stoeckle and his colleagues are hoping to get back on the water when the COVID-19 pandemic is over. Salter’s Atlantic cod project has funding to finish a 5-year comparison of eDNA and trawl surveys by 2022.

Because eDNA sampling costs so much less than trawling, it can be done more frequently, offering more accurate maps of fish abundance as species move around over the season. “If there’s a good correlation between eDNA and fish abundance, then you’ll be able to fill a lot of gaps,” Nielsen says. Salter imagines weekly eDNA surveys to track how fish populations are changing.

But eDNA alone can’t provide information on age, size, and sex of fish, which biologists need to forecast population changes. That means it won’t replace trawl surveys outright, at least not anytime soon.