U.S. government agencies monitoring fisheries, endangered species, and environmental impacts ought to leverage the DNA present in every drop of seawater, say the organizers of a conference on marine environmental DNA (eDNA), held at Rockefeller University in New York City in November 2018. Biological surveys based on eDNA are reliable and poised to cut costs and save time, they argue in a report released last week.
The report calls for the U.S. National Oceanic and Atmospheric Administration (NOAA) and other government agencies that survey marine life to add the technology to their standard palette of assessment techniques.
“We are exploring all pathways to get the critical information of what animals are where and how many there are,” says conference attendee Michael Weise, who manages the Office of Naval Research’s Marine Mammals and Biology program in Arlington, Virginia. “We are already developing our capabilities using eDNA and we will continue to push that forward. There are gaps and challenges, but I think they are surmountable in the near term.”
Animals leave behind a trail of genetic material as they move through their environment, often in the form of skin cells. Scientists can collect these loose fragments of DNA from soil or water and analyze them to ferret out their source. In the ocean, the DNA trail goes cold after about 24 hours, meaning that any species that shows up in analysis can’t be too far off. For researchers and resource managers trying to find animals in a vast, opaque sea, the technique offers new opportunities.
To sample eDNA, researchers push seawater through a very fine filter. The DNA can then be pulled off the filter, quantitative ecologist Christopher Jerde of the University of California, Santa Barbara, explains. After collecting the DNA from the water sample, researchers can isolate segments of genetic code unique to a species, called genetic markers. These genetic markers can then be compared to a library of such markers to figure out what they came from.
The technique could supplement and eventually supplant collecting entire organisms, says Jerde, who works on eDNA but was not involved in the conference report. “It takes a lot of work to physically survey the oceans—you need so many different setups to capture different species,” he says. “The cost savings [of eDNA] is massive, and because it’s so quick and easy to collect water, you’re able to do it across broad geographical regions.”
Conference organizer and co-author of the report Mark Stoeckle of Rockefeller University has developed an eDNA tool called Go Fish that can identify species in a sample in 3 days or less at a cost of $15 for a single species and $8 for each additional species. Using a different analysis, a single liter of water can reveal the identity of all animals nearby. Testing water for stray DNA also doesn’t harm the animals being studied, whereas many traditional methods injure or kill their subjects.
The techniques, which were first tested in the ocean about 7 years ago, have thus far been used by researchers, but not on the scale of government monitoring. For instance, scoops of seawater detected great white sharks off the coast of Southern California in a 2018 study by Jerde and others published in Frontiers in Marine Science. The technology could one day be deployed in shark-detecting buoys, he says.
Other researchers have used eDNA to study whale sharks, killer whales, and whole ecosystems. On a local scale, Stoeckle used eDNA to detect the arrival of winter flounder in New York Harbor, marking the beginning of the season in which regulations forbid dredging.
The usefulness of eDNA rests on the strength of the genetic library scientists use to interpret it, an area Stoeckle says is still developing, especially for invertebrate species. In waters near humans, scientists must also be wary of contamination. “If tilapia and Atlantic salmon DNA show up in the East River in New York [City], the likelihood is that that genetic material came from human wastewater,” Stoeckle says.
Stoeckle and report co-author Jesse Ausubel, a frequent collaborator also at Rockefeller University, are optimistic that NOAA and other government organizations could simply tack eDNA technology on to existing methods.
Ausubel says he and other conference organizers had encouraging conversations in late 2018 with high-level officials at NOAA and the U.S. Navy. The report’s other recommendations include establishing long-term eDNA monitoring sites to track ecosystems over time and exploring the potential of eDNA to inform decisions such as setting commercial quotas.
Ausubel is convinced of eDNA’s promise. “I’ve been trying to do biodiversity studies for 30 years, and this is a revolution.”