Tucked into a closet-sized room in a NOAA facility on the shore of Lake Washington in Seattle are a trio of beige and gray plastic boxes that research biologist Kim Parsons calls her “most sensitive babies.”
The boxes – state-of-the-art scientific instruments – are part of the reason that Parsons and her team have temporarily decamped to this building at Sand Point while road construction is ongoing near the agency’s Montlake facility. “It’s the pile driving that we’re most concerned about,” Parsons explains.
The devices use lasers, impossibly fine wires, and thumbnail-sized glass slides seeded with “lawns” of 1,200 short sequences of molecules known as nucleotides to perform feats such as distinguishing one ecotype of killer whale from another or cataloging the biodiversity found at a particular location in Puget Sound, all based on traces of genetic material in the water.
As such, “they all like things to be very precise,” Parsons says of the machines. “They don’t like to be jostled.” Hence the complicated logistics, all in service of a powerful up-and-coming technique for understanding the biology of the Salish Sea known as environmental DNA (eDNA).
University of Washington professor of marine and environmental affairs Ryan Kelly likened the emergence of eDNA to the invention of the telescope or the microscope, offering “a bit of a revolution in how we see the world.”
Living things are constantly shedding bits of genetic material called DNA into the environment through skin cells, hair, mucus, saliva, feces, and so on. Over the last ten years, researchers have realized that they could apply well-established molecular techniques not just to organisms or bits of tissue but to environmental samples of water, soil, or even air.
In a presentation to the Salish Sea Science Roundtable in May, University of Washington professor of marine and environmental affairs Ryan Kelly likened the emergence of eDNA to the invention of the telescope or the microscope, offering “a bit of a revolution in how we see the world.”
Analyzing the DNA in environmental samples enables scientists to answer questions about organisms that live in or have recently passed through that environment, often at larger scale or with reduced human effort compared to traditional methods, and sometimes without ever seeing the organism of interest at all.
For example, where exactly are invasive European green crabs (Carcinus maenas) establishing a beachhead in Puget Sound? Traditionally, agencies have tracked and managed the invasion with traps, but that’s labor intensive and trap coverage tends to be concentrated where the crabs are already known to be present. In a 2022 study, scientists demonstrated that eDNA is on par with trap data: European green crab DNA was detectable in water samples from the vicinity of all traps that had crabs in them.
Not only that, but the scientists detected European green crab DNA in water samples from some locations where traps remained empty. This likely reflects the movement of larval crabs into new areas where adults have not yet been spotted, the researchers concluded.
“You can detect green crab with eDNA before the adults are there,” Kelly, a member of the study team, told Salish Sea Currents in an interview. “From the perspective of early detection and rapid response for an invasive species, that’s gold.”
As well as tracking the spread of invasive species, eDNA can be ideal for keeping tabs on endangered ones. Kelly and his collaborators are now investigating whether eDNA can be used to monitor the status of yelloweye rockfish (Sebastes ruberrimus). Rockfish are difficult to monitor and sample because, well, they live among rocks, and eDNA could offer a more practical solution – as well as one that would involve less disturbance to the fish.
A key question is whether eDNA can reliably distinguish the Puget Sound population of the fish, which is listed as threatened under the federal Endangered Species Act, from healthy populations elsewhere, as well as from a myriad of closely related rockfish species in Puget Sound. If the method can thread that difficult needle, that would be powerful evidence in favor of using eDNA to monitor endangered species more generally, Kelly says.
Kelly is the director of the eDNA Collaborative, a program housed at the University of Washington and funded by the David and Lucille Packard Foundation and Oceankind that aims to make eDNA research more accessible to scientists around the world. Since the center was set up two years ago, it has awarded 150 microgrants to researchers from over 40 countries on 6 continents and has hosted 9 visiting scholars to learn more about eDNA techniques.
Kelly and other UW scientists who are part of the eDNA Collaborative often tackle questions about Puget Sound biology that are directly relevant to policy and management, while also developing eDNA methods that are more widely applicable.
For example, a team including eDNA Collaborative researchers looked for DNA from four salmonid species (cutthroat trout, Oncorhynchus clarkii; coho salmon, O. kisutch; rainbow trout, O. mykiss; and sockeye salmon, O. nerka) in water samples taken from above and below two culverts over the course of 18 months before, during, and after the replacement of the culverts to improve fish passage.
“It feels like magic, still,” says study team member Elizabeth Allan, senior scientist with the eDNA Collaborative, who has been involved in eDNA research for nearly a decade. “You take a Nalgene bottle, you put it in a creek, and you can see the whole tree of life.”
One of the culverts had not blocked fish passage to begin with, the researchers reported in a paper published in 2023. The second culvert was blocking fish passage, but the replacement improved the situation.
“So not only is it picking up the signal that there’s a problem, we can tell you, yeah, your solution actually is a solution,” Kelly says.
In the coming years, the State of Washington will spend billions of dollars on court-mandated culvert replacements to improve fish passage. In the future, eDNA could be used to help prioritize these expensive, time-consuming, and disruptive projects and to monitor their effects, Kelly says.
In fact, there’s increasing precedent for using eDNA to guide policy and management decisions. Evidence from eDNA has been ruled admissible in federal court to establish the presence or absence of invasive or endangered species and has been used in federal rulemaking around endangered species as well.
Still, such a new field involves many unknowns. “We’re still in our infancy in terms of understanding how far DNA moves in the environment, how long it lasts,” Parsons says. Getting a handle on these dynamics is necessary to answer more complex questions than simply recording the presence or absence of species in an area.
But the Puget Sound region may offer a unique opportunity to gain insight into the details of marine eDNA transport and persistence. It starts with a quartet of dolphins who live at the U.S. Navy base in Bangor, on Hood Canal. The dolphins are part of a once top-secret program to monitor the waters around the base for swimming intruders and protect the nuclear weapons deployed there.
A team including NOAA and eDNA Collaborative researchers has been tracking the movement of DNA from these dolphins. “These aren’t native dolphins. They’re Atlantic bottlenose dolphins,” Kelly explains. “So because of that, when I find Atlantic bottlenose dolphin DNA anywhere in the Hood Canal, I know exactly where it came from.”
The other piece of the puzzle is LiveOcean, an unusually detailed and high-resolution oceanographic model of the Salish Sea and the Washington coast. In a project that is part of a larger, 5-year effort funded by the Office of Naval Research to use eDNA to understand cetacean presence and movements along the West Coast of the United States, researchers have so far demonstrated that the actual movements of dolphin DNA in the water correspond well to the predictions of the model.
They have also established that the eDNA only persists about 24-48 hours and travels about 1-10 kilometers before sinking or being degraded by microbes. “You need a lot of elements to come together to actually answer that question in a quantitative way,” Kelly says. The exact numbers may not generalize to other parts of the ocean, he says, but “all of this is really putting details on the intuition that eDNA is sampling very, very small areas in space and time.”
Similarly, NOAA scientists are analyzing DNA from endangered southern resident killer whales (Orcinus orca) in water samples collected in Puget Sound to gain insight into the dynamics of killer whale eDNA.
eDNA probably won’t be directly helpful in monitoring the whales in Puget Sound because hydrophone and visual sighting networks are so robust in inland waters. Instead, “We’ve used our opportunity to collect water around killer whales to optimize some of our assays,” Parsons says. “We know who was there. We know how many were there. So it’s giving us a unique opportunity to use those samples as a testing ground.”
The insights gleaned could enable the researchers to use eDNA in other, less-studied parts of the southern residents’ range, such as to understand what food sources are drawing them to the outer coast and the western part of the Strait of Juan de Fuca, where the whales have been spending more time in recent years as salmon runs in Puget Sound have declined.
With the rapid proliferation of eDNA research in Puget Sound and elsewhere, scientists and agencies involved in these studies have begun a push for standardization of eDNA methodologies, saying there’s a need to establish best practices for carrying out eDNA research and consistent ways of using it in management. With that in mind, the White House Office of Science and Technology Policy released a national aquatic eDNA strategy for the United States.
Among the eDNA Collaborative’s activities are testing ways to make reliable eDNA methods cheaper and faster for use in the Global South, a group of developing countries in the Southern Hemisphere, and other lower resourced areas. Shana Hirsch, a social scientist with the Collaborative, liaises with communities in the Global South to make sure the methodologies and standards that are being developed are relevant and feasible for them.
But there’s less of a split between the needs of these communities and the needs of stakeholders in the Puget Sound region than one might imagine. “Environmental DNA is only just starting to be used by managers in our region,” Hirsch says. “And so in a lot of ways, we’re all in the same boat.”
That boat, meanwhile, is chugging along. On a recent Friday afternoon, Parsons found herself in a deserted lab after everyone else had gone home for the weekend, standing in front of one of her beige plastic boxes which she said was “angry with me right now.” It turned out the machine’s memory was full, she reported as she downloaded data onto a thumb drive.
“It's absolutely wild,” Parsons said. “We get millions of sequences off of this from every single sample. One of our greatest challenges is how to manage all the data and how to make sure we don't run out of storage space.” That challenge will only grow in the future, as NOAA scientists aim to integrate visual sightings, hydrophone, and eDNA data from killer whales during 2025-26 research cruises, among other efforts. Meanwhile researchers from the eDNA Collaborative plan projects including training citizen scientists on Vashon Island monitor native fish populations and detect green crabs. It’s not hard to imagine the region awash in a coming flood of eDNA data.