During the annual salmon run last fall, 91̽�� researchers pulled salmon DNA out of thin air and used it to estimate the number of fish that passed through the adjacent river. , a 91̽��research scientist of marine and environmental affairs, began formulating the driving hypothesis for the study while hiking on the Olympic Peninsula.

“I saw the fish jumping and the water splashing and I started thinking — could we recover their genetic material from the air?,” he said.

The researchers placed air filters at several sites on Issaquah Creek, near the Issaquah Salmon Hatchery in Washington. To their amazement, the filters captured Coho salmon DNA, even 10 to 12 feet from the river. Scientists collect environmental DNA, or eDNA, to identify species living in or passing through an area, but few have attempted to track aquatic species by sampling air.

This study, , shows that eDNA can move between air and water — a possibility scientists hadn’t accounted for even though aquatic animal DNA sometimes appears in airborne study data.

The researchers then merged air and water eDNA with the hatchery’s visual counts in a model to track how salmon numbers rose and fell during the fall migration. Although the amount of salmon DNA in the air was 25,000 times less than what was observed in the water, its concentration still varied with observed migratory trends.

“This work is at the edge of what is possible with eDNA,” said senior author , a 91̽��professor of marine and environmental affairs and director of . “It pushes the boundaries way further than I thought we could.”

Researchers have streamlined the process of sampling eDNA over the past decade. Water and air are reservoirs for discarded bits of skin, hair and other DNA-rich detritus. Like a footprint, eDNA flags the presence of a species nearby.

After hatching, young salmon migrate to the ocean for one to several years before returning to the same stream to spawn. They leap and thrash near the surface of the water, likely shedding eDNA in the process. Every year, as the fish pass through migratory bottlenecks, people count them to gauge population health, set catch limits and monitor rehabilitation efforts.

Ip began to wonder about remote monitoring efforts while watching the fish wiggle upstream. eDNA has become a valuable tool for tracking endangered and invasive species. He developed an experiment to test the air for salmon DNA in conjunction with colleagues at the UW.

“This is Aden’s baby,” said Kelly. “He arrived saying ‘I know you can get eDNA from the water, but I want to do something nobody has done before.’”

Researchers placed filters 10 to 12 feet from the stream and left them out for 24 hours on six different days between August and October, testing four filter types each time. Three were vertical filters and the fourth was an open 2-liter tub of deionized water to capture settling particles.

In the lab, they washed eDNA from the filter and measured its concentration with a Coho salmon-specific tag to a DNA amplification method called polymerase chain reaction. They referenced air and water eDNA concentration and visual counts to track population changes, assuming that each method has its own margin of error, and the true number of fish is unknown.

The airborne eDNA concentration fluctuated with the visual counts reported by the hatchery, suggesting that this could become a useful tool for tracking salmon populations. The strategy is more remote-friendly than other methods because it does not require electricity.

“This technique quantitatively links air, water and fish,” Ip said. “Airborne eDNA doesn’t give us a headcount, but it does tell us where salmon are and what their relative abundance is in different streams.”

There are still a number of variables to account for, such as rain, wind, humidity and temperature, that the researchers plan to continue exploring in future studies.

“Right now, we’re pushing the boundaries of possibility,” Kelly said. “Eventually, we will develop the technique, as we have for waterborne eDNA, into something that can help guide management and policy.”

For more information, contact Aden Yincheong Ip at adenip@uw.edu

Co-authors include , a 91̽��postdoctoral researcher in the School of Marine and Environmental Affairs and , chief scientist at the eDNA collaborative in the School of Marine and Environmental Affairs at UW. 

This research was funded by the David and Lucile Packard Foundation and Oceankind.

To help struggling salmon populations, the state of Washington is legally required to replace hundreds of culverts that divert streams under roadways. The state transportation department is replacing old, rusting metal pipes with broad, concrete promenades that provide more gradual gradients and gentler flows for salmon swimming upstream to access more spawning grounds. The of the effort will last 17 years and cost $3.8 billion.

But how successful are these projects at boosting fish traffic? A team from the 91̽�� and the National Oceanic and Atmospheric Administration performed genetic sleuthing during two culvert replacements in 2021-22 near the city of Bellingham. Post-intervention monitoring shows that upgrading one culvert — which went under Interstate-5 — had a big impact, and the other culvert may not have been as much of a barrier. Construction did not disrupt fish populations at either site.

The will appear in a forthcoming issue of Environmental Applications.

“This was an amazing study to work on, both in terms of the science and the broader implications. We demonstrated that we can measure the impact of management interventions using only DNA recovered from the water,” said lead author , who began the project as a 91̽��postdoctoral researcher in marine and environmental affairs and is now chief scientist at the UW-based .

For the study, the researchers didn’t catch or count a single fish. Instead, from March 2021 to December 2022 — before, during and after the project — they collected water samples each month at locations just upstream and downstream of the culvert. Back in the lab, they sequenced the fragments of floating DNA to identify the type and amount of DNA of salmonid species present.

The study used a new type of monitoring known as “environmental DNA,” or eDNA. Fragments of DNA floating in the environment on scales, scat, fur or other material can help researchers detect which species are nearby, rather than relying on visual counts, cameras or traps.

A fish’s DNA stays in the water for a day or two. The researchers aimed to use the culvert project as a model for the use of eDNA in environmental impact reporting, more generally.

The study focused on along Padden Creek, a roughly 3-mile creek flowing from Padden Lake to Bellingham Bay. One culvert replacement was a major upgrade under I-5. DNA results show improvement for the four species of interest: cutthroat trout, coho salmon, rainbow trout and sockeye salmon. The other project, a smaller culvert replacement under state Route 11, or Old Fairhaven Parkway, had less impact: Trout and salmon DNA were present at similar levels before and after construction, meaning the older culvert may have been passable to fish.

“It is clear that not all things that are marked as a blockage to salmon are, in fact, blockages to salmon,” Allan said. “In the future, DNA sampling upstream of culverts might be something to add to the prioritization process.”

The results could help support across the West Coast and in Alaska.

“Environmental DNA offers a pretty different way of seeing the world,” said co-lead author , a 91̽��associate professor of marine and environmental affairs. “We can see thousands of species in a liter of water, in a way that no other sampling method can. And what makes eDNA really attractive is it’s easily repeatable and scalable.”

Researchers collected water samples using a high-tech backpack donated by Smith-Root, a company based in Vancouver, Washington. They sequenced about 52 million fragments of DNA in total, about half of which were for the four salmonid species of interest.

Researchers also surveyed five other creeks as controls. In the future, the authors say, engineers or surveyors could collect water samples for environmental monitoring more easily than surveying and identifying fish, making it simpler to combine with other measurements.

“If you had to go out there with another method and find and count fish, it would take all day,” Kelly said. “So eDNA offers a real savings in terms of in terms of time and effort in the field.”

Other co-authors are postdoctoral researcher , master’s student and research scientist , all in the 91̽��School of Marine and Environmental Affairs; and and at NOAA. The research was funded by Oceankind, a grantmaking organization based in California, and by the Washington State Department of Transportation.

For more information, contact Allan at eallan@uw.edu or Kelly at rpkelly@uw.edu.

A new effort at the 91̽�� aims to accelerate eDNA research by supporting existing projects and building a network of practitioners to advance the nascent field. Called the , the team is based in the College of the Environment with leadership and program staff from the School of Marine and Environmental Affairs.

For about a decade, scientists have honed the craft of using genetic material in the environment — known as eDNA — to detect and monitor organisms for environmental science and conservation. In a marine environment, for example, scientists can collect water samples from a specific location, then extract DNA to discern which species were present recently in that area, having never seen the animals themselves.

This bit of molecular wizardry is now becoming routine for scientists — even prompting a commitment from the U.S. Navy to use eDNA to map the locations of marine mammals — and the eDNA Collaborative aims to help the technique make the leap into everyday use for people and governments everywhere.

It can be hard to monitor and gather data across large areas using standard techniques of observing and counting various species, and eDNA techniques aim to supplement standard approaches to data collection and monitoring. This data can then inform state and federal decisions about wildlife conservation and management. For example, the team helped roll out a molecular method to help Washington find invasive European green crabs as they threaten to invade the waters of Puget Sound. Such practical applications are what turn a technology from being an interesting niche into a foundational tool on which agencies rely.

But adopting new technologies requires building familiarity and trust, and this is where the eDNA Collaborative comes in. The Collaborative’s director, , a 91̽��professor of marine and environmental affairs, likened the young field of eDNA research to how various new technologies develop and take off.

“Experimentation is how technologies develop, and as with the early days of any new tech, it’s a soup of ideas with eDNA research,” Kelly said. “While people are still inventing, we don’t want to impose standards in a top-down way. We want to encourage best practices without squelching creativity. That’s what this Collaborative will help do: accelerate the field from the bottom up.”

The initiative will focus on three main areas: Supporting existing eDNA research projects at UW; granting seed money to new eDNA research ventures outside the 91̽��and the United States; and supporting a visiting scholar program to connect eDNA practitioners and encourage networking and information-sharing. The goal is to move more of the techniques developed in the lab out into practice in the field, helping the best ideas rise to the surface faster.

“Environmental DNA is an entirely new way of seeing the living world, and we’re just learning how to take advantage of it for purposes of management and conservation. At the Collaborative, we wake up every day thinking about how to move this technology into routine practice for people and institutions around the world,” said Eily Andruszkiewicz Allan, chief scientist at the Collaborative.

The Collaborative is funded initially with a $1 million grant from the David & Lucile Packard Foundation. The team also recently secured a $7.5 million grant from the U.S. Navy — in collaboration with the National Oceanic and Atmospheric Administration and Scripps Institution of Oceanography — for a five-year project to use eDNA to map the locations of marine mammals in the ocean.

The goal is to help the U.S. Navy reduce harm to marine mammals by better understanding where those animals are in space and time. Most of the eDNA sampling activity will begin this fall and center around Seattle and San Diego. eDNA methods will fold into other existing work, including visual and acoustic surveys, to eventually produce a West Coast-wide estimate of where marine mammals are in the ocean.

Other ongoing projects include:

• Monitoring for the invasive European green crab throughout Puget Sound and Washington’s outer coast
• Developing eDNA as a tool for
• Using eDNA to monitor the presence of salmon in streams to gauge the effectiveness of culvert replacement projects in Washington
• Assessing seasonal changes in Norwegian fjords for the country’s salmon industry

For more information, contact Kelly at rpkelly@uw.edu, Allan at eallan@uw.edu and program manager Cara Sucher at csucher@uw.edu or email the Collaborative at ednacollab@uw.edu. Contact U.S. Navy program officer Mike Weise for questions about the marine mammal monitoring grant: michael.j.weise@navy.mil.

Follow the eDNA Collaborative on Twitter at .