AVERY COOPER: Scientists are traveling all around Washington to figure out exactly what fish are living in rivers and streams. They’re using some high tech equipment to search out even the most “underloved” freshwater fish. NWPB’s senior environmental correspondent Courtney Flatt has the story.

COURTNEY FLATT: These days there are fewer critters in Washington’s rivers and streams.

Marie  Winkowski specializes in native aquatic species for the Washington Department of Fish and Wildlife. She says many things are contributing to this biodiversity loss. 

MARIE WINKOWSKI: “ In many cases, I think it's the idea of death by a thousand cuts. Anthropogenic factors …” 

FLATT: Like the ways people are changing the habitat: pollution, dams, draining wetlands.

WINKOWSKI: “climate change exasperating all of that.”

FLATT: By increasing water temperatures and changing water flows.

WINKOWSKI: “ And in addition to that, we have a lack of data on a lot of our non-game fishes, and a lot of those fishes are species of greatest conservation need.” 

FLATT: Freshwater fish like bottom-dwelling sculpin and shellfish like western ridged mussels.

WINKOWSKI: “underloved species.”

FLATT: Most of those fish you don’t fish for, they don’t get a lot of attention. Or funding.

WINKOWSKI: “ Because really you can't preserve or protect something if you don't know where it is exactly.”

FLATT: So, these researchers set out to do a statewide census for freshwater species. Winkowski says this is a first-of-its-kind study — mostly because of how big the project is.

The work began in 2023. Since then, they’ve mapped out places from the Wenatchee River to Willapa Bay, with more still to go. They take random samples that allow them to extrapolate what’s in the rest of the river or stream.

The state is creating  an interactive map of everything they find. The hope is people use it as they plan for restoration work or make development decisions.

WINKOWSKI: “Then they preemptively plan ahead or plan around those species before they go ahead and work in water.”

To do all this as quickly and efficiently as possible, they’re using something called environmental-DNA, or e-DNA.

WINKOWSKI: “We're all sort of shedding DNA all the time.”

FLATT: Fish and shellfish shed their DNA in the water. 

WINKOWSKI: “When we take a water sample, we're filtering it and then we collect bits of e-DNA that are in the water.”

Thousands of samples are sent to a genetics lab. For this project, they’re using a special technique called metabarcoding. That means they can get information on all sorts of species … all at once.

WINKOWSKI: “ Then from that DNA we compare it to a reference database that's available online, where we have examples of DNA.”

FLATT: If they find DNA, that’s a clear sign that fish or shellfish are living nearby. It doesn’t tell researchers how many fish are in the water. Those studies can come next.

And they don’t only find fish. 

WINKOWSKI: “Aquatic amphibians, beaver, macroinvertebrates.”

FLATT: Sometimes people, too.. 

The cool thing is, Winkowski says, they don’t have to bother the fish to get all this info.
 
To collect the e-DNA, fisheries technician Cami Boesch pulls out a backpack. 

WINKOWSKI: “ It looks like Ghostbusters. It really does. But it’s a very fancy pump, essentially.”

The technicians take a seat on the banks of the Cle Elum River. Boesch wears plastic gloves and doesn’t touch any of the filters to avoid contamination.

She connects a filter to a long plastic tube and sticks it in the water.

BOESCH: “So now it’s getting comfortable and sitting for about five minutes.”

FLATT: Traditionally, this sort of survey would be conducted by electrofishing or snorkeling – which would take several hours per site. Now, they’re able to collect three samples in minutes.

BOESCH: “This  job does make me notice things that I, like, wouldn't notice before: little details of the stream or seeing little macroinvertebrates crawling around.”

FLATT: The researchers hope it’ll help others notice the “underloved species” they haven’t seen before. The data has already found lamprey in a few places biologists didn’t expect. 

This census could take another six years. After that, they hope to keep tracking it overtime.

I’m Courtney Flatt, on the banks of the Cle Elum River.