Several years ago, researchers with Washington’s Department of Fish and Wildlife started noticing fewer and fewer critters in the state’s freshwater ecosystems.
There’s not really one that’s causing the biodiversity loss, said Marie Winkowski, the native aquatic species unit lead with the department.
“In many cases, I think it's the idea of death by a thousand cuts,” she said.
People are changing the habitat through things like pollution, dams and draining wetlands. And climate change is exacerbating the problems by increasing water temperatures and changing water flows, Winkowski said.
“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,” she said.
Like bottom-dwelling sculpin, a freshwater fish, and western ridged mussels, a freshwater shellfish. Most of those “underloved species” don’t get a lot of attention or funding, Winkowski said.
“Really, you can't preserve or protect something if you don't know where it is exactly,” she said.
So, they set out to do just that across every watershed in the state. It’s a first-of-its-kind study, mostly because of how big the project is, Winkowski said.
The aquatic biodiversity study began in 2023. Since then, researchers have mapped out places from the Wenatchee River to Willapa Bay, with more still to go. The survey could take another six years.
The study is funded through the state’s Biodiversity Proviso and the Climate Commitment Act. The 2025-2027 biennial and supplemental budgets cut the department’s biodiversity efforts by $2 million per fiscal year. That means this census work might take a little longer to complete, Winkowski said.
“We really need consistent funding and long-term monitoring to answer those questions and track changes over time,” she said. “(That’s) really important to understand how are species doing.”
Mapping the state
Random samples allow researchers to extrapolate what’s in the rest of the river or stream.
To do all this work quickly and efficiently, the team is using something called environmental-DNA, or eDNA.
“We're all sort of shedding DNA all the time,” Winkowski said. “When we take a water sample, we're filtering it and then we collect bits of e-DNA that are in the water.”
Those samples – thousands of them – are sent to a genetics lab. Then scientists use a technique called metabarcoding, which basically gives them information on all sorts of species all at once instead of information on one specific species.
Skylar Wolf, an inland fisheries biologist for the department, said they can compare those massive amounts of genetic information to a large database — that already has genetic information on file.
“If you think back to high school science, and you think about DNA, essentially, what we're doing is generating sequences from our samples that we take in these streams and comparing it to known sequences that come from those known species,” Wolf said.
If they find DNA, that’s a clear sign of what’s living nearby. However, the information doesn’t tell them the number of a particular species present. Those studies can come next.
In addition to freshwater fish and shellfish, they’ve found all sorts of aquatic amphibians, beaver and macroinvertebrates. That data will be available to other researchers as well.
“Sometimes it feels like a puzzle when you're trying to put it all together,” Winkowski said.
They’ve also found DNA from people, too, near places where people fish or swim.
A challenge is that the census collects data from a snapshot of time, typically from July-October, instead of year round. Also, it can be harder to detect the e-DNA from some species, like lamprey that can be buried in the riverbottom.
The cool thing is, Winkowski said, they don’t have to bother the fish to get all this info.
Collecting samples
To collect the e-DNA, fisheries technician Cami Boesch pulls out a backpack. “ It looks like Ghostbusters. It really does. But it’s a very fancy pump, essentially,” Winkowski said.
Boesch and Seila Lai, a biodiversity technician with the department, take a seat on the banks of the Cle Elum River. First they run the equipment with deionized water to make sure there’s no contamination.
“So basically, just making sure that we aren't touching the water. And then making sure that we have clean hands for the whole time we're doing it,” she said, wiping bleach on her hands.
“Then we make sure the bleach dries so that we're not bleaching the DNA off the filter at all,” she said.
Boesch then connects a filter to a long plastic tube and sticks it in the water.
“So now it’s getting comfortable and sitting for about five minutes,” she said with a chuckle.
Traditionally, this sort of survey would be conducted by electrofishing or snorkeling – which would take several hours. With the e-DNA equipment, they’re able to collect three samples in minutes.
They also measure things like the stream flow, temperature and pH, which can affect how much e-DNA is present in the water.
“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,” Boesch said.
Planning ahead
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. It’s also helped provide more data for species of greatest conservation need, like the mountain sucker in the Yakima River.
“Sometimes we're just focusing on sort of the larger charismatic species or the ones that we're fishing for,” Winkowski said. “But when you think about the ecosystem as a whole, every component of that is really valuable and important.”
The “underloved species” could be an important part of the food web. They can also be an important part of the ecosystem, like freshwater mussels, which filter gallons of water per day.
They’ve created an interactive map of everything they’ve found so far – available for anyone to use. The team will continue to add to the map until all the samples have been collected and analyzed. The hope is people can use the data and maps as they plan for restoration work or development decisions.
“Then they preemptively plan ahead or plan around those species and think, ‘Okay, well, I definitely want to look for freshwater mussels here,’ before they go ahead and work in water,” Winkowski said.
