Biologists look for clues about belugas in the Kenai River

Mar 2, 2021

KPC student Teresa Becher (middle) and Semester by the Bay students Kaitlyn Roberts (left) and Abigail Stephens take samples from the Warren Ames Memorial Bridge this February.
Credit Debbie Boege-Tobin

Cook Inlet belugas used to follow salmon through the Kenai River in the summer. Now, they’re mostly just spotted in other seasons.

Researchers from NOAA Fisheries aren’t sure why. It’s one of many questions they’re asking about the endangered population to better understand why the belugas aren’t rebounding and how the agency can support their recovery.

A study featuring a relatively new DNA sampling technique might help them find answers.

NOAA Fisheries geneticist Kim Parsons, who’s leading the project, said it’s like getting clues from a crime scene.

“All organisms are continually shedding genetic material into our environment," she said. "So in the soil, in the air and in the water there are all these cells floating around that represent the community of organisms that are in the water at that time.”

It’s called environmental DNA, or eDNA. As they swim through the Kenai River, fish shed tiny bits of eDNA — in skin cells, feces, even mucous. Researchers are collecting this eDNA from the river to understand which species of fish are there.

They’re looking at fish because that’s what belugas eat. Scientists say knowing more about the belugas’ diet will help them understand how they’re sustaining themselves in the winter and what’s keeping their population from rebounding.

“So that we can try to learn a little bit more about how the beluga movements are responding to changes in the prey base," she said.

eDNA is a relatively new concept. Alaska researchers have previously collected and sequenced samples of eDNA to study Pacific salmon and harbor porpoise.

To collect samples from the Kenai River, NOAA partnered with a field team from the Kachemak Bay Campus of Kenai Peninsula College.

KPC Biology Professor Debbie Boege-Tobin is leading that team. She said on one hand, the fact that the whales are in the river at all could be a promising sign that there’s enough prey there to support them through the winter.

“But it also makes me nervous because we know that at times of the year when there’s lots of potential prey there, like in the summertime, they don’t seem to be using it. And that question puzzles me," she said.

Once or twice a month, Boege-Tobin and a team of students take water samples from two spots on the Kenai River, at the City Docks and Warren Ames Bridge. They collect samples both at the river’s surface and a few meters down, so they can capture a wide range of genetic signatures.

The river water, containing low levels of eDNA, is emptied into something as simple as a sterile Nalgene.

“It’s low tech, it’s accessible, and we can collect a lot of samples that way," Parsons said. "We just require a hearty field team who’s willing to go out there in kinds of conditions to lower the bottle for us off the dock or boat or bridge, wherever we’re sampling from.”

Boege-Tobin and her team started collecting samples in November. They’ll keep collecting until May.

Once they’ve filled their vials, the team runs the water it’s collected through a filter in a lab in Homer. The remaining material goes to Parsons in Seattle for sequencing. There, they can use it to identify and quantify the prey species in the river.

It’s a pilot study, so it’s relatively preliminary. eDNA is not a perfect science yet.

“The tricky thing about eDNA is that we’re still in the early stages of understanding how that signal moves in the environment," Parsons said.

In a river, researchers can capture genetic signals as they move downstream. In a marine environment, that material is moved by wind and currents, and could settle and sink.

If researchers find the eDNA methodology successful, they can take what they’ve learned and apply it to other sites in Cook Inlet. Boege-Tobin also said they can use the data they collect to set some measures to protect the belugas.

“So hopefully, if we find out when they’re relying on the river, on the Kenai River in this case, we could potentially put in place some sort of management policies or measures to set aside some of that habitat for them," she said.

Researchers said they’ll have preliminary analysis by the end of the year.

Correction: An earlier version of the story said belugas are mostly spotted in the Kenai River in the winter. They’re also found  there regularly in the spring and fall.