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Science and Technology

Science Fiction Becomes Reality For Species Surveys

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Tom Banse
/
Northwest News Network
Postdoc researcher Jimmy O'Donnell at the UW lab bench where he processes eDNA samples.

On the original "Star Trek" series, landing parties from the starship Enterprise used a versatile device they called the Tricorder to instantly read out what was in their surroundings.

So imagine being able to detect rare or invasive species, study biodiversity or to estimate fish abundance with just a scoop of air or a dip of water. It would be like science fiction come true.

The Tricorder was dreamed up in the mid-1960s. Now more than 40 years later, environmental researchers and surveyors can match Captain Kirk and Mr. Spock -- sort of. Science fiction is indeed becoming reality through a new sampling technology called environmental DNA.

"It's a really good analogy because essentially we can take a sample of soil or air -- or in our case -- water and we can sequence the DNA out of it and tell you what is there,” said University of Washington Professor Ryan Kelly describing the technique called environmental DNA - or eDNA for short.

Our scientists haven't yet miniaturized the process into a handheld device like in Star Trek, but give it a few years.

Practical DNA screening

For now, here's how this works. Kelly said all living creatures are constantly shedding or pooping their telltale DNA into the environment.

In Kelly's Seattle lab, his team filters out and amplifies the genetic material. They are currently working with water samples collected from Puget Sound.

Ryan said the cost of gene sequencing has "plummeted in recent years." That makes DNA screening practical.

"This is already very competitive and will be sort of a slam dunk for some monitoring applications in the near future,” he said.

Environmental DNA can be used in two ways. One is to identify the suite of creatures around a place. The other is to confirm the presence or absence of a specific critter, typically an invasive or endangered species.

Caren Goldberg runs the new eDNA lab at Washington State University in Pullman. She's one of the first biologists in the Northwest to take the tool from demonstration experiments to practical application.

"It is extremely useful for species that are really hard to find,” Goldberg said.

Goldberg sees potential to get answers more efficiently, safely and with less destruction compared to traditional survey techniques such as electrofishing, snorkeling or netting.

No more searching necessary

"I have spent many hours looking for species that I was pretty sure were there -- looking under rocks, looking in the water, doing all kinds of surveys,” she said.

Goldberg recently analyzed samples collected by Idaho Fish and Game biologists from lakes and wetlands in north Idaho. No more searching necessary. The sensitive DNA screening confirmed the northern leopard frog has disappeared from that part of its range.

She's also been hired in Washington to locate where a tiny invader -- the New Zealand mudsnail -- has spread.

Now, the federal Bureau of Land Management wants Goldberg to look for the Columbia spotted frog in eastern Oregon and Nevada. That rare frog is a candidate for federal threatened species listing.

"We're absolutely at this point where proof-of-concept has been established,” Golberg said. “I don't think everyone is on board necessarily yet, but I think the majority of the people are on board."

Natural resource managers are looking for evidence that eDNA methods are getting better at reporting what's there with a low number of errors.

This has gotten the most scrutiny in the Great Lakes region where both false positives and missed detections have occurred while monitoring for invasive Asian carp. A related research goal is to pin down better how long environmental DNA lingers and how far it can drift in different environments.

‘Another tool in the toolbox’

Field biologists are not going to be replaced by robots just yet, say scientists working with the technology. But the old-fashioned field work could soon be more targeted or prioritized.

"This is not going to replace all the other tools," Boise-based U.S. Geological Service ecologist David Pilliod said. "It's another tool in the toolbox."

Pilliod described the results of a study involving Chinook salmon that was just published online in the journal Biological Conservation. He, Goldberg and lead author Matthew Laramie, another USGS scientist from Boise, tested their ability to detect endangered spring Chinook in the Methow and Okanogan River basins of north central Washington.

In the study, the eDNA showed high reliability in detecting Chinook in places where the fish were known to be present. The molecular sampling also found traces of Chinook in some tributaries where they were not expected.

"One area where eDNA might help is detecting where fish are recolonizing," Pilliod said in an interview. The federal government and Colville Confederated Tribes are spending millions on recovery plans for upper Columbia River fish runs. Solid information about the distribution of the fish is useful both to measure progress and to allocate habitat restoration grants.