SEATTLE  Wed Dec 31, 2014 4:40pm

 

It's a familiar scene in science fiction stories: Explorers arrive on a new world, and quickly determine what's in their surroundings with a high-tech device that checks for breathable air and signs of other life forms.

Here on earth, science fiction is becoming reality through a new sampling technology called environmental DNA, or eDNA for short. It allows scientists, like ecologist Ryan Kelly, to detect rare or invasive species, study biodiversity or estimate fish abundance with just a scoop of air or a dip of water.

"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."

That's because all living creatures are constantly shedding or excreting their telltale DNA into the environment. In Kelly's lab at the University of Washington in Seattle, his team filters out and amplifies the genetic material. They are currently working with water samples collected from Puget Sound.

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

 

Identifying what's there and what's not

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

Caren Goldberg, who runs the new eDNA lab at Washington State University in Pullman, Washington, is one of the first biologists in the northwestern U.S. to take the tool from demonstration experiments to practical application.

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

Goldberg sees the potential to get answers more efficiently, safely and with less destruction compared to traditional survey techniques such as snorkeling, netting or using an electric current to temporarily stun the fish.

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

In fact, this newer way to figure out what's where is rapidly catching on around the world. In Vietnam, zoologists are using it to locate the last wild specimens of the Yangtze giant softshell turtle. In Trinidad, a researcher is using eDNA to track down endangered golden treefrogs. And in Madagascar, it's being used to identify amphibian diseases.

For her part, Goldberg has used the sensitive DNA screening to confirm the local extinction of a leopard frog in northern Idaho. She's also been hired to determine the extent of the spread of the New Zealand mudsnail, a tiny invasive that is infesting Washington state's lakes and streams.

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

 

A new tool for biologists

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," said Boise-based U.S. Geological Service (USGS) ecologist David Pilliod. "It's another tool in the toolbox."

Pilliod described the results of 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 salmon 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," said Pilliod in an interview.

The federal government and Colville Confederated Tribes, a federally recognized American Indian tribe, 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.

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 received 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 more accurately pin down how long environmental DNA lingers and how far it can drift in different environments.