Biologist Shaun Clements stands in the winter mist in a coastal Oregon forest. He’s holding a small vial of clear liquid.
“We should be safe mixing it now, right?” he asks his colleague Kevin Weitemier above the sound of a rushing stream a few feet away.
Weitemier brings a second vial, full of stream water. In deliberate, seeming choreographed movements, usually associated with ritual, they pour the liquid back and forth between the small containers to mix — two, then three times — never spilling a drop.
Clements looks down at the clock. It’s 12:29 pm.
“We’ve got one minute,” he says.
12:30 is go-time.
The two move out into the cold stream with the vials. Clements is in the main stream. Weitemier is closer to shore.
“Ok,” Clements calls out.
At the same moment, they tip the containers on end. Two trillion particles of lab-created DNA falls into the rushing water. It’s an experiment to figure out how far and how quickly environmental DNA – or “eDNA” – travels in different kinds of streams.
Occasionally a big idea comes along that promises revolutionize the world – think about things like self-driving cars. For biologists – especially those who work with fish and other aquatic plants and animals – eDNA is one of those big ideas. The technology is starting to revolutionize how we protect native animals and ensure invasive species don’t take hold.
The easiest way to understand eDNA is to imagine yourself relaxing in a steamy hot tub. As you’re soaking there, a bubble splashes water into your mouth and you spit it out. A day’s worth of dead skin sloughs off. Finally toasty warm, you get out of the tub.
The you-flavored broth left behind is full of your DNA. It has become part of the larger environment. And even long after you’re gone, that DNA could be detected if someone knew what to look for.
The same holds true for any organism in any body of water.
“All these little critters out there, they’re shedding DNA from their skin cells, urine, feces,” Clements explains.
Clements works for the Oregon Department of Fish and Wildlife. He says Oregon has a lot of waterways and the state doesn’t have the resources to fully monitor endangered fish, look for invasive plants or check in on all the other native species, including potentially mammals like river otters, beavers and bats.
With eDNA, doing all of this could get much cheaper and easier.
“Just by taking a water sample, you can tell somewhere in basin above you, there was this range of species and something about their relative abundance,” he says.
And this potential has fisheries biologists excited for what lies ahead.
“eDNA sampling really can be a game changer,” says U.S. Forest Service fisheries biologist Mike Young.
So Many Variables
Young says biologists and fisheries managers in the West are already really good at using eDNA to find bull trout in small streams. That’s because he and other scientists have been working for years to figure what exactly it means when you find bull trout DNA in a water sample. They know what a positive detection indicates about bull trout presence and relative population numbers.
“But let’s say we’re trying to sample to detect western pearl shell mussels in larger stream… or Pacific lamprey, or trying to find invasive species in reservoir,” Young says. “Each water will come with its own probability of detection that’s specific to that species and habitat pair.”
DNA will travel differently depending on the habitat and the species you’re looking for.
Where and how much DNA you find in water can be affected by:
- the speed and direction that water flows
- how much sunlight hits the water
- how much DNA-eating bacteria are present
- season, rainfall and temperature
- what kind of organism you’re trying to detect
And this is only a partial list. Consequently, there are dozens upon dozens of variables that still need to be tested.
Scientists are only really beginning to scratch the surface. Even so, the technology is beginning to prove its worth – for bull trout monitoring in the West and for keeping track of invasive Asian carp, which pose a huge threat to the Great Lakes region.
“We don’t have to know everything about it [eDNA] to make it useful - as long as we’re accounting for errors,” says Caren Goldberg, an ecologist at the Washington State University.
Refine, Refine, Refine
The work of refining the science of eDNA is what ODFW’s Clements is doing out in the woods near Alsea, Oregon.
After dropping the synthetic DNA into the stream, he and Weitemier jumped in their car and bounced along a logging road. They stopped at a pink flag marking their fourth collection site about a half-mile downstream.
“I wasn’t sure I was going to be the person standing in the stream, but I thought there was a possibility,” says Weitemier, who drew the proverbial short straw.
Like other scientists in place at the team’s three other collection sites, Weitemier will be thigh-deep in the icy-cold stream for the next hour, taking water samples at regular intervals to see if they can capture any of the DNA released upstream.
“There was a lot of DNA in there – trillions of DNA particles. But that was being diluted into millions of liters of this stream,” says Weitemier. “So we might only recover a very small proportion… especially, [where] I was sampling at the farthest point from where we put it in”
The samples will be taken back to the Oregon Hatchery Research Center to be filtered. Then the filters will be taken back to the Center for Genome Research and Biocomputing at Oregon State University, where Weitmier works. Even if they captured the synthetic DNA, other issues could arise.
“Then the test we use to recover them may not be sensitive enough to see them. But we don’t know. That’s what we’re testing,” he says.
But if all goes as planned here, and OSU is able to detect the DNA, ODFW’s Shaun Clements will repeat this experiment at sites throughout Oregon. He’ll use the information he gleans from the field tests to figure out how the agency can start using eDNA to monitor and manage fish and wildlife.
“Scientists always say more data is better, managers always say we need to know now,” he says. “So, we anticipate that along the way we’ll learn a lot.”