DNA tracker a 'breakthrough' in measuring invasive species

A breakthrough discovery stunned a team of Flathead Lake Biological Station researchers during the first official field test of their “DNA Tracker” at Lake Mead in April. Next month, the team will be putting the results to the test on Flathead Lake.

Researcher and technologist Cody Youngbull completed the prototype for the world’s first portable DNA detection device in August of last year, and while the creation of the device in itself opened up a new world for field research on DNA detection, an accidental mix-up during its first field test revealed even greater potential.

At around the size of a shoebox, the “DNA Tracker” works by comparing filtered samples taken from the lake and comparing it to a template for a specific type of DNA to look for matching types of DNA in the sample.

However, in preparing to travel to the Quagga mussel-infested waters of Lake Mead, which lies in both Arizona and Nevada, Youngbull grabbed the wrong kind of filter for the device to collect the DNA cells they were searching for.

A crucial part of the device, the filter is supposed to trap the cells and other particles with DNA inside on a screen while the excess water is thrown out.

The filter Youngbull grabbed, however, was too small and caught more than just the desired particles.

The mistake was not discovered until the bio station team arrived at their destination after having spent thousands of dollars on travel, equipment, reservations and other expenses. Without the correct filter, hopes of using the device to extract DNA from the water plummeted, so the team made an effort to salvage the trip by trying what Youngbull said most other scientists would have thought to be a pointless test.

They filtered the samples using what they had, but rather than testing what was left on the filter, they tested the water that had gone through.

Once water has been that thoroughly filtered, Youngbull explained, all that is left are free molecules, or molecules not held together or contained within cells.

Among them, Youngbull found, was eDNA, or environmental DNA, and a lot of it.

The device measured not only the presence of Quagga mussels in the water, but the quantity of eDNA from the mussels floating freely throughout the lake, allowing the team to view a gradient of where concentrations were highest.

According to Youngbull, eDNA molecules are left behind when an organism dies and its cells containing DNA break down, releasing traces of that organism’s presence into the water.

The problem with eDNA testing, or molecular detection, however, is that it is gone in a matter of minutes. Unprotected by cell walls, it is rapidly broken down by sunlight or consumed by other organisms before a sample can make it back to a lab for testing.

Because of this, little research has been done with eDNA so far, but the portability of the “DNA Tracker” has proved to be a game changer, allowing researchers to test the samples they collect immediately before the eDNA can break down.

The device’s ability to detect eDNA also eliminates the need for the extraction, or filtering, of DNA from the water, a time-consuming and usually costly process.

“What this means now is there is no more front end,” Youngbull said. “This is what we should have been doing for a long time.”

Once fed a sample, the tracker takes about 45 minutes to produce results.

Youngbull and his team took their discovery a step further and tested a boat that recently left the mussel-infested lake. The results showed an incredibly high count of eDNA presence on the boat, according to Youngbull, but after decontamination, a re-test came back completely negative for mussel eDNA.

“No one’s ever done that before,” Youngbull said. “That’s a world’s first, and this is a taste of what’s to come at the vehicle checkpoints here.”

Officials currently rely on a method of detecting invasive species called microscopy, which requires the visual sighting of a DNA cell under a microscope.

The problem with that method, Youngbull said, is that by the time you are able to view a living, whole cell under a microscope, the examined water source likely already holds an established, thriving population.

With eDNA testing, however, Youngbull said researchers can pick up even the most minute traces of a species in the water, meaning it can catch the invaders before they are firmly established.

Youngbull called it “one step closer to the DNA smoke alarm,” and he hopes that in the future, his device, and molecular detection as a whole, will gain the acceptance he feels it deserves in order to be used as a viable method of protecting the Flathead Basin’s waters.

For now, however, Youngbull said he will be working with the Confederated Salish and Kootenai Tribes to begin implementing the technology around the lake as soon as next month, with the U.S. Fish and Wildlife Service funding the deployment of the device for at least one of the vehicle-check stations near Polson.

Though Youngbull said that other methods of detecting the presence of invasive mussels, like microscopy and mussel-sniffing dogs, are still relevant and valuable, he feels that eDNA is the Flathead’s best hope for preventing an invasion.

“There aren’t any problems with eDNA,” Youngbull said. At least none that can’t be prevented, he added.

Despite years of skepticism by both government and environmental officials about the validity of using eDNA to identify a species’ presence, Youngbull said the information provided by molecular detection is valid and much more valuable as an early warning system than microscopy.

“We should start including this data whenever possible,” Youngbull said. “Even stopping one boat is making a difference.”

What comes next for the development of the DNA tracker, Youngbull said, is getting it out of the prototype stage and into the production stage — getting more of the devices built and sent out to other scientists who can further advance the study and research of eDNA.

Youngbull said he too plans to begin redirecting much of his research to understanding eDNA and its implications in not only detecting invasive mussels, but in furthering the study of other species in habitats worldwide.

Reporter Mary Cloud Taylor can be reached at 758-4459 or mtaylor@dailyinterlake.com.