Aquatic invasive species detection goes CSI with eDNA

Post by Jenny Seifert, UWEX Aquatic Invasive Species Outreach Specialist

Peering into a bucket of mud, Maureen Ferry felt like she was looking for a needle in a haystack. That needle was the New Zealand mud snail, a teeny tiny invasive species that was discovered in Black Earth creek , and she and fellow WDNR employees were trying to confirm its presence in the creek.

Eventually, their eyes adjusted, and they realized the bucket was not actually filled with mud, but innumerable mud snails!

New Zealand mud snails are teeny tiny (this dime is normal sized, we swear), which makes using eDNA technology an easier way to detect them. Credit: Paul Skawinski

Hard-to-detect aquatic invasive species like the mud snails are one example of why some resource managers are raving about a new(ish) technology that helps them sniff out unwanted exotic critters: environmental DNA, or eDNA.

Much like the forensics used to solve crimes, eDNA allows managers to use genetic evidence to trace the tracks of an invasive species in a lake or stream, giving them clues as to whether the species is guilty or innocent of an invasion.

“All living things shed DNA, and we can pick it up in the environment,” explains Ferry, who is the statewide aquatic invasive species monitoring coordinator for the WDNR.

They pick up this DNA by collecting water samples from sites they think a certain invasive could be hiding and then extracting all of the genetic material floating around in the water. Using a chemical reaction, they can screen the DNA soup for genetic markers specific to the suspected invader. If the genetic markers appear, it tips managers as to whether the species may have been at the scene and how many of them there might be.

The beauty of this technology is the improved efficiency it gives managers in detecting invasive species. While it won’t help them actually find the needles, it gives them a lead on where in the haystack to look for them, so they can better target their traditional sampling methods, which are otherwise more time consuming.

“It’s a really powerful tool that can help us make better decisions about how we manage our natural resources,” says Chris Merkes, a geneticist at the U.S. Geological Survey (USGS) who is involved in a partnership with WDNR and the UW-Stevens Point Cooperative Fish Unit to develop and use eDNA technology to monitor the New Zealand mud snail and another troublesome invader, the round goby.

In fact, this month WDNR and USGS will test out a new eDNA tool to investigate whether the round goby, an invasive fish, has moved into Lake Winnebago. It has already invaded the lower Fox River down stream of Lake Winnebago, and WDNR is trying to prevent it from getting into Lake Winnebago. The concern is, an invasion to the lake could give it access to 17 percent of the state’s inland waterways. So this new eDNA tool could help WDNR make more efficient use of its resources by indicating areas where fisheries managers should look for round goby.

The cool thing about this upgraded tool is, once tested, you won’t need to be an expert geneticist to use it. Developed by USGS, it’s a simplified and portable DNA detection kit that allows nearly anyone to perform the genetic testing anywhere. All data detectives will need is a cup of water and an hour to get a reading of whether the goby’s DNA is present or absent from the water.

Volunteers process samples during the test run of a portable eDNA kit for Asian Carp. A similar kit, but designed for the round goby, will be tested this month. Credit: USGS.

The hope is, down the line, the simpler kits will make it easy for citizens to get involved in round goby surveillance in the Winnebago basin, which will put more detectives on the case and make it easier for the DNR to monitor the nuisance fish and make effective decisions.

But even if the eDNA technique detects a species’ genetic material, the suspect is still innocent until proven guilty. There can be red herrings like false negatives or positives, and sometimes genetic evidence is not enough to confirm whether the species is actually in the waterbody – that DNA could be merely a remnant left in the belly of a predator, for example. Sleuthing actual specimens from the lake or stream with traditional sample methods, like fish shocking and catching them in nets, are the only way to close a case.

“It’s a complicated equilibrium that we’re trying to assess, and there’s no finite way to understand exactly how many organisms are in a system at any given time,” says Merkes.

Shortcomings aside, Merkes is excited about the technology’s potential. He thinks it could someday help natural resource agencies improve the conservation of native species.

For example, managers could use it to monitor changes in fish populations at the molecular level, which could inform fishing guidelines, or they could use it to study lake microbiomes to determine their vulnerability to invasive species or diseases.

“Any time we can gain information about a natural system without disrupting it is a great thing,” says Merkes, referring to the non-invasive nature of the mere water sample needed for eDNA as another perk of the technology, compared to trapping methods.

As for the New Zealand mud snail, while it is established Black Earth Creek and Badger Mill Creak in southwest Wisconsin, eDNA evidence collected by WDNR has shown the snail is, so far, innocent of invading other sites in Wisconsin.

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