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Scientists using DNA to track invasive species

The Natural Resources Research Institute is researching best use of eDNA to detect zebra mussels and other invaders in Minnesota lakes.

Researchers working with water samples in a laboratory setting
Researcher Anna Totsch uses a micro pipette to measure water samples for eDNA testing Jan. 19 at the University of Minnesota Duluth's Natural Resources Research Institute.
Clint Austin / Duluth News Tribune
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DULUTH — Scientists at the Natural Resources Research Institute are trying to develop the best methods to check for aquatic invasive species in Minnesota lakes by simply testing a sample of water from the lake.

If any zebra mussels, carp or other invading creature are present in the lake, their DNA will be in the water, an unmistakable fingerprint left behind by their feces, flakes of skin or fish slime.

No zebra mussel DNA, no zebra mussels.

Scientists worldwide have already done the job of sequencing the DNA for most of the problematic critters, so they know what to look for. Now, the hope is for a standardized system for collecting and processing water samples to find so-called environmental DNA, or eDNA, will allow lake associations, conservation groups, natural resources agencies and others to check lakes to see if new invaders have arrived.

Filling a vial with water and sending it to a lab for testing is a lot easier and less expensive than combing a lake for the actual animal, especially for very small or secretive ones. That means more lakes can be tested more often, with a better chance at finding new invasions before they take hold. That may help resource managers fight back sooner, especially as new methods are developed to eradicate invaders. Environmental DNA could even be used to quickly and easily test ships' ballast water, a known pathway for new invaders from afar.


Researchers working with water samples in a laboratory setting.
Researcher Anna Totsch loads water samples into a centrifuge.
Clint Austin / Duluth News Tribune

What scientists don’t know yet is how much water they need to collect and sample, when it should be collected or where on the lake. It might be possible to test for multiple species with just one water sample from each lake per year. Or it might take different samples taken at different times and locations to check for multiple invaders.

“Should you collect in midsummer or spring? Near shore or down deep? The answer might be different for each species,” said Josh Dumke, a lead researcher on the project at NRRI, a branch of the University of Minnesota Duluth.

Researchers last summer took samples from 13 lakes across the state, about half known to have invaders and half believed to still be free from the pests. Eight more lakes will be sampled in 2022. They are homing in on four key invasives: zebra mussels, spiny water fleas, common carp and rusty crayfish.

The NRRI work hopes to find a recipe everyone will use before the field work to the lab when they look for eDNA for those four species.

NRRI DNA from invasive species
Josh Dumke, rear, and Collin Krochalk of the Natural Resources Research Institute in Duluth lower a device called a Van Dorn to collect a water sample from the bottom of Pike Lake in 2021. Samples collected at several Minnesota lakes now are being analyzed in an NRRI laboratory to find any DNA in the lake water left behind by invasive species.
Contributed / Natural Resources Research Institute

While Dumke oversaw the field work, NRRI microbiologist Chan Lan Chun is heading the laboratory work with help from research scientists and grad students. It’s a painstaking process to run hundreds of tiny samples through the machinery that can pull out and identify specific strands of DNA. Scientists have to be extra careful that samples don’t cross contaminate.

It’s not that scientists haven’t already been using eDNA to check for invaders. But no one has developed an established protocol so there’s a standard method across all fields.

Researchers working with water samples in a laboratory setting.
Researcher Chan Lan Chun shows the inside of a freezer unit used to store water samples. The freezer is at a temperature of -77º Celsius or -106.6º Fahrenheit.
Clint Austin / Duluth News Tribune

“Some are taking maybe a liter of water and maybe another is taking 100 milliliters. There’s no system in the place that all (researchers) work from,” Chun said. “Even deciding which water filter to use (in laboratory work), everyone is different now.”

Chun likened the eDNA work to forensic scientists investigating a crime: They can tell if a body was at the scene even when they don't have the body.


Gretchen Hansen, a professor at the University of Minnesota’s department of Fisheries, Wildlife and Conservation Biology and co-lead on the eDNA project, said she thinks standardized eDNA resting will allow scientists and resource managers to see how far and wide the spread of invasives really is.

Researchers working with water samples in a laboratory setting.
A tray containing 96 vessels to test water samples for the presence of eDNA at the University of Minnesota Duluth's Natural Resources Research Institute.
Clint Austin / Duluth News Tribune

“Our current knowledge is based on opportunistic sampling … people happen to find something and report it,” Hansen noted. That doesn’t give a true representation of where the species might be, she said. “We believe the use of eDNA offers a potential to rapidly and accurately determine the distribution of aquatic invasive species in Minnesota lakes.”

Someday, Hansen noted, eDNA might be used to determine where endangered species exist or even the abundance of a species in a particular lake, with more eDNA indicating more of that species.

The project was supported by the Minnesota Aquatic Invasive Species Research Center at the University's Twin Cities campus, with funding from the Minnesota Environment and Natural Resources Trust Fund that's stocked with the state’s profits from the lottery.

NRRI using DNA to track invaisve species
Anna Totsch, a graduate student doing research at UMD's Natural Resources Research Institute, takes a sample of water from Pike Lake near Duluth in 2021 as Collin Krochalk, NRRI research technician, looks on. NRRI scientists are looking at using DNA in lakes to determine where invasive species are located.
Contributed / Natural Resources Research Institute
New study finds fishing line highest among potential pathways spreading the invasive species.

Infested waters list growing

While it may seem like aquatic invasive species are everywhere, that's not yet the case in Minnesota. And that’s why it’s so important to take steps to keep them from spreading — namely cleaning, draining and drying all boats, trailers, fishing gear, scuba gear and water sports gear before moving them from one lake to another.

About 8% of Minnesota's more than 11,000 lakes are on the infested waters list with at least one invasive species. Less than 4% of Minnesota lakes are listed as infested with zebra mussels. As of November, 270 lakes and wetlands are known to have zebra mussels and another 232 are considered likely infested with zebra mussels because they are closely connected to a waterway where zebra mussels have been found.

Source: Minnesota Department of Natural Resources


Researchers working with water samples in a laboratory setting.
A vial containing a water sample that will be tested for eDNA at the Natural Resources Research Institute.
Clint Austin / Duluth News Tribune

What is environmental DNA?

DNA, short for deoxyribonucleic acid, is the hereditary material in living organisms that contains the biological instructions for building and maintaining them. The chemical structure of DNA is the same for all organisms, but differences exist in the order of the DNA building blocks, known as base pairs. Unique sequences of base pairs, particularly repeating patterns, provide a means to identify species, populations and even individuals.

Environmental DNA, eDNA, is nuclear or mitochondrial DNA that is released from an organism into the environment. Sources of eDNA include feces, mucus, shed skin and hair and carcasses. eDNA can be detected in cellular or dissolved form.

In aquatic environments, eDNA is diluted and distributed by currents and other hydrological processes, but it only lasts about 7–21 days, depending on environmental conditions. Exposure to UVB radiation, acidity, heat, and endo- and exonucleases can degrade eDNA.

Source: U.S. Geological Survey

Researchers working with water samples in a laboratory setting.
Researchers Chan Lan Chun, left, and Adelle Keppers discuss the process of extracting environmental DNA or eDNA from water samples.
Clint Austin / Duluth News Tribune
Researchers working with water samples in a laboratory setting.
The University of Minnesota Duluth's Natural Resources Research Institute.
Clint Austin / Duluth News Tribune

John Myers reports on the outdoors, natural resources and the environment for the Duluth News Tribune. You can reach him at jmyers@duluthnews.com.
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