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Montana Researchers Developing New Early Detection Methods For Invasive Mussels

Phil Matson collects a water sample from Flathead Lake for use in e-DNA testing for quagga and zebra mussels.
Nicky Ouellet
Montana Public Radio
Phil Matson collects a water sample from Flathead Lake for use in e-DNA testing for quagga and zebra mussels.

Wherever you go, you leave behind a tiny trace of yourself, a fingerprint even smaller than a cell that says you were here. Every organism does this, including the invasive quagga and zebra mussels the state is trying to keep out of Montana. This summer, a team of scientists in the Flathead Valley is using cutting-edge technology to detect the mussels’ genetic fingerprints sooner. They say early detection may offer the only hope for eradicating the mussels if they do get here.

Phil Matson is gearing up for a day on the Jesse-B research vessel sampling Flathead Lake, not for the invasive mussels themselves, but for the presence of their DNA.

"We're gonna take some samples from the surface of the lake, and we're gonna take some samples from the bottom of the lake," he explains.

The University of Montana’s Flathead Lake Biological Station uses what’s called environmental DNA, or e-DNA — basically, bits of genes floating around in the water — to determine if a specific species has been in the lake.

"The DNA gets sloughed off through feces, or dead cells, just like we have our skin, our skin sloughs off. That DNA is very concentrated and it collects in the water, so any time that we collect some water, we'll be able to extract the DNA from that," Matson says.

This sampling method has been around for years. It’s often used to find where threatened and endangered species are, and then target those areas for population recovery.

Now, a team at Bio Station is pioneering how to detect quagga and zebra mussels specifically, with the hope that positively identifying them in a water body could help managers halt their spread.

Matson is doing the first step of this method on the boat. Today Matson will sample seven sites around Flathead Lake, taking six samples at each site; two each of a surface sample, a deep sample and a control.

He starts by soaking all his equipment in bleach to kill off anything that could throw off the results.

"The devil's in the details. You miss one piece of equipment and the whole day is kind of shot," he says.

Next we head to the sample site.

He drops a very fine-mesh net 9 meters under the startlingly clear water using a winch, and holds another net just under the surface as Jim Craft, our pilot, slowly trolls forward.

"Jim's got it down to a science, you can hear him, he's shifting all the time, the clicks trying to go forwards, backwards, forwards, keep it at the right pace," Matson says.

After a minute, the nets come up and Matson uses a syringe of ethanol to coax the green and brown gunk trapped in his net into a test tube.

This is what he’s after — that green and brown gunk is a mix of algae, plankton and bits of genetic material that hold the answer to whether Flathead Lake has mussels in it. With samples successfully collected, we head back to the lab.

That green and brown gunk is a mix of algae, plankton and bits of genetic material that hold the answer to whether Flathead Lake has mussels in it. One sample comes from 9 meters deep, the other from the surface.
Credit Nicky Ouellet
That green and brown gunk is a mix of algae, plankton and bits of genetic material that hold the answer to whether Flathead Lake has mussels in it. One sample comes from 9 meters deep, the other from the surface.

This next part is where the Bio Station is pioneering the science. They’ve mapped the invasive mussel’s DNA, and found a tiny section that only the mussels have. This little segment of DNA is like a key. They can introduce this little segment of DNA — this key — to a sample from the lake. If the lake sample has actual mussel DNA in it, that DNA will react with the little key segment.

"Basically it's a jigsaw puzzle," says Shawn Devlin, an assistant research professor at the Bio Station. He says a highly sensitive machine can see and count these tiny reactions.

"So, we get this little glow in the system." [Angel chorus sound]

The machine doesn’t actually make that sound, but it forces this reaction to happen over and over so it’s easier to see, and after 40 or so times, it has a good idea how many strands of mussel DNA were in the sample to begin with. The Bio Station samples 31 different places around the lake, so between the location and the number of DNA hits, "we can really focus in and say we probably have an infestation there, by using the relative abundance of those genes moving closer to the point where we think that colony is established ."

Devlin says sampling e-DNA has huge advantages.

"What I find is the most compelling reason to use it, is that it will detect the presence of the organism at any life stage, at any time of year. So if we can go out and we can find them, say, before the breeding cycle begins in June and July, and we find them in April, we might be able to do something about them much more quickly."

The drawbacks are that it takes a huge investment of time and money on the front end to develop and tweak this method, and processing a sample in the lab can take a few days. It’s also a little expensive. It costs between $65 to $120 to run a set of samples.

So, the Bio Station is pioneering another early detection sampling technique that’s smaller, faster and even more precise. This method uses a sample size so small, only one strand of DNA can fit inside. The same key DNA segment is introduced, if mussel DNA is present the sample will glow, and the whole process happens in less than an hour. They plan to use it in the field at boat inspection sites.

Boat propeller encrusted with invasive mussels.
Credit National Parks Service (PD)
Quagga mussels cover an outboard motor at Lake Mead National Recreation Area.

"We'll take a suitcase and it'll have a plug coming out the back that we plug into a cigarette lighter, and a tube coming out the front that will suck our sample into the system. Then give it a few minutes, and we can do the next sample, and the next sample. And based on when the reaction time comes through — anywhere from 45 minutes to 60 minutes later, we'll know what sample we're getting data for, and we'll understand if there is DNA from zebra mussels or quagga mussels within that timeframe" Devlin explains.

The idea is to eliminate human error at inspection stations.

Separate from the Bio Station’s research, Montana Fish, Wildlife and Parks is also sampling Montana’s lakes for zebra and quagga mussels.

Stacy Schmidt works in the state’s aquatic invasive species lab in Helena. She says the sampling part is pretty similar to what the Bio Station does, but back in the lab, she’s looking at the samples under a microscope to see actual baby mussels.

"Our microscope is a dissecting microscope that's set up to have cross polarized light capability," Schmidt says.

Think of polarized sunglasses. Take two pairs, rotate one 90 degrees, and everything will look kind of black.

"And when you do that with a microscope, it turns everything black, but it causes certain minerals to glow. And one of those minerals that glows is the shells of bivalves, so it makes them really easy to pick up," Schmidt says.

This gives much more concrete proof that mussels are present in a water body than e-DNA, where a positive hit could be proof of a living mussel, a dead mussel or a mussel byproduct like poop.

"From a management perspective, when you're looking at the presence of the DNA of a species, versus collecting a sample where you have a baby mussel in front of you, from a management perspective it's totally different," Schmidt says.

But Schmidt also acknowledges there are some challenges with FWP’s methodology. It only works at certain times of the year when baby mussels are floating around in the water. It also takes a few years to train a lab technician to analyze a sample, which makes staffing the lab a challenge.

Schmidt says FWP is trying out a bunch of sampling methods this year to find out which one makes the most sense or how to use multiple methods in harmony.

"We don’t want to be so set in our ways that we're ignoring better tools as they're being developed. That’s the whole mantra of the AIS program. It’s dynamic, it’s ever changing," she says.

None of the samples taken by the Bio Station or FWP this year have positively identified quagga or zebra mussels. One real test will come next week, when a team of divers from the U.S. Fish and Wildlife Service takes a look at boulders in the bottom of Tiber Reservoir to see if they can find an adult colony.

Nicky is MTPR's Flathead-area reporter.
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