Lindsay Chadderton taking water samples in the Chicago River
Lindsay Chadderton taking water samples in the Chicago River Credit: Chris Jerde

The test that detected the Asian carp’s environmental DNA, or eDNA, above the electric barrier is new: it was developed in the past year by New Zealand scientist Lindsay Chadderton and scientists at Notre Dame. They say this is the first time DNA testing has been used on such a scale to find evidence of invasive fish in freshwater, and they think their method will ultimately be used around the globe to detect invasive species and protect endangered ones.

In January 2007 the Nature Conservancy hired Chadderton, an aquatic ecologist, as the first director of aquatic invasive species for its Great Lakes Project, a program to rejuvenate and protect the ecosystem of the lakes. Chadderton had been working with invasive species for New Zealand’s Department of Conservation, where he’d spent 16 years, and soon after he arrived in the midwest he and the team from Notre Dame—David Lodge, the university’s director of aquatic conservation, and research assistant professors Andrew Mahon and Christopher Jerde—began experimenting with DNA detection. They were pleasantly surprised to find themselves able to detect species-specific DNA in running water. Now this technology has taken center stage in perhaps the most politically charged invasive species controversy ever to hit the Great Lakes region.

How did the eDNA test come about?

About 18 months ago I had a conversation with Andy Mahon and said, “What do you reckon?” about trying to see if we could detect DNA in the water column. He said, “Let’s give it a go.” So Andy, Chris Jerde, and I set out doing some really simple trials, putting fish in buckets, seeing if we could detect DNA. Once we saw we could do that, we went out to a local river and found we could detect common carp in the river. At the same time we were playing around with this technique, Chris was also doing a modeling study of Asian carp in the Sanitary and Ship Canal. He thought the fish should be much higher up [the canal] than current methods were saying they were. So last April we went out with the Army Corps and took water samples in the Illinois River where large numbers of bighead and silver carp were known to be present. The day we went out the river was in flood, running five foot above normal river height, and as we drove home with our samples Andy Mahon and I looked at each and said, “Well, it was a nice idea.” We were highly skeptical that we would detect anything because the river at that point is really large, maybe up to 200 meters wide and 10 meters deep, and it was flowing really quickly. We thought any DNA would be flushed out of the system. Hence, when we found we could detect DNA even in small [500 milliliter] water samples, we were really surprised. We then started sampling moving up the Des Plaines River into areas where few Asian carp had ever been recorded, and into areas supposedly above the invasion front, to see if our detection methods were more sensitive than standard electric fishing and static nets. Chris Jerde’s dispersal modeling suggested the fish should have made it at least to the electric barriers designed to prevent the carp getting upstream, so we were not surprised to find evidence of fish. Once we found DNA below the barrier and coupled that with some dispersal modeling done by Chris, a math biologist, we were also not that surprised we found DNA above the barrier. We did the first trials in April 2009 and the first tests in June.

How does the DNA test work?

We go out, take between 60 and 100 two-liter water samples, put them in coolers on ice to slow natural breakdown, and bring them back to the laboratory. Within 24 hours of collection we filter each sample through really fine filter paper . . . to remove any particles in the water, including any possible cells. Then we extract the DNA off the filter paper, using kits that break the cells open and release the DNA. We then use a centrifuge to take the liquid off, and that gives us a DNA extract. Then we amplify—sort of clone—the species-specific DNA we’re looking for so we have enough to detect, and we run these on simple gels that allow us to compare each sample with controls that contain the target DNA.

The Army Corps of Engineers and state officials have repeatedly stated that no Asian carp have been found above the electric barrier. How confident are you of the DNA tests?

Yes, the DNA testing is new, and like any new tool, there’s always going to be a healthy level of skepticism. But we are confident that our results are real, and the more testing we do this confidence increases. In the criminal justice system we regularly use DNA to place people at the scene of a crime. People, like other animals, shed DNA into the environment—skin, hair, bodily fluids. Carp do the same thing—DNA cells associated with mucus or sloughed off from the gills, attached to scales, shed from the gut system, and contained in feces and urine. Once those cells are released into the water they are held in suspension for some time and we are simply collecting them in the water column. We’re looking for evidence of a species, instead of individuals like you do with people, but the principles are the same.

Could that DNA have gotten there by a mechanism other than fish being present? There have been various suggestions that carp could have got there by other pathways, like barges carrying water [from the Asian-carp-infested Illinois River]. But since August the barge operators have not discharged water [from downstream] above the barriers, and barges don’t get into the North Branch of the Chicago River or the Des Plaines River, where we have found carp DNA. The other pathways like birds or wastewater also don’t explain the overall pattern,

And the last thing that gives us confidence is the fact we can go back to certain places and repeatedly detect DNA. These results are not chance events, and the distribution is consistent with the movement of fish. For example, the number of positive samples decreases as we get closer to the barrier. That’s consistent with an upstream invasion.

Why are the Asian carp moving past the barrier at all? They don’t know there’s good habitat farther on, do they?

It’s probably just an innate sense. These fish prefer slow-flowing water and the canal is probably not particularly good habitat for them. It’s like a box, there are not a lot of places to get out of the current so we’d expect these fish to continue to pushing up through the system searching for better food or habitat. With any population there are dispersers that keep moving and other animals that hang around. For one thing, if you’re at the front of the pack there might be more food. If you’ve got hundreds of thousands of individuals behind you all feeding in the same water—wouldn’t you want to be up front?

When the fish in the canal were poisoned in December just south of the electric barrier [see previous story for more], just one dead Asian carp was found. Why was that, if there are so many Asian carp in the system? Were you surprised?

We didn’t expect to see many if any Asian carp, as when they are killed by rotenone they sink. It was cold, which makes them slower to decompose and bloat and float. There were apparently large numbers of fish on the bottom being fed on by crayfish and other invertebrates not affected by the fish poison. All these conditions would have acted to prevent the fish floating to the surface.

You’ve spoken of using a “Judas carp” to find Asian carp already past the barrier and possibly in Lake Michigan. What is it?

It’s one way to track fish down. We think some fish have gotten into Lake Michigan—it’s the most plausible explanation for what we have found. So if we want to stop Asian carp we need to track them down and prevent them from spawning. One way would be to use Judas fish. These are fish with a transmitter attached to them. You follow the Judas fish around, and once it’s hanging out you encircle the area and fish it out or treat it [with rotenone or another poison]. The technique is used to control invasive species around the world. The Aussies have used it very successfully to control and almost eradicate common carp in two lakes in Tasmania. We need to remove the Asian carp between the barrier and the Great Lakes, and we could use the Judas fish to locate areas to treat.

Do you think we could actually find the probably very few Asian carp in Lake Michigan?

When the carp are in the lake they have an Achilles’ heel—they need long distances of running water to successfully spawn. So while it’s going to be hard to find them in the lake itself, the fact they will likely need to go inland and upstream to spawn may make the search easier. There’s a lot we can learn from the sea lamprey control program, which is the poster child of integrated aquatic pest management. [The government spends about $18 million a year fighting invasive sea lampreys, which latch on to Great Lakes fish and suck their blood. Lamprey need to move inland to spawn, and fishery managers employ various barriers on the Great Lakes streams to block and capture them. They also poison the larvae, and release thousands of sterile male lampreys to mate with the females.]

Could you apply rotenone to all the canals and rivers leading into the lake?

Treating the whole thing would be something you’d want to explore. There are other methods you could use, like electrofishing or seining. But treating the waterway with a fish poison like rotenone is the only surefire way of making sure you got them all.

Do you still have faith in the electric barrier? It’s a numbers game—the more fish that get into the lake the greater likelihood we will see successful establishment. We know the largest numbers of fish are still below the barrier and we need to keep them there. Over the last two to three years the upper barrier has been taken down for maintenance on at least one occasion, on the assumption Asian carp weren’t present. But Chris [Jerde] estimated the carp probably made it to right below the barrier two to three years ago, and it seems possible that during the 2008 maintenance operations fish got through.

Another idea is to aerate the water and use the bubbles as the medium for a piercing noise the carp can’t tolerate. Would that combination work?

Acoustic bubble barriers are likely to be effective in the short term, although studies suggest they are likely to keep out only 70 to 80 percent of fish. They are probably less effective than the electric barrier but can be put in place rapidly and could be used above the barrier near Lake Michigan to buy time.

You are pretty certain Asian carp are in Lake Michigan. Does that mean the worst fears of environmental groups—that the lake will be taken over by Asian carp—will come true?

It’s definitely not game over. We’ve got some amount of time. There’s got to be enough fish, they’ve got to find each other, they’ve got to find suitable spawning habitat, their eggs have to survive and hatch, the larvae have to survive. At each stage all sorts of things could go wrong, there’s still lots of uncertainty.

If we look at invasion history around the U.S. and the world, invasive species often don’t do what we expect. They may not end up being more than a nuisance, but they could conversely end up being a disaster. We won’t know until it happens, at which stage it’s too late. It seems incredibly risky or foolhardy to let these things into the Great Lakes unchecked. We know enough about them to be really concerned about the potential consequences. There is too much at stake. And we never really know what exactly is going to happen until it happens.

Since Lake Michigan has relatively sparse plankton and Asian carp need faster-moving water to spawn, it doesn’t sound like it’s even an ideal habitat for them.

In their native range, they prefer slow-flowing or standing water, like lakes—except for when spawning. The big issue is whether there is enough food. This is likely to vary across each of the Great Lakes and some recent work suggests that in the open water of most lakes there isn’t enough food. But that research work didn’t take into account all possible food sources—like the larva of [invasive] zebra and quagga mussels. Everybody generally accepts that Asian carp are probably likely to do well in Lake Erie and in embayments in Lake Michigan like Green Bay.

They’ve already been found in Lake Erie, right?

About five bighead carp [a species of Asian carp] have been found in Lake Erie over the last 14 or so years. The assumption is these fish represent individual releases. At least two of them were in really good condition—they were fat and large.

You mentioned them eating zebra and quagga mussel larvae. Could a silver lining of an Asian carp invasion be that they would curb these invasive mussels?

No. These mussels are pumping out so many larvae it seems highly unlikely the carp would have any effect.

How else could the eDNA test be used?

The question of invasives in an aquatic environment is a global issue. This will probably become a standard tool in the toolbox, not only for detecting aquatic invasive species but also for detecting rare species that we want to protect. The same problems we have in terms of finding low numbers of early invaders biologists face in trying to find rare native species like sturgeon that they want to protect.

You’ve said “ecological separation” is the only certain long-term solution to the carp menace, and ecological separation means what it says—severing Lake Michigan from the rivers and canals that artificially connect it to the Mississippi basin.

Yes, this is true, but it should still be possible to develop solutions that achieve this while still allowing the waterway system to maintain its many other functions.

What about the proposal to close the locks four days a week or a few times a month? Wouldn’t the carp still get through on the days the locks were open?

Intermittent closure of the locks might at best slow but would seem unlikely to prevent passage of Asian carp. But if intermittent lock closure is coupled with establishing acoustic, bubble, light, and other fish deterrents in and around the lock chamber, as well as periodic treatment downstream of the lock to remove any resident fish, then it could help.

What do you envision when you say the waterway system could maintain its functions with the locks closed? Barge operators and tour boat companies have said it would ruin their businesses.

This is a really complex issue, but simplistically, there are four major uses of the waterway that could be impacted by lock closure, but each has olutions that could minimize or hopefully avoid long-term impacts.

First, the waterway is used for alleviating flooding by discharging water into the lake during high flow events. A partial solution could be to use sets of special screens, which are routinely used on dams and water intake structures to prevent passage of aquatic organisms. . . .

The second concern is the river and lakefront boat tours in downtown Chicago. Development of passenger transit facilities across the waterfront could allow people to efficiently move between boats in the river and lakefront. This would require changes to existing tour operations but would still allow the tours to continue and the facility could be developed into a tourism attraction.

Then there’s the movement of bulk cargo. My understanding is that much of the cargo is off-loaded or on-loaded onto larger or smaller vessels in the Calumet Harbor directly upstream of the O’Brien Lock. A state-of-the-art cargo transfer facility or intermodal facility could presumably be designed and built to allow the movement of bulk cargo across separation structures, including the closed locks. . . . This might even increase canal usage and make it a much more effective transport system than we have now. . . 

Finally there is the concern about movement of recreational boaters. There are numerous examples around the world where boat lifts are used to move recreational watercraft across physical barriers. Depending on the traffic volumes, and the type and number of lifts, this could be as efficient as moving through a lock, with the added benefit that you could clean, inspect, and remove any aquatic invasive species while the craft are out of the water.   v

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