Environmental DNA Used to Provide Early Detection of Invasive Crayfish

5 October 2016, at 1:00am

US - A University of Illinois researcher and his colleagues have analyzed environmental DNA (eDNA) to successfully detect the presence of the highly invasive rusty crayfish in a dozen Wisconsin lakes.

Using eDNA to monitor hard to detect species can provide early warnings of newly arrived invasive species.

“The lakes in the Boulder Junction area have had long-term monitoring from the University of Wisconsin and the University of Notre Dame, so we had an existing gradient of lakes where this invasive crayfish had never been observed to lakes where we know rusty crayfish are abundant,” says U of I aquatic ecologist Eric Larson.

“Using the eDNA tool we succeeded in detecting rusty crayfish in lakes where this species is very rare. This suggests that the tool could be used to monitor for early warning of new invasions in other regions, which would let us enact control or eradication measures when they’re most feasible.”

In the study, samples were analyzed using a small white machine that could be easily mistaken for a bread maker. Inside, a computer with a laser heats and cools the samples of DNA over and over in a chemical solution. During each cycle, the double strands of DNA are separated, then built up again.

The duplication is exponential so millions of copies are created within a very short time. Beforehand, a dye is attached to the DNA, making it easier for researchers to identify each organism’s DNA and quantify it.

Mr Larson’s colleague Mark Davis, coordinator of the Collaborative Ecological Genetics Laboratory at the Illinois Natural History Survey, explains that every living thing is constantly sloughing off cells and all of those cells contain DNA. But eDNA isn’t like what you get if you take a blood sample from a salamander. That would be “clean DNA.” You already know it’s from a salamander.

“The eDNA from a lake is ‘dirty’ DNA,” Mr Davis says. “It’s degraded, broken down so you have very small fragments and few copies. With chemistry and technology, we amplify it. Using bioinformatics, the computer wades through the information to give us a full complex of what’s in that sample—whether it be invertebrates, fish, reptiles, amphibians, birds—anything that may be coming into contact with the water or soil. With eDNA, it’s exciting because you don’t know what you’ll find.”

Mr Davis says there are still eDNA problems to solve. “Right now we can tell if an organism is present or not. But knowing the exact number of individuals is difficult. For example, we often don’t know the rate an organism sheds DNA or if they shed more at different times. How quickly does it degrade?”

Further Reading

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