Environmental DNA technology helping MSU researchers more accurately examine aquatic communities

Two MSU researchers are using innovative technology that extracts DNA from lake water samples, painting a clearer picture of what lies beneath the water's surface.

Research team members Nick Sard and Rebecca Selby comparing environmental DNA and traditional surveys of diversity and abundance.
Research team members Nick Sard and Rebecca Selby comparing environmental DNA and traditional surveys of diversity and abundance.

In 2002, the Michigan Department of Natural Resources (MDNR) created the Status and Trends Program, which helps the agency take inventory of the state’s lakes and streams to inform management decisions.

Traditionally geared toward fish, techniques for species identification and population estimates have included gill nets, trap nets and electrofishing. It’s a tried-and-true process but also laborious. Michigan has more than 11,000 inland lakes, making it unrealistic to survey them all.

Researchers in the Michigan State University Department of Fisheries and Wildlife are testing a relatively new technology that could drastically reduce the time and resource expenditure. By taking several water samples, which are then passed through a fine mesh filter and analyzed in the lab, scientists can extract DNA information from a variety of living organisms.

Environmental DNA (eDNA) techniques have been around for more than a decade, but the science has taken a significant leap in recent years. Early eDNA studies were searching for the absence or presence of a single species, either invasive or threatened. Now scientists can observe entire aquatic communities, from fish and invertebrates to insects and plants.

Each of these organisms leaves traces of DNA that can persist in the environment for weeks. This DNA may come from skin cells, scales, damaged tissue, waste or free DNA. By obtaining samples from different areas at varying depths, a clearer image of the ecosystem begins to emerge.

Leading the charge for MSU are Kim Scribner, a professor, and John Robinson, an assistant professor, both in the Department of Fisheries and Wildlife. Scribner and Robinson have been partnering with postdoctoral researchers, graduate students, undergraduates, the MDNR and the Michigan Department of Environment, Great Lakes and Energy (EGLE).

Their first eDNA projects have been efforts to compare findings with the Status and Trends Program. The team has surveyed 22 lakes around the state, taking 40 to 50 water samples from each. The analysis then takes place on the MSU campus.

“The outcomes tend to be similar to the traditional methods, in that we find a lot of the same things,” Robinson said. “But with eDNA it’s much more sensitive. We find rarer species, including rare invasives, that would be hard to capture otherwise.”

Scribner believes that the efficiency of eDNA makes it an attractive methodology.

“You’re getting more bang for your buck,” he said. “It’s easier to get information from more bodies of water in a shorter amount of time, and it’s more accurate. When we use eDNA as compared to traditional sampling, we get much higher species accumulation curves, meaning that when we take multiple samples from the same area, we find more and more species each time. Agencies such as the MDNR and the U.S. Fish and Wildlife Service have already expressed interest in our findings.”

But applications of eDNA technologies span far beyond general population estimates. About five years ago when he first started to explore eDNA, Scribner became interested in how it could address an assortment of ecological questions around invasive and threatened species, and how human development influences inland lake ecosystems. When Robinson joined the university a year later, he added his expertise to the mix.

One of the primary concerns is the sheer number of invasive species posing problems in Michigan waters and how that influences native wildlife. Scribner thinks that by getting a more complete picture of what’s in the water, researchers can better understand why certain lakes are more susceptible to infestation. EGLE and the Great Lakes Restoration Initiative have partnered in these studies.

“There has been a lot of work done with eDNA and well-known invasives such as Asian carp,” Scribner said. “This is obviously an area of emphasis for management agencies because they want to know if Asian carp are there.

“But there are many more species that can do tremendous damage. If we can understand the food chain by seeing what’s present, we can inform management agencies about lakes and streams that are potentially at greatest risk. It would, for example, be easier for an invasive to establish in an open system than in one where food is scarce due to native species.”

Asian carp almost immediately became a nuisance when they were introduced to the U.S. in the 1970s. After being intentionally placed in controlled settings to feed on algal blooms, invasive snails and vegetation, some escaped and established breeding populations. Asian carp have ravaged portions of the Mississippi River, the Missouri River and the Illinois River, among others, devouring food that’s essential for native species.

Many organizations with a vested interest in the Great Lakes have tried to keep Asian carp out of these waters for years. A $7 billion annual fishing industry is at stake.

Although Scribner and Robinson haven’t ventured into projects at the scale of the Great Lakes yet, Scribner said it’s likely they’ll move toward that in the future. In the meantime, Robinson said it’s possible for Asian carp to appear in inland lakes, so they will continue to monitor.

More common invasives such as round goby are found regularly in inland lakes and the Great Lakes. Accidentally brought from Asia to North America, round goby are small fish that outcompete native fish for food and habitat.

Abundant invasives like these often have a harmful effect on threatened species, gobbling up important food sources. Human development can also change the environment, making it less suitable for certain plants and wildlife. Scribner and Robinson are working with the MDNR to use eDNA to test for the presence of threatened species such as the lake herring.

“It can be really difficult to capture threatened species using traditional methods, but with eDNA we can see if they’ve been in a particular location recently,” Scribner said. “The lake herring is an example of an important fish that has seen dwindling numbers in inland lakes. Before we write them off completely, we can see if any DNA appears in our water samples. This technology can provide a glimmer of hope to restoring these populations.”

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