$1.95M NSF Grant Fuels Penn State Research on Environmental DNA Dynamics

A bottle of water sampled from a lake or river can reveal what fish, amphibians insects and bacteria are present, thanks to environmental DNA (eDNA), the genetic material shed by organisms. This way of measuring transforms scientists’ ability to determine the extent of aquatic life in various water bodies, according to a team led by Daniel Allen, assistant professor of aquatic ecology in Penn State’s College of Agricultural Sciences.

The U.S. National Science Foundation awarded Allen and his team, which includes partners at the University of Alabama and the University of North Texas, a $1.95 million, five-year grant to support a project focused on analyzing how eDNA moves in streams across the continent.

The technology has been used to search for invasive Asian carp in waterways flowing into the Great Lakes, American eels in streams in the Susquehanna River basin and hellbenders in mountain streams of the eastern United States. Yet, despite the rapid advances and adoption of this approach, scientists know very little about how eDNA degrades in nature, and the lack of understanding about the fate of eDNA in streams and rivers presents a major challenge for interpreting an eDNA “hit,” Allen said.

In collaboration with Arial Shogren, assistant professor in the Department of Biological Sciences at the University of Alabama, and Zacchaeus Compson, assistant professor in the Department of Biological Sciences at the University of North Texas, Allen will investigate the environmental factors that promote or inhibit eDNA movement in streams.

The research will focus on three mechanisms controlling the fate of eDNA — degradation, deposition and transport — in 24 streams across the U.S. The streams are part of the National Ecological Observatory Network (NEON), which comprises terrestrial, aquatic, atmospheric and remote-sensing measurement infrastructure and cyberinfrastructure to deliver standardized, calibrated data to the scientific community through a single, openly accessible data portal.

“Data provided by the NEON streams will allow us to understand ‘eDNA spiraling,’ a term that has been used to describe the fate of eDNA as it flows downstream, where it can be degraded by microbes, deposited in streambed sediments, resuspended from the streambed and transported further downstream,” Allen said. The researchers will test how water chemistry and microbial communities affect eDNA fate and conduct eDNA spiraling experiments at NEON stream sites.

The researchers will replicate eDNA-spiraling experiments in two NEON streams and in the Shaver’s Creek watershed in the Shale Hills Critical Zone Observatory near Penn State’s University Park campus to determine whether eDNA from some species persists longer than that from other species in streams. The researchers also will try to determine if eDNA particle size influences eDNA spiraling metrics.

“To test this, we will release a novel source of environmental DNA into streams across United States, and then track how far we can collect it,” Allen said. “We will be developing methods that use a commercial fish that doesn’t exist in those streams, and then use it to make an eDNA slurry.”

Finally, the research team will participate in the NSF-funded Emerge program, which broadens participation in freshwater science by training undergraduate, graduate and early career scientists from underrepresented groups in data analysis and visualization. The researchers plan to offer in-person workshops on bioinformatics of DNA at all three participating universities.

The prospect of conducting innovative studies like this eDNA research project is what brought Allen to Penn State, he said.

“I knew Penn State has strong expertise in these kinds of genetic, DNA-based approaches,” said Allen, who also is a faculty member of the Institute of Energy and the Environment. “We have the Genomics Core Facility and the One Health Microbiome Center in the Huck Institute of the Life Sciences. When I moved here, I was able to start up a new lab at Penn State with the equipment that I would need to be able to use these DNA-based approaches.”