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USGS Science is Refining eDNA Techniques and Developing New Applications 


Geneticist in lab using a pipette to extract a sample from a centrifuge tube
Geneticist, Kylle Roy, extracts DNA from samples to detect Ceratocystis, a fungal pathogen that causes rapid ohia death. Samples have been acquired using aerial spore traps, by collecting wood shavings from ohia trees, or by collecting frass (excrement) of wood-boring beetles.  Photo by Karen Courtot, USGS

More than 6,500 nonindigenous species are now established in the United States, and new species are still arriving. When an introduced, nonnative disease, parasite, plant, or animal begins to spread or expand its range from its point of introduction, and when the species has the potential to cause harm to the environment, the economy, or to human health, it is considered an invasive species. Research by the U.S. Geological Survey is leading to new techniques in the use of environmental DNA, or eDNA, to detect invasive species and their spread.

“The cost of invasive species impacts everyone,” said Cynthia Tam, USGS Biological Threats and Invasive Species Research Program Coordinator. “Farmers, ranchers, businesses, and local, state, tribal, territorial, and federal governments are all working to control the economic, health, and environmental threats these invaders pose. USGS science is supporting their work with science that delivers reliable information about invasive species below the waterline and, increasingly, above ground.”

How does eDNA work? The cells of all living things include DNA, the basic building blocks of life. Skin, fur, hair, scales, and waste all carry these cells, and when they are shed, an organism’s DNA is also shed into the surrounding environment. USGS scientists studying invasive species collect air, water or soil samples, and analyze it to determine whether the DNA of a target invasive species is present.

The first glimpse of a new invading species may be eDNA. A master of camouflage, the Burmese python is a nonindigenous, invasive species that had been identified in the Florida Everglades by about 2000. Margaret Hunter, a USGS scientist with the Wetlands and Aquatic Research Center in Gainesville, Florida, used eDNA research to investigate whether Burmese pythons were moving out from the Everglades. Her research indicated the presence of Burmese python northeast of the Everglades on the Arthur M. Marshall Loxahatchee National Wildlife Refuge 2 years before there was visual confirmation of the snake on the refuge.

Environmental DNA is an indirect method of identifying whether a species is present, and it has inherent challenges for researchers and land managers. Analysis of eDNA sampling is more complicated than noting the presence or absence of DNA in a given sample. Scientists with the USGS Upper Midwest Environmental Sciences Center in LaCrosse, Wisconsin, and the Columbia Environmental Research Center in Columbia, Missouri, are working together to develop quantitative tools to guide sampling design and estimate detection probability, which allows USGS to provide better context for interpreting results when working with land managers. 

More than a decade ago, UMESC and CERC scientists were leaders in the use of eDNA in efforts to protect the Great Lakes from the spread of invasive carps, including bighead, black, grass, and silver carps. Environmental DNA remains an important tool in tracking invasive carp, saving time and money in invasive carp removal efforts. Today, USGS scientists are working with the U.S. Fish and Wildlife Service and the U.S. Army Corps of Engineers to continue developing eDNA research in support of the needs of natural resource managers.

USGS scientist Nate Jensen displays an invasive bighead carp collected on the Illinois River. The fish was collected as part of research into the anatomy and physiology of invasive carp. USGS photo.

Scientists looking for the DNA of Burmese python and invasive carp used protocols designed for sampling water, but in Hawaiʻi, USGS researchers exploring connections between the nonindigenous insect and the nonindigenous fungus behind a lethal tree disease had to invent new sampling methods.

The ʻōhiʻa tree is a dominant tree species with both cultural and economic importance throughout the Hawaiian Islands. Since 2010, the species has been succumbing to a disease called “rapid ʻōhiʻa death,” and research has pointed to excrement from invasive ambrosia beetles as being the carrier of the fungal pathogens behind rapid ʻōhiʻa death. Scientists with USGS wanted to know if the pathogens were airborne in ambrosia beetle excrement.

Answering that question resulted in USGS researchers developing a low-cost method of sampling airborne eDNA. Researchers designed wooden traps to hold glass slides and attached the traps to thin strips of metal that can be placed at any height. The glass slides are greased to secure the microscopic environmental debris carried in the wind. Low-tech as well as low-cost, the traps were designed to be easy for land managers to make, install, and collect slides from for shipment to scientists for analysis. The traps are already being used by other agencies studying other plant diseases.

Image shows an aerial spore trap, which is a tall piece of metal with a collector, there are trees and gras in back ground
USGS scientists designed a low-cost, easy-to-build method of sampling the air for eDNA. Photo by Kylle Roy, USGS

While the methods and use of eDNA for invasive species research have come a long way in a short time, in many ways eDNA still hinges on scientists being in the right place at the right time to collect samples. Research Ecologist Adam Sepulveda at the USGS Northern Rocky Mountain Science Center in Bozeman, Montana, and Research Hydrologist Elliot Barnhart at the USGS Wyoming-Montana Water Science Center in Helena, Montana, are exploring whether combining robotics with USGS streamgages can overcome that inherent challenge.

Research on eDNA itself has suggested that humans and robots are about even in their ability to detect the eDNA of species that are present in the environment. Where robotics excel over humans is in establishing when DNA is not present, Sepulveda said. A researcher who visits a site five times and gets five negative results cannot say with certainty that a given species’ eDNA is not present. A robot can easily perform 100 samples, and if those samples are all negative, land managers and scientists can have greater confidence that the DNA in question is not present.   

Sepulveda was inspired by marine biologists at the Monterey Bay Aquarium Research Institute, who like land-based scientists in the West, do their research in remote areas. As part of his research on invasive zebra mussels and quagga mussels, Sepulveda partnered with the institute to install robots at USGS streamgages in the Yellowstone and Snake rivers. Robots built for the ocean are overkill in most streamgage sites, so future research will look at how robots can be adapted for shallower, freshwater locations, how to design sample plans for robotic collection, and ultimately whether adding robots to streamgages is worth the cost.

“Environmental DNA research is allowing USGS scientists to give resource managers a new window into invasive and native species that may affect decisions today, and in the future,” Tam said. “Even more importantly, USGS science is serving as the foundation to the work of others.”


A robotic sampler is lowered into its metal housing.
The Monterey Bay Aquarium Research Institute (MBARI) robotic sampler is shown being lowered into its metal housing. Photo by Cheryl Miller, USGS