Environmental DNA (eDNA): Combining Technology and Biology to Detect Aquatic Invasive Species and Pathogens

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Using DNA, USGS researchers are able to detect the presence of invasive species in aquatic ecosystems. The DNA they use is literally floating around in the environment and is called environmental DNA (eDNA) and is a powerful tool for the early detection of invasive species and pathogens, which can cause serious ecological and economic damage. USGS researchers are also combining the use of eDNA with robotic technology and have deployed automated, robotic eDNA samplers that can detect invasive species in aquatic systems. By combining biology and technology, USGS science can help resource managers detect invasive species and other biological hazards early or monitor their spread, which may provide managers with adequate time and flexibility in developing management strategies, including invasive species control.


Nonnative species can be ecologically disruptive and economically damaging, and early detection is important for developing robust monitoring and control strategies. However, trying to find a handful of individuals invading new habitat can be nearly impossible, especially if those individuals are small or well-hidden as is commonly the case in aquatic systems.

Sealing MBARI Environmental Sample Processor (robot) into its housing

Sealing robotic eDNA sampler into its housing (Credit: Cheryl Eddy Miller, USGS. Public domain.)

To address this issue, scientists use biology and the aquatic habitat the invasive species live in and turn those factors into a tool they can use. Organisms shed and excrete DNA into the environment, and this DNA, termed environmental DNA (eDNA), can be found suspended in the water, making it accessible to researchers who have the means to extract it from water samples. Using eDNA can be a more effective approach to detect difficult-to-find invasive species than using nets, electro shocking, visual surveys, or other traditional means of detecting aquatic invasive species.

Using eDNA can be part of an early warning system letting resource managers know that invasive species are now present in a habitat that they were previously not. Early detection of invasive species may provide managers flexibility in how they develop their management strategies and could increase the chances of successful control efforts because the invasive species’ population numbers might be relatively low at the time of detection. Once an invasive species gets well established in a habitat, controlling that species can become very difficult and expensive.   

NOROCK Research

Using eDNA: Testing water samples from rivers in Oregon, Colorado, Idaho, Montana, Wyoming, and Minnesota, we have successfully used eDNA to detect invasive species. Specifically, we have been able to detect the DNA of nonnative fish, aquatic weeds, and aquatic invertebrates, such as mussel and snail species, and a microscopic parasite that causes proliferative kidney disease in fish, which can cause fish kills in the salmon family (salmon, trout, char, etc.). We have repeatedly used eDNA sampling to detect dreissenid mussel (zebra and quagga mussels) DNA from rivers, lakes and reservoirs. This is particularly exciting because zebra and quagga mussels are a notoriously ecologically and economically harmful group of invasive species that grow on hard surfaces and can damage water pipes and other infrastructure, recreational vehicles, and even other organisms like turtles. They can also outcompete native mussels, disrupt native aquatic communities, and alter how aquatic ecosystems function. Once dreissenid mussels become well established, they are extremely difficult to manage, so having an early detection system that warns managers these mussels have started to occupy a new habitat could be very valuable in controlling these invaders before their numbers become overwhelming.  

eDNA and Robots: We, along with our collaborators from other USGS Science Centers and the Monterey Bay Aquarium Research Institute, deployed robotic eDNA samplers to test if they could provide as reliable, timely eDNA samples as those collected by humans. Our results indicate that the robotic sampler could provide samples of similar quality as those taken by humans. In contrast to humans, the robotic samplers can be programed to take samples at a higher frequency than a human could take them, which could be a serious advantage when trying to detect potentially harmful invasive species as early as possible.