Use of Robotic DNA Samplers That Can Rapidly Detect Invasive Aquatic Species

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USGS researchers and their collaborators demonstrated the efficacy of using robotic environmental DNA samplers for bio surveillance in freshwater systems, showing that samples collected, processed, and preserved by robotic sampler detect organism DNA in the environment at rates comparable to those collected traditionally by human technicians.

Outside casing of robotic environmental DNA aquatic sampler

Outside casing of robotic environmental DNA aquatic sampler. From the outside, the sampler unit looks rather humble. However, a lot of complicated work gets done in there, including taking and processing aquatic samples for DNA analysis. (Credit: Elliott Barnhart, USGS Wyoming-Montana Water Science Center. Public domain.)

USGS researchers Adam Sepulveda (Northern Rocky Mountain Science Center, NOROCK) and Elliott Barnhart (Wyoming-Montana Water Science Center, WY-MT WSC) and colleagues at WY-MT WSC, Idaho Water Science Center, and Upper Midwest Environmental Science Center have successfully used a robotic environmental DNA (eDNA) sampler for organism detection in streams and to determine if real-time bio surveillance may be feasible. The study was funded in part by the USGS National Innovation Center and partnered with the Monterey Bay Aquarium Research Institute (MBARI)  The recently published paper in Scientific Reports describes the use and testing of autonomous, robotic eDNA samplers to collect and process samples collected at a high frequency for detecting human and fish pathogens and non-native species at USGS streamgages in freshwater aquatic environments. This new study finds that samples collected, processed, and preserved by robotic samplers detect organism presence at a similar rate compared to traditionally collected samples by a technician. Robotic sampling has several advantages over humans in that these robots have been designed to withstand harsh oceanic environments and could be deployed safely where there are hazards such as radioactive sites or water-borne viruses. Additionally, the robot can be programmed to sample at any time, day or night, and can have a higher sampling frequency (hourly or daily, for example) than is feasible or cost effective using human labor. Higher-frequency sampling can be important when looking for species that are not widespread in an ecosystem, because finding the DNA of those organisms is a bit like finding a needle in a haystack - you have to look at more hay to find the needle.

The eDNA robot, or Environmental Sample Processor, can collect, filter, and preserve water samples for later analysis, and although not used for this study, it can perform selected rapid, on-site analyses. These features coupled with telemetry capabilities to communicate results to end-users may provide early warning of disease, invasive species, and related water-quality issues, giving resource managers time to protect human and ecosystem health. Invasive aquatic species can have serious effects on native communities and local and regional economies. Early detection of invasive species increases the likelihood of controlling and limiting their dispersal and preventing widespread ecological and economic damage. Research using the eDNA sampler will continue with funding from the U.S. Fish and Wildlife Service to detect the invasive Quagga and Zebra mussels. 


Sceintific Reports Paper: Sepulveda, A.J., Birch, J.M., Barnhart, E.P., Merkes, C.M., Yamahara, K.M., Marin, R., III, Kinsey, S.M., Wright, P.R., and Schmidt, C., 2020, Robotic environmental DNA bio-surveillance of freshwater health: Scientific Reports,

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Date published: July 19, 2019
Status: Active

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