Using Robots in the River: Biosurveillance at USGS streamgages

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For more than a decade, researchers around the world have shown that sampling a water body and analyzing for DNA (a method known as eDNA) is an effective method to detect an organism in the water. The challenge is that finding organisms that are not very abundant requires a lot of samples to locate this needle in a haystack.  Enter the "lab in a can", the water quality sampling and processing robot.

A recently completed study demonstrated the effectiveness of using streamgages as locations for sampling for eDNA (DNA fragments that are shed by an organism into the environment). However, in order to find the species of interest, especially an organism that is new to the ecosystme, many samples must be collected.


Sealing MBARI Environmental Sample Processor (robot) into its housing

Sealing MBARI Environmental Sample Processor into its housing

(Credit: Cheryl Miller, USGS. Public domain.)

During the summers of 2018 and 2019, USGS researchers, funded in part by the USGS National Innovation Center, partnered with the Monterey Bay Aquarium Research Institute (MBARI) to use a robotic sampler to collect water from the river one to two times per day. The robot processed and preserved the DNA filtered from the water sample for analyses at a lab in the fall.

The results are in: Data show that samples collected by the robot and by traditional manual sampling provided similar information about the organisms of interest in the ecosystem. Additionally, robotic sampling has an advantage over humans because it can be programmed to sample any time of day or night, and can have a higher frequency of sampling (hourly or daily, for example) that is not feasible or cost effective with a person.

Not only did the robotic sampler deployed at the Snake River near Irwin, Idaho streamgage show that the robot can collect similar samples, it provided an example as to how technology can be integrated into the USGS streamgage network to help partners understand and address issues such as detection of aquatic invasive species or fish and human pathogens.

By installing the robot at a streamgage, additional data, such as streamflow and water quality, help us interpret the DNA data, to gain a better understanding of how the organism is behaving, and eventually those data may be able to be used to forecast the presence and movement of an invasive or pathogenic organism.