November 9, 2022

New partnership advances DNA-detecting technology to help monitor aquatic health

Grassy riverbank of the Yellowstone River with a USGS stream gage shed on the left and a white truck parked adjacent

A new partnership between MBARI and USGS is developing a portable robotic sampler to detect invasive species, pathogens, parasites, and other threats to our nation’s rivers and streams. Image: Jim Birch © 2018 MBARI

A new cooperative agreement between MBARI and the U.S. Geological Survey (USGS) will develop portable robotic DNA samplers capable of independently monitoring the health of rivers and streams. This partnership will help advance detection of invasive species, pathogens, and parasites that cause ecological and economic damage to aquatic systems. These biological threats can wreak havoc on our waterways, threaten commercial and recreational fishing industries, and promote the spread of zoonotic diseases that can impact humans.

Researchers with the USGS have also launched a new program, building on earlier work, called Rapid eDNA Assessment and Deployment Initiative and Network, or READI-Net, which tests for DNA fragments in the water known as environmental DNA (eDNA). READI-Net will enhance early detection and rapid-response methods to help resource managers contain and control aquatic biological threats.

A large, cylindrical Environmental Sample Processor with its internal components exposed

MBARI’s Environmental Sample Processor (ESP) can help monitor aquatic health. A new portable eDNA sampler will enable nimble deployments of this technology. Image courtesy of Devin Jones, USGS

“Freshwater environments are critical for ecosystem health and provide valuable resources for food and recreation,” said Adam Sepulveda, a USGS scientist and the project lead. “The USGS has successfully used eDNA methods and robotic samplers as an early-detection strategy for biological threats to important aquatic systems.” For example, the USGS has engaged in eDNA survey campaigns for invasive carp, dreissenid mussels, round gobies, and Burmese pythons in water basins across the country.

Robotic samplers can help researchers search for hard-to-find organisms by detecting their DNA in the water. The current MBARI-designed sampler, called the Environmental Sample Processor (ESP), was built to be a sturdy 181-kilogram (400-pound) machine for use in rugged marine environments. Scientists need a more compact and nimble design for easier deployment in freshwater rivers and streams. As part of the new agreement, MBARI and USGS will design a new robotic eDNA sampler. This device will be smaller and lighter, with an easy-to-use computer to facilitate deployments and wireless connectivity so researchers can control sampling remotely.

“MBARI will design the eDNA samplers to be roughly the size of a microwave oven so they are easily carried and will fit into USGS streamgages for possible deployment across the nation,” said Jim Birch, director of the SURF Center at MBARI. “These new eDNA samplers will provide high-quality data for scientists, leading to effective monitoring for aquatic biological threats.”

The eDNA robot will be programmed to take samples frequently, at any time of day, and will collect large amounts of data that must be managed and analyzed. The USGS READI-Net researchers will develop field and laboratory procedures to acquire high-quality data, produce analytical tools to process and validate large volumes of information, and create products for the public and decision-makers, such as resource managers, to easily visualize the results.

Funding for this new partnership comes from President Biden’s Bipartisan Infrastructure Law. The Bipartisan Infrastructure Law is advancing scientific innovation through a $510.7 million investment for the USGS, which is supporting integrated mapping and interpretation of mineral resources data, the preservation of data from geochemical samples from the Earth Mapping Resource Initiative (Earth MRI), and a replacement facility for the USGS energy and minerals research center in Boulder, Colorado, as well as other resources for scientists.

Article adapted from a news release from USGS.

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Kevin Gomes

Information Engineering Group Lead