Fishing for genes via eDNA

Just as steelhead trout migrate from saltwater to freshwater and back, Environmental Sample Processors (ESPs)—first developed by the Monterey Bay Aquarium Research Institute (MBARI) for studies in the ocean—have been getting a lot of use in freshwater over the last five years.

Kevan Yamahara and Doug Pargett install a pump system downstream of a fish trap in Scott Creek. The pump system feeds water to an Environmental Sample Processor to sample the DNA of fish in the stream. Photo © 2019 MBARI/Kim Fulton-Bennett

This spring, MBARI’s ESP team installed an instrument to collect samples of “environmental DNA” from a coastal creek just north of Monterey Bay. Researchers will use these samples to track populations of threatened steelhead trout, endangered coho salmon, and invasive species in the creek.

In the process, they could help revolutionize environmental monitoring and fisheries management nationwide.

The research is a joint project of MBARI and the Monterey Bay Aquarium, with funding from the Arthur Vining Davis Foundations as part of their newly launched Environmental Engagement, Stewardship & Solutions program. The work is being carried out in collaboration with the National Oceanic and Atmospheric Administration (NOAA). It is part of MBARI’s continuing effort to provide scientific data with direct application for ocean and wildlife conservation.

Automated sampling around the clock

Environmental DNA (eDNA) is similar to the forensics used in criminal court cases. But instead of trying to find DNA in bits of hair or saliva at a crime scene, eDNA researchers can simply collect samples of water. These water samples will contain tiny particles of skin, mucus, waste, or other organic matter from the animals that live in the water. Researchers filter the water to concentrate these particles, extract the DNA, and then sequence it. By doing so, they can identify what kinds of animals live in the water and, in some cases, how abundant their populations are.

The research team installs the Environmental Sample Processor (ESP) at Scott Creek in northern Santa Cruz County. Photo © 2019 MBARI/Kim Fulton-Bennett

It’s possible to collect water samples for eDNA analysis just by dipping a sterile container into a body of water. But MBARI’s ESP collects and processes water samples automatically, as frequently as once an hour. This allows researchers to study how fish populations in a stretch of river change at different times of day—or over periods as long as months.

Collecting samples frequently and repeatedly is important for eDNA work because DNA degrades over time. If a fish passes through a stretch of river, its residual DNA might only be detectable for a few days afterward. Figuring out how long DNA persists in the water is one of the research goals of the current project. Another is to compare the results of eDNA analyses with the observations of trained wildlife biologists who count fish in California streams.

Years of preparation and testing

The ESP can also collect information about the temperature and chemistry of stream water, which can be correlated with the results of the eDNA analyses.

The proof-of-concept for the effectiveness of eDNA sampling in ocean water was confirmed in tests at the Monterey Bay Aquarium’s Open Sea exhibit.

Kevan Yamahara, an MBARI research specialist, has been working on eDNA for almost five years. Several years ago, he helped assess the effectiveness of eDNA by testing water from the Open Sea Exhibit at the Monterey Bay Aquarium, where aquarists already knew precisely what fish were present. That landmark study was instrumental in showing that eDNA analyses of ocean water could potentially be used for resource management in the wild. That led to MBARI’s use of the technology in NOAA’s five-year, $7 million Marine Biodiversity Observation Networks (MBON) program.

Yamahara performed a pilot study of the eDNA of steelhead trout in the Carmel River, near Monterey. He will be conducting additional eDNA research in the Carmel River as part of the current grant from the Arthur Vining Davis Foundations.

The most recent ESP deployment was in Scott Creek, a small coastal stream the flows into the ocean in northern Santa Cruz County. Scott Creek is a particularly interesting location from a conservation perspective. Not only does it support an active run of steelhead trout, it is also the southernmost body of water in California to support coho salmon (though in very small numbers). It is at risk of being colonized by two invasive species: striped bass and New Zealand mud snails.

– Kim Fulton-Bennett

Learn more about the work of the Monterey Bay Aquarium Research Institute.

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