Environmental DNA reveals secrets of the creek and beyond

By Brittney J. Miller, Monterey Herald

A plop of rain met California ground and trickled into a creek. There it scraped against fish and slipped through their gills, stealing traces of each encounter. The droplet then carried the genetic souvenirs downstream until it reached an innovative device that helped unlock the secrets of the creek’s creatures.

“We call this a microbiology lab in a can,” said Jim Birch, director of the SURF center at the Moss Landing-based Monterey Bay Aquarium Research Institute, or MBARI.

That “can” is actually MBARI’s environmental sample processor, a $200,000 robotic laboratory the size of a 50-gallon drum. It gathers genetic clues — cells, mucus, feces — from ecosystems that are collectively dubbed environmental DNA, or eDNA.

MBARI staff installs an environmental sample processor to collect water from Scott Creek for later genomic analysis to detect coho salmon, steelhead trout and invasive species. (Kim Fulton-Bennett/ MBARI) 

In a project on Scott Creek north of Davenport in Santa Cruz County, the device produced one of the nation’s largest single-site eDNA data collections. From April 2019 to April 2020, scientists uncovered details about endangered and invasive species in the freshwater ecosystem. Now a scientific paper in the works, the study reinforces the growing interest in detecting and better protecting hard-to-find species using eDNA monitoring instead of more invasive techniques such as fish counts.

“It has that ability to do that without having to put a lot of nets in the water,” said MBARI’s Kevan Yamahara, a specialist on the device and one of the paper’s authors.

Worldwide interest in eDNA’s ability to detect rare organisms has expanded over the past few decades. The new technology rediscovered a rare aquatic insect population in the United Kingdom. It detected more mammals than traditional camera traps in the Canadian wilderness. It helped track the spread of the coronavirus.

In Scott Creek, MBARI’s device pumped water from the creek’s flow and pushed it through a filter several times a day. Once the filter collected enough materials, the machine applied a preservative. According to Yamahara, each filter was then shelved in a carousel similar to the bullet-loaded chamber of a gun. Once the carousel filled with 132 samples, researchers collected the data and took it to their Moss Landing lab.

Nearly 700 samples emerged from the yearlong monitoring. Researchers focused on the creek’s endangered coho salmon and threatened steelhead trout populations, both commercially important fish. Since Scott Creek is one of the southernmost points where coho salmon come to lay eggs, it’s crucial to know how the species is faring, said Birch, who is also an author of the soon-to-be-submitted research manuscript.

In the creek, the device sat next to a more established monitoring tool: a weir operated by the National Oceanic and Atmospheric Administration. Birch said that the weir, a perforated “flow-through dam,” has allowed NOAA staff to tally, inspect and release fish on a seasonal basis for two decades.

The fish counts continued throughout the project and allowed for comparisons of traditional and emerging monitoring techniques. From the samples, the team gleaned that the amount of steelhead trout DNA usually surpassed that of coho salmon. This complemented the numbers observed in the NOAA fish traps, according to Ryan Searcy, an environmental engineering doctoral student at Stanford and the research paper’s lead author.

The collected eDNA also provided seasonal data that mirrored the suspected life histories of species through winter rains, summer dry spells and most days in between. The information unveiled the best times to conduct eDNA sampling for certain species, Yamahara said.

The highest concentrations of coho salmon eDNA, for example, appeared during the winter when the fish were thought to be migrating and laying eggs. During the fall, when the creek’s flow diminished, so did the amount of salmon eDNA. The findings gave researchers confidence in the data and suggested that the new monitoring methods could be well-suited for documenting the behaviors of migratory fish, Searcy said.

Alex Hay, a researcher with the NOAA Southwest Fisheries Science Center, left, and Kevan Yamahara, an ESP specialist at MBARI, observe a rainbow trout retrieved from the downstream weir at Scott Creek. (Todd Walsh/MBARI) 

The data revealed other secrets of the creek: The team found that less than 1% of the eDNA came from invasive species. That low number offers hope that species like the New Zealand mudsnail and striped bass are not yet present in the creek, Searcy said. Such monitoring could offer scientists early warning signs for invasive species before ever observing them, Yamahara said.

“You don’t have to actually physically go and physically look for those specimens,” Yamahara said. “You can just take a water sample and process it.”

MBARI’s environmental sample processor traveled around the world when it was unveiled in the late 2000s, Birch said. The version of the Scott Creek device has since transformed into a new model the size of two basketballs.

Researchers included the upgraded tech in underwater autonomous vehicles now used to explore marine habitats like those in Monterey Bay, Birch said. They’re also used in the Great Lakes to track harmful algae blooms, Yamahara said.

As eDNA monitoring evolves from stationary machinery to traveling endeavors across ecosystems, Yamahara hopes that the technology will progress even more for use in freshwater habitats like Scott Creek. But while the device could revolutionize ecosystem monitoring, the prototype has limitations.

Research specialist Kevan Yamahara, left, and mechanical engineer Doug Pargett secure the hoses that will carry water samples from the fish trap to the ESP. (Kim Fulton-Bennett/MBARI) 

The sheer amount of genetic information the new devices provide, for instance, can overwhelm labs, Birch said. To fix this problem, he’d like to see future versions of the tech do that analysis on-site.

“That’s really the Holy Grail — the brass ring — that we are trying to push for here at MBARI … to go beyond the simple sampling and do the processing onboard as well,” he said.

There were also discrepancies between old and new monitoring strategies. The team detected fish eDNA more frequently than the fish were counted in NOAA’s fish traps. That’s unexpected but not unheard of in the field, according to Searcy, especially since detected eDNA could belong to fish upstream of the sampling site.

Since each technique reveals different details about species, they should be seen as complementary at this point, the researchers say. That combination is valuable and rare in the greater Bay Area, said Brian Allee, the lead fisheries biologist at the South Bay Clean Creeks Coalition who was not involved in the study.

While the device’s $200,000 price tag can limit its use, Allee would like to see its eDNA monitoring applied to local urban streams to further investigate endangered species.

“What we really want are wild populations spawning on their own on a sustainable basis,” he said. “That has been a difficult process — one in which technology is important since we can’t turn the clock back to the Lewis and Clark era.”

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