Environmental DNA reveals the secrets of a California creek and beyond

Dec 26, 2021 at 1:50pm

Brittney Miller

A plop of rain met parched 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. 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.
In a project on Scott Creek north of Davenport, 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 brought 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.
Continue reading the article from The Mercury News here