A raindrop hit the parched California soil and spilled into a stream. There he scratched the fish and glided through their gills, stealing traces of every encounter. The droplet then carried the genetic memories downstream until it reached an innovative device that helped unlock the secrets of the creek’s creatures.
“We call it a microbiology lab in a box,” said Jim Birch, director of the SURF center of the Monterey Bay Aquarium Research Institute, based in Moss Landing.
This “box” is actually the environmental sample processor for MBARI, a $ 200,000 robotic lab the size of a 50 gallon barrel. It brings together genetic clues – cells, mucus, feces – from ecosystems collectively called environmental DNA or eDNA.
In a project on Scott Creek north of Davenport, the device produced one of the largest collections of eDNA data at a single site in the country. From April 2019 to April 2020, scientists discovered details of threatened and invasive species in the freshwater ecosystem. Now a scientific paper in preparation, the study reinforces growing interest in detecting and better protecting hard-to-find species using electronic DNA monitoring instead of more invasive techniques such as counting fish.
“It has this ability to do this without having to put a lot of nets in the water,” said Kevan Yamahara of MBARI, a device specialist and one of the authors of the article.
Global interest in the ability of eDNA to detect rare organisms has grown over the past decades. The new technology rediscovered a rare aquatic insect population in the UK. This detected more mammals than traditional camera traps in the Canadian wilderness. This helped to follow the spread of the coronavirus.
At Scott Creek, MBARI’s device pumped water from the creek and pushed it through a filter several times a day. Once the filter had collected enough material, the machine applied a preservative. According to Yamahara, each filter was then stored in a carousel similar to the chamber loaded with bullets from a pistol. Once the carousel is full of 132 samples, the researchers collected the data and brought to their lab in Moss Landing.
Focus on salmon
Almost 700 samples emerged from monitoring throughout the year. Researchers focused on endangered coho salmon and endangered populations of the stream’s rainbow trout, two commercially important fish. Since Scott Creek is one of the southernmost points where coho salmon come to lay their eggs, it’s crucial to know how the species is doing, said Birch, who is also an author of the soon-to-submit 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 the weir, a perforated “flow dam”, has allowed NOAA personnel to count, inspect and release fish on a seasonal basis for two decades.
Fish counts continued throughout the project and made it possible to compare traditional and emerging monitoring techniques. From the samples, the team concluded that the amount of DNA from rainbow trout generally exceeded that of coho salmon. This completed the observed figures in NOAA fish traps, according to Ryan Searcy, a Stanford environmental engineering doctoral student and lead author of the research paper.
The collected eDNA also provided seasonal data that reflected the presumed life histories of the species through winter rains, summer droughts, and most days in between. The information revealed the best times to perform eDNA sampling for certain species, Yamahara said.
The highest concentrations of coho salmon eDNA, for example, occurred during the winter when the fish were thought to be migrating and laying eggs. In the fall, when the stream’s flow decreased, the amount of salmon eDNA also decreased. The results gave researchers confidence in the data and suggested that the new monitoring methods might be well suited to documenting the behaviors of migrating fish, Searcy said.
The data revealed other secrets of the creek: The team found that less than 1% of eDNA came from invasive species. That low number gives hope that species like the New Zealand snail and striped bass are not yet present in the creek, Searcy said. Such monitoring could offer scientists warning signs of invasive species before they even see them, Yamahara said.
“You don’t have to physically go looking for these specimens,” Yamahara said. “You can just take a water sample and process it. “
MBARI’s environmental sample processor toured the world when it was unveiled in the late 2000s, Birch said. The Scott Creek version of the device has since evolved into a new model the size of two basketballs.
Researchers have included the improved technology in autonomous underwater vehicles now used to explore marine habitats like those in Monterey Bay, Birch said. They are also used in the Great Lakes to track harmful algal blooms, Yamahara said.
As eDNA monitoring evolves from stationary machinery to efforts to move through ecosystems, Yamahara hopes the technology will advance even further for use in freshwater habitats like Scott Creek. But while the device could revolutionize the monitoring of ecosystems, the prototype has limits.
The large amount of genetic information provided by new devices, for example, can overwhelm labs, Birch said. To solve this problem, he would like future versions of the technology to do this analysis on site.
“It really is the holy grail – the brass ring – that we are trying to promote here at MBARI… to go beyond just sampling and also do the processing on board,” he said.
Monitoring the old, the new
There were also discrepancies between the old and the new monitoring strategies. The team detected eDNA from fish more frequently than fish were counted in NOAA fish traps. This is unexpected but not unknown in the field, according to Searcy, especially since the detected eDNA could belong to fish upstream of the sampling site.
Since each technique reveals different details about the species, they should be seen as complementary at this point, according to the researchers. This combination is valuable and rare in the Greater Bay Area, said Brian Allee, senior fisheries biologist with the South Bay Clean Creeks Coalition, who was not involved in the study.
While the device’s price may limit its use, Allee would like to see its eDNA surveillance applied to local urban flows to further investigate endangered species.
“What we really want are wild populations that reproduce on their own in a sustainable way,” he said. “It’s been a difficult process – a process where technology is important because we can’t go back to the Lewis and Clark era. “