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Environmental DNA reveals secrets of the creek and beyond – Monterey Herald

Environmental DNA reveals secrets of the creek and beyond – Monterey Herald

Environmental DNA reveals secrets of the creek and beyond – Monterey Herald

A drop of rain met the California desert ground and trickled into the creek. It scraped against fish and slipped under their gills, taking traces from each encounter. The droplet carried the genetic memories downstream until it reached an ingenious device that unlocks the secrets of creek creatures.

Jim Birch, director at the SURF Center at the Moss Landing-based Monterey Bay Aquarium Research Institute, described it as a microbiology laboratory in a can.

This can is actually a MBARIs environmental sample processor, a $200,000 robotic lab the size of a 50-gallon drum. It collects genetic clues from cells, mucus, and feces of ecosystems that are collectively known as environmental DNA, or EDNA.

Alex Hay, a researcher at the NOAA Southwest Fisheries Science Center (left), observing a rainbow trout retrieved at Scott Creek’s downstream weir (right). (Photo by Todd Walsh. 2019 MBARI.

The largest single-site eDNA data collection in the country was created by a Scott Creek project north of Davenport. Scientists discovered details about threatened and invasive species in the freshwater ecosystem from April 2019 to April 2020. The study, now a scientific paper, reinforces the growing interest and protection of hard-to find species using eDNA monitoring rather than more invasive techniques like fish count.

It can do that without needing to put a lot more nets in the water, according to Kevan Yamahara, a specialist and one of the paper authors.

The ability of eDNAs to detect rare organisms has been gaining worldwide attention over the past several decades. The technology has helped to rediscovered a small but important population of aquatic insects in the United Kingdom. It detected more mammals than traditional camera traps found in the Canadian wilderness. It was able to track the spread of coronavirus.

Kevan Yamahara (Research Specialist) and Doug Pargett (Mechanical Engineer) secure the hoses to transport water samples from a fish trap to the ESP. (Photo by Kim Fulton Bennett, 2019 MBARI).

MBARIs used a pump to draw water from Scott Creek and then pushed it through a filter multiple times per day. Once the filter had collected enough materials, the machine applied preservative. Yamahara said that each filter was placed in a carousel, similar to a gun’s bullet-loaded chamber. Researchers collected the data from the carousel that contained 132 samples and brought it to Moss Landing.

Nearly 700 samples were collected during the yearlong monitoring. Researchers focused on the endangered coho salmon and threatened steelhead trout population of the creeks, which are both economically important fish. Birch, who is also the author the soon-to be-submitted research manuscript, said Scott Creek is the most southern point where coho salmon lay eggs.

The device was located in the creek next to a more reliable monitoring tool, a National Oceanic and Atmospheric Administration weir. Birch explained that the weir is a perforated, flow-through dam that has allowed NOAA staff to count, inspect and release fish on an annual basis for 20 years.

MBARI staff install an environment sample processor to collect water in Scotts Creek (northern Santa Cruz County). This will be used for genomic analysis to identify invasive species and coho salmon. (Photo by Kim Fulton Bennett, 2019 MBARI).

The fish counts were kept going throughout the project, allowing for comparisons between traditional and new monitoring techniques. The team learned that the amount and quality of the steelhead trout’s DNA was higher than that of the coho salmon. Ryan Searcy, a Stanford environmental engineering doctoral student and the lead author of the research papers, said that this was in addition to the NOAA fish traps numbers.

The eDNA collected provided seasonal data that mirrored species’ life histories through winter rains, summer dry spells, or any other day in between. Yamahara explained that this information revealed the best times to sample eDNA for certain species.

For example, the winter was when coho salmon DNA eDNA was at its highest concentration. This is because the fish were believed to be migrating or laying eggs. The amount of salmon DNA decreased as the creeks flowed less in the fall. Searcy stated that the findings gave confidence to the researchers and suggested that new monitoring methods could be suited for documenting the behavior of migratory fish.

Other secrets were revealed by the data. The team discovered that less then 1% of the eDNA originated from invasive species. Searcy stated that the low number suggests that species like the New Zealand Mudsnail and the striped bass are not yet in the creek. Yamahara said that such monitoring could provide scientists with early warning signs about invasive species before they are actually observed.

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

Birch stated that the MBARI’s environmental sample processor was a hit all over the world after its unveiling in the late 2000s. The Scott Creek device was redesigned to be the same size as two basketballs.

Birch explained that the technology was used by researchers to create autonomous underwater vehicles for exploring marine habitats, such as those at Monterey Bay. Yamahara also said they are used in the Great Lakes for monitoring harmful algal blooms.

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Yamahara hopes that eDNA monitoring will move from stationary machinery to mobile devices across ecosystems. Yamahara also hopes that the technology will be more useful in freshwater habitats such as Scott Creek. Although the prototype could revolutionize ecosystem monitoring it has some limitations.

Birch said that the sheer amount of genetic data these new devices provide can overwhelm labs. Birch said he would like to see future tech perform this analysis on-site in order to fix this problem.

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 differences between the old and new monitoring strategies. The team detected fish DNA more often than the NOAAs fish traps. Searcy said that this is not common, but not unusual in the field. This is especially true since eDNA may be from fish downstream of the sampling site.

Researchers say that each technique provides different information about species, so they should be considered complementary. This combination is rare in the Bay Area, according Brian Allee (lead fisheries biologist, South Bay Clean Creeks Coalition), who was not involved with the study.

Although the device’s price tag may limit its use, Allee would love to see its eDNA monitoring applied in local urban streams to further investigate endangered animals.

He said that what we really want is wild populations that spawn on their own on an ongoing basis. It has been a difficult process. Technology is essential because we can’t go back to the Lewis and Clark era.

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