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Environmental DNA reveals secrets of creek, beyond – Santa Cruz Sentinel
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Environmental DNA reveals secrets of creek, beyond – Santa Cruz Sentinel

Environmental DNA reveals secrets of creek, beyond – Santa Cruz Sentinel

A drop of rain met dry California ground, and it trickled into a stream. It scraped against fish, then slipped through their veins, stealing 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 described it as a microbiology lab in an can. Director of the SURF Center at the Moss Landing-based Monterey Bay Aquarium Research Institute.

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.

Scott Creek projectThe north of Davenport, theOne of the largest single-site eDNA data collection in the country was created by device. From April 2019 through April 2020, scientists discovered details about endangered species and invasive species in the freshwater ecosystem. The study is now a scientific paper. It reinforces the growing interest and protection of hard-to-find species by using eDNA monitoring, instead of more invasive techniques like fish counts.

It is able to do this without needing to put many nets in water, according MBARIs Kevan Yamahara who is a specialist on the device, and one the papers authors.

Over the past decade, eDNAs ability detect rare organisms has attracted a lot of attention around the world. The new technology RediscoveredIt is a rare species of aquatic insect in the United Kingdom. It is extremely rare. Detected In the Canadian wilderness, there are more mammals than traditional cameras traps. It TrackedThe spread of the coronavirus.

Alex Hay, a researcher for the NOAA Southwest Fisheries Science Center (MBARI), holds a rainbow-colored trout retrieved by Scott Creek. (Todd Walsh/MBARI)

MBARIs device was used to pump water from Scott Creek’s stream and push it through a filter several time per day. Once the filter had collected enough materials, the machine applied preservative. Yamahara explained that each filter was then placed in a carousel that resembled a gun’s bullet-loaded chamber. Once the carousel was filled with, each filter was placed in a carousel. 132The data was collected from samples and then the researchers brought it to Moss Landing..

Salmon is the focus

Nearly 700 samples were collected over the course of the yearlong monitoring. Researchers focused on the endangered coho salmon and threatened populations of steelhead trout, which are both commercially important fish. Scott Creek is one the most important rivers in the area.Southernmost pointsBirch, who is also the author of the report, said that coho salmon are known to lay eggs in areas where they are found. soon-to-be-submitted Research manuscript.

The device was situated in the creek alongside a more established monitoring instrument: a National Oceanic and Atmospheric Administration (NOAA) weir. Birch stated that the weir, which is a perforated flow through dam, has allowed NOAA staff for over two decades to count, inspect, and release fish on a seasonal schedule.

The fish counts were maintained throughout the project. This allowed for comparisons of emerging and traditional monitoring techniques. The team discovered that the amount of steelhead trout genetic material was often higher than that of coho salmon. This confirmed the numbers. Ryan Searcy, an environmental engineering doctoral candidate at Stanford and the lead author of the research papers, stated that the NOAA fish traps were used.

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

The winter is when coho salmon eggs eDNA were at their highest concentrations. The amount of salmon eDNA decreased in fall when the creeks were less flowing. 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.

Results from data

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

MBARI staff installs an environment sample processor to collect water at Scott Creek for genomic analysis. This will allow them to identify invasive species, steelhead trout, and coho salmon. (Kim Fulton-Bennett/ MBARI)

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 globe after its unveiling in the late 2000s. Since then, the Scott Creek device is now a model the size of two basketballs.

Birch stated that researchers included the upgraded technology in underwater autonomous vehicles, which are now used to explore marine habitats such as those in Monterey Bay. Yamahara also said they are used in the Great Lakes for monitoring harmful algae blooms.

Yamahara hopes that eDNA monitoring will become more mobile and adaptable to different ecosystems as it evolves. The prototype is not perfect, but it could revolutionize ecosystem monitoring.

Birch said that the new devices can provide so much genetic information that it 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.

Monitoring old, new

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.

Kevan Yamahara, a researcher, and Doug Pargett, a mechanical engineer, secure the hoses to transport water samples from ESP to fish trap. (Kim Fulton-Bennett/MBARI)

Researchers say that each technique provides different details about species and should therefore be considered complementary. This combination is rare and valuable in the greater Bay Area, according to Brian Allee, a lead fisheries biologist at South Bay Clean Creeks Coalition, who was not part of the study.

Although the price tag of the device can limit its usage, Allee would like to see its eDNA Monitoring applied to local urban streams in order to further investigate endangered species.

He stated that wild populations should be able to spawn on their terms on a sustainable basis. This has been a difficult process, but technology is crucial as we cannot go back to the Lewis and Clark era.

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