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Environmental DNA reveals the secrets of the creek and beyond

Environmental DNA reveals the secrets of the creek and beyond

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

A plop, a drop of rain, met the California desert ground and trickled into the creek. It brushed against fish, and then slipped through their gills to steal traces of 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 of the SURF centre at the Moss Landing-based Monterey Bay Aquarium Research Institute) said, “This is a microbiology lab inside 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 cells, mucus and feces from ecosystems. These are collectively called environmental DNA, or just 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. 

One of the largest single-site eDNA collections in the nation was produced by the device at Scott Creek, north of Davenport. From April 2019 through April 2020, scientists discovered details about endangered and invasive species within the freshwater ecosystem. The study is now a scientific paper. It reinforces the growing interest to detect and better protect hard-to-find species by using eDNA monitoring, instead of more invasive techniques like fish counts.

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.

Over the past decade, eDNAs ability detect rare organisms has attracted a lot of attention around the world. The technology has helped to rediscovered a small but important population of aquatic insects in the United Kingdom. It detected more mammals in Canada than traditional camera traps. It was instrumental in tracking the spread of the 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 took the data from the carousel containing 132 samples and returned it to Moss Landing.

Nearly 700 samples were collected over the course of the yearlong monitoring. The creek’s threatened coho salmon and steelhead trout populations were the focus of the yearlong monitoring. These are both commercially important fish. Birch, who is also the author the soon-to be-submitted research manuscript, said Scott Creek is one the most southern points 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 installed an environmental sample processor to take water from Scotts Creek in northern Santa Cruz County. This water will then be used for later genomic analysis to determine if there are any invasive species or 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 discovered that the amount of steelhead trout genetic material was often higher than that of 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 reflected the possible life histories of species through winter rains, dry spells in summer and all days 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 DNA decreased as the creeks flowed less in the fall. Searcy stated that the results gave confidence to researchers and suggested new monitoring methods might be well-suited for documenting migratory fish behavior.

Other secrets of the creek were also revealed by the data. The team discovered that less then 1% of the eDNA was derived 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 stated that such monitoring could give scientists early warning signs of invasive species, allowing them to be detected before they are observed.

Yamahara stated that you don’t have to physically search for the specimens. You can simply take a water sample, and then process it.

Birch stated that the environmental sample processor for MBARIs traveled the globe when it was first revealed in the late 2000s. Since then, the Scott Creek device has been redesigned into a model that is 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 stated that they are also used in the Great Lakes to monitor harmful algal blooms.

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Yamahara hopes that eDNA monitors will become more mobile and can be used in freshwater habitats like Scott Creek. The prototype is not perfect, but it could revolutionize ecosystem monitoring.

Birch stated that labs can be overwhelmed by the sheer amount of genetic data provided by these new devices. Birch would like to see future versions that can do this type of analysis on-site.

He stated that that is the Holy Grail, the brass ring. MBARI is trying to push for this ring to be used onboard to process the samples.

There were also differences in the results of old and new monitoring techniques. The team detected fish eDNA much more often than fish caught in 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 and they should 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.

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