March 14, 2025It’s our mission at River Partners to learn more about the wildlife which call our statewide river-restoration sites home. And over the last couple of years, we’ve added new, innovative science and monitoring techniques to do this that are being deployed in the San Joaquin Valley, which will advance conservation efforts throughout California and beyond.
Last year, for example, during our Before-After Control-Impact studies, the deployment of acoustic recording units captured sounds of birdsongs; point counts documented bird species diversity and abundance at specific moments in time; and motion-activated cameras gave us glimpses of raptors in flight, among other animal action. Now, River Partners is getting another high-tech assist to glean even more data about what lives, or has lived, in areas along San Joaquin Valley rivers that we have either restored or are in the process of revitalizing.
As part of a suite of funding from the California Wildlife Conservation Board (WCB) for floodplain restoration and research in the San Joaquin Valley, River Partners collected hundreds of soil samples this winter to be tested for environmental DNA, or eDNA.
eDNA is a revolutionary research tool and offers a powerful and relatively simple and non-invasive way to understand the biodiversity of ecosystems. The results will provide a snapshot of species present in an area and allow River Partners to detect the presence of species that are rare, endangered, or elusive. Results may also show us the presence of invasive species of vegetation before they become established.
Throughout the month of February, 600 samples were collected at 22 sites and were sent to our project partners eDNA Explorer and CALeDNA, from the University of California, Santa Cruz, for analysis—600 more samples will be collected from the same sites over the summer. Results from this cutting-edge science will provide a richer understanding of the life forms that walk, fly, swim, and grow on our restoration sites.
WCB Executive Director Rebecca Fris said her agency’s mission is protecting biodiversity, creating and restoring habitat for fish and wildlife, and protecting that into the future. The eDNA research and data that come from it align nicely with that mission.
“If the eDNA work is really providing some better understanding of how things are working on the ground, we’re always interested in supporting that,” Fris said. “We also hope to learn from all the research that’s done and share that information broadly as things come out of what River Partners is finding in the work itself.”
Adding eDNA to its lineup of data gathering methods gives River Partners a deeper bench as we continue to fulfill our mission of creating healthy and resilient ecosystems throughout California, benefiting people, the environment, and even California’s world-class economy. And if we can now gather and investigate life’s building blocks in the San Joaquin Valley, River Partners Associate Director of Restoration Science Emma Havstad said that’s just another way to inform our future work.
“Ecosystems are incredibly complex, and in order to get good work done, sometimes we pretend that they’re simpler,” she said. “We shouldn’t let that complexity stop us from doing things that we know are good. But the eDNA is a way of exploring more deeply the complexity of the systems we need to rebuild.”
Data on an “Unprecedented” Scale
DNA sheds naturally from skin, fur, bones, feathers, plant detritus, fungi, and waste. Extracting and analyzing the DNA that’s settled in soil can reveal the presence of hundreds of species, even those that are difficult or impossible to detect through other methods.
At five different locations along a transect (a line) strategically selected for their wildlife activity at each restoration site, our scientists first don a pair of latex gloves before clearing away any vegetation and larger debris. Then, at three different points no more than 12 inches from each other, soil is scooped into a small vial and marked with a corresponding label indicating the restoration site and location.
“A really interesting thing about taking the samples along the transects, you get to see the changes in the soil type,” said River Partners Associate Restoration Scientist Diego Garcia, who collected samples at Dos Rios State Park, the San Luis National Wildlife Refuge, and our Bear Creek Ranch (located about 17 miles west of Merced) restoration sites. “Sometimes the soil has more clay, or maybe one site has more biomass than others. It’s cool to see.”
After releasing any air bubbles lodged in the soil sample with a skinny twig or sturdy grass, the vial is capped and placed in a plastic bag. Our scientists then note on an app where the sample was collected, snapping a few photos to document the location. The samples are then whisked off to CALeDNA in Santa Cruz for analysis. Within a few months, River Partners will receive a report of which species’ DNA were within the 600 soil samples collected.
Clockwise from top left: Restoration Science Ecologist Annie Booth collects samples in Eplin Tract; Restoration Science Ecologist Dr. Sarah Gaffney at San Luis National Wildlife Refuge; Associate Restoration Scientist Claudia Delgado (left) and Associate Director of Restoration Science Emma Havstad at San Luis National Wildlife Refuge; Booth at Arena Plains; Associate Restoration Scientist Diego Garcia at Bear Creek Ranch
Then, in four or five months, we’ll do it all over and collect 600 more, for 1,200 total soil samples.
“We’ll come back to these sites in summer to collect again,” Garcia said, “so we can compare samples from the winter with samples from the summer to see what that tells us about the site and which species are using the site each season.”
One of the things that excites Havstad about the eDNA research is the sheer volume of information we’ll get, calling it “unprecedented.”
“The fact that we can send CALeDNA 600 samples and get thousands of species hits and that we have the capacity to do this blows my mind,” she said, “and that they have sequenced so many species that they’ll be able to tell us what our little soil samples have in them.”
To get an idea of the wealth of species data eDNA can analyze, back in spring 2022, River Partners conducted its first eDNA testing at the 300-acre Grayson Riverbend Preserve along the San Joaquin River in Stanislaus County. After collecting just 67 samples at four different locations at Grayson, the results revealed the presence of 33 distinct vertebrate species and 97 distinct invertebrate species. It also showed evidence of 589 different species of bacteria and archaea and 654 different species of fungi.
All of this data can help inform our future restoration efforts, from the wildlife we expect (and hope) to see to the vegetation we plant to give native plants and trees a better shot of thriving.
Driving Watershed-Scale Restoration
The WCB funding for eDNA research arrived just in time for River Partners as we increase the pace and scale of our restoration impact across the San Joaquin Valley during this critical decade. eDNA is translating research into action, providing actionable insights, and informing future restoration projects with data-driven improvements.
Working with eDNA helps River Partners interpret and understand the myriad complexities of ecosystems we can’t see or collect every day and which we haven’t measured on our projects. Havstad said there’s so much just from the soil community alone that we don’t know or understand—like, for example, the impact of decades of agricultural production on the soil.
“The whole framework of restoration is this idea of putting certain components on the landscape, wildlife is attracted to that, and then it builds,” she said. “But if the things that we’re putting here to start with are missing key components, eDNA is a way for us to learn and take corrective action so that our projects are more successful to help create a more diverse community of species.”
As DNA-extraction technology has advanced, so has its accessibility. Democratizing the data collection is allowing communities far beyond the San Joaquin Valley to participate in ecological research and restoration. And websites like eDNA Explorer and CALeDNA are publicly accessible repositories for eDNA research and findings.
“These kits are being shipped all across the world,” Havstad said. “It opens up the possibility of inviting so many other community members to help us in the work here and around the world to do restoration in other places.”
By adding eDNA to its roster of monitoring methods, River Partners can now become more strategic in what, when, and where our science teams monitor, while providing a wider view of the life that calls the San Joaquin Valley home—or used to.
“There are always more things you could measure, there are always things that would be interesting to know about a restoration site—but, often we have to choose,” Havstad said. “Are we going to survey for birds or are we going to survey for mammals? eDNA is a way of saying, ‘maybe we don’t have to do all this picking and choosing.’ We can have this method to get a more complete picture on an affordable and efficient scale.”
And with the possibility of a flood of information coming our way within the next several months about our restoration methods, the wildlife, and the San Joaquin Valley, success can come in different forms.
“To me, success from a research project is always a concrete outcome of what we are going to try differently in the next restoration that we plan. If this project results in some key findings of soil modifications that we want to do, soil health improvements that we need to do, or a better understanding of what is missing from our restoration sites for least Bell’s vireo or some of the focal species so that we have some concrete ideas of how to improve our restoration, that would be success to me,” Havstad said. “And then, it would be cool if we found something that was rare, that we didn’t know was out there.”
With partnerships like WCB, CALeDNA, eDNA Explorer, and California State Parks and Recreation in place, these kinds of advancements at River Partners are made possible.
“We have lots of partnerships with universities and scientists that are really trying to push that cutting edge and understand how to move forward. All of this relates back to our need to understand and protect the biodiversity knowing how important that is in California especially,” said Fris of the WCB. “The huge suite of questions that is still outstanding is critical to continue to try to learn about—and River Partners is helping to answer those questions.”
Lead photo courtesy of Sarit Laschinsky/CapRadio
