River Partners announces results of eDNA research, collections across the San Joaquin Valley

The San Joaquin Valley has plenty to discover, much of which is hidden in the dirt.

Last year, scientists from the nonprofit River Partners fanned out across the region, collecting samples at multiple locations to learn more about the different species that live there —- using a research tool called environmental DNA (eDNA.)

One of the collections took place at Dos Rios State Park near Modesto, with researchers digging across numerous tracts to fill small test tubes with soil and mud.

Last month, River Partners announced it has received the data from these collections, and the results will help guide the future of restoration and conservation work in the region.

Dr. Sarah Gaffney is a Senior Scientist with River Partners, and Julie Stanford is the CEO of eDNA Explorer. They spoke with Insight Host Vicki Gonzalez about the process of identifying thousands of species in one small sample.

This interview has been edited for length and clarity.

Interview highlights

Julie, as the CEO of eDNA Explorer, what exactly is environmental DNA?

STANFORD: eDNA is basically the dead cells, skin or all the eDNA particles that slough off any living thing. All of us, right now, have a cloud of it around us. In fact, if you had a COVID PCR test where you sent your samples to a lab, that was actually an eDNA test looking for COVID in your mucus.

How long has the study of eDNA been around, and been used in biology and conservation?

STANFORD: It’s been around for a really long time. About 30 years ago a gentleman named Andrew Ogram discovered that you could sequence this genetic material that can be found in water, sediment, and soil. At first, he used it to study microbes. Then maybe 14 years ago the field opened up to really use that genetic material to get a bird's-eye view on all organisms in a sample. Animals, insects, plants, fungi, microbes, all of that became possible.

I'd say in the last like 10 years, it's really started to leave academia and turn into a more mainstream resource for understanding what's happening in an ecosystem.

How long has River Partners been using eDNA? Is it exciting to use this tool to better understand the areas you’re working in?

GAFFNEY: Our big project last year was our first time. It was super exciting. We are always looking for more tools in the toolbox to assess restoration outcomes, and eDNA was a great opportunity. 

How does it complement those other tools that you have?

GAFFNEY: Normally we go out and assess our vegetation by percent cover, learning what species are there. We do point counts for bird data collection, or stick out wildlife cameras. But we can't always see all of the animals — maybe we didn't put a camera in the right place — and there’s just so much acreage to our sites that we might not catch every single plant.

River Partners Restoration Scientist Diego Garcia surveys a collection site at Dos Rios State Park near Modesto, Feb. 28, 2025.Sarit Laschinsky/CapRadio

But most importantly, the eDNA is really helping us understand the soil microbiome at all of our sites — what’s going on with the bacteria and the fungi.

You recently got the eDNA results back. What did they include?

GAFFNEY: So many different things. We found some invasive plant species that we didn't know were in the area — we want to go out and actually try to see if we can see those on the ground, do some early detection and rapid response. We found some really cool animals like the California tiger salamander, the western spadefoot [toad.] These are species of special concern. We saw a badger in some of our Kern sites. Badgers are very elusive and come out at night, so it's hard to find them on a camera sometimes. 

The Insight team joined River Partners for one collection last year at Dos Rios State Park. But how many sites did you take samples from? 

GAFFNEY: We sampled around 20 sites — 10 planning sites that we're going to implement restoration on, and then 10 other reference sites. We have a few sites in the Kern Valley. We have Panorama Vista Preserve, which we restored over the last 10 years, serving as a reference site for more work that we want to do along the Kern River in Bakersfield. We have agricultural sites near Merced in the San Luis National Wildlife Refuge, and then a bunch of sites up near Modesto.

River Partners Restoration Scientist Diego Garcia scoops a soil sample for eDNA testing at Dos Rios State Park near Modesto, Feb. 28, 2025.Sarit Laschinsky/CapRadio

How does the team decide where to take their samples? What makes a good site? 

GAFFNEY: This was part of a much larger monitoring effort. We had a large grant from the state to plan 6,000 acres of restoration. This is part of a larger baseline survey of what is going on at all of our sites before implementation, so then later we can collect data post-implementation and really attribute any improvements to our restoration.

Sampling was done in the winter and summer. What’s the purpose of collecting them across different seasons? 

STANFORD: That was one of our questions: does it make sense to sample both seasons? And we really found there were different communities in terms of understanding [when] larger animals, or small mice, were out and about at different times. But then, if you looked under the surface at the soil, we also saw differences in those communities.

To get a really rich view of what's really going on, we thought it actually does make sense to sample at both times. And it makes sense —  when you look around, winter looks really different than summer just to the naked eye. Then we can start answering questions. Why is it that this site might have a richer plant community than this other site? Why are some threatened species more attracted to this area? Is it seasonal or is there actually something else going on?

Can you also use eDNA to kind of learn about what used to live there? 

STANFORD: Yeah! It's really interesting with soil. The DNA lasts anywhere from days to weeks, or if you dig down into the core — people studying ancient eDNA can actually look back in time thousands of years and see what might have been there. eDNA is basically sugar, and so things are eating it all the time, but just enough can be saved — especially if soil is really dry — to get that backwards view.