Pilot study incorporates eDNA identification methods into routine stream monitoring

SCCWRP and its partners have shown in a proof-of-concept study that regional stream monitoring programs can be used to track endangered and invasive aquatic species using the environmental DNA – or eDNA – they have shed into their environment.

The three-year pilot study, completed in March, involved incorporating molecular sampling and analysis methods into routine stream monitoring programs in the San Diego region. Researchers successfully identified multiple species that passed through the water column, including the Arroyo toad, stickleback, steelhead and pond turtle – all endangered – and the swamp red crayfish, an invasive species from the southeastern U.S.

Incorporating eDNA methods into routine stream monitoring programs has the potential to provide additional lines of evidence about ecological health, helping stream managers paint a more comprehensive picture of overall condition.

Having information about specific target species also could inform management efforts to better protect specific endangered and vulnerable organisms – and to better control the spread of invasive organisms.

These organisms traditionally have been impractical and/or costly to monitor in aquatic environments because of their motility and often disparate distribution. Consequently, most stream monitoring programs in California are built around tracking more ubiquitous species that can be readily sampled in the field, including insects and algae.

During the SCCWRP-led study, researchers developed a series of custom genetic probes to identify target organisms; a DNA quantification method known as ddPCR (droplet digital polymerase chain reaction) was used to quantify DNA levels for target species. ddPCR already is routinely used to identify bacterial indicators of fecal contamination in aquatic environments.

The application of molecular methods to identify eDNA, however, remains in its infancy. eDNA methods are largely confined to the individual research labs that developed the methods. Not only do different labs use different methods – and different variations of methods – to identify the same target organisms, but there also is not yet agreement among labs about how to standardize eDNA methods to ensure results are comparable.

SCCWRP, which holds a leadership role on the California Water Quality Monitoring Council’s Molecular Methods Workgroup, is working to standardize eDNA methods so they can be incorporated into routine stream monitoring programs statewide.

SCCWRP and its partners also are working to better define how to interpret the strength of eDNA signals. Signal strength in a water sample is influenced by a number of environmental factors, including organism shedding rates, water velocity, temperature, and grazing activity. Furthermore, the ability to detect eDNA from known upstream sources can be highly variable, according to the initial findings of ongoing SCCWRP investigations.

A final study report is expected to be published this summer.

For more information, contact Dr. Susanna Theroux.