Citation:

Waits, E., L. Smith, AND D. Linz. California aquatic environmental DNA (eDNA). U.S. Environmental Protection Agency, Washington, DC, 2025. https://doi.org/10.23719/1532153

Impact/Purpose:

Living organisms constantly shed DNA into the environment. Conservation and management of imperiled freshwater species requires the identification and enumeration of extant populations; however, monitoring efforts often overlook or underestimate species occupancy due to cryptic life history, low abundances, and habitat fragmentation. Environmental DNA (eDNA) offers a non-invasive approach to detect freshwater species sight-unseen. Environmental DNA monitoring also allows assessment on a spatial scale that would not be feasible for traditional biomonitoring alone. In scenarios of limited conservation resources, eDNA surveillance can augment traditional biomonitoring surveys and guide more localized traditional sampling events.

Description:

We evaluated the utility of environmental DNA (eDNA) methodology to detect the critically-endangered delta smelt and other species of concern in the Yolo Bypass and in Vernal pools located in the Central Valley. These areas are critical habitat for many aquatic species in the Sacramento River watershed, CA. Water samples for eDNA analysis were collected over a 12-month period in coordination with the California Interagency Ecological Program (IEP), which has a long-term monitoring program to collect baseline data on juvenile and adult fish and water quality data in the Yolo Bypass. eDNA samples were interrogated using piscine metabarcoding assays, as well as species-specific TaqMan assays targeting delta smelt, Chinook salmon, Sacramento pikeminnow, Sacramento splittail, longfin smelt, giant garner snake, California tiger salamander, and vernal pool brachiopod species.  Results from eDNA surveillance were compared to survey data from traditional monitoring events across the water year. eDNA methods successfully detected focal species when visually observed and, in some cases, when not. For example, traditional survey methods (rotary screw traps, fyke nets, beach seine, etc.) in the Yolo Bypass detected only a single delta smelt across 156 sampling events during the 12 months. Alternatively, positive delta smelt eDNA detections were observed on three occasions across 15 sampling events during the water year, including on the day of the visual observation. We propose eDNA is a valuable tool that can be used to augment traditional monitoring programs and enable higher spatial and temporal resolution, especially for species difficult to detect due to limited abundances.

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