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A Protocol to Monitor Wild Delta Smelt Using Environmental DNA

A Protocol to Monitor Wild Delta Smelt Using Environmental DNA

Delta Smelt, photo by Peter Johnson, USFWS

Background and Significance of Study

The GVL is using environmental DNA (eDNA) to detect Delta Smelt in the San Francisco Estuary and Delta. Previously, GVL researchers developed a genetic assay that detects Delta Smelt in predator gut contents (Baerwald et al. 2011, Brandl et al. 2015). Now, we are using this assay to detect the presence of Delta Smelt in water using trace amounts of DNA left by fish.

The goal of this project is to develop a tool that can be used to augment existing monitoring of delta smelt. eDNA is a promising new tool in conservation and monitoring. Adequate monitoring of endangered species like delta smelt can be challenging. Not only are the fish hard to find, but trawling may harm populations. eDNA, on the other hand, is a non-invasive monitoring method. In addition, eDNA detects fish of any life stage and in habitats that may be inaccessible to traditional trawling.

The purpose of this project is to assess variables that affect Delta Smelt eDNA detection and put the results in a biological context. Developing and evaluating eDNA for Delta Smelt monitoring includes testing water from cultured smelt tanks, field experiments using cultured Delta Smelt, and field sampling coordinated with the USFWS Enhanced Delta Smelt Monitoring (EDSM) survey. This work helps to determine best practices for eDNA sampling and interpretations of positive (and negative) eDNA detections of Delta Smelt in the San Francisco Estuary. Accurate interpretation of eDNA detections increases the value of eDNA for Delta Smelt management, and likely has value for eDNA sampling of any rare fish in a dynamic estuarine environment.


This project is funded by the CA Department of Water Resources and the CA Department of Fish and Wildlife.


Ann Holmes, Mandi Finger, Andrea Schreier, Tien-Chieh Hung (UC Davis)

Ted Sommer, Brian Schreier, Brian Mahardja, Melinda Baerwald (DWR)

Jeff Rodzen (CDFW)

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