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Environmental DNA Metabarcoding in the San Francisco Estuary

Multi-year, multi-institution collaborative project funded by CA Department of Fish and Wildlife and CA Proposition 1

Environmental DNA Metabarcoding in the San Francisco Estuary

Project Summary

Environmental DNA (eDNA) refers to DNA originating from skin/scales, mucus, gametes, or feces that can be isolated from water and used to detect target species or reconstruct whole communities (metabarcoding) (Figure 1). In this project we are developing an eDNA metabarcoding protocol to complement existing monitoring surveys. We are creating a custom reference DNA sequence database for native and invasive fish, mussels, and macroinvertebrates present in the San Francisco Estuary (SFE). We will optimize a molecular and computational pipeline for eDNA metabarcoding and groundtruth the method against three SFE monitoring efforts, each using different sampling gear. We will investigate the relationship between eDNA sequence read count and biomass or abundance. Finally, we will determine the ability of metabarcoding to detect fish and macroinvertebrate assemblages across large and small spatial scales and over time. Our overarching goal is to develop a non-invasive, low cost monitoring tool that can be used in conjunction with existing monitoring programs or used alone to assess biological community composition at locations of interest in the SFE.

Project Significance

This project will allow more accurate and comprehensive biomonitoring and will enable better science-based decision making for managers. It will also promote increased scientific understanding of the SFE ecosystem. Multiple conservation benefits are expected to result from completion of this project. An important example is the ability to monitor whole communities, from individual water samples, that will allow managers to detect and potentially mitigate rapid shifts in SFE biological communities that are predicted to occur as the climate warms.


Objective 1: Develop robust molecular methods and a computational pipeline for detection of SFE fish and macroinvertebrates by eDNA metabarcoding of water samples. Furthermore, we will build a DNA reference sequence database for SFE fishes, mussels and other invertebrates for this and future studies, and will create a metabarcoding protocol that will enable detection of these organisms from aquatic eDNA samples.

Objective 2: Compare eDNA metabarcoding head-to-head with existing and historical monitoring data from three ongoing ecological surveys using diverse conventional sampling gear and evaluate the accuracy of fish abundance and biomass estimates from eDNA metabarcoding data. These surveys are the enhanced delta smelt monitoring survey (EDSM), the DWR Yolo Bypass rotary screw trap, and the UC Davis Suisun Marsh Fish Study otter trawl (Figure 2). We will determine the value of eDNA metabarcoding as a survey technique by comparing species detections between it and conventional gears. We will determine whether eDNA copy/read number is positively correlated with fish species’ abundance/biomass (EDSM survey only).

Objective 3: Evaluate factors that influence eDNA detection of species of interest (e.g. rare or invasive species) and suites of species (e.g. benthic fishes and invertebrates) on two spatial scales, within and between habitats, along with temporal variation. We will determine if fine-scale spatial sampling provides higher detection rates for rare or invasive species; we will determine if surface sampling effectively detects benthic species and if benthic sampling effectively detects pelagic species. As the UC Davis Suisun Marsh Fish Study otter trawl detects fishes and some macroinvertebrates, metabarcoding results from these eDNA samples will be compared to otter trawl data to assess (presence/absence) the accuracy of both fish and invertebrate detections.

Project Team

Andrea Schreier, Principal Investigator, Adjunct Assistant Professor, University of California, Davis

Ravi NagarajanAssistant Project Scientist, University of California, Davis

Ann HolmesGraduate Student, University of California, Davis

Melinda BaerwaldEnvironmental Program Manager, California Department of Water Resources

Brian Schreier, Senior Environmental Scientist, California Department of Water Resources

Andrew RypelAssociate Professor, University of California, Davis

Larry Brown, Research Biologist, US Geological Survey, California Water Science Center

Mallory Bedwell, Environmental Scientist, California Department of Water Resources

Alisha GoodblaLab Manager, University of California, Davis

Project Collaborators

CA Department of Fish and Wildlife: Martha Volkoff, Heather Perry, Ian Ralston, Chelsea Callahan, Jim Snider

UC Davis: Ted Grosholz, Jessica Weidenfeld

CA Department of Water Resources: Betsy Wells, Jesse Adams

US Fish and Wildlife Service (Delta Juvenile Fish Monitoring Program): Catherine Johnston, Brian Mahardja

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