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Project: Developing an eDNA Metabarcoding Protocol to Improve Fish and Mussel Monitoring in the San Francisco Estuary

Description: Funding for this Project will be used to develop a non-invasive, low cost monitoring tool that can be used in conjunction with existing Interagency Ecological Program (IEP) monitoring programs or used alone to assess biological community composition at locations of interest in the San Francisco Estuary (SFE). To achieve this goal, results of this project will: 1) create a comprehensive reference sequence database for native and invasive fish, mussels, and common macroinvertebrates in the SFE; 2) develop molecular and computational methods necessary for eDNA metabarcoding, 3) collect water alongside three existing IEP surveys and compare how well metabarcoding analysis detects species assemblages relative to conventional gears; 4) determine if metabarcoding metrics such as read count can be used to estimate abundance or biomass; and 5) determine whether time of sample collection or microhabitat conditions affect metabarcoding detection rates.

Reference Number: 3600BQ1996023

Implemented By: Regents of the University of California, Davis

Objective: Specific objectives are to: 1) Develop robust molecular methods and a computational pipeline for detection of SFE fish, mussels, and other benthic macroinvertebrates by eDNA metabarcoding of water samples. 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 accuracy of abundance and biomass estimates from eDNA metabarcoding data. 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 bivalves) on two spatial scales, within and between habitats, along with temporal variation.

Type: Monitoring, Research/Planning (including Science)

Total Cost: $419,742.00

Project Status: Project Implementation

On Time?: Yes    Within Scope?: Yes    Within Budget?: Yes

Estimated Completion: 9/30/2022    Actual Completion:

Associated Counties:

Project Benefits a Disadvantaged Community (or SDAC): No

Contribution SourcesContribution DateContribution Amount
Prop. 1, Water Quality, Ecosystem Restoration and Fish Protection Facilities - Delta10/16/2019$419,742.00

Project MetricMetric TopicQuantityUnit
MonitoringAt-risk Species Monitoring/Assessment  
Research/Planning (including Science)Mapping: Habitat  

Water Action Plan Target

Achieve the Co-Equal Goals for the DeltaAction Description
Protect and Restore Important EcosystemsAction Description


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