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Management theme
Delta As Place
Environmental Conditions
Flood Risk And Land Use Management
Governance
Habitat Management
Invasive / Non-native Species Management
Native Species Management
Water Quality
Water Supply Management
Science theme
Amphibians And Reptiles
Aquatic Vegetation
Biological Resource Use
Channelized Habitats
Climate Science
Environmental Conditions
Fish
Floodplain
Food Webs
Habitat Changes
Hydrologic Changes
Hydrology And Hydrodynamics
Invasive / Non-native Species
Invertebrates
Land Use And Human Activities
Landform And Natural Disturbance
Mammals
Modeling
Nutrients, Energy And Food Web
Riparian Habitats
Sediment
Social Impacts
Social Science
Species
Terrestrial Habitats
Tidal Wetlands
Traditional Knowledge
Vulnerability Assessment
Water Quality
Weather And Climate
Type
Core Monitoring
Status And Trend Monitoring
Synthesis
Targeted Foundational Research
Targeted Immediate Research
Unsure
Delta region
Cache Slough Complex
East Delta
Entire Delta
North Delta
South Delta
Suisun Marsh
Twitchell And Sherman Complex
West Delta
Yolo Bypass
Yolo Bypass And Cache Slough Complex
Status
Awarded / Initiating
Complete
In Progress / Ongoing
Advanced
Science function
Data Application / Analytics
Data Application – Data Analysis
Data Application – Information Management
Data Application – Modeling
Data Application – Science Communication / Knowledge Synthesis
Monitoring – Effectiveness
Monitoring – Implementation
Monitoring – Status And Trends
Planning And Guidance
Research
Management actions
Agricultural Production
Carbon Markets
Climate Change Mitigation
Creation Of Favorable Habitat Conditions For Native Species
Flood Control
Ghg Emissions
Groundwater Protection & Management
Habitat Protection / Enhancement / Restoration
Improving Methods And/or Infrastructure For Science And Monitoring
Invasive Species Control And Management
Land Use Designation
Methylmercury Tmdl
Natural Environmental Flows
Pathways Of Introduction Of Invasives
Pollution Control
Population Enhancement Of Listed Species
Predation
Salinity Gate Management
Sea-level Rise Accommodation
Subsidence Reversal
Wastewater Management
Water Conveyance / Infrastructure
Water Demand
Water Operations
Water Storage
Wetland Resilience
Wetlands
Science topics
Above-highwater Refugia
Agriculture
Air Temperature
Algae
Ammonia
Amphibians And Reptiles
Aquatic Vegetation
Arsenic
Atmosphere
Backwater
Bedload
Benthic
Benthos
Bioaccumulation
Biosentinels
Birds
Bivalve
Brazilian Waterweed
Cadmium
California Tiger Salamander
Carbon
Carbon Storage
Chemistry
Chinook Salmon
Chlorophyll A / B
Climate Change
Conductivity
Constituent Of Emerging Concern Cec
Copper
Corbicula/potamocorbula
Crustaceans
Cyanobacteria
Delta Islands
Delta Smelt
Deposition
Detritus
Direction
Dissolved Oxygen
Docks And Ports
Dredging
Drought
Emergent Macrophytes
Endangered Species
Endocrine Disruptors
Energy And Mines
Environmental Drivers
Epiphytic Algae
Erosion
Estuaries
Evaporation / Evapotranspiration
Extreme Heat
Extreme Storms
Fecal Coliform / E. Coli
Fish
Fishing
Flame Retardants
Floating Aquatic Vegetation
Flood
Flows
Flushing Rates
Food Webs
Forest Harvesting
Forests
Fungicides
Giant Garter Snake
Giant Reed
Green Sturgeon
Greenhouse Gas Ghg
Groundwater
Gulls
Habitat
Habitat Restoration
Harmful Algal Blooms Hab
Herbicides
Hg And Methyl Mercury
Historical Ecology
Hunting
Hydrocarbons / Polycyclic Aromatic Hydrocarbons Pah
Insecticides
Insects
Intertidal / Transition Zones
Invasive / Non Native Species
Invertebrates
Jellyfish
Land Elevation
Landscape Change
Landscape Metrics
Lead
Levees
Light
Longfin Smelt
Main Channels
Mammals
Managed Ponds
Marsh Wildlife
Methylmercury
Microplastics
Mollusks
Mudflats
Mysis
Nitrogen
Nitrogen / Ammonia
Non-forested Vegetation
Non-resident / Overwintering Birds
Nutria
Nutrients
Open Water
Other Discharge Contaminants
Other Species
Other Zooplankton
Outflow
Pacific Flyway
Pelagic Fish
Pesticides
Ph
Phosphorous
Phragmites
Phytoplankton
Polychlorinated Biphenyl Pcb
Precipitation
Predation
Primary Production
Rail Lines
Recreation & Tourism
Remote Sensing
Residence Time
Resilience
Restoration
Restoration Planning
Riparian Wildlife
Roads And Bridges
Rodenticides
Sacramento Splittail
Salinity
Salmon Migration
Salmon Rearing
Salt Marsh Harvest Mouse
Saltwater / Freshwater Marshes
Sav/fav
Sea Level Rise
Seasonally Flooded
Sediments
Seismicity
Selenium
Shorebirds
Sloughs
Snowpack / Snow Water Equivalent Swe
Socio-economic Drivers
Soil
Solar Irradiance
Spongeplant
Stage
Steelhead Trout
Stormwater Runoff / Drainage
Striped Bass
Sturgeon
Submerged Aquatic Vegetation
Subsidence
Surface Water / Flow
Suspended Sediment
Temperature
Terrestrial Wildlife
Tidal Wetlands
Tides
Toxicity
Turbidity
Urban Development
Velocity
Vessels And Shipping Channels
Wastewater Discharge
Water
Water Conveyance / Infrastructure
Water Hyacinth
Water Intakes, Fish Screens & Passage
Water Management
Water Operations / Exports
Water Storage
Water Temperature
Water Use / Demand
Waterfowl
Waves
Wetland Mapping
Wetlands
White Sturgeon
Wildfire
Wind
Yellow Star Thistle
Zinc
Zooplankton
Science action area
1a. Establish Publicly Accessible Repositories, Interactive Platforms, And Protocols For Sharing Information, Products, And Tools Associated With Monitoring And Modeling Efforts, In Support Of Forecast And Scenario Development, Timely Decision-making, And
1b. Develop Tools To Assist Adaptive Management In The Delta
1c. Identify And Implement Large-scale Experiments That Can Address Uncertainties In The Outcomes Of Management Actions For Water Supply, Ecosystem Function, And Socioeconomic Conditions In The Delta.
2a. Evaluate And Update Monitoring Programs To Ensure Their Ability To Track And Inform The Management Of Climate Change Impacts, Emerging Stressors, And Changes In Species Distributions.
2b: Identify And Prioritize Important Data Sources That Should Be Interconnected To Promote Collaboration And Provide The Technology Necessary To Easily Access This Information
3a. Conduct Studies To Inform Restoration And Approaches To Protecting Human Communities That Are Resilient To Interannual Hydrologic Variation And Climate Change Impacts.
3b. Develop Integrated Frameworks, Data Visualization Tools, And Models Of The Delta Social-ecological System That Evaluate The Distribution Of Environmental Benefits And Burdens Of Management Actions Alongside Anticipated Climate Change Impacts.
4a. Use Multi-method Approaches (e.g., Surveys, Interviews, Oral Histories, And/or Observations) To Develop An Understanding Of How Human Communities’ Values, And Uses Of Cultural, Recreational, Agricultural, And Natural Resources Vary Across Geography, D
4b. Synthesize Existing Data And Collaboratively Develop Additional Long-term Data Collection And Monitoring Strategies To Address Knowledge Gaps On Human Communities Within The Delta And Those Reliant On The Delta, With The Goal Of Tracking And Modeling
4c. Measure And Evaluate The Effects Of Using Co-production Or Community Science Approaches (in Management And Planning Processes) On Communities' Perceptions Of Governance And On Institutional Outcomes, Such As Implementation Or Innovation.
4c: Understand Mechanisms For Observed Relationships Between Flows And Aquatic Species
5a: Advance Integrated Modeling Through Efforts Such As An Open Delta Collaboratory (physical Or Virtual) That Promotes The Use Of Models In Guiding Policy.
5b. Identify Thresholds In The Survival And Health Of Managed Fish And Wildlife Species With Respect To Environmental Variables (e.g., Flow, Temperature, Dissolved Oxygen) And Location-specific Survival Probabilities To Develop Strategies That Will Suppor
6a. Evaluate How Climate Change, Sea Level Rise, And More Frequent Extremes Will Impact Habitats, Water Supply, Water Quality, Sediment Supply, Long-term Species Persistence, Primary Productivity, And Food Webs.
6e. Predict And Test How Water Allocation And Supply Decisions, And Ecological Flow Scenarios Should Change Under Projected Climate Change To Maintain Habitat Conditions, Access Of Target Species To Critical Habitat, And Interactions Among Native And Inva
N/a (project Initiated Prior To 2017)
Saa Action Area 1 (2017-2021): Invest In Assessing The Human Dimensions Of Natural Resource Management Decisions
Saa Action Area 2 (2017-2021): Capitalize On Existing Data Through Increasing Science Synthesis
Saa Action Area 3 (2017-2021): Develop Tools And Methods To Support And Evaluate Habitat Restoration
Saa Action Area 4 (2017-2021): Improve Understanding Of Interactions Between Stressors And Managed Species And Their Communities
Saa Action Area 5 (2017-2021): Modernize Monitoring, Data Management, And Modeling
Saa Need 1 (2022-2026): Improve Coordination And Integration Of Large-scale Experiments, Data Collection, And Evaluation Across Scales And Institutions
Saa Need 2 (2022-2026): Enhance Monitoring And Model Interoperability, Integration, And Forecasting.
Saa Need 3 (2022-2026): Expand Multi-benefit Approaches To Managing The Delta As A Social-ecological System
Saa Need 4 (2022-2026): Build And Integrate Knowledge On Social Processes And Human Behavior To Support Effective And Equitable Management
Saa Need 5 (2022-2026): Acquire New Knowledge And Synthesize Existing Knowledge Of Interacting Stressors To Support Species Recovery
Saa Need 6 (2022-2026): Assess And Anticipate Climate Change Impacts To Support Successful Adaptation Strategies
Unspecified
Start year
End year
Organizations and funding programs
Lead implementing organization
Audubon Canyon Ranch
CALFED Bay-Delta Program
California Department of Conservation [DOC]
California Department of Fish and Wildlife [CDFW]
California Department of Forestry and Fire Protection [CALFIRE]
California Department of Parks and Recreation [PARKS]
California Department of Pesticide Regulation [DPR]
California Department of Transportation [Caltrans]
California Department of Water Resource [DWR]
California Energy Commission [CEC]
California Rice Commission
California Sea Grant
California State Coastal Conservancy
California State University - East Bay
California State University Long Beach
California State University Maritime Academy
California State University [CSU]
California State Water Resources Control Board [SWRCB]
California Water Board - Central Valley Region
Central Valley Regional Water Quality Control Board [Central Valley RWQCB]
Coastal Conservation and Research, Inc.
Contra Costa Water District [CCWD]
Cornell University - Lab of Ornithology
Cramer Fish Sciences
Delta Regional Monitoring Program [RMP]
Delta Stewardship Council
Delta Stewardship Council - Delta Science Program
DigitalGlobe
East Bay Municipal Utilities District
European Space Agency
Goddard Space Flight Center
Hydrofocus Inc.
Land IQ
MarineTraffic
Metropolitan Water District of Southern California
Michigan State University
National Aeronautics and Space Administration [NASA]
National Agricultural Statistics Service [NASS]
National Audubon Society
National Marine Fisheries Service [NMFS]
National Oceanic and Atmospheric Administration [NOAA]
Oregon State University
Pacific Flyway Council
Pacific States Marine Fisheries Commission [PSMFC]
Pardee RAND Graduate School
Point Blue Conservation Science
Port of Stockton Board of Commissioners
Portland State University
R2 Resource Consultants Inc.
Sacramento-San Joaquin Delta Conservancy
San Diego State University
San Francisco Estuary Institute [SFEI]
San Francisco State University [SFSU]
San Francisco State University, Estuary & Ocean Science Center
San Joaquin County and Delta Water Quality Coalition [SJCDWQC]
Santa Clara University
Sierra Streams Institute
Southern California Stormwater Monitoring Coalition [SMC]
Stanford University
State Water Contractors [SWC]
Suisun Resource Conservation District
The Institute for Bird Populations
U.S. Army Corps of Engineers [USACE]
U.S. Bureau of Reclamation [USBR]
U.S. Department of Agriculture [USDA]
U.S. Department of Energy - Office of Biological and Environmental Research [DOE-BER]
U.S. Department of Transportation [DoT]
U.S. Environmental Protection Agency [USEPA]
U.S. Fish and Wildlife Service [USFWS]
U.S. Geological Survey [USGS]
UNAVCO
University of California
University of California - Berkeley [UC Berkeley]
University of California - Davis [UC Davis]
University of California - Los Angeles [UCLA]
University of California - Merced [UC Merced]
University of California - Riverside [UC Riverside]
University of California - San Diego [UCSD]
University of California - Santa Barbara [UCSB]
University of California - Santa Cruz [UCSC]
University of Maryland - Center for Environmental Science
University of Vermont, USGS Vermont Cooperative Fish and Wildlife Research Unit
University of Washington [UW]
Virginia Institute of Marine Science
Westside San Joaquin River Watershed Coalition
Woodland-Davis Clean Water Agency
Partner implementing organizations
Agricultural Coalitions: Landowners membership fees
Anchor QEA
Bachand and Associates
Bureau of Transportation Statistics [BTS]
California Cooperative Anadromous Fish and Habitat Data Program [CalFish]
California Department of Conservation [DOC]
California Department of Fish and Wildlife [CDFW]
California Department of Food and Agriculture [CDFA]
California Department of Forestry and Fire Protection [CALFIRE]
California Department of Parks and Recreation [PARKS]
California Department of Pesticide Regulation [DPR]
California Department of Public Health [CDPH]
California Department of Water Resource [DWR]
California Environmental Protection Agency [CalEPA]
California Heritage: Indigenous Research Project
California Institute of Technology Jet Propulsion Laboratory
California Institute of Technology [Caltech]
California Landscape Conservation Cooperative [CALCC]
California Natural Resources Agency [CNRA]
California Office of Environmental Health Hazard Assessment [OEHHA]
California State Board of Equalization
California State Coastal Conservancy
California State Lands Commission [CSLC]
California State University [CSU]
California State Water Resources Control Board [SWRCB]
Central Valley Flood Protection Board [CVFPB]
Central Valley Joint Venture
Central Washington University [CWU]
Chapman University
Collaborative Adaptive Management Team [CAMT]
Conservation Farms and Ranches
Cramer Fish Sciences
Delta Conservancy
Delta Stewardship Council
Delta Stewardship Council - Delta Science Program
Department of Fish and Game [DFG]
Desert Research Institute [DRI]
Ducks Unlimited
East Bay Municipal Utilities District
EcoMetric Consulting
Environmental Science Associates
Fishery Foundation of California
FloodSAFE Environmental Stewardship and Statewide Resources Office [FESSRO]
Hydrofocus Inc.
ICF International Inc.
International Institute for Applied Systems Analysis
Interstate Council on Water Policy [ICWP]
Koy'o Land Conservancy
Land IQ
Lawrence Berkeley National Laboratory [LBNL]
Lawrence Livermore National Laboratory
Maine Prairie High School
Manomet Inc.
Metropolitan Water District of Southern California
Michigan State University
Moss Landing Marine Laboratories [MLML]
National Aeronautics and Space Administration [NASA]
National Agricultural Statistics Service [NASS]
National Agriculture Imagery Program [NAIP]
National Audubon Society
National Marine Fisheries Service [NMFS]
National Oceanic and Atmospheric Administration [NOAA]
National Science Foundation [NSF]
National Wetlands Inventory - Many Supporting Organizations
NatureServe
Northwest Alliance for Computational Science and Engineering - PRISM Climate Group
Pacific Northwest National Laboratory
Pacific States Marine Fisheries Commission [PSMFC]
Point Blue Conservation Science
Purdue University
RAND Corporation
Resource Management Associates [RMA]
Restore the Delta
Rohde Environmental Consulting, LLC
SUNY College of Envir. Science & Forestry
Sacramento Regional County Sanitation District [Regional San]
Sacramento-San Joaquin Delta Conservancy
San Francisco Bay Bird Observatory
San Francisco Bay Conservation & Development Commission [BCDC]
San Francisco Estuary Institute [SFEI]
San Francisco State University [SFSU]
San Joaquin County Resource Conservation District
San Joaquin Valley Drainage Authority
Santa Clara University
Shingle Springs Band of Miwok Indians
Solano Land Trust
South Yuba River Citizens League
Southern California Coastal Water Research Project [SCCWRP]
Southern California Stormwater Monitoring Coalition [SMC]
Southwest Climate Adaptation Science Center
State Water Contractors [SWC]
Suisun Resource Conservation District
Texas A&M
The Nature Conservancy
U.S. Army Corps of Engineers [USACE]
U.S. Bureau of Indian Affairs [BIA]
U.S. Bureau of Land Management [BLM]
U.S. Bureau of Reclamation [USBR]
U.S. Census Bureau
U.S. Department of Agriculture [USDA]
U.S. Department of Defense [DoD]
U.S. Department of Energy [DOE]
U.S. Energy Information Administration [EIA]
U.S. Environmental Protection Agency [USEPA]
U.S. Fish and Wildlife Service [USFWS]
U.S. Forestry Service [USFS]
U.S. Geological Survey [USGS]
U.S. National Park Service [NPS]
University of British Columbia [UBC]
University of California - Berkeley [UC Berkeley]
University of California - Davis [UC Davis]
University of California - Irvine [UCI]
University of California - Merced [UC Merced]
University of California - San Diego [UCSD]
University of California - Santa Barbara [UCSB]
University of California - Santa Cruz [UCSC]
University of Kansas
University of South Carolina
University of Washington [UW]
Utah State University
Washington Department of Fish and Wildlife
Western Ecosystems Technology Inc.
Western States Water Council [WSWC]
Wolf Creek Community Alliance
Yuba River Management Team
Primary funding organizations
CALFED Bay-Delta Program
California Department of Fish and Wildlife [CDFW]
California Department of Water Resource [DWR]
Delta Regional Monitoring Program [RMP]
Delta Stewardship Council
Interagency Ecological Program [IEP]
State Water Contractors [SWC]
U.S. Bureau of Reclamation [USBR]
U.S. Environmental Protection Agency [USEPA]
U.S. Fish and Wildlife Service [USFWS]
U.S. Geological Survey [USGS]
Funding programs
California Department of Fish and Wildlife CDFW - Prop 1
Delta Regional Monitoring Program RMP
Delta Science Program - Delta Science Solicitations
Delta Science Program - Operation Baseline
Delta Science Program and California Sea Grant - Delta Science Fellows Program
Interagency Ecological Program IEP
Funding Sources
CalFED Bay Delta Fund CBDF
California Department of Fish and Wildlife CDFW - General Fund
California Department of Fish and Wildlife CDFW - Prop 1
Delta Stewardship Council - General Fund
Proposition 50
Proposition 84
Wetland Program Development Grant
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Records
Currently, sorted by last updated
Last updated
Title
Download
Title
Directed Outflow Project
Lead
U.S. Bureau of Reclamation [USBR]
Description
The U.S. Bureau of Reclamation (USBR) and California Department of Water Resources (DWR), along with collaborators, are continuing efforts to evaluate the hypothesized benefits of outflow and outflow alteration for Delta Smelt. The collective aim of these efforts is to better inform management actions that will bolster and stabilize the Delta Smelt population. The planned five-year Directed Outflow Project (DOP) seeks to assist in evaluating the overarching hypothesis that habitat quality and quantity is improved in the summer/fall when X2 is below 81 km and the LSZ occurs in Suisun Bay and Marsh, and this improvement in habitat conditions will translate into a greater catch density, health, and growth for Delta Smelt using this area
Science topics
Delta Smelt
,
Fish
,
Flows
,
Water management
Updated
November 17, 2022
Title
Fish Diet and Condition
Lead
California Department of Fish and Wildlife [CDFW]
Description
Description The Diet and Condition study has provided information on the food habits of pelagic fishes in the estuary since 2005. We focus on the temporal and spatial differences in diet composition and feeding success of Delta Smelt, Striped Bass, Threadfin Shad, Longfin Smelt, Mississippi Silversides, and American Shad. Need Data from this project has been used to inform the Fall Low Salinity Habitat Program (FLaSH), Directed Outflow Project (DOP), and Management, Analysis and Synthesis Team reports, as well as life history models used for the conservation of fish and their habitats. Understanding what prey are utilized for food in the context of available prey, with the associated body-condition of fish, helps clarify the existence and timing of food limitation for young pelagic fish in the estuary. This work began as part of the Pelagic Organism Decline investigations and continued as a contributor to FLaSH investigations during which we in collaborated with the Fish Health Monitoring Project. Recently staff completed Longfin Smelt diet investigations as part element #296 (Longfin Smelt Investigations – in response to a litigation agreement) that will also contribute to the Longfin Smelt Conceptual Model and Synthesis effort (element #320). Finally, we will process Delta Smelt diets from investigations prompted by the Delta Smelt Resilience Strategy, and as part of the DOP. Objectives 1. What are the diets of pelagic fishes (especially Delta Smelt and Longfin Smelt) in the estuary and do they vary regionally or temporally? 2. Is there evidence of reduced feeding success spatially or temporally in the estuary? 3. Is feeding success associated with changes in relative weight or condition of fish? 4. Is there seasonal and regional overlap of diets between species (with a focus on age-0 Delta Smelt, Longfin Smelt, Striped Bass, Prickly Sculpin, Pacific Herring, and Threadfin Shad)?
Science topics
None specified
Updated
April 29, 2022
Title
Aquatic Habitat Sampling Platform: Standardized Fish Community Sampling Across Habitat Types
Lead
U.S. Bureau of Reclamation [USBR]
Description
Description The Aquatic Habitat Sampling Platform (AHSP) is an integrated aquatic species and habitat sampling system that can effectively monitor aquatic organisms and reveal habitat associations while having minimal or no “take” of sensitive species. Further development and deployment of the AHSP will expand data collection to shallow and off-channel habitat, while offering the capability to transition to deeper and open water habitats, providing reliable sampling efficiency estimates (e.g., probability fish detection) and “catch” per unit effort (i.e., number of individual species per volume of water sampled) and improving our knowledge about populations, habitat associations and major stressors of key organisms within the San Francisco Estuary (Estuary). Need Within the Estuary, numerous monitoring techniques are used. However, monitoring weaknesses for determining fish status and trends include: 1) restricted locations available for some techniques;2) limited ability to simultaneously assess zooplankton and fish larvae;and 3) difficulty in estimating fish population size due to lack of gear efficiency information (Honey et al. 2004). Furthermore, past attempts at integrated abundance indices from more than one sampling method have had limited success. Although there continues to be considerable collaborative monitoring and research devoted to understanding Central Valley fish species, coordination among activities has been difficult. Other issues include permitting take of listed species and time-consuming monitoring with extended periods of down time due to sample post-processing of fish and invertebrate species. Identification of key microhabitats for each lifestage and attributes and linking associated physical parameters such as habitat features (e.g., depth, structure, channel type) and water quality is needed. Objectives • Test AHSP operation within the Estuary while providing information highly relevant to pressing Delta management issues (IEP 2016); • Provide detailed information on distribution and approximate abundance of adult Delta Smelt within identified habitat types (Biological Opinion on the Long-Term Operational Criteria and Plan for coordination of the Central Valley Project and State Water Project;https://www.fws.gov/sfbaydelta/documents/SWPCVP_OPs_BO_12-15_final_OCR.pdf);and • Assess habitat associations and diurnal behavior of Delta Smelt and other fishes (Durand 2015).
Science topics
Delta Smelt
Updated
April 29, 2022
Title
Central Valley Salmonid Coordinated Genetic Monitoring [Year 4]
Lead
U.S. Bureau of Reclamation [USBR]
Description
Description This work will include tasks to rapidly identify winter-run Chinook juvenile salmon at the CVP/SWP salvage facilities, process juvenile salmonid tissues from various CVPIA and IEP fish monitoring stations, and support coordination of genetic monitoring across the CVP and SJRRP programs. PIs: Josh Israel (USBR);Scott Blankenship (Cramer Fish Science);Ken Bannister (USFWS);John Carlos Garza (NOAA-Fisheries);Brett Harvey (DWR);Noble Hendrix (QEDA);Rachel Johnson (NOAA-Fisheries);Mariah Meek (UC Davis);Kevin Reece (DWR) Need This study is needed due to the limited accuracy of Lenght at Date stock identification. Inaccurate identification of Chinook salmon is problematic because it compromises the management value of data collected from standard monitoring programs. This project will improve the science and management value of the Central Valley salmon monitoring network, supported through IEP and Central Valley Project Improvement Act (CVPIA) monitoring stations, by accurately determining stock identification of multiple Chinook salmon stocks across their distribution. Classification tables will be developed to characterize monthly and seasonal accuracy between length-at-date and genetic race assignment at IEP and BiOp monitoring locations. This multi-year dataset will be used to evaluate the likelihood of accurate assignment and potential biophysical explanatory variables influencing genetic accuracy. Objectives Improve accuracy of CVPIA and IEP monitoring programs by providing genetic stock identification information for tissues collected from Red Bluff, Knights Landing, DJFMP, salvage facilities and San Joaquin River fish monitoring stations. Samples will be collected from all four runs of Chinook salmon based on length-at-date (i.e., samples will be collected from Chinook of various sizes throughout the sampling period).
Science topics
Chinook Salmon
Updated
April 29, 2022
Title
Enhanced Acoustic Tagging, Analysis, and Real-Time Monitoring
Lead
National Oceanic and Atmospheric Administration [NOAA]
Description
Description This project tracks the movement and survival of wild and hatchery juvenile Chinook salmon with a large acoustic receiver network (JSATS), including real-time receivers, and the development of real-time metrics and retrospective modeling of juvenile salmon migration data. Need There is a well-documented need for improved detection and associated modeling of salmon migration and survival in the Central Valley. Understanding salmon survival and movement dynamics in the Delta and its tributaries is critical to the operation of state and federal water projects, recovery of ESA-listed species, and sport and commercial fisheries management. Objectives • Maintain 20 real-time JSATS receivers: will provide information on migrating salmon smolt location and timing of Delta entry and exist, which is key for informing time-sensitive decisions • Deployment of autonomous JSATS receiver array: this will provide fine-scale reach-specific survival and movement rates • Development of new metrics for the real-time data: this will inform key management relevant questions, such how many fish are entrained at critical junctions • Development of real-time website to convey movement and survival rates of acoustic tagged juvenile salmonids at various real-time locations in the Sacramento River and Delta.
Science topics
Salmon migration
Updated
April 29, 2022
Title
Suisun Marsh Salinity Control Gate Study
Lead
California Department of Water Resource [DWR]
Description
Description Suisun Bay and Marsh are a key part of the habitat for Delta Smelt, but during drier periods such as summer, Delta Smelt may be at least partially excluded from Suisun Marsh due to high salinities. The purpose of this proposal is to provide scientific support a management action for Smelt, operation of the Suisun Marsh Salinity Control Gates (SMSCG). This facility is currently to tidally pump water into the Marsh to improve fall and winter habitat conditions for waterfowl, but could also provide a tool to manage aquatic habitat for Delta Smelt in other periods. Specifically, by using the SMSCG to direct more fresh water in Suisun Marsh, our prediction is that reduced salinities will improve habitat conditions for Delta Smelt in the region. Need The status of Delta Smelt is dire. As part of the Resources Agency's Delta Smelt Resiliency Strategy, in August 2018 we conducted pilot operations of the SMSCG to support Delta Smelt , with promising results. Based on this early success, we expect that the SMSCG will be used as a seasonal tool to support Delta Smelt in summer-fall in coming years as part of the coming FWS Biological Opinion and DFW ITP. Neither has been completed, but SMSCG operations for fish are expected to be required in each. Hence, the proposed study is intended to provide a scientific evaluation and guidance for an expected SMSCG action in 2020. Objectives The primary objective of this project is to evaluate the effectiveness of the SMSCG action. Questions to be addressed include: • Did the action improve habitat conditions for Delta Smelt in the Suisun Region? • Does the Suisun Region typically have better habitat and food web conditions than the upstream River Region? • Do Delta Smelt respond favorably to the SMSCG flow action? • Does operation of the SMSCG affect other fishes and clams?
Science topics
Salinity
Updated
April 29, 2022
Title
Physiological and Behavioral Effects of Domestication on Delta Smelt
Lead
California Department of Water Resource [DWR]
Description
Description Due to the continued population decline of Delta Smelt and the threat of extinction, conservation efforts may include future supplementation practices using the refuge population of Delta Smelt at the Fish Conservation and Culture Laboratory (FCCL) in Byron, CA to assist in maintaining the wild population. Prior to any supplementation planning, it is first critical to determine if Delta Smelt with varying levels of domestication indices (i.e. level of hatchery ancestry) respond differently, both physiologically and behaviorally, to various habitat conditions. This project aims to provide a better understanding of the effects of domestication on captive Delta Smelt (Hypomesus transpacificus) by assessing the refuge population at the FCCL. Three studies will be conducted exploring if domestication index (i.e. the level of hatchery ancestry) affects the physiological and behavioral performance of Delta Smelt in response to physical handling and climate change stressors. Need Physiological and behavioral changes of hatchery fish due to domestication could lead to unintended detrimental effects in the wild;therefore, research characterizing the alterations of hatchery Delta Smelt across levels of domestication indices are warranted to understand the effects of captivity and how they might shape future supplementation and conservation strategies. For example, identification of differences among groups of Delta Smelt with varied domestication index may create the need for domestication management and the implementation of altered hatchery practices. This project will provide relevant and timely information for conservation managers and adaptive restoration strategies and dovetail with the recommendations from the 2017 Delta Smelt Supplementation Workshop. As such, this study is included in the supplementation studies work plan which came out of that workshop. Specifically, this project fits within two topics in the IEP Science Strategy: Effects of Climate Change and Extreme Events and Restoring Native Species and Communities. Objectives 1. To characterize domestication effects on hatchery Delta Smelt by synthesizing existing/historical datasets on growth and reproduction of fish at the FCCL since the start of the hatchery program. 2. To identify the impacts of domestication index on the physiological stress response of Delta Smelt following handling stress. 3. To determine the effects of domestication index on individual and group swimming behavior, responses to predation, and responses within the context of climate change factors including warming and increased salinity.
Science topics
Delta Smelt
Updated
June 13, 2024
Title
Developing an eDNA metabarcoding protocol to improve fish and mussel monitoring in the San Francisco Estuary
Lead
National Oceanic and Atmospheric Administration [NOAA]
Description
Description We propose to develop an eDNA metabarcoding protocol to complement existing IEP monitoring surveys and assess the effects of management activities such as habitat restoration or flow alteration. We will develop a reference sequence database for native and invasive fish, mussels, and other macroinvertebrates present in the San Francisco Estuary (SFE). We will optimize a molecular and computational pipeline for metabarcoding and ground truth the method against three SFE monitoring efforts, each using different sampling gear. We will investigate the relationship between eDNA sequence read count and fish biomass or abundance (EDSM survey). Finally, we will determine the ability of metabarcoding to detect fish and macroinvertebrate assemblages across large and small spatial scales and over time. Need Our overarching goal is to develop a non-invasive, low cost monitoring tool that can be used in conjunction with existing IEP monitoring programs or used alone to assess biological community composition at locations of interest in the SFE. This proposal is related to the 2020 – 2024 IEP Science Strategy by creating a new monitoring tool that can assist in two main areas: 1) Restoring Bay-Delta native fishes and community interactions and 2) assessing effects of flow alteration on Bay-delta aquatic resources. Broadly, this study will inform management decisions by supporting and augmenting existing monitoring surveys in the SFE. It will also lead to a richer and more complete understanding of SFE ecology. This study is not explicitly required by law or agreement, and to our knowledge is neither a recommended action nor a result from an IEP review or synthesis effort. Objectives Objective 1: Develop robust molecular methods and a computational pipeline for detection of SFE fish and macroinvertebrates by eDNA metabarcoding of water 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 accuracy of fish abundance and biomass estimates from eDNA metabarcoding data. 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.
Science topics
Fish
Updated
April 29, 2022
Title
Predation Dynamics Across Reach-Specific Gradients in Juvenile Salmon Survival
Lead
U.S. Geological Survey [USGS]
Description
Description The overarching goal of this project is to determine if predation by piscivorous fishes is an important explanatory driver of survival of juvenile Chinook Salmon emigrating through the north Delta. To achieve this goal, we seek to determine if variation in reach-specific characteristics of predation dynamics covary with survival of acoustictagged juvenile Chinook Salmon collected during the study period. This will be accomplished by comparing reach-specific characteristics of the piscivore community and its observed and modeled consumption of juvenile Chinook Salmon across a range of environmental conditions. Need This is not a mandated study but it addresses an important research need. Objectives • How does the piscivore community (species composition, size structure, and abundance) vary across specific migratory pathways (river reaches) in the North Delta? • To what extent do environmental conditions (e.g., water temperature, turbidity, and discharge) control the consumption of juvenile Chinook Salmon? • Do characteristics of the predator community explain variation in survival of acoustic tagged salmon collected during the study period?
Science topics
Predation
Updated
April 29, 2022
Title
Directed Field Collections
Lead
California Department of Fish and Wildlife [CDFW]
Description
Description The Direct Field Collections element (-089) provides funding support for expanded field collections, allowing CDFW to provide other, IEP-approved researchers access to research-capable boats and experienced operators, and thus the ability to safely sample the upper San Francisco Estuary. This element most recently facilitated investigations associated with the Fall Low Salinity Habitat (FLaSH) project and the Directed Outflow Project (DOP). Need This element allows CDFW and thus IEP to provide boat and operator time to assist collaborating researchers leading approved IEP projects with “on-the-water” sampling. There is no mandate for this element. Objectives To provide CDFW operational flexibility to assist collaborating researchers leading approved IEP projects with access to CDFW boat operators and boats to complete "onthe-water" sampling.
Science topics
None specified
Updated
April 29, 2022
Title
North Delta Flow Action: Role of Improved Yolo Bypass Flows on Delta Food Web Dynamics
Lead
California Department of Water Resource [DWR]
Description
Description In a collaborative effort between CA Department of Water Resources, US Bureau of Reclamation, CA Department of Fish and Wildlife, United States Geological Survey, San Francisco State University, and UC Davis, this study will investigate the role of augmented summer and fall flows in the Yolo Bypass and North Delta areas on lower trophic food web dynamics and the benefits to listed fish species. Using both continuous and discrete sampling approaches, this study will relate hydrologic patterns to chlorophyll-a, nutrients and primary productivity, plankton densities and composition (phytoplankton and zooplankton), contaminant concentrations, as well as water quality parameters such as electrical conductivity, turbidity, temperature, and dissolved oxygen. In addition, caged hatchery Delta Smelt will be monitored to determine the effects of the managed flow action and increased food web productivity on fish survival, growth, and behavior. Need Due to the food-limited nature of the San Francisco Estuary, it is critical to understand mechanisms that result in successful food web productivity including phytoplankton blooms. Food limitation is one of the primary hypothesized causes of the Pelagic Organism Decline. In 2011 and 2012 there was evidence that a moderate Yolo Bypass flow pulse during fall agricultural drainage periods was followed by phytoplankton blooms in the lower Sacramento River. Managed flow actions in the following years showed an increase in food web productivity could be repeated;however, results varied across years and flow actions indicating more research is warranted to understand correlations between flow and abiotic conditions, and the biological response of the food web. The increases of summer/fall flows in North Delta, has been considered a management strategy as part of complying with USFWS Delta Smelt Biological Opinion Action 4. The augmentation of flows through the Yolo Bypass/North Delta is also included as one of several Delta Smelt Resiliency Strategies by Natural Resources Agency. Objectives • Determine if managed flow actions through the Yolo Bypass stimulate increased primary productivity locally and downstream, and if it is repeatable. • Characterize how nutrients, chlorophyll and plankton (composition and density) in the Toe Drain, Cache Slough Complex, and lower Sacramento River change in response to flow pulses. • Determine if nutrient subsidies of the source water and downstream are limited by abiotic and biotic factors. • Characterize spatial differences and transport of pesticide contaminants in the Yolo Bypass in response to the flow actions. • Determine survival, growth and behavior of caged hatchery Delta Smelt before and after the flow action in the Yolo Bypass.
Science topics
Flows
,
Water management
Updated
June 13, 2024
Title
Estimating Abundance of Juvenile Winter-run Chinook Salmon Entering and Exiting the Delta [SAIL]
Lead
U.S. Fish and Wildlife Service [USFWS]
Description
Description This is a continuation of a five year project funded by CDWR and CDFW and the Central Valley Project Improvement Act in 2017. The objective of the project is to improve estimates of population abundances for fall, winter and spring run juvenile Chinook Salmon at Sacramento and Chipps Island by improving efficiency estimates using data from releases of coded wire tags (CWT), acoustic tags (AT), and by genetically sampling the trawl catch in 2018. The project will (1) develop statistical models for estimating trawl efficiencies using 2016-2018 data for paired AT-CWT releases of winter run and fall-run Chinook Salmon;(2) use 2018 genetic sampling of trawl catch in combination with efficiency estimates to estimate population abundances of fall, spring and winter run at Sacramento and Chipps Island in 2018;(3) implement trawl efficiency studies for multiple salmon runs in 2018 informed by the 2016 and 2017 results and in coordination with hatcheries for inclusion of AT fish with existing CWT releases;and (4) combine trawl efficiencies with genetic samples of trawl catch to provide estimates of fall, spring and winter-run salmon abundance (with estimated precision) entering and exiting the Delta in 2018. Need There is growing appreciation that a salmon monitoring network that could quantitative estimates of abundance is desirable to improve our knowledge and resolution of life stage success and movement across the landscape (Salmon SAIL conceptual models 2016). Objectives (1) Estimate the population-level status and trends for winter run;and status of spring and fall run;(2) evaluate production estimates for juvenile winter-run Chinook Salmon entering the Delta used in water project take development;(3) provide estimates of winter and fall run-specific freshwater cohort strength to support ocean harvest management decisions;(4) establish a time series of winter, spring and fall run-specific production estimates at key locations for incorporation into life cycle models.
Science topics
Chinook Salmon
Updated
April 29, 2022
Title
Reconstructing Juvenile Salmon Growth, Condition, and Delta Habitat Use in 2014-15 Drought and Beyond [SAIL]
Lead
University of California - Davis [UC Davis]
Description
Description Life history diversity buffers salmon populations over space (e.g. the use of natal and non-natal rearing habitats and time (e.g. variable migration timing resulting in greater probability of meeting optimal ocean conditions). Historically the Sacramento-San Joaquin Delta provided critical salmon rearing habitat, but urban expansion, water diversions and species introductions have resulted in inhospitable conditions unlikely to meet rearing needs. This study fills critical data gaps regarding Delta rearing by juvenile Chinook salmon – primarily to determine the annual migrant portfolio (proportion of different populations and life stages) and the relative success of Delta vs. natal rearing (inferred by rearing duration, growth rate, diet and condition). We quantify the extent to which Delta rearing contributes to salmon population resiliency under different environmental conditions, including drought (2014-15) and flood conditions (2017, 2019), and provide baseline data to provide insights into population-level responses to future habitat restoration and climate change. The study uses annual collections of fall & late fall run salmon samples from sites upstream (Mossdale/Sherwood Harbor), within, and downstream (Chipps Island) of the Delta sampled by the IEP Delta Juvenile Fish Monitoring Program (DJFMP). Need Annual monitoring surveys routinely sample salmon entering and leaving the Delta, but the extent to which these juveniles rear there is virtually unknown, and has been highlighted as a critical data gap for parameterizing the NMFS Chinook salmon life cycle model (S. Lindley NOAA pers. comm.). There are limited tools available to monitor habitat use by native fishes, with most efforts providing a snapshot of fish presence/absence or abundance. Tagging studies provide key information about migratory pathways and survival through stretches of the Delta, but are typically limited to larger individuals and often use hatchery smolts with different rearing needs and seareadiness to the smaller individuals most likely to use Delta habitats. Otoliths represent a unique tool to reconstruct fish age, natal origin, growth history, movement patterns, and habitat use, even in fry <40mm fork length. Objectives We will use juvenile salmon collected by the IEP Delta Juvenile Fish Monitoring Program to assess: 1. Contributions of different rivers & hatcheries to sites upstream, within & downstream of the Delta. 2. Delta habitat use (frequency, duration) and success (growth rates, condition and diet). 3. Mechanisms governing juvenile salmon outmigration timing from the natal tributary.
Science topics
None specified
Updated
April 29, 2022
Title
Enhanced Delta Smelt Monitoring [EDSM]
Lead
U.S. Fish and Wildlife Service [USFWS]
Description
Description The Enhanced Delta Smelt Monitoring (EDSM) program is a year-round monitoring program comprised of multiple crews trawling concurrently at multiple sites in predefined strata within the San Francisco Estuary. Post-larval Delta Smelt are targeted approximately April through June using 20mm trawling gear, and Kodiak trawling gear is employed the remainder of the year. Gear efficiency experiments and shallow water sampling elements are incorporated when possible. Need The declining Delta Smelt population has highlighted the need to keep improving the array of information that supports our understanding of the factors affecting Delta Smelt population dynamics and management decisions to minimize adverse effects of water operations on the population. EDSM has biological significance and potential conservation benefit by providing data to resource managers on nearly all life stages of endangered Delta Smelt and near-real-time data on the juvenile and adult life stages. EDSM data is provided to the Smelt Working Group and other managers in near realtime to help inform management decisions during the entrainment season. Objectives • To estimate the total abundance of Delta Smelt, along with standard errors or confidence intervals, on a weekly to bi-weekly basis for various life stages (postlarvae, juveniles, sub-adults, adults) throughout the year; • To estimate the spatial distribution of Delta Smelt at a management relevant temporal and spatial resolution;and • To provide data that support management decisions and address scientific questions to further understanding of sampling efficiency, drivers of Delta Smelt population patterns, and other conservation and management-relevant topics.
Science topics
Delta Smelt
Updated
April 29, 2022
Title
Effect of Outflow Alteration upon Delta Smelt Habitat, Condition and Survival
Lead
U.S. Bureau of Reclamation [USBR]
Description
Description The Directed Outflow Project (DOP) is a continuing collaborative effort among a dozen state, federal and non-governmental groups. The DOP will employ a focused spatial and temporal approach to evaluate mechanistic hypotheses directly related to the rationales provided for the summer Delta outflow action and Yolo Bypass Toe Drain action to benefit Delta Smelt, with direct relevance to the fall outflow action. Paired data collections (same location and time) of abiotic and biotic habitat constituents to test specific hypotheses will assist in avoiding prior shortcomings of using data collected for different studies/hypotheses and/or across variable spatial/temporal scales (as discussed in MAST [2015] and elsewhere). Sampling will occur during the Delta Smelt juvenile rearing-stage, a period known to be associated with the location of the low salinity zone (LSZ). Results should strengthen our understanding of the mechanisms and drivers impacting Delta Smelt vital rates and associated habitat features with a focus on outflow conditions. Results should assist in evaluating the benefit and feasibility of future flow augmentation actions for managers and decision makers. Results from this and other related studies will inform evaluations on which particular outflow-related action or group of actions provides the most benefit for Delta Smelt. Need Requests and plans for water management actions related to augmentation of Delta outflow have proceeded and are expected to proceed in the future. However, there is uncertainty and disagreement regarding the mechanistic relationship of Delta outflow during the rearing period to Delta Smelt vital rates and habitat, and the hypothesized benefit of outflow alteration for Delta Smelt. Delta outflow has experienced reductions in recent years, coinciding with the collapse of the Delta Smelt. Reduced outflow has been linked to reductions in habitat suitability in Suisun Bay and Marsh and movement of the LSZ to the Confluence of the Sacramento-San Joaquin River where little connection to shallow open water habitats exists. Objectives The DOP’s main objective will be to evaluate the hypothesized benefit of outflow alteration for Delta Smelt and its habitat in coordination with all stakeholder groups. The following process and product related sub-objectives will facilitate progression toward this evaluation objective. • Test mechanistic hypotheses addressing the rationale behind outflow-based actions to benefit Delta Smelt. • Concurrently sample fish and measure abiotic/biotic habitat conditions at each randomly selected location along the salinity and habitat gradient of the north to western Delta along the Sacramento River during the summer and fall.
Science topics
Delta Smelt
Updated
April 29, 2022
Title
Integrating Measurement of Fish Body Condition within the Delta Juvenile Fish Monitoring Program [DJFMP]
Lead
U.S. Fish and Wildlife Service [USFWS]
Description
Description The aim of this pilot effort is to begin assessing methods and developing protocols for incorporating measurement of fish body condition (Fulton’s Condition Index, K) into standard Delta Juvenile Fish Monitoring Program (DJFMP) sampling. Need The goal of this study is to examine the utility of fish body condition as a measure for DJFMP to evaluate underlying factors driving fish health and survival in the Sacramento and San Joaquin River-Delta system. This will provide a more complete assessment of how condition metrics vary for common fish species that are sensitive to differences in environmental conditions, filling a fundamental data gap in our existing monitoring program. Objectives • Establish a pilot sampling design and methods for collection of data from fish sampled through DJFMP. • Assess the utility and expand the use of body condition to include up to 7 species of commonly sampled fishes. • Develop protocols for incorporating new methods into DJFMP sampling.
Science topics
Fish
Updated
April 29, 2022
Title
Extracting Better Information from Long-Term Monitoring Data: Estimating Occupancy and Abundance of Near-Shore Fishes in the Sacramento-San Joaquin River Delta
Lead
U.S. Fish and Wildlife Service [USFWS]
Description
Description The purpose of this study is to expand IEP monitoring and inference to other dominant near-shore, littoral habitats not sampled by beach seines through the use of boat electrofishing. To accomplish this we will sample key littoral fish species across various near-shore habitats in order to determine how best to estimate abundance, occupancy, capture probabilities, and related environmental drivers. Need Expanding DJFMP sampling to other habitats throughout the Delta will allow our program to detect and monitor fishes and ecological trends through time, alleviating a recognized data gap. Current sampling relies on data collected through non-random fixed point sampling of unobstructed habitats, which limits the utility of our data to inform management decision. Objectives • Design boat electrofishing survey methods to expand DJFMP’s monitoring into habitats and locations not sampled by beach seining. • Design and develop field and data analysis methods for estimating capture probability and abundance using boat electrofishing techniques. • Predict spatio-temporal distribution of habitats occupied by key littoral species.
Science topics
Habitat
Updated
April 29, 2022