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  • Title

    Habitat Values of Native SAV [Submerged Aquatic Vegetation] in the Low Salinity Zone of San Francisco Estuary

    Lead San Francisco State University [SFSU]
    Description We will investigate the importance of native submerged aquatic vegetation (SAV) in providing food web support for native fish species in the low salinity zone of the San Francisco Bay-Delta. These SAV beds, composed primarily of Stuckenia pectinata (sago pondweed), are an extensive feature along many of the islands in Suisun Bay and the west Delta, yet almost nothing is known of their seasonal or interannual patterns, their invertebrate communities, or how their physical structure or food resources influence use by native fishes. We hypothesize that the position of these beds in the shallow subtidal zone along the islands increases habitat options adjacent to wetlands and channels for numerous fish species, including species of concern such as delta smelt and chinook salmon. The objectives of this project are to: 1) characterize patterns in habitat structure, community composition, and productivity of SAV beds in four locations in Suisun Bay and the western Delta over a three year period (with comparisons to non-native Egeria densa beds), 2) document the epifaunal invertebrate community composition and abundance in the Stuckenia beds, 3) assess fish use of these beds through seining and acoustic monitoring of hatchery-tagged fish, 4) utilize stable isotope analyses to evaluate food web relationships within and among the beds, and 5) begin preliminary evaluation of the potential to restore native SAV to subsided lands in this region.
    Science topics Chinook Salmon, Green sturgeon, White Sturgeon, Sacramento Splittail, Delta Smelt, Steelhead Trout
    Updated April 29, 2022
  • Title

    Synchrony of Native Fish Movements: Synthesis Science Towards Adaptive Water Management in the Central Valley (FishSync)

    Lead University of California - Davis [UC Davis]
    Description Salmon and other native California fishes are in decline and increasingly targeted for enhanced conservation. Acoustic telemetry technologies have emerged, allowing researchers to track fish routes through the Central Valley. Yet while the use of acoustic telemetry has widened, little synthesis has occurred on the large, growing, and expensive datasets that already exist. The main goal of the project is to conduct a synthesis study of existing and high priority telemetry datasets for native and non-native fishes in the Central Valley. Using synchrony of movement rates, through space and time, we will develop a novel behavior-based statistical framework to gain understanding into the environmental conditions that promote movement/passage of diverse native fishes in the Central Valley. The project includes a Technical Advisory Group, composed of members of multiple conservation teams. The group will inform each step of study, strengthen syntheses, and enable rapid communication of results to decision makers. In total, the project will analyze 10 to 15 high-quality telemetry datasets encompassing a range of native fishes and life stages. This synthesis will yield major insights into water management practices that could help improve survival of native fish.
    Science topics Chinook Salmon, Fish, Salmon migration, Steelhead Trout, Sturgeon, White Sturgeon
    Updated December 4, 2022
  • Title

    Delta Regional Monitoring Program

    Lead San Francisco Estuary Institute [SFEI]
    Description The Delta Regional Monitoring Program (RMP) is a stakeholder-directed project formed to develop water quality data necessary for improving our understanding of Delta water quality issues.
    Science topics Hg and methyl mercury, Insecticides, Rodenticides, Herbicides, Fungicides, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Striped bass, Fish
    Updated April 29, 2022
  • Title

    20-mm Survey [Delta Smelt distribution monitoring]

    Lead California Department of Fish and Wildlife [CDFW]
    Description California Department of Fish and Wildlife (CDFW) conducts the 20-mm Survey annually to monitor the distribution and relative abundance of larval and juvenile Delta Smelt (Hypomesus transpacificus) in the upper San Francisco Bay Estuary. The survey began in 1995 and supplies near real-time catch data to water and fisheries managers as part of an adaptive management strategy to limit the risk of Delta Smelt entrainment during water exports Data collected: temperature, electro-conductivity, water transparency, turbidity, water volume, tidal stage, fish, and zooplankton.
    Science topics Stage, Tides, Other zooplankton, Water temperature, Turbidity, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Benthos
    Updated April 29, 2022
  • Title

    Fall Midwater Trawl Survey [FMWT]

    Lead California Department of Fish and Wildlife [CDFW]
    Description The FMWT was initiated to determine the relative abundance and distribution of age-0 striped bass (Morone saxatilis), delta smelt (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), American shad (Alosa sapidissima), splittail (Pogonichthys macrolepidotus), and threadfin shad (Dorosoma petenense) in the estuary. FMWT has sampled annually since it's inception in 1967, with the exceptions of 1974 and 1979, when sampling was not conducted. The FMWT samples 122 stations each month from September to December and a subset of these data is used to calculate an annual abundance index.
    Science topics Stage, Mysis, Other zooplankton, Water temperature, Turbidity, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail
    Updated April 29, 2022
  • Title

    Lower Sacramento River Green Sturgeon Telemetry Monitoring

    Lead California Department of Fish and Wildlife [CDFW]
    Description To better understand emigration, California Department of Fish and Wildlife is undertaking a collaborative effort with University of California Davis Biotelemetry Laboratory to capture and acoustically tag 100 green sturgeons and 100 white sturgeons per year for three years. CDFW staff conducted sampling by deploying and tending 33-m variable mesh gill nets anchored with 18-kg pyramid weights. Juvenile sturgeon are surgically implanted with Vemco® V9 69 kHz acoustic transmitters and released near the point of capture. An array of Vemco® acoustic receivers deployed throughout the SFBDE collect detection data for acoustically tagged juvenile sturgeons. To date, (January 2018) CDFW and UCD staff tagged 16 juvenile green sturgeon and 11 juvenile white sturgeon over 159 days of sampling effort.
    Science topics Green sturgeon, White Sturgeon
    Updated April 29, 2022
  • Title

    California Natural Diversity Database [CNDDB]

    Lead California Department of Fish and Wildlife [CDFW]
    Description The California Natural Diversity Database (CNDDB) is an inventory of the status and locations of rare plants and animals in California. CNDDB staff work with partners to maintain current lists of rare species, as well as to maintain an ever-growing database of GIS-mapped locations for these species. The CNDDB is a "natural heritage program" and is part of a nationwide network of similar programs overseen by NatureServe (formerly part of The Nature Conservancy). All natural heritage programs provide location and natural history information on special status plants, animals, and natural communities to the public, other agencies, and conservation organizations. The data help drive conservation decisions, aid in the environmental review of projects and land use changes, and provide baseline data helpful in recovering endangered species and for research projects.
    Science topics Mudflats, Intertidal / transition zones, Above-highwater refugia, Main channels, Sloughs, Backwater, Submerged aquatic vegetation, Floating aquatic vegetation, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Non-forested vegetation, Delta islands, Pacific flyway, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Pelagic fish, Benthos, Salt marsh harvest mouse, Waterfowl, Shorebirds, Gulls, Giant garter snake, California tiger salamander, Insects, Mollusks, Crustaceans, Striped bass, Corbicula/Potamocorbula, Nutria, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Saltwater / freshwater marshes, Habitat, Other species, Fish, Mammals, Birds, Amphibians and reptiles, Invertebrates, Invasive / non native species, Non-resident / overwintering birds
    Updated April 29, 2022
  • Title

    Central Valley Angler Survey

    Lead California Department of Fish and Wildlife [CDFW]
    Description CDFW uses a stratified sampling design to interview anglers and check catches in the Delta and throughout the Sacramento system. Focus of the program is on salmonids, but they also record striped bass and sturgeon data, as available.
    Science topics Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Fish
    Updated April 29, 2022
  • Title

    San Francisco Bay Study

    Lead California Department of Fish and Wildlife [CDFW]
    Description The San Francisco Bay Study (Bay Study) was established in 1980 to determine the effects of freshwater outflow on the abundance and distribution of fish and mobile crustaceans in the San Francisco Estuary, primarily downstream of the Sacramento-San Joaquin Delta. Sampling ranges from south of the Dumbarton Bridge in South San Francisco Bay, to just west of Alcatraz Island in Central San Francisco Bay, throughout San Pablo and Suisun bays, north to the confluence Steamboat and Cache sloughs on the Sacramento River, and east to Old River Flats on the San Joaquin River. The open water or boat survey samples 52 stations monthly: 35 original stations, 7 stations added in 1988, 4 stations added in 1991, and 6 stations added in 1994. The study included a beach seine survey, discontinued in 1987, and a shore-based ringnet survey for crabs, discontinued in 1994. The Bay Study uses a 42-foot stern trawler to sample with 2 trawl nets at each open water station. The otter trawl, which samples demersal fishes, shrimp, and crabs, is towed against the current at a standard engine rpm for 5 minutes then retrieved. The midwater trawl, which samples pelagic fishes, is towed with the current at a standard engine rpm for 12 minutes and retrieved obliquely such that all depths are sampled equally. The open water survey included a plankton net that sampled larval fish and crustaceans, but this was discontinued in 1989. Fish, caridean shrimp, and brachyuran crabs are identified, measured, and counted. Shrimp and crabs are also sexed. Sampling effort is quantified (i.e. distance towed, volume of water filtered) and salinity, water temperature, Secchi depth, and station depth are measured;wave height, tide, cloud cover, and tow direction are categorized. The length, catch, and effort data is used to calculate catch-per-unit-effort (CPUE) by species and age class. The CPUE data is used to calculate monthly and annual abundance indices, which are used to track seasonal and annual population trends. Important factors that control or regulate abundance and distribution of fish and mobile crustaceans in the estuary include salinity, temperature, freshwater outflow, ocean temperature, upwelling, and surface currents, primary and secondary productivity, and introduced species. We are interested in how species respond to changes in the physical environment on several temporal scales - seasonal, annual, decadal, and longer. We produce several annual Status and Trends reports that summarize recent changes for the most commonly collected species. These reports are published in the Spring issue of the IEP Newsletter, which can be found at http://iep.water.ca.gov/report/newsletter. The 1999 IEP Technical Report, "Report on the 1980-1995 Fish, Shrimp, and Crab Sampling in the San Francisco Estuary, California", is a good source of basic information. This report is out-of-print, but can be found at www.water.ca.gov/iep/docs/tech_rpts/tech_rprt_63_toc.html. website: https://water.ca.gov/-/media/DWR-Website/Web-Pages/Programs/Environmental-Services/Interagency-Ecological-Program/Files/2019-IEP-Work-Plan_2018-12-11.pdf?la=en&hash=C305D1B1DA7931D95E8676247669F098F26A28FA
    Science topics Water temperature, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Crustaceans, Conductivity, Mammals
    Updated April 29, 2022
  • Title

    Smelt Larva Survey

    Lead California State Water Resources Control Board [SWRCB]
    Description The Smelt Larva Survey provides near real-time distribution data for longfin smelt larvae in the Delta, Suisun Bay and Suisun Marsh. Sampling takes place within the first two weeks in January and repeats every other week through the second week in March. Each 4-day survey consists of a single 10-minute oblique tow conducted at each of the 35 survey locations (see map) using an egg and larva net. The 505-micron mesh net is hung on a rigid frame shaped like an inverted-U, which in turn is attached to skis to prevent it from digging into the bottom when deployed. The net mouth area measures 0.37 m2. The conical net tapers back from the frame 3.35 m to a 1-liter cod-end jar, which collects and concentrates the sample. Immediately after each tow, juvenile fishes are removed, identified, measured and returned to the water immediately, and the remaining larvae are preserved in 10% formalin for later identification in the Lab in Stockton.
    Science topics Stage, Salinity, Water temperature, Turbidity, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Conductivity
    Updated April 29, 2022
  • Title

    Spring Kodiak Trawl Survey

    Lead California Department of Fish and Wildlife [CDFW]
    Description The Spring Kodiak Trawl Survey (SKT) has sampled annually since its inception in 2002. The SKT determines the relative abundance and distribution of spawning delta smelt (Hypomesus transpacificus). The SKT samples 40 stations each month from January to May. These 40 stations range from San Pablo Bay upstream to Stockton on the San Joaquin River, Walnut Grove on the Sacramento River, and the Sacramento Deep Water Ship Channel. Each 'Delta-wide' survey takes approximately 4 - 5 days per month to complete. Historically, 'Delta-wide' surveys were followed by a 'Supplemental' survey two weeks later to intensively sample areas of highest delta smelt concentration to estimate the proportion of male and female delta smelt that were in pre-spawning, spawning and spent maturation stages. Beginning in 2008, in an effort to minimize take of spawning adults, routine 'Supplemental' surveys were discontinued and are now only conducted under the recommendation of the Smelt Working Group and the approval of managers.
    Science topics Stage, Salinity, Water temperature, Turbidity, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Conductivity, Other species
    Updated April 29, 2022
  • Title

    Sturgeon Study

    Lead California Department of Water Resource [DWR]
    Description Staff of the Sturgeon Study make estimates of sturgeon abundance, relative abundance, harvest rate, and survival rate by using data from Commercial Passenger Fishing Vessels (Party Boats;CPFV), various creel surveys, and a mark-recapture program. We monitor the relative abundance of sturgeon by calculating catch per unit effort (CPUE) from data submitted by Commercial Passenger Fishing Vessels. The Department's Marine Region compiles the data, we request the data at intervals, and we calculate CPUE. By applying tags to sturgeon and monitoring the subsequent ratio of tagged fish to untagged fish, we calculate sturgeon abundance, relative abundance, harvest rate, and survival rate. During August-October we use nets in San Pablo Bay and/or Suisun Bay to collect sturgeon, then we tag and release them on-site. Each tag includes our mailing address and a unique code, and some tags include a reward value. By posting "Tagged-fish Wanted" posters around the Estuary and making presentations, we encourage anglers to return tags to us. We also recover tags by talking with anglers during various creel surveys.
    Science topics Main channels, Green sturgeon, White Sturgeon, Habitat
    Updated April 29, 2022
  • Title

    Summer Townet Survey

    Lead California Department of Fish and Wildlife [CDFW]
    Description The Summer Townet (STN) Survey was initiated in 1959 to determine relative distribution and abundance of young of the year (age-0) striped bass (Morone saxatilis) in the Delta. To predict fishery recruitment, the survey calculates an index to measure age-0 striped bass year class strength. This index is based on abundance when age-0 striped bass attain a mean length of 38.1 mm. In contrast, the delta smelt (Hypomesus transpacificus) index is the average of the first two survey indices. The delta smelt index was developed about 1990 in response to declining delta smelt abundance. It has proven valuable in gauging the health of the estuary;delta smelt abundance trend data was used as supporting evidence for their listing as threatened in 1992 under the Federal and State Endangered Species Acts. It appears that zooplankton data are also collected.
    Science topics Mysis, Other zooplankton, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Striped bass, Fish
    Updated April 29, 2022
  • Title

    Suisun Marsh Fish Study

    Lead University of California - Davis [UC Davis]
    Description The University of California, Davis has been involved in fish and wildlife monitoring and research within Suisun Marsh for 35 years and has been instrumental in detecting important trends associated with naturally fluctuating environmental conditions as well as anthropogenic influences. Research has included a 35+ year time series on the fish and invertebrate communities of the slough networks, research on waterfowl nesting patterns and population biology, and research on the demography of salt marsh harvest mouse. The Suisun Marsh Fish Study anchors this effort as it is the longest established survey in Suisun marsh. It will continue the research of Professor Peter Moyle under the direction of John Durand, and will focus upon the detection of changes in the aquatic ecosystem in response to developing stressors in the San Francisco Estuary (SFE). This time series is designed to further our understanding of the ecology and function of the fish community residing within Suisun Marsh and the San Francisco Estuary (SFE), and acts as one of the key surveys with Interagency Ecological Program's monitoring effort.
    Science topics Stage, Tides, Salinity, Water temperature, Dissolved oxygen, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Pelagic fish, Benthos, Salt marsh harvest mouse, Mollusks, Crustaceans, Striped bass, Corbicula/Potamocorbula, Conductivity, Environmental drivers, Other species, Fish, Invertebrates
    Updated April 29, 2022
  • Title

    Fish Salvage and Genetic Analysis

    Lead U.S. Bureau of Reclamation [USBR]
    Description The State Water Project (SWP), operated by the California Department of Water Resources (DWR), and the Central Valley Project (CVP), operated by the U.S. Bureau of Reclamation, export water out of the San Francisco Bay Delta for urban and agricultural use in California. Salvage of fish at both facilities is conducted 24 hours a day, seven days a week at regular intervals. Since 1957, the U.S. Bureau of Reclamation (USBR) has salvaged fish at the Tracy Fish Collection Facility (TFCF). CDFW's Fish Facilities Unit, in cooperation with DWR, began salvaging fish at the Skinner Delta Fish Protective Facility (SDFPF) in 1968. Fish salvage and loss rates are used to determine the need for changes in operations in response to National Marine Fisheries Service (NMFS) regulatory requirements. Salvage and loss monitoring includes daily monitoring and reporting of estimated loss of salvaged fish, as well as monitoring and reporting of salvaged Coded Wired Tagged (CWT) hatchery fish. This information is widely used by West Coast fisheries agencies to collect information on natural and hatchery-reared stocks of salmon and steelhead. Our state-of-the-art genetic analysis techniques are used to quantify salvage rates of listed runs of California's Central Valley juvenile Chinook Salmon. We also utilize advanced genetic analysis techniques to identify different populations of Central Valley juvenile Chinook Salmon, and actively participate in development of new analysis methods.
    Science topics Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Striped bass, Fish, Invasive / non native species
    Updated April 29, 2022
  • Title

    Yolo Bypass Fish Monitoring

    Lead California Department of Water Resource [DWR]
    Description California Department of Water Resources (DWR) has operated a fisheries monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: (1) collect baseline data on lower trophic levels (phytoplankton, zooplankton, and aquatic insects), juvenile fish and adult fish, hydrology, and water quality parameters;(2) investigation of the temporal and seasonal patterns in chlorophyll-a concentrations, including whether high concentrations are exported from the Bypass during agricultural and natural flow events and the possibility of manipulating bypass flows to benefit listed species like Delta Smelt (Hypomesus transpacificus) and Chinook salmon (Oncorhynchus tshawytscha). The YBFMP operates a rotary screw trap and fyke trap, and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts.
    Science topics Surface water / flow, Stage, Velocity, Direction, Tides, Flood, Chlorophyll A / B, Phytoplankton, Other zooplankton, Water temperature, Dissolved oxygen, pH, Turbidity, Other discharge contaminants, Mudflats, Intertidal / transition zones, Main channels, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Insects, Striped bass, Conductivity, Saltwater / freshwater marshes, Fish, Invasive / non native species
    Updated April 29, 2022
  • Title

    Fish Restoration Program Monitoring

    Lead California Department of Fish and Wildlife [CDFW]
    Description The Fish Restoration Program (FRP), an inter-agency agreement between the California Department of Fish and Wildlife (CDFW) and the California Department of Water Resources (DWR), will restore at least 8,000 acres of tidal wetlands in the Sacramento-San Joaquin Delta (Delta) and Suisun Marsh pursuant to requirements in federal Biological Opinions and the California Incidental Take Permit for operation of the State Water Project and Central Valley Project. The rationale for restoration is that state or federally listed fish species, Delta Smelt Hypomesus transpacificus, spring-run and winter-run Central Valley Chinook Salmon Oncorhynchus tshawytscha, and Longfin Smelt Spirinchus thaleichthys will benefit from increased availability of habitat and food web resources. The CDFW FRP Monitoring Team is responsible for monitoring the biological effectiveness of individual FRP tidal wetland restoration projects. Fish catch, invertebrate catch, and water quality data have been collected as baseline monitoring data and to determine the most efficient methods for monitoring wetland restoration efforts.
    Science topics Nitrogen / ammonia, Phosphorous, Carbon, Chlorophyll A / B, Phytoplankton, Other zooplankton, Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Submerged aquatic vegetation, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Insects, Mollusks, Crustaceans, Invertebrates
    Updated April 29, 2022
  • Title

    White Sturgeon Telemetry Synthesis

    Lead Cramer Fish Sciences
    Description Acoustic telemetry studies are expensive and logistically demanding. A new study to tag and monitor 315 White Sturgeon would require a massive field effort by a large team, but by pooling and leveraging existing datasets, this sample size and analysis will be achieved at a fraction of the cost and effort. In recognition of the efficiencies gained by this approach, the Delta Stewardship Council’s Science Program lists the synthesis and analysis of existing telemetry datasets in Science Action Area (SAA) 2. This project directly addresses SAA 2 by capitalizing on existing White Sturgeon telemetry data through the synthesis of three existing large telemetry dataset to understand system-wide White Sturgeon movements. This contract will synthesize existing long-term acoustic telemetry datasets in order to address high priority research questions for the management of White Sturgeon in the San Francisco Estuary system. These questions include: 1. What is the periodicity of spawning migrations by tagged White Sturgeon, and how do these estimates compare to those from previous, single-basin studies? 2. What is the scope and variability of inter-basin movements exhibited by tagged adult White Sturgeon across years? 3. Is there individual fidelity to specific migration routes or sites within each river basin? 4. Do White Sturgeon migrating through the Yolo Bypass experience delays in reaching spawning grounds relative to fish using the mainstem Sacramento River or San Joaquin River routes? 5. Is the onset of upstream migration movement by individuals associated with a characteristic flow rate or event? This contract will serve as a model for future telemetry synthesis studies by adhering to best practices in scientific computing for reproducible, transparent research, and by making all parts of the data and analysis accessible to the broader Delta research community.
    Science topics Environmental drivers, Fish, Flows, White Sturgeon
    Updated February 1, 2024