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  • Title

    Delta Wetland Resilience and Blue Carbon

    Lead San Francisco Estuary Institute [SFEI]
    Description This project estimates carbon storage for the past, present and future Delta, as well as GHG fluxes and elevation change based on chosen restoration and rice farming scenarios in the future Delta using the Delta Landscape Scenario Planning Tool. The project also investigates how well the current organic matter parameterizations and inorganic sediment parameterization in the Marsh Equilibrium Model (MEM) represent Delta marsh accretion processes. Knowledge of marsh accretion and migration will be used to develop a spatial conceptual model of marsh resilience in the Delta.
    Science topics Carbon, Greenhouse gas GHG, Resilience, Sea level rise, Subsidence, Wetlands
    Updated October 13, 2023
  • Title

    Delta Landscapes Project

    Lead San Francisco Estuary Institute [SFEI]
    Description The Delta Landscapes Project has developed a body of work to inform landscape-scale restoration of the Sacramento-San Joaquin Delta ecosystem. The project is built on knowledge, first published in 2012’s Delta Historical Ecology Investigation, of how the Delta ecosystem functioned in the early 1800s (prior to the California Gold Rush and subsequent landscape-level changes).
    Science topics Landscape metrics, Restoration planning, Marsh wildlife, Riparian wildlife, Terrestrial wildlife, Fish
    Updated April 29, 2022
  • Title

    Delta Landscape Scenario Planning Tool

    Lead San Francisco Estuary Institute [SFEI]
    Description The Delta Landscapes Scenario Planning Tool is a set of resources to assist users with developing, analyzing, and evaluating different land use scenarios in the Delta. The tool is designed to inform ongoing and future restoration planning efforts by assessing how proposed projects will affect a suite of landscape metrics relating to desired ecosystem functions.
    Science topics Fish, Landscape metrics, Marsh wildlife, Restoration planning, Riparian wildlife, Sea level rise, Terrestrial wildlife
    Updated November 17, 2022
  • Title

    Landscape Visioning Pilot Application for Staten Island

    Lead San Francisco Estuary Institute [SFEI]
    Description A demonstration project to define possible future land use scenarios for Staten island (“visions”) and leverage existing tools/resources to analyze and compare these scenarios.
    Science topics Habitat restoration, Carbon storage
    Updated April 29, 2022
  • Title

    Delta Salmon Rearing Project

    Lead San Francisco Estuary Institute [SFEI]
    Description This project summarizes existing research and knowledge around suitable rearing habitat for Chinook salmon in the Sacramento-San Joaquin Delta;identifies areas of suitability for rearing salmon using a combined suitability analysis of four mapped habitat parameters;and provides recommendations for types of restoration needed to improve or restore rearing habitat, as well as to identify where in the Delta these restoration efforts could be prioritized.
    Science topics Salmon rearing, Salmon migration, Habitat restoration
    Updated April 29, 2022
  • Title

    Do light, nutrient, and salinity interactions drive the “bad Suisun” phenomenon? A physiological assessment of biological hotspots in the San Francisco Bay-Delta

    Lead University of California - Santa Cruz [UCSC]
    Description This project assessed the physiological basis for reduced phytoplankton growth in Suisun Bay, prior to the major upgrade at the Sacramento Regional Wastewater Treatment Plant (SRWTP), which is responsible for 90% of the nitrogen released into the bay. The work involved analyzing almost three decades of historical eld data from the bay-delta and using it to build a model to evaluate environmental drivers of phytoplankton biomass. Discoveries from the eld data were then tested through laboratory culturing experiments. By illuminating the interacting e ects of bottom- up drivers (light, nutrients, salinity) on phytoplankton, this research helps provide a fundamental understanding of this complex ecosystem.
    Science topics Ammonia, Flushing rates, Light, Open water, Pelagic fish, Phytoplankton, Salinity, Wastewater discharge, Water temperature
    Updated November 17, 2022
  • Title

    Next Generation Multi-Hazard Levee Risk Assessment

    Lead University of California - Los Angeles [UCLA]
    Description In June 2004, a 350-foot levee section gave way west of Stockton, flooding crops and more than a dozen homes, and challenging state officials to protect the state's water supply. What is the risk of that happening again somewhere in the Delta? In light of agricultural fields sinking, the sea level rising, more frequent and severe floods occurring, and earthquakes looming, improvements are estimated to cost $3.8 - $4.3 billion over the next few decades. This study combines 3-D representations with information on the levee’s structure to analyze how different levees respond to floods, sea level rise, and earthquakes. State officials released the last Delta Risk Management Strategy a decade ago. Since then, scientists have collected significant amounts of data and have developed new procedures to compute the risk of failure. This work will produce new Delta-wide data sets important for characterizing the hazards coming from floods and earthquakes. It will also develop the best method to conduct levee hazard assessments. Applying this new method will ensure wise investments and effective threat mitigation Delta-wide.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Tidal Wetland Restoration in the Bay-Delta Region: Developing Tools to Measure Carbon Sequestration, Subsidence Reversal, and Climate Resiliance 2021

    Lead California State University [CSU]
    Description Tidal marshes are important ecosystems in the San Francisco-Bay Delta. They remove carbon from the atmosphere, build up soils that buffer our communities from sea level rise, mitigate excessive nutrients (like nitrogen), and provide critical habitat and food resources for a diversity of species. It is difficult to predict how tidal marshes change naturally over time versus as a response to climate change, restoration and water quality changes. This project provides the first ever multi-year dataset of the complete carbon budget of a tidal marsh. This dataset will be used to predict seasonal and annual carbon budgets in tidal marshes over a range of salinities. The model will assess the sustainability of existing and potential restored tidal wetland benefits over the next 100 years using remote sensing data. The model will be an open-source tool designed for use by wetland managers and decision makers in the Bay-Delta region. This project supports ongoing initiatives to restore tidal wetlands in the Delta and our ability to manage them in a changing world.
    Science topics None specified
    Updated April 29, 2022
  • Title

    An Improved Genomics Tool for Characterizing Life History Diversity and Promoting Resilience in Central Valley Chinook Salmon

    Lead Michigan State University
    Description This study will improve our ability to protect the diversity of traits in Chinook salmon. The diversity of Chinook salmon migration timing is decreasing in the Central Valley. A key roadblock to protecting diversity is the current inability to rapidly and inexpensively identify large numbers of individuals from different populations during their migration to the ocean. This study addresses this information gap by leveraging pre-existing genomic data to develop a new technique that will allow scientists to identify individuals to life history type and location. For example, this study will potentially be able to identify Fall Run Chinook that are from the Sacramento versus the San Joaquin River basins. This information, in combination with data on water temperature and river flows, can determine the relationship between environmental conditions and juvenile salmon life history diversity. The information generated by this work will provide managers with the ability to accurately monitor the effect of key management actions on the different Central Valley Chinook salmon populations.
    Science topics Chinook Salmon, Estuaries, Fish, Habitat restoration, Resilience, Salmon rearing
    Updated November 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

    Changes in Organic Carbon and Food Resources in Response to Historical Events in the Sacramento-San Joaquin Delta: A Synthesis Project

    Lead Virginia Institute of Marine Science
    Description Recent management strategies in the Delta rely on habitat restoration and water quality improvement to restore ecosystem function. However, current monitoring programs have been limited in their ability to measure ecosystem functions such as food webs. This study explores changes to the sources, quantity, and quality of organic carbon that support the Delta food web. Data from fifteen sites selected to represent the dominant sub-habitats in the Delta will identify the available food resources. The project examines how food resources are affected by wastewater treatment and habitat restoration. Information about organic carbon in the historic and current Delta will aid in establishing realistic goals and targets for ongoing and future restoration efforts in the Delta.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Estuarine fish community responses to climate, flow, and habitat

    Lead University of California - Berkeley [UC Berkeley]
    Description The goal of this research is to better understand how climate change will affect fishes with different life histories and habitat associations across the San Francisco Estuary. Existing datasets will be incorporated in synthetic analyses and cutting-edge statistical models to identify fish community responses to climate, flows, and habitats along the estuarine salinity gradient. This synthesis-science project will use rich long-term datasets that have been collected by Bay-Delta researchers for decades that will then be analyzed in a reproducible and open science framework. It will also support efforts by the Interagency Ecological Program’s Climate Change Project Work Team.
    Science topics Estuaries
    Updated April 29, 2022
  • Title

    Using existing datasets to understand multi-scale changes in and controls on biogeochemistry in the SF Bay-Delta

    Lead University of California - Santa Cruz [UCSC]
    Description In collaboration with the United States Geological Survey, this research will explore temporal and spatial variability of carbon and nitrogen biogeochemistry across the San Francisco Bay-Delta. This science synthesis will capitalize on existing multi-year isotope datasets to gain new insights useful for understanding future changes in the system. The results generated from this two-year data synthesis project will be useful for improving our current understanding of factors driving changes in SF Bay-Delta biogeochemical processes. Results will also be informative for understanding the imminent changes coming to the from the Sacramento Regional Wastewater Treatment Plant upgrade.
    Science topics Nitrogen
    Updated November 17, 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

    Assessing sea-level rise and flooding changes in the Sacramento/San Joaquin Delta using historical water-level records

    Lead California State University [CSU]
    Description The project aims to recover, digitize, and analyze more than 1300 station years of ‘lost-and-forgotten’ water level records collected from 1857 to 1982 in the Sacramento-San Joaquin Delta. These measurements, augmented by modern data, will improve our understanding of tidal, flood, and sea level trends in the system. By determining ‘hotspots’ of habitat and flood risk sensitivity, the results may be used to better focus future scientific and management priorities, to protect the environment, manage flood risk, and enhance community resilience to climate change
    Science topics Backwater, Climate change, Environmental drivers, Estuaries, Land elevation, Levees, Outflow, Sea level rise, Stage, Subsidence, Surface water / flow, Tides, Velocity, Vessels and shipping channels, Water, Wind
    Updated October 10, 2023
  • Title

    Open-Source Resources for the Sacramento-San Joaquin Delta Telemetry Research Community

    Lead Cramer Fish Sciences
    Description There is a great deal of telemetry data amassed from studies in the Sacramento-San Joaquin Delta. It continues to grow every year with special studies and monitoring efforts. Multiple research priorities surrounding fish ecology in the Delta could be addressed, at least in part, by synthesizing the myriad telemetry data sets that exist; this work would benefit greatly from the centralization and standardization of data workflows surrounding telemetry research. With the guidance of a PIT Advisory Team, we plan to establish a collection of open-source, technology-agnostic, accessible resources to support a reproducible and transparent telemetry data workflow for researchers in the region. The workflow and resources do not invent new procedures, rather improve and standardize those already used by the telemetry research community. This will bring us in closer alignment with centralized, coordinated data workflows that have been successfully implemented in other regions and data communities. The final open-source set of resources will include a design and roadmap for implementing a central telemetry database and workflow, an R package for the preparation, QA/QC, and basic analysis of telemetry data, and a regional workshop offering training programs in the proposed telemetry data workflow.
    Science topics Chinook Salmon, Fish, Other species, Salmon migration, Steelhead Trout, Striped bass, Sturgeon
    Updated December 22, 2023
  • Title

    Standard Operating Procedure for Diagnosing and Addressing Predator Detections in Salmon Telemetry Data

    Lead University of Washington [UW]
    Description Tag predation is a complicating factor in juvenile salmon telemetry studies that can bias results, delay timely reporting, and prevent effective data synthesis. This project addresses the problem by (1) characterizing predatory fish movement patterns from existing telemetry data in the Delta; (2) developing a standard operating procedure for diagnosing and handling detections of predated tags in salmon telemetry studies; and (3) implementing the recommendations in a software package in Program R that includes code, a “library” of expected predator behaviors, and example vignettes. The R package will be freely available for download at www.cbr.washington.edu.
    Science topics Chinook Salmon, Endangered species, Fish, Intertidal / transition zones, Invasive / non native species, Predation, Salmon migration, Steelhead Trout, Striped bass
    Updated December 26, 2023
  • Title

    Impacts of predation and habitat on Central Valley Chinook smolt survival

    Lead University of Vermont, USGS Vermont Cooperative Fish and Wildlife Research Unit
    Description The Sacramento River in California’s Central Valley has been highly modified over the past 150 years due to mining, urbanization, and impoundment/diversion of river flow to provide water for municipal, industrial, and agricultural needs. Land use changes combined with high levels of harvest have been accompanied by drastic declines in native salmon populations, including the once abundant Chinook salmon (Oncorhynchus tshawytscha). Further, the region has been subject to the introduction and widespread establishment of non-native fish species, some of which are predators of juvenile salmon. Of the four historic ecotypes of Chinook salmon (fall, late-fall, winter, and spring runs), winter- and spring-runs have been most impacted and are currently listed as endangered and threatened respectively under the US Endangered Species act. Past research has illustrated how smoltification of juvenile salmon and outmigration from freshwater to the ocean is a time of increased mortality, and reduced survival at this life stage can impact the number of reproducing adults returning to the system in subsequent years. While these studies have provided valuable information on how habitat and environmental conditions experienced by migrating Chinook salmon smolts can affect survival, they have primarily focused on individual ecotypes during the portion of the year where downstream migrations occur. However, variation in smolt size and migration timing among ecotypes can expose migrating fish to differing environmental conditions and levels of exposure to predation, which can present distinct risks for outmigration survival. To identify the areas and environmental conditions which have the greatest relative impact on juvenile survival for each ecotype, this project will use over ten years of data (2012-2022) from acoustically tagged smolts representing all four Chinook salmon ecotypes in the Sacramento River/Central Valley. Combining these data will increase sample size relative to previous studies, the range of environmental conditions (e.g., temperature, flow, and predator abundance) modeled, the range of fish sizes, and thus, the statistical power of our analyses. We hypothesize that each ecotype will have different factors that will be the primary drivers of mortality experienced during outmigration. To test our hypotheses, we will implement Cormack-Jolly-Seber (CJS) mark-recapture models to estimate both the probability of survival through reaches of the Sacramento River delineated by acoustic receivers, and the detection probability in each reach. Survival will be modeled as a function of individual, release group, reach-specific, and time-varying covariates. Further, to examine the relative impact of predation on smolt survival, we will include an additional covariate representing predator-prey encounter rates using the Mean Free-path Length model. Finally, model selection will be applied to a series of CJS models to assess the relative impact of each covariate on smolt survival for each of the four Chinook ecotypes.
    Science topics Chinook Salmon, Environmental drivers, Fish, Flows, Habitat, Predation, Salmon migration, Water temperature
    Updated February 2, 2024
  • 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