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  • Title

    Delta Landscapes Primary Production Project

    Lead San Francisco Estuary Institute [SFEI]
    Description This project compares first-order estimates of primary production among five major groups of primary producers, historically and today, to better identify the potential food production of different habitat types, and inform restoration actions that could increase food availability for wildlife.
    Science topics Primary production, Phytoplankton, Emergent macrophytes, Epiphytic algae, SAV/FAV
    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

    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

    Soil type as a driver of agricultural climate change response in the Sacramento-San Joaquin Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description This research project aims to increase understanding of how iron-rich peatland soils cycle carbon, nitrogen, and phosphorus in the delta and establish how carbon and nitrogen biogeochemistry and greenhouse gas emissions vary with management practices and crop type. It also explores how a drier future climate will influence biogeochemistry and greenhouse gas emissions in iron-rich soils and how to best adapt land management practices. The goal of this research is to identify agricultural practices that can generate a portfolio of climate change adaptation and greenhouse gas mitigation strategies for delta farmers. The greenhouse gas data collected as part of this research also helped to generate increasingly accurate emission offset credits for potential wetland restoration projects in California’s Cap-and-Trade program.
    Science topics Agriculture, Carbon, Nitrogen, Phosphorous, Soil
    Updated November 17, 2022
  • Title

    Operation Baseline Project 2B: Phytoplankton, CSU Maritime Academy

    Lead California State University Maritime Academy
    Description Planned upgrades to the Sacramento Regional wastewater treatment plant (Regional San) between 2019 and 2021 will reduce total nitrogen inputs by >60% and shift the dominant form of nitrogen entering the Delta from ammonium (NH4) to nitrate (NO3). These changes will affect the Delta in ways unforeseeable with existing knowledge. The focus of this project is to quantify the links between wastewater nitrogen and phytoplankton standing stock, community composition and carbon and nitrogen production. Working in collaboration with the other two Operation Baseline projects, we will: 1. validate in situ monitoring approaches for phytoplankton standing stock and community composition (i.e. using size-fractionated chlorophyll-a and diagnostic phytopigments via HPLC) and 2. provide estimates of ambient and nitrogen-saturated phytoplankton NH4 and NO3 uptake rates as well as C uptake. Phytoplankton N and C uptake rates will be made along spatial gradients in nitrogen and water residence time (Task 1) and in three wetland habitats with varying influence from wastewater nitrogen (Task 3). Together with the other proposals, this project will provide much needed baseline characterization of nutrient processes in the Delta prior to Regional San upgrades.
    Science topics Algae, Floating aquatic vegetation, Food webs, Nitrogen / ammonia, Open water, Other discharge contaminants, Phytoplankton, Submerged aquatic vegetation, Wastewater discharge, Water operations / exports, Wetlands, Zooplankton
    Updated December 14, 2022
  • Title

    Operation Baseline Project 2C: Zooplankton, Romberg Tiburon Center, SFSU

    Lead San Francisco State University [SFSU]
    Description This project will examine responses of zooplankton (copepods) to variations in the foodweb attributable to nutrient sources. At each wetland site we will determine spatial abundance patterns and rates of reproduction, growth, and mortality. These will be integrated with information on phytoplankton and physical dynamics to determine how population dynamics responds to nutrient conditions. Stable isotopes will be used to assess nutrient source contributions to growth.
    Science topics Algae, Floating aquatic vegetation, Food webs, Nitrogen / ammonia, Open water, Other discharge contaminants, Phytoplankton, Submerged aquatic vegetation, Wastewater discharge, Water operations / exports, Wetlands, Zooplankton
    Updated December 14, 2022
  • Title

    Investigation of the resilience of the salt marsh harvest mouse and best management practices in response to climate change

    Lead University of California - Davis [UC Davis]
    Description This study aimed to investigate the response of the salt marsh harvest mouse to several threats of climate change, including extreme annual climate cycles and sea level rise. The study was based on ongoing population surveys in the Suisun Marsh, and a study of upland/elevated refuge throughout the species’ range, over the two-year study. It also involved the piloting of advance remote detection technology (camera traps, audio detectors, and digital mouse traps) and effective, affordable high tide refuge (islands and trellises). Finally, ongoing trapping efforts at established survey sites is providing data for ongoing analysis on the effects of weather patterns and space needs of populations.
    Science topics Climate change, Salt marsh harvest mouse, Saltwater / freshwater marshes
    Updated November 17, 2022
  • Title

    Effects of copper exposure on the olfactory response of Delta smelt [Hypomesus transpacificus]: Investigating linkages between morphological and behavioral anti-predator response

    Lead University of California - Davis [UC Davis]
    Description This study aimed to address the question of how water-borne copper can affect the ability of delta smelt to detect predator related odorants and conduct essential behaviors. To do this, the project included a thorough morphological and cytological study of the delta smelt olfactory organ, which had previously not been well-studied. The researchers also characterized the olfactory mediated antipredatory response to alarm cues and assessed the effects of copper exposure on the anti-predator behavior and morphology of the olfactory rosette of delta smelt.
    Science topics Copper, Delta Smelt, Toxicity
    Updated November 17, 2022
  • Title

    Effect of temperature and salinity on physiological performance and growth of longfin smelt: Developing a captive culture for a threatened species in the Sacramento- San Joaquin Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description This research project aimed to improve understanding of the physiological requirements for survival and reproduction across the entire life history of longfin smelt (from egg to larvae to juvenile to reproducing adult). The overall goals of this project were to assist in developing a captive longfin smelt culture and assess longfin smelt responses to multiple stressors across all life stages, which has been difficult because of extremely low (<10%) larval survival of these fish.
    Science topics Delta Smelt, Longfin Smelt, Salinity, Temperature
    Updated November 17, 2022
  • Title

    Reevaluating ecosystem functioning and carbon storage potential of a coastal wetland through integration of lateral and vertical carbon flux estimates

    Lead University of Washington [UW]
    Description This study aims to produce an integrated, net ecosystem carbon budget for Suisun Marsh, a representative ecosystem in the delta. This project combines diverse measurements on land and in the adjacent marine environment to produce the first directly measured, complete carbon budget for a coastal wetland habitat. This work has generated a more complete picture of the potential of wetland preservation for greenhouse gas reduction, as well as the processes that shape wetland accretion and resilience to sea-level rise. The project will provide vital information for understanding the ecosystem services, food webs, and carbon storage potential of the region’s wetlands, as well as provide new methodology that could be used by researchers around the world.
    Science topics Atmosphere, Carbon, Carbon storage, Evaporation / evapotranspiration, Non-forested vegetation, Sea level rise, Sediments, Surface water / flow, Wetlands
    Updated November 17, 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

    Simulating methylmercury production and transport at the sediment-water interface to improve the water quality in the Delta

    Lead University of California - Merced [UC Merced]
    Description The aim of this project was to improve basic knowledge of mercury cycling and aid management of net methylmercury production in the delta by developing a kinetic-thermodynamic reaction model that describes and quantifies mercury cycling in delta sediments. The model was used to assess uncertainties and estimate methylation and demethylation rates — the processes by which methylmercury is produced and breaks down. In addition, the project examined coupling of mercury cycling with cycling of iron, sulfur, and manganese.
    Science topics Bioaccumulation, Chemistry, Hg and methyl mercury
    Updated November 17, 2022
  • Title

    Defining habitat quality for young-of-year longfin smelt: Historical otolith-based reconstructions of growth and salinity history in relation to geography, climate, and outflow

    Lead University of California - Davis [UC Davis]
    Description This project aimed to use experiments to develop new otolith-based tools for longfin smelt and to then apply them to an extensive collection of archived wild Longfin Smelt specimens, to build a better understanding of longfin smelt life history, habitat use, and the interactions between stressors and abundance. In addition, the project aims to improve the understanding of how longfin smelt populations are affected by freshwater outflow. The project also aims to provide tools to support and evaluate habitat restoration, and facilitate development of a plan to recover this threatened species.
    Science topics Longfin Smelt, Outflow, Salinity
    Updated November 17, 2022
  • Title

    Operation Baseline Project 1: Conceptual Framework

    Lead Delta Stewardship Council
    Description A multidisciplinary team will develop a thorough conceptual model that will describe current conditions and consider changes from the WWTP upgrade. The model will be used to identify the highest priority science questions and investigations to pursue before, during, and after the plant upgrade.
    Science topics Algae, Floating aquatic vegetation, Food webs, Nitrogen / ammonia, Open water, Other discharge contaminants, Phytoplankton, Submerged aquatic vegetation, Wastewater discharge, Water operations / exports, Wetlands, Zooplankton
    Updated December 14, 2022
  • Title

    Operation Baseline Project 2A1: USGS Pilot Studies

    Lead U.S. Geological Survey [USGS]
    Description Two pilot studies were funded to establish a baseline in open water and shallow wetland habitats prior to the WWTP upgrade. Study 1: Nutrient concentrations, transformation rates, and links to the foodweb. Study 2: Method to improve monitoring using fixed stations coupled with high-speed boat measurements
    Science topics Algae, Floating aquatic vegetation, Food webs, Nitrogen / ammonia, Open water, Other discharge contaminants, Phytoplankton, Submerged aquatic vegetation, Wastewater discharge, Water operations / exports, Wetlands, Zooplankton
    Updated December 14, 2022
  • Title

    Operation Baseline Project 2A2: USGS Pilot Studies - Isotopes

    Lead U.S. Geological Survey [USGS]
    Description Evaluate the usefulness of stable isotopes to trace nutrients form effluent water
    Science topics Algae, Floating aquatic vegetation, Food webs, Nitrogen / ammonia, Open water, Other discharge contaminants, Phytoplankton, Submerged aquatic vegetation, Wastewater discharge, Water operations / exports, Wetlands, Zooplankton
    Updated December 14, 2022
  • Title

    Nutritional Quality of Zooplankton as Prey for Fish in the Sacramento-San Joaquin Dalta

    Lead University of California - Davis [UC Davis]
    Description Primary consumers (zooplankton) are a critical trophic link for energy transfer to upper trophic levels and a key food source for threatened and endangered fish species in the Delta. The zooplankton community was shaped by large spatial and temporal changes in both abundances and species composition that affected quantity of zooplankton carbon. It is also expected that taxonomic shifts affected quality of zooplankton carbon for fish due to altering biomass transfer at the base of the food web that can profoundly influence nutritional quality and population dynamics at higher trophic levels. Yet the biochemical composition of plankton remains largely unstudied in this system despite the fact that the importance of zooplankton nutritional quality for fish is one potential major component for the long-term decline and more recent collapse of pelagic fish species. The proposed research aims to measure essential nutritional status (stoichiometry, fatty acids, sterols) for zooplankton taxa and will calculate food-quality indices for fish. On the basis of nutritional plankton and biomass values, spatial patterns as well as long-term and recent changes in plankton quality associated with compositional shifts will be estimated. We propose that through integrating plankton food-quality into the management and restoration plan for the Delta, the dynamics of the ecosystem can be viewed from a new perspective that has key implications for understanding the decline in pelagic organisms.
    Science topics Zooplankton
    Updated April 29, 2022
  • Title

    An Open-Source, Three-Dimensional Unstructured-Grid Model of the Sacramento/San Joaquin Delta: Model Construction and Application to Delta Hydrodynamics and Temperature Variability

    Lead Stanford University
    Description Motivated by the need to predict transport in the Delta, this project will apply the open-source, unstructured-grid computer model, SUNTANS (Stanford Unstructured Nonhydrostatic Terrain following Adaptive Navier Stokes simulator) to the Sacramento/San Joaquin Delta. SUNTANS solves the governing equations of fluid flow on a grid that permits fine detail in areas of particular interest in the Delta, while allowing us to include the entirety of the Bay/Delta system so as to properly model oceanic and estuarine influences on the Delta We have two aims:(1) to carry out the model development needed to apply SUNTANS to the Delta;(2) to apply the model to look at aspects of the physical variability of the Delta that are critical to ecosystem function and to understanding how physical processes in the Delta affect ecosystem function, most notably entrainment of fish and other organisms by the export facilities. In particular, we propose to look at flow behavior at channel junctions, a key aspect of Delta hydrodynamics that influences dispersion in the Delta and thus the transport of biota, nutrients and contaminants. We also will examine the dynamics of spatial and temperature variability in the Delta in response to tides, atmospheric forcing, river flows, and diversions, variability that must be properly calculated to forecast how climate change and altered project operations may affect key species like Delta Smelt. We will carry out new fieldwork to support our modeling.
    Science topics Water temperature
    Updated April 29, 2022
  • Title

    Integrating Ecosystems, Flood Control, Agriculture, and Water Supply Benefits: An Application to the Yolo Bypass

    Lead University of California - Davis [UC Davis]
    Description The Yolo Bypass presents an opportunity to develop mechanisms governing the management of flows across floodplains that balance ecosystem services with economic and recreational functions, and to study the untapped potential of such floodplains to play a role in conjunctive surface and groundwater management. Analysis to the necessary high degree of spatial resolution for such management decisions is generally lacking for the Yolo Bypass. This proposal seeks funding for an interdisciplinary study to better understand the economic, hydrologic, and ecological functioning of land and water across the bypass, and to develop tools that use this knowledge in identifying promising strategies for the timing and configuration of spring inundation. Agronomic, economic, and hydraulic models will be used with formal interviews to study the relationship between flooding and six Yolo Bypass functions: (1) Agricultural Economics, (2) Waterfowl management, (3) Native Fish habitat, (4) Flood Control, (5) Groundwater storage, and (6) Recreation. Data from these first efforts will be incorporated into an optimization model that identifies promising inundation alternatives for ecosystem services which minimize costs to landowners and waterfowl managers, and maximize potential conjunctive use benefits. This synthesis answers the Delta Science Program's request for coupled hydrologic and ecosystem models, and for water and ecosystem management decision support system development.
    Science topics None specified
    Updated April 29, 2022
  • Title

    CASCaDE II: Computational Asessments of Scenarios of Change for the Delta Ecosystem

    Lead U.S. Geological Survey [USGS]
    Description This proposal builds upon an existing model-based effort to develop a holistic view of the Bay-Delta-River-Watershed system. CASCaDE I developed a set of linked models to assess Delta ecosystem response to climate change. In CASCaDE II, we propose to refine and extend those modeling capabilities to assess Delta ecosystem response to changes in climate and physical configuration. With a new state-of-the-art hydrodynamic and sediment model at its core, CASCaDE II will link models of climate, hydrology, hydrodynamics, sediment, geomorphology, phytoplankton, bivalves, contaminants, marsh accretion, and fish. Our goals are to apply these linked models to 1) better understand Delta ecosystem function, 2) assess possible futures of the Delta under scenarios of climate and structural change, and 3) provide science-based information to support the DSC in its co-equal goals of water supply and ecosystem protection. The tools developed will provide an objective basis for anticipating and diagnosing Delta ecosystem responses to planned and unplanned changes. Experiments using the linked models are designed to address questions such as: How will climate change, together with new conveyance structures or increased flooded island habitat, alter water flow and drinking water quality? With projected changes in residence time, turbidity, temperature, and salinity, how will primary productivity, invasive bivalves, marsh processes, contaminant dynamics, and fish populations respond?
    Science topics None specified
    Updated April 29, 2022
  • Title

    Quantifying the contribution of tidal flow variations to survival of juvenile Chinook salmon

    Lead U.S. Geological Survey [USGS]
    Description The purpose of this project is to quantify how tides in the Delta influence survival of juvenile salmon. Juvenile salmon survival increases when there is more flow and the river is less tidally influenced. We hypothesize that the increase in survival is because of reduced travel times causing less exposure to predators. This project will test this hypothesis using multiple models including ones that can predict how management actions that modify tidal patterns affect juvenile salmon survival.
    Science topics Chinook Salmon, Salmon migration, Surface water / flow, Tides, Water management
    Updated January 29, 2024
  • Title

    Assessing Sediment Nutrient Storage and Release in the Delta: Linking Benthic Nutrient Cycling to Restoration, Aquatic Vegetation, Phytoplankton Productivity, and Harmful Algal Blooms

    Lead U.S. Geological Survey [USGS]
    Description Nutrients in sediment play a large role in influencing food webs, harmful algal blooms, aquatic vegetation, and drinking water quality. This study will investigate the amount, types, and dynamics of nutrients in Delta sediments. It will also examine sediment microbial communities that mediate these processes. Results of this study will help determine how the planned reduction in nutrient inputs to the Delta will effect sediment nutrients and microbial communities following the upgrade of the Sacramento Regional County Sanitation District’s wastewater treatment plant. Data will also inform how wetland restoration and invasive aquatic vegetation influence sediment nutrients and microbial communities. These data will contribute to improving computer models that inform large-scale nutrient management actions.
    Science topics Aquatic vegetation, Benthic, Cyanobacteria, Harmful algal blooms HAB, Nitrogen, Nitrogen / ammonia, Nutrients, Phytoplankton, Sediments
    Updated May 14, 2024
  • Title

    Low-Cost Satellite Remote Sensing of the Sacramento-San Joaquin Delta to Enhance Mapping for Invasive and Native Aquatic Vegetation

    Lead University of California - Davis [UC Davis]
    Description Invasive aquatic vegetation (IAV) acts as an ecosystem engineer by changing habitat conditions and water quality. This negatively affects the survival of native species. Over the past 15 years, IAV has more than doubled its footprint in the Sacramento-San Joaquin Delta waterways. The State of California spends millions of dollars each year to control IAV in the Delta-Suisun region and costs are likely to continue to rise. Gaining a better understanding of the spread, life history characteristics, and potential vulnerabilities of these species can lead to more effective control strategies. The recent launch of the Sentinel-2 satellite can fill temporal gaps left by annual airborne surveys. This study will create a data pipeline for sustained, low-cost satellite-based monitoring of aquatic and marsh vegetation year-round. To quantify one of the Delta Plan performance measures, the time and degree of floodplain inundation for the Yolo Bypass will be measured. This study will result in new metrics to measure progress toward habitat goals in several restoration sites.
    Science topics Aquatic vegetation, Invasive / non native species
    Updated November 18, 2022
  • Title

    Resolving Contradictions in Foodweb Support for Native Pelagic Fishes

    Lead San Francisco State University [SFSU]
    Description Much research in the Delta has focused on foodweb dynamics, stimulated by evidence that low productivity of plankton is linked to declines in several fish species including the endangered delta smelt. Pseudodiaptomus forbesi is the most abundant copepod (small crustaceans) in the Delta in summer. It is an important food source for many fishes and makes up about half of the food of delta smelt. This study focuses on the feeding, reproduction, and growth of copepods as essential foodweb support for fishes. This work investigates four diverse habitats including two open-water channels and two shallow habitats. The researchers will measure copepods´ feeding rates on microscopic plants and animals, and relate feeding to their rates of growth and reproduction. Computer models will be used to estimate their movement and death rates. These results will show the sources of nutrition used for growth and reproduction of these key organisms. Results will inform how food webs respond to large scale changes in the Delta ecosystem, for example, restoration and the Sacramento wastewater treatment plant upgrade.
    Science topics None specified
    Updated April 29, 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

    Recreational Hunting as an Ecosystem Service of Restoration in the Bay-Delta Watershed

    Lead Santa Clara University
    Description Ecological restoration in the Bay-Delta watershed provides increased access to hunting opportunities for recreational hunters in the region in addition to benefitting native flora and fauna. While increased hunting is not always considered an economic benefit, it is a dividend from investments in habitat restoration. This research will quantify in dollars the economic impact of restoring sites and opening them for hunting. The study will survey members of the public at restored sites in the Bay-Delta and Sacramento River regions that have resulted in new and/or improved hunting access. In addition to the economic analysis, the survey will shed light on two other issues: 1) whether there is a tradeoff among recreational usage, carbon storage, and habitat quality for restored sites, and 2) whether current users perceive an unmet need for recreational access in the region. These analyses will be useful in explaining multi-benefit restoration projects to stakeholders and policymakers, and informative to future decision-making.
    Science topics Hunting
    Updated December 7, 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

    Integrated Science and Management of Nutrient, Salt, and Mercury Export from San Joaquin River Wetland Tributaries to the Delta

    Lead University of California - Merced [UC Merced]
    Description Mercury, salinity, and nutrients such as nitrogen and phosphorus are major contaminants of concern and are an understudied source of water quality impairment to the Delta. This study will (1) examine seasonal variation and transfer of salt, nutrients, and mercury out of managed wetlands;(2) establish and verify whether other routinely monitored water components can serve as reliable alternatives (proxies) for detecting mercury and nutrients;(3) integrate monitoring data and proxy relationships to estimate levels of contaminants;and (4) develop science-based strategies for adaptive co-management of salt, nutrients, and mercury from seasonal wetlands to improve water quality in the Delta. Outcomes from this study will provide improved best practices and guidelines for management of salt, nutrients, and mercury in wetlands. Results will also address key knowledge gaps identified in the Delta Nutrient Research Plan and provide support for the Delta Mercury Control Plan.
    Science topics Nutrients, Salinity, Hg and methyl mercury
    Updated April 29, 2022
  • Title

    Risk of fish predation within and across tidal wetland complexes

    Lead University of California - Davis [UC Davis]
    Description This study focuses on understanding how restored tidal wetlands with different physical configurations function as refuge and rearing habitat for fishes, including native and imperiled species such as delta smelt and juvenile Chinook salmon. This research will assess the spatial distribution of predation risk as it varies within and across tidal wetlands. The proposed research will generate a statistical model that helps predict predation outcomes from various restored tidal wetland designs and channel configurations. This will be a powerful tool for managers to forecast how proposed habitat restoration or water management actions may impact native fish populations.
    Science topics Tidal wetlands
    Updated April 29, 2022
  • Title

    Phytoplankton and cyanobacteria growth and response to stressors

    Lead University of California - Davis [UC Davis]
    Description Pesticide and nutrient inputs from human activities are present in the Sacramenot-San Joaquin Bay-Delta, but the impact of these stressors together on algae is not well known. This research will examine the impacts of herbicides and nutrients on the growth and stress responses of phytoplankton and cyanobacteria present in the San Francisco Estuary. The algae in the delta are diverse with critical ecological effects, ranging from toxin-producing cyanobacteria that form hazardous algal blooms to benthic diatoms and green algae that make up the bulk of the aquatic food web. Contaminants and herbicides can cause changes in algae cellular health which may impact population growth. Understanding algal sub-lethal stress responses will improve our understanding of stressors on the bay-delta food web and bloom formation.
    Science topics Phytoplankton, Cyanobacteria
    Updated April 29, 2022
  • Title

    Wetland carbon sequestration and impacts of climate change

    Lead California State University [CSU]
    Description This project aims to improve understanding of atmospheric and hydrologic carbon fluxes in a restored tidal salt marsh in the South San Francisco Bay. I will use soil chambers to measure how much carbon dioxide and methane is taken in and emitted from the marsh. The project will also examine how spatial variability in marsh surface cover impact these exchanges. Shahan will use the data collected in this study to create a biogeochemical model that estimates the carbon budgets of wetlands in the Bay-Delta. A complete carbon budget will illuminate relationships between carbon fluxes and environmental variables. This information can support more informed management of wetlands, as well as allow researchers and decision makers to more effectively plan wetland restoration to be effective in managing carbon fluxes in the face of possible impacts due to climate change.
    Science topics Wetlands
    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

    Environmental geochemistry and tidal wetland support of pelagic food webs

    Lead University of California - Davis [UC Davis]
    Description This project aims to characterize and quantify where detrital material (decaying plant matter) originates within wetlands, the composition of that material, and how export of detrital particles occurs. This project will combine powerful characterization tools and techniques that scale from molecules to ecosystems to assess spatial and temporal trends in particle sources, species and composition. Because restoration in the Sacramento-San Joaquin Delta will fundamentally alter particle distribution and food availability for aquatic organisms, this study will inform habitat restoration efforts and the revival of native fish populations. The tools developed and adapted for this project may inform management response during extreme conditions and climate events by helping to identify areas that may act as refugia for species.
    Science topics Wetlands
    Updated April 29, 2022
  • Title

    The effect of temperature on predation of juvenile salmonids

    Lead University of California - Davis [UC Davis]
    Description This study will investigate fish swim performance in response to temperature, using salmon and two of its known predators: largemouth bass and Sacramento pikeminnow. The researcher will assess swim performance metrics and predation risk inside and outside the ideal thermal range of each species to determine if a temperature advantage predicts salmon survival in predation scenarios. This project’s results will provide a mechanistic understanding of how temperature stress may influence mortality risk of juvenile Chinook salmon through predation, which will offer a more holistic perspective on the management of this species
    Science topics Temperature
    Updated April 29, 2022
  • Title

    Pesticide risk analyses and management actions, chemical fate and transport

    Lead University of California - Santa Barbara [UCSB]
    Description This project work will model the risk of pesticide pollution in 225 sub-catchments of the Sacramento-San Joaquin Bay-Delta. The model will account for water management practices, land use, pesticide use rates, and cumulative pesticide stress. Additionally, this work will produce a web-based tool to simulate current and future risks based on the ranking of primary sources of pesticide contribution. This work will provide a framework to predict risk from chemical stressors. Specific objectives are: (1) enhanced pro-active chemical risk assessment, (2) creation of a tool which enables science-based chemical use decisions, (3) improved risk screening for vulnerable areas, and (4) identification of adverse effects of current and future chemical use strategies.
    Science topics Herbicides
    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

    Nitrogen cycling and ecosystem metabolism before and after regulatory action

    Lead Stanford University
    Description This project focuses on nitrogen and carbon cycling within the Bay-Delta, both before and after planned 2021 upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP). We will measure in situ benthic nitrate (NO3- ) and oxygen (O2) fluxes using a new non-invasive technique, which provides high frequency continuous data over a much larger sediment surface area than traditional methods. The SRTWP currently represents one of the largest point sources of nitrogen to the Bay-Delta, with the upgrades projected to cut nitrogen outputs from the plant by ~65%. This project will help assess the efficacy of this major management action and our results will add to biogeochemical models for the Bay-Delta.
    Science topics Nitrogen / ammonia
    Updated April 29, 2022
  • Title

    Understanding the Scale and Mechanisms of Connectivity between Splittail Populations and the Implications for Management

    Lead U.S. Bureau of Reclamation [USBR]
    Description Our proposal seeks to add four elements, telemetry, genetics, physiology, and modeling, to an existing research effort on splittail. The study addresses the hypothesis that there is no difference in population dynamics between the two distinct splittail populations. To address this hypothesis we are conducting a collaborative, interdisciplinary study that includes an intensive field effort combined with state-of-the-art laboratory tools that can determine the natal origins, historical habitat use, feeding, and general health of adult splittail. With this proposal we seek to leverage additional funds that were not previously available to add the four new elements. The telemetry component will take advantage of the expansive existing array of receivers deployed in the estuary to evaluate the movements and migration of splittail. The genetic component will provide a precise means to assign individuals to their respective population, determine sex ratios, and to estimate the effective size of the populations. The physiology component will determine if the newly discovered Petaluma/Napa population of splittail exhibits different requirements and tolerances than the Central Valley population. The modeling component will apply the cumulative information gained by the overall study to evaluate the sensitivity of splittail persistence to demographic variability in population dynamics. This work will directly address the Priority Research Topics presented in the PSP.
    Science topics Sacramento Splittail
    Updated April 29, 2022
  • Title

    Linking Trophic Ecology with Slough and Wetland Hydrodynamics, Food Web Production and Fish Abundance in Suisun Marsh

    Lead University of California - Davis [UC Davis]
    Description Suisun Marsh remains one of the most productive regions of the San Francisco Estuary (SFE), fueling interest in the Marsh as a model for restoring estuarine function to the region in the future. The UC Davis Suisun Marsh Fish Survey has 30 years of data on physical structure, water quality, benthic and pelagic invertebrates and fish. We will use these and other data to explore patterns of fish abundance in relation to zooplankton, slough geomorphology, and regional hydrodynamics. Our goal is to understand and predict the kinds of physical variability and structure that create attractive habitat for fish, in order to 1) serve as a template for wetland and subtidal habitat restoration in the Estuary and 2) anticipate the effects of sea level rise, levee failure and salinity increases that are expected to have a large impact on the Marsh in the near future. A comprehensive literature and data search will pull together known information for synthesis. Cluster analysis will identify slough complexes into types of functional habitat. Predictive maximum likelihood, hierarchical and multivariate autoregressive models will be used to predict how foodwebs and fish respond to environmental factors. Finally, coupled hydrodynamic-life history models for zooplankton will demonstrate how production is regulated by slough morphology. Results will be integrated as a white paper on the history, current functioning, and future of the Marsh.
    Science topics Levees, Climate change
    Updated April 29, 2022
  • Title

    The Role of Microcystis Blooms in the Delta Foodweb: A Functional Approach

    Lead San Francisco State University [SFSU]
    Description We propose a collaborative investigation of blooms of the toxic, cyanobacteria Microcystis in the San Francisco Estuary Delta including how blooms develop, identification of toxic species and strains, controls on toxin production, and foodweb effects. The research will address Delta Science Program Priority Research Topic 2 and Research Topic 5 in the CALFED-funded analysis of ammonium issues in the Estuary. The appearance of Microcystis in the Delta was coincident with the POD, suggesting a link. The spatial and temporal scales of Microcystis blooms was identified with their environmental covariates but a mechanistic analysis of the conditions that distinguish bloom periods and locations, which are critical for ecosystem modeling and management, are still lacking. Our objectives are to determine: 1- the biotic and abiotic factors controlling Microcystis bloom formation and toxin production;2- how Microcystis strains and microbial associations influence toxicity;3- the role of Microcystis in the Delta pelagic food web and its effect on the POD through zooplankton grazing. Our 3-year work plan comprises 2 years of laboratory and field work (contrasting bloom and non bloom locations). Experiments will be conducted to determine mechanisms driving observed in situ patterns. We will synthesize the results and clarify the environmental-bloom-food web effects in a useable format for management efforts aimed towards water supply, fisheries and recreational use of the Delta.
    Science topics Harmful algal blooms HAB
    Updated April 29, 2022
  • Title

    Functional diversity and predator dynamics along the Sacramento and San Joaquin River Delta

    Lead University of California - Santa Cruz [UCSC]
    Description This project's objectives are to: 1) determine snake species diversity and relative abundance, 2) establish resources available and examine the functional role that snakes play along field sites within the Sacramento-San Joaquin River Delta, 3) document predator-prey interactions, and 4) assess the thermal physiology of snakes and the thermal profile of microhabitats along the Sacramento-San Joaquin Delta.
    Science topics Habitat, Invasive / non native species
    Updated May 8, 2024
  • Title

    Identification of environmental conditions driving cyanobacterial multi-species blooms and their toxicity using genome resolved metagenomics

    Lead University of California - Berkeley [UC Berkeley]
    Description In recent years the Sacramento-San Joaquin Delta has seen an increase in toxigenic cyanobacterial diversity and abundance during harmful cyanobacterial bloom events (cyanoHABs). This increased cyanobacterial diversity parallels an increase in the number of detected toxins during cyanoHABs outside of the typical microcystins that have been previously identified. Currently there are critical knowledge gaps around the full toxigenic potential of rising diversity of cyanobacterial species, and how the total microbial community of cyanoHABs interacts within itself and with external abiotic factors in ways that may promote the expansion of new and diverse cyanoHABs. The goal of this study is to use genome-resolved metagenomics to study the genetic diversity and metabolic and toxigenic potential of cyanoHABs to i) identify cyanobacterial taxa composition and their potential for toxins biosynthesis ii) characterize species succession dynamics and metabolic processes of the full microbial community during cyanobacterial bloom phases, iii) correlate environmental factors and toxin titers with biological components of diverse bloom phases to explain the development of cyanobacterial multi-species dominated bloom.
    Science topics Cyanobacteria, Harmful algal blooms HAB
    Updated May 8, 2024
  • Title

    Fish out of breath: Assessing, developing, and validating physiological bioindicators of hypoxia across the Delta

    Lead University of California - San Diego [UCSD]
    Description This proposal seeks to generate two management tools to optimize ongoing conservation efforts (e.g. wetland restoration, fish supplementation) by accomplishing the following 4 objectives: Objective 1) use controlled laboratory experiments to identify temperature-dependent hypoxia tolerance data (Pcrit) for ChinookSalmon smolts and juvenile Delta Smelt. Objective 2) compile existing temperature and DO monitoring data across the SFE. Objective 3) generate metabolic indices using the newly-generated physiological data (Obj. 1) and existing environmentalinformation (Obj. 2) to examine spatial and temporal patterns in metabolic stress for each species. Objective 4) explore and develop an otolith-based bioindicator to identify past hypoxia exposure.
    Science topics Chinook Salmon, Delta Smelt, Dissolved oxygen, Temperature
    Updated May 8, 2024
  • Title

    Using high frequency flux measurements to constrain dissolved inorganic carbon in a tidal wetland carbon budget

    Lead California State University - East Bay
    Description The main purpose of this project is to determine how much carbon (C) is annually sequestered and exported laterally in a tidal wetland environment through the calculation of a net ecosystem C budget. C hydrologic export, mainly in the form of dissolved inorganic C (DIC), is poorly constrained and can pose a significant component of a wetland C budget that is often overlooked. This project intends to reduce that uncertainty by providing a better understanding of the biogeochemical drivers of C cycling and give further insight into wetland management decision-making.
    Science topics Carbon, Restoration, Tidal wetlands
    Updated November 30, 2022
  • Title

    Restoring tidal marsh foodwebs: assessing restoration effects on trophic interactions and energy flows in the San Francisco Bay-Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description The objective of this research on tidal marsh food webs is to examine whether and how restoration (via breaching dikes) may translate into recovery of diverse energy pathways and trophic interactions between basal resources, primary consumers, and predators. By comparing food webs at several tidal marshes, I will answer the following questions: (1) How does food web structure vary between reference and restored tidal marshes over time (seasons and years) and across a salinity gradient? (2)What mechanisms explain variation in food web structure within and between reference and restored tidal marshes–are they related to energy flows (food quantity, quality, transfer efficiency), community composition, or both? (3) What role do non-native species play in potentially shifting food web structure–e.g., changing community membership, sequestering energy from natives? This project builds on a large breadth of research that has used stable isotopes to characterize tidal marsh food webs in the Bay-Delta and other regions.
    Science topics Food webs, Wetlands
    Updated May 8, 2024
  • Title

    Harmonizing pesticide risk management of the Bay Delta watershed

    Lead University of California - Santa Barbara [UCSB]
    Description Objective One: Employ high-resolution irrigation data to predict pesticide risks in the Bay Delta Watershed (BDW). This effort will enable more accurate prediction of health hazards given irrigation is a key driver of pesticide transport to surface and ground water. The effects of irrigation methods to pesticide transport vary significantly in their contribution of pesticides to runoff/leachate due to effects on pesticide build-up/wash-off and soil moisture conditions antecedent to precipitation. Objective Two: Provide harmonized species indicators of pesticide toxic burden releases for the Bay Delta which consider diverse resident taxa and human health. California benefits from a plethora of academic researchers, environmental advocacy groups, municipalities, and government groups working to protect the environment. Due to the complexities of this work, efforts often focus on a particular taxa or environmental compartment. This introduces a significant challenge in evaluating the pros and cons of any particular pesticide use. Currently, 79 of the 208 watersheds near the Delta which receive agricultural pesticide applications have increasing pesticide toxic burdens to aquatic taxa. Enabling evaluation of chemical alternatives which reduce toxic burdens across taxa is important to restoring ecosystem health. Objective Three. Quantify the variability of pesticide degradation and the significance to pesticide risk in the BDW. The degree to which pesticides remain in the soils of the BDW increases their probability for accumulation, transport, and nontarget affects. Degradation is highly variable in soils; an investigation of 10 pesticides in 8 soil types under equivalent conditions demonstrated a mean difference of 540% in the minimum and maximum rate of degradation for pesticides evaluated. Yet, researchers and regulators often only employ the median observed rate of degradation which may under predict risks to waterbodies of the BDW.
    Science topics Pesticides
    Updated November 30, 2022
  • Title

    Mapping the adaptation governance network of the Delta

    Lead University of California - Davis [UC Davis]
    Description Climate adaptation in the San Joaquin-Sacramento Delta involves multiple agencies, communities, venues, projects, and issues. Understanding how learning and cooperation occurs within this complex governance network is critical for carrying out effective and equitable adaptation. The main objective of this project is to understand how and why human communities (e.g., community organizations, local governments, and Tribal entities) are engaged in this governance system and the drivers of learning and cooperation for climate adaptation. To accomplish this, we will map the network of current adaptation actors, institutions, and actions, assess their engagement in the governance system, and conduct in-depth case studies on existing adaptation projects in the San Joaquin – Sacramento Delta.
    Science topics Climate change
    Updated May 8, 2024
  • Title

    Science for adaptive management of juvenile spring-run Chinook salmon in the San Joaquin River

    Lead University of California - Davis [UC Davis]
    Description Spring-run Chinook salmon rehabilitation efforts are intensifying on the San Joaquin River. Over the last three years, UC Davis has successfully tracked movement, behavior, reach-specific survival, and route selection for reintroduced juvenile spring-run Chinook salmon in this ecosystem. In 2019, information on salmon tracking was combined with state-of-art habitat (fast limnological automated measurements or “FLAMe”) and physiological (e.g. fish condition, survival and transcriptomic) approaches. Results from this work are ongoing but have yielded actionable information on key habitats and management strategies for promoting salmon life-cycles in the San Joaquin River and central Delta. Now UC Davis will further explore promising recent findings. First, the analysis of an additional year of juvenile salmon tracking will occur to glean more survival information across different water year conditions. This information would be married with expanded FLAMe surveys in space and time along with a second year of physiological assays using caged fish. UC Davis will also evaluate the ‘transport effect’ on salmon, in an attempt to explain consistently high losses of JSATS-tagged salmon through the restoration area. Numerous other synergies exist with new and ongoing telemetry work that will be benefitted by a continuation of this work. The goal is to provide actionable science, and open access data, with a high potential to facilitate adaptive management in the San Joaquin River and central Delta.
    Science topics Chinook Salmon, Endangered species, Estuaries, Fish, Habitat restoration
    Updated October 3, 2023
  • Title

    Integrating social and ecological research to control invasive species: fostering collective action among private and public stakeholders

    Lead Suisun Resource Conservation District
    Description This project will establish an integrated pest management approach for Phragmites (Common reed), an aggressive invasive plant in Delta wetlands. Results will highlight social and cultural barriers to collective action for invasive species control, and include communication tools for developing a regional strategy for Common reed control.
    Science topics Invasive / non native species, Pesticides, Phragmites, Socio-economic drivers
    Updated October 13, 2023