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  • Title

    Quantifying Factors Affecting Migration Routing and Survival of Juvenile Late-Fall Chinook Salmon in the Sacramento-San Joaquin River Delta

    Lead U.S. Geological Survey [USGS]
    Description Juvenile Chinook salmon emigrating from natal tributaries of the Sacramento River must negotiate the Sacramento-San Joaquin River Delta where they disperse among the Delta's complex channel network. Natural processes and water management actions affect the fraction of the population using different migration routes through the Delta and survival within those routes, but quantifying these relationships has proven difficult. Since 2006, acoustic telemetry techniques have been used to quantify both movement among migration routes and survival within routes, providing the first insights into how route-specific survival contributes to population-level survival in the Delta. In this project, we propose to use existing acoustic telemetry data from multiple sources to 1) Quantify factors affecting migration routing of juvenile salmon emigrating from the Sacramento River, 2) Quantify factors affecting survival of juvenile salmon within specific migration routes, and 3) Simulate population-level survival through the Delta under a limited number of historical and operational scenarios. Collating telemetry data from multiple sources over numerous years offers a unique opportunity to identify important relationships that might otherwise be difficult to detect for any particular study in a given year. Quantifying such relationships is critical to informing resource management that seeks to balance use of water resources with recovery of endangered salmon populations.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Impact of Urbanization on Chinook Salmon, Steelhead Trout, and Their Prey: a Case Study of the American River

    Lead University of California - Berkeley [UC Berkeley]
    Description The American River provides spawning/rearing habitat for Chinook salmon and steelhead, yet passes through 30 miles of dense urban development. Urban runoff contains pyrethroid insecticides that cause the river to become toxic to standard testing species with every storm event. This study will go beyond observed toxicity, and address toxicity to chironomids, caddisflies, and mayflies, key diet components of juvenile fish in the river. A bioenergetic model will be used to evaluate effects of food web changes on young salmonids. Our key approach is the use of river-side systems with flowing river water that allow us to replicate realistic pesticide exposures, while controlling other variables. We will determine sensitivity to pyrethroids and fipronil of salmonid prey taxa, and expose them, as well as standard testing species, in the flow-through systems through six storm events. We will maintain experimental streams containing riverine benthic invertebrate communities, and measure response to the pyrethroid pulses. To supplement analyses of the indirect, food web-mediated effects, we will measure endocrine effects through vitellogenin induction in salmon and steelhead. Finally, one treatment includes river water from which organic contaminants have been removed by activated charcoal, to help establish cause of toxicity. The goal is to determine if known toxicity in the American River is a threat to benthic invertebrates and, through the food web, to salmon and steelhead.
    Science topics Chinook Salmon, Steelhead Trout, Above-highwater refugia, Other discharge contaminants, Food webs
    Updated April 29, 2022
  • 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

    Physiological Mechanisms of Environmental tolerance in Delta Smelt [Hypomesus transpacificus]: From Molecules to Adverse Outcomes

    Lead University of California - Davis [UC Davis]
    Description The proposed project directly addresses priority research detailed by the Delta Science Program to protect native fishes that depend on the Bay-Delta system focusing on adaptations to local habitats and physiological tolerances to key environmental stressors;in delta smelt (Hypomesus transpacificus). Temperature and salinity changes associated with anthropogenic climate change are likely to further exacerbate delta smelt population declines. We hypothesize that delta smelt tolerance to forecasted temperature rises and salinity intrusions into the Bay-Delta system can be assessed at a mechanistic level, and that acclimation thresholds can be established by means of genomic responses. This proposal builds upon successful development of a cDNA microarray for delta smelt containing approximately 2000 individual gene fragments, and the subsequent application of biomarkers for assessing the effects of chemical stressors on larval development with links to swimming behavior. We propose to develop a Next Generation oligonucleotide microarray in delta smelt, with ca. 15K genes, in order to assess mechanistic tolerance to changes in gemperature and salinity. Genomic studies will be conducted integrating effects on energetic activity and swimming performance studies, in an interdisciplinary approach that will permit the establishment of links between tolerance mechanisms and adverse outcomes.
    Science topics Delta Smelt, Water temperature, Salinity, Turbidity
    Updated April 29, 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 June 17, 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 October 3, 2024
  • 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

    Evaluating Juvenile Salmonid Behavioral Responses to Hydrodynamic Conditions in the Sacramento-San Joaquin Delta

    Lead State Water Contractors [SWC]
    Description This study combines detailed model predictions with salmonid tracking data to inform how river flows affect steelhead movement through the Delta. This project leverages an existing 6-year data set to support analysis of salmonid behavioral responses across a broad range of water years. The study will evaluate behavior relative to flow under existing regulatory requirements (Old and Middle River Flow and the Inflow to Export ratio), evaluate five new potential water management metrics identified by the Collaborative Adaptive Management Team Salmonid Scoping Team, and improve the understanding of what conditions affect survival.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Impact of Temperature and Contaminants on Chinook Salmon Survival: A Multi-Stressor Approach

    Lead National Marine Fisheries Service [NMFS]
    Description The decline of native salmon species has resulted in their protection under the U.S. Endangered Species Act and the California Endangered Species Act. Disease and predation are primary drivers of mortality as salmon migrate. Multiple stressors, such as exposure to contaminants and elevated temperature, can impact rates of disease and predation of salmon as they migrate to the ocean. This study examines how contaminant exposures at different temperatures affects salmon health. Specifically, the study investigates the sensitivity of salmon to a contaminant mixture of bifenthrin (a pyrethoid pesticide) and triclosan (an antibacterial added to personal care products). Both contaminants can alter fish swimming behavior and critical physiological functions. Similarly, temperature stress can impact fish physiology and behavior, as well as exacerbate the adverse effects of contaminants.
    Science topics None specified
    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

    An Evaluation of Sublethal and Latent Pyrethroid Toxicity Across a Salinity Gradient in Two Delta Fish Species

    Lead Oregon State University
    Description Pyrethroids are a type of insecticide frequently detected in the San Francisco Bay and Delta (SFBD). They are highly toxic to fishes and may contribute to their decline. The Central Valley Water Resources Control Board has adopted regulations for many pyrethroids. These concentration goals for Delta surface waters are quite stringent. However, they do not take into account non-lethal effects in fishes, particularly during the early life stages and at the salinity conditions we see in the SFBD. Understanding non-lethal effects in fish is vital to influencing population health. This study investigates pyrethroid toxicity on Delta smelt and Inland Silverside embryos, while accounting for changing SFBD salinity and other factors such as sediment. Results will inform the development of pesticide regulation criteria and control efforts, furthering the protection of SFBD fishes.
    Science topics None specified
    Updated April 29, 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

    Improving Green Sturgeon Population and Migration Monitoring

    Lead University of California - Santa Cruz [UCSC]
    Description Green sturgeon is a listed species under the federal Endangered Species Act. This project supports the recovery and management of the southern distinct population segment of green sturgeon by improving population and migration monitoring. Improved monitoring is recommended in multiple initiatives to help protect this species, such as the Green Sturgeon Recovery Plan. There is some uncertainty on whether the most appropriate green sturgeon monitoring techniques are being used. This project compares the different estimation and monitoring techniques to identify the superior protocol. To compare the effectiveness of different techniques, scientists will monitor green sturgeon in the Sacramento River using sonar technology. Monitoring data will be used to estimate the population size and death rates due to by-catch. This project will also review and synthesize past acoustic telemetry data to determine if the data can be modeled to improve population size estimates.
    Science topics Green sturgeon
    Updated June 3, 2024
  • 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

    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
  • 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

    Non-Invasive Environmental DNA Monitoring to Support Tidal Wetland Restoration

    Lead University of California - Davis [UC Davis]
    Description In this project we use single-species and multi-species environmental DNA (eDNA) approaches to monitor tidal wetland restoration sites and paired reference sites (existing, unrestored tidal wetlands located near restoration sites) in the San Francisco Bay Delta (SFBD). We are working in coordination with the CDFW Fish Restoration Program (FRP) and other collaborators so our eDNA detections can be paired with physical detections of fishes from their trawling efforts. Ultra-sensitive DNA single species detection methods are being used to identify restoration site use by listed species (Delta Smelt, Longfin Smelt, winter- and spring-run Chinook Salmon) while the DNA metabarcoding approach will evaluate entire fish communities (groups of different fish species) at restored and reference sites. Aside from revealing restored habitat use by other fishes, metabarcoding will reveal potential ecological interactions between Endangered Species Act listed and non-listed species, through concurrent detection in time and space. Sampling throughout the year will allow us to identify seasonal trends in fish use of restored and reference sites. This project will demonstrate the utility of eDNA detection as a non-invasive (no take), cost-effective monitoring tool that can complement conventional surveys of restored tidal wetlands in the SFBD. Our results can be incorporated into an adaptive monitoring framework for tidal wetland restoration, to increase success of future restoration projects.
    Science topics Chinook Salmon, Delta Smelt, Endangered species, Estuaries, Fish, Green sturgeon, Habitat, Habitat restoration, Invasive / non native species, Invertebrates, Longfin Smelt, Mollusks, Pelagic fish, Restoration, Restoration planning, Sacramento Splittail, Salmon migration, Salmon rearing, Steelhead Trout, Striped bass, Sturgeon, Tidal wetlands, Wetlands, White Sturgeon
    Updated May 24, 2024
  • Title

    From Microbes to Zooplankton, What Defines a Beneficial Wetland?

    Lead San Francisco State University, Estuary & Ocean Science Center
    Description Our study will characterize species diversity at multiple levels of biological organization in the water column of restoring wetlands in the upper San Francisco Estuary and Delta (SFE), from bacteria to fishes. In doing so, we will also describe the foodweb benefits being provided to larval fishes, including longfin smelt, through additional dietary DNA analysis. We will use the species diversity we find in the water column to identify a subset of biota that are indicative of the conditions present in wetlands in different stages of restoration (early, intermediate, and mature) and identify connections between those indicators to the foodweb resources being provided to higher trophic levels. We will study 3-4 wetlands in each of 3 stages: early (unvegetated), intermediate (partially vegetated and partially channelized), and mature (fully vegetated and channelized) wetlands.
    Science topics Crustaceans, Cyanobacteria, Estuaries, Fish, Food webs, Habitat, Habitat restoration, Insects, Invertebrates, Longfin Smelt, Other species, Other zooplankton, Pelagic fish, Phytoplankton, Predation, Restoration, Salinity, Saltwater / freshwater marshes, Tidal wetlands, Wetlands, Zooplankton
    Updated January 31, 2024
  • 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 May 21, 2024
  • Title

    The Relative Contributions of Contaminants to Ecological Risk in the Upper San Francisco Estuary

    Lead Delta Stewardship Council - Delta Science Program
    Description This project developed methods to calculate risk of mixtures of pesticides for the Upper San Francisco Estuary (USFE). We used curve fitting to estimate the exposure-response curves for each individual chemical and then the mixture. For the mixtures, the models were normalized for specific ECx values. In that way, the curve fitting was optimized for effects that are comparable to most threshold values. A Bayesian network was built that incorporated five different pesticides and mercury. The input distributions of the contaminants were measured amounts from each of the six risk regions. We also explored three different methods of combining the results of the three pathways – additive, average, and expert judgement. The initial result was the BN model’s Predicted Fish Mortality (%). The Sensitivity analysis (mutual information) identified the most important components of the Bayesian network in determining the toxicity. The top two pathways were the Malathion/Diazinon Mortality pathway and the Mercury Mortality pathway. For the individual nodes Mercury, Bifenthrin and Season were key. Currently, we are completing the risk assessment network by adding Chinook salmon and Delta smelt population pathways to estimate risk to the six Risk Regions. A major accomplishment was the demonstration that curve fitting using additive models for mixtures can be used to estimate fish toxicity in this proof-of-concept model. Bifenthrin, the specific risk region, and season were the inputs that were most important to the calculation. Factors determining macroinvertebrate community structure were identified using multivariate tools. Water quality parameters were the most important in determining clusters of similar macrobenthic communities. Because contaminants were not statistically significant in determining these patterns, further analysis of macroinvertebrate community structure was postponed. At this time, the techniques applied in this program appear applicable to estimating risk due to the variety of chemicals and other stressors to the multiple endpoints under management in the USFE.
    Science topics None specified
    Updated January 24, 2024
  • Title

    Carbon Biogeochemical Cycling in Tidal Wetlands: Exploring Lateral Carbon Exchange and Sequestration Potential

    Lead University of California - Berkeley [UC Berkeley]
    Description Tidal wetlands, at the interface of land and ocean, play a critical role in carbon biogeochemical cycling and have the potential to provide major feedback to the Earth system through greenhouse gas exchange and long-term carbon sequestration. However, the efficiency of carbon sequestration in tidal systems relies on both vertical carbon exchange with the atmosphere and lateral tidal exchange with adjacent water bodies. Unfortunately, the importance of hydrologic carbon fluxes has been largely overlooked, leaving a crucial aspect of coastal wetland net carbon balance unaddressed. We employed an integrated approach to quantify vertical and lateral carbon exchange and studied their dynamics, combining eddy covariance flux measurements with on-site water quality and tidal discharge measurements, as well as manual 24h surface water samplings. Our measurements were conducted in a recently restored tidal freshwater marsh in the Sacramento-San Joaquin Delta, CA, that stands out in global networks like FLUXNET and Ameriflux owing to its impressive net ecosystem exchange of -850 g C m-2 yr-1. Using wavelet decomposition, we examined the variability of carbon exchange (CO2 and CH4) across different timescales. Through information theory and mutual information analysis, we assessed the factors influencing both vertical and lateral exchanges. Our preliminary findings suggest that variability in carbon exchange is largest at the diel scale, with plant gross primary productivity and tidal fluctuations in depth having the most significant interactions with CO2 and CH4 fluxes, respectively. Furthermore, our tidal cycle samplings revealed that dissolved inorganic carbon dominates the fraction of lateral carbon loss, accounting for approximately 80% of the export. Remarkably, similarities existed between the values for net lateral carbon export and ecosystem respiration, signifying that the dissolved, terrestrial-to-ocean carbon flux could represent one of the primary fates of the fixed carbon in this tidal ecosystem. These large dissolved inorganic carbon fluxes and their chemical speciation, are important to consider when estimating the climate mitigation potential of restored tidal wetlands.
    Science topics Carbon, Carbon storage, Greenhouse gas GHG
    Updated January 30, 2024
  • Title

    Suisun Landscapes: historical ecology, functional metrics, and community priorities for landscape planning

    Lead San Francisco Estuary Institute [SFEI]
    Description

    To support management planning in Suisun Marsh, this project is developing a body of science and tools to understand past, present, and potential future changes to the Marsh’s ecological patterns, processes, and functions. This project builds on SFEI’s prior work in the Delta, extending historical ecology mapping, landscape change studies, and the Landscape Scenario Planning Tool to cover Suisun's historical and present-day landscapes. Through spatially explicit representations of the historical function and condition of the marsh and analyses of landscape metrics, this project is evaluating changes over time in landscape support for ecosystem functions and services in Suisun. In order to incorporate diverse perspectives into planning resources, project activities include engagement with local tribes and community members to understand community interests, priorities, and uses of the Marsh. Findings will be shared through a report and article for both technical and general audiences, and spatial analyses and data layers will be made available through the Landscape Scenario Planning Tool.

     
    Science topics None specified
    Updated October 10, 2024
  • Title

    The effects of climate change on the life history of spring-run Chinook Salmon through time

    Lead University of California - Santa Cruz [UCSC]
    Description

    Chinook Salmon (Oncorhynchus tshawytscha) populations in California are in decline due to the combined effects of habitat degradation, water diversions, and shifting climate regimes. This project uses archival tissues (otoliths, vertebrae) from modern and ancient spring-run Chinook Salmon to understand how shifts in migration timing and habitat use allowed salmon to cope with highly variable environmental conditions. We will learn how salmon responded to the recent drought and flood periods (2012-2020 CE), the California Gold Rush Period (~1835-1870 CE), the Little Ice Age (~1560-1780 CE), and the Megadrought Period (~1200-1410 CE). This effort will provide the insights needed for developing climate-adapted conservation actions to support salmon into the future.
    Science topics Chemistry, Chinook Salmon, Climate change, Environmental drivers, Fish, Habitat, Salmon rearing
    Updated April 8, 2025