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  • Title

    Directed Outflow Project

    Lead U.S. Bureau of Reclamation [USBR]
    Description The U.S. Bureau of Reclamation (USBR) and California Department of Water Resources (DWR), along with collaborators, are continuing efforts to evaluate the hypothesized benefits of outflow and outflow alteration for Delta Smelt. The collective aim of these efforts is to better inform management actions that will bolster and stabilize the Delta Smelt population. The planned five-year Directed Outflow Project (DOP) seeks to assist in evaluating the overarching hypothesis that habitat quality and quantity is improved in the summer/fall when X2 is below 81 km and the LSZ occurs in Suisun Bay and Marsh, and this improvement in habitat conditions will translate into a greater catch density, health, and growth for Delta Smelt using this area
    Science topics Delta Smelt, Fish, Flows, Water management
    Updated November 17, 2022
  • Title

    Delta Historical Ecology

    Lead San Francisco Estuary Institute [SFEI]
    Description The San Francisco Estuary Institute-Aquatic Science Center, in collaboration with the California Department of Fish and Game, completed a historical ecology study of the Sacramento-San Joaquin Delta. The project improves understanding of what the Delta looked like and how it functioned prior to the significant modification that has occurred over the last 160 years.
    Science topics Historical ecology, Landscape change
    Updated May 23, 2023
  • 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

    Landscape Visioning Pilot Application for Staten Island

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

    Delta Regional Monitoring Program Mercury Monitoring

    Lead Delta Regional Monitoring Program [RMP]
    Description Monitoring of sport fish and water was conducted by the Delta Regional Monitoring Program (Delta RMP) from August 2016 to April 2017 to begin to address the highest priority information needs related to implementation of the Sacramento–San Joaquin Delta Estuary Total Maximum Daily Load (TMDL) for Methylmercury (Wood et al. 2010). Two species of sport fish, largemouth bass (Micropterus salmoides) and spotted bass (Micropterus punctulatus), were collected at six sampling locations in August and September 2016. The length-adjusted (350 mm) mean methylmercury (measured as total mercury, which is a routinely used proxy for methylmercury in predator fish) concentration in bass ranged from 0.15 mg/kg or parts per million (ppm) wet weight at Little Potato Slough to 0.61 ppm at the Sacramento River at Freeport. Water samples were collected on four occasions from August 2016 through April 2017. Concentrations of methylmercury in unfiltered water ranged from 0.021 to 0.22 ng/L or parts per trillion. Concentrations of total mercury in unfiltered water ranged from 0.91 to 13 ng/L. Over 99% of the lab results for this project met the requirements of the Delta RMP Quality Assurance Program Plan, and all data were reportable. This data report presents the methods and results for the first year of monitoring. Historic data from the same or nearby monitoring stations from 1998 to 2011 are also presented to provide context. Monitoring results for both sport fish and water were generally comparable to historic observations. For the next several years, annual monitoring of sport fish will be conducted to firmly establish baseline concentrations and interannual variation in support of monitoring of long-term trends as an essential performance measure for the TMDL. Monitoring of water will solidify the linkage analysis (the quantitative relationship between methylmercury in water and methylmercury in sport fish) in the TMDL. Water monitoring will also provide data that will be useful in verifying patterns and trends predicted by numerical models of mercury transport and cycling being developed for the Delta and Yolo Bypass by the California Department of Water Resources (DWR).
    Science topics Biosentinels, Fish, Methylmercury, Restoration, Water
    Updated November 17, 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

    Habitat, hatcheries, and nonnative predators interact to affect juvenile salmon behavior and survival

    Lead University of California - Santa Cruz [UCSC]
    Description Chinook salmon are an iconic part of California’s environment and heritage, and important both economically and culturally. In the Sacramento River, the winter-run Chinook population is endangered, and there is strong interest in restoring these populations. To do so, resource managers need to better understand the pressures on wild populations. Predation by nonnative predators affects survival of young salmon but may also affect the behavior of salmon. Changes to salmon behavior also have costs but are not currently considered in management. Managers need information on how predators affect juvenile salmon behavior, how they might vary under different conditions, and how they scale up to affect populations.
    Science topics Chinook Salmon, Fishing
    Updated November 17, 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

    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

    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

    The effects of early hypersaline acclimation due to climate change on the toxicity of pyrethroid, an insecticide, in salmonids.

    Lead University of California - Riverside [UC Riverside]
    Description Sea level rise and drought are expected to result in hypersaline waterways in the Delta. Endangered Chinook salmon and Steelhead trout go through smoltification to be able to live and mature in saline environments. However, with salinities and temperatures increasing in historically freshwater areas, these fish may be facing new stressors. Pesticide runoff into the Delta is common due to the urbanization and agriculture of many regions and can adversely affect fish. Additionally, previous research has shown that salinity exposure increases the toxicity of contaminants in anadromous fish, and it is had been demonstrated that bifenthrin, a common insecticide in the Bay, can have endocrine disrupting effects on juvenile salmonids. This project will examine the impacts of hypersaline conditions, various temperatures, and exposure to bifenthrin on the development and survival of juvenile Chinook salmon and Steelhead trout. Specifically, it will: Test the impacts of premature hypersaline acclimation and temperature on the survivial and smoltification process of a range of juvenile salmonids; Test the combined impacts of premature hypersaline acclimation, temperature, and bifenthrin exposure on smoltification, survival and behavior;and Predict the population level effects of drought and pesticide runoff on the health of endangered salmonids Additionally, this research will provide information to CA Department of Pesticide Regulation for potential pesticide management in the Delta, as well as to the CA Department of Fish and Wildlife for conservation practices of endangered juvenile salmonids in the Delta.
    Science topics Salinity
    Updated April 29, 2022
  • Title

    Identifying the Causes of Feminization of Chinook Salmon in the Sacramento and San Joaquin River System

    Lead University of California - Berkeley [UC Berkeley]
    Description Purpose was to assess the potential importance of endocrine-disrupting chemical contaminants to salmon and other resident speices of waters that are discharged into the San Francisco-San Joaquin Delta.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    How Abiotic Processes, Biotic Processes, and Their Interactions Sustain Habiata Charactersitics and Functions in River Channels and Their Floodplains: An Investigation of How a Reach of the Merced River Responds to Restoration

    Lead University of California - Santa Barbara [UCSB]
    Description The purpose of this project is to determine how river restoration affects the abundance and distribution of salmonid and non-salmonid fishes at critical life stages. The proposal involves field survey of hydraulics, sedimentation processes, channel changes, habitat conditions, invertebrate and fish communities and their interactions.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Review of Four Juvenile Salmon Coded Wire Tag Experiements Conducted in the Delta

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description The US Fish and Wildlife Service, Stockton Fish and Wildlife Office, has since the mid-1980s conducted several multi-year release-recovery experiments with coded-wire-tagged juvenile Chinook salmon. The objectives of the studies were (1) to estimate survival through the lower portions of the Sacramento and San Joaquin river systems, the California Delta, and (2) to quantify the factors affecting survival. Four of these studies, listed more or less by their historical start dates, are the Delta Cross Channel, Interior, Delta Action 8, and VAMP experiments.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Predicting the Effects of Invasive Hydrozoa [Jellyfish] on Pelagic Organisms Under Changing Salinity and Temperature Regimes

    Lead University of California - Davis [UC Davis]
    Description The purpose of this project seeks to investigate the potential effects of jellyfish, a devising invader of some ecosystems, on the SFE ecosystem, to determine the key factors allowing successful establishment and spread of these species, and to predict future effects and spread of the invasions.
    Science topics Water temperature, Salinity, Pelagic fish, Jellyfish
    Updated April 29, 2022
  • Title

    Quantitative Indicators and Life History Implications of Environmental Stress on Sturgeon

    Lead University of California - Davis [UC Davis]
    Description The purpose of this project is to analyze the effects of the pollutants on the overall fitness of different life stages of the green and white sturgeon. This research will significantly enhance our understanding of stressors on sturgeon and allow further development of life history models.
    Science topics Water temperature, Salinity, Pelagic fish, Methylmercury, Sturgeon
    Updated April 29, 2022
  • Title

    Comparison of Nutrient Sources and Phytoplankton Growth and Species Composition in Two Rivers: Their Roles in Determining Productivity and Food Web Conditions in Suisun Bay and the Delta

    Lead San Francisco State University [SFSU]
    Description
    Science topics Phytoplankton, Pelagic fish, Nitrogen / ammonia
    Updated April 29, 2022
  • Title

    The Transport and Dispersion of Rafting Vegetation in the Sacramento-San Joaquin Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description The research we are proposing here is focused on developing a thorough, mechanistic understanding of how rafting vegetation, such as hyacinths or egeria, is transported in the Sacramento-San Joaquin Delta. Our approach is to examine in detail the forces that act on rafts of vegetation, and the resulting raft accelerations, to establish a predictive model of raft pathlines. Our model development will be built around a series of field experiments that include measurements of raft movement using GPS-logging drifters integrated into rafts, tidal and wind-forcing using a boat mounted current profiler and an anemometer, and direct estimation of the water-induced shear stress using a point velocity meter incorporated into the actual rafts. These field observations will be used to critically evaluate a numerical model of both channel (tidal) flows and resulting raft movement. Our initial development will include a highly-resolved channel flow model, which will explicitly capture more lateral variability, including low velocity side “pockets”, than is typically resolved with Delta scale hydrodynamic models. Initially, this will allow us to carefully evaluate the quality of our raft tracking calculations. Once the approach is established to be accurate, however, these high-resolution flows will be used to numerically calculate the effective advection and dispersion of rafts in the Delta channel under consideration. This analysis will be focused on parameterizing the effects on raft transport of structures and processes that are unresolved in typical Delta hydrodynamics models. An example of a process that is likely to be important to parameterize is the trapping and retention of rafts along the perimeter of channels due to off-axis wind forcing, and the resulting along-channel dispersion of rafts. In order to examine the effective advection and dispersion of rafts in Delta channels, we propose to pursue this combination of field and numerical studies of raft transport in locations of increasing complexity: first in idealized, straight channels, then in a natural, sinuous channel and a channel junction, and finally throughout the entire Delta. Our research is strongly motivated by the desire to provide a predictive model of dispersion in the Delta for floating objects that respond to both wind and tidal forcing. Immediate applications involve the movement of hyacinth rafts and egeria to evaluate potential management strategies. Important future applications are likely to include consideration of other biological invasions, due to the potential for rafts to provide a transport pathway, and analysis of the movement of accidental or intentional releases of floating material in the Delta.
    Science topics None specified
    Updated November 29, 2022
  • Title

    Pilot Mark-Recapture Study to Estimate Delta Smelt Pre-Screen Loss and Salvage Efficiency

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description The purpose of this project is to perform a study to determine whether it is feasible to quantify entrainment losses of juvenile and adult delta smelt due to water exports. This information is critical to better understanding the movement of Delta smelt in the system.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Are Apparent Sex Reversed Chinook Salmon a Symptom of Genotoxicity?

    Lead University of California - Davis [UC Davis]
    Description Goal was to test the relative importance of chemical stressors on population viability and genetic diversity for fall-run Chinook salmon (in association with environmental contaminant exposure in the Central Valley delta).
    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

    Foodweb Support for the Threatened Delta Smelt and Other Estuarine Fishes in Suisun Bay and the Western Sacramento-San Joaquin Delta

    Lead San Francisco State University [SFSU]
    Description The purpose of the project is to increase understanding of the foodweb supporting delta smelt and other estuarine species. This research is important because: 1) it could lead to increased foodweb support for the threatened delta smelt and 2) identify potential mechanisms underlying relationships of abundance or survival of some fish to freshwater flow.
    Science topics Delta Smelt
    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

    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

    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

    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

    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

    Consequences of Phragmites invasion for community function in Suisun Marsh

    Lead University of California - Davis [UC Davis]
    Description This project aims to quantify the impacts of common reed (Phragmites) invasion on community structure and ecosystem function during early stages of tidal restoration in wetlands. The study will focus on the Tule Red Tidal Restoration site in Suisun Marsh. The research aims to produce a conceptual model that will describe habitat structure, invertebrate communities, and predator use of wetlands affected by Phragmites invasion. The conceptual model resulting from this study will guide future predictions of wetland response to invasion and to develop mitigation strategies. Data collected will also support food web models and the understanding of invasive plants as stressors, as well as foster translational science to the management community.
    Science topics Invasive / non native species
    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

    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

    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

    Survivial and Migratory Pattern of Central Valley Juvenile Salmonids

    Lead University of California - Davis [UC Davis]
    Description The purpose of this project is to determine the survival and movement patterns of late-fall Chinook salmon smolts and steelhead smolts as they migrate downstream. This information is important to better understand how salmon move through the system.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Understanding the Effects Of Nutrient Forms, Nutrient Ratios and Light Availability on the Lower Food Web of the Delta

    Lead University of Maryland - Center for Environmental Science
    Description This proposed study addresses how changes in nutrient form, ratio and loading (water quality) affect the lower pelagic food web that ultimately determines the quality and quantity of food for Delta fishes. Shifts in algal composition and food availability have been implicated in fish decline, but identifying the changes at the base of the food web that are linked to changes in nutrients has been difficult because of the complexity of factors contributing to stress on the food web. Nutrients may shape community composition in complex ways;they do not have to be limiting to be important drivers of plankton communities. Elevated nutrients, particularly chemically reduced forms of nitrogen (N), may be inhibitory rather than stimulatory. We hypothesize that when NO3- is proportionately abundant relative to NH4+ (and the N:P ratio is suitable), diatoms will dominate, but when NH4+ is proportionately abundant, cyanobacteria or flagellates will dominate. Reduced light availability will lead to communities with higher bacterial abundance, and/or higher proportions of flagellates able to alter their nutrition towards mixotrophy. This proposal will directly test these relationships by conducting experimental manipulations with different ambient communities from different sites and seasons. Data will be interpreted with respect to the long-term trends reported for the Bay Delta and supplied as an integrated product for management efforts concerned with water quality and fisheries.
    Science topics Nutrients, Food webs
    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

    Phytoplankton Communities in the San Francisco Estuary: Monitoring and Management using a Submersible Spectrofluorometer

    Lead California Department of Water Resource [DWR]
    Description The purpose of this project is to evaluate a new submersible spectrofluorometer, the bbe FluoroProbe, for phytoplankton monitoring and management in the SFE. Secondly, this project seeks to investigate high-frequency patterns in spatial phytoplankton group distributions among Delta habitats and along gradients from the western Delta and northern San Francisco Bay.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Biomass and Toxicity of a Newly Established Bloom of the Cyanobacteria Microcystis aeruginosa and its Potential Impact on Beneficial Use in the Sacramento-San Joaquin Delta

    Lead California Department of Water Resource [DWR]
    Description Monitoring and simple analysis of the extent of this cyanobacteria in the Delta, and preliminary exploration of the impacts of cystins on drinking water quality, and human and wildlife health.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Fish Diet and Condition

    Lead California Department of Fish and Wildlife [CDFW]
    Description Description The Diet and Condition study has provided information on the food habits of pelagic fishes in the estuary since 2005. We focus on the temporal and spatial differences in diet composition and feeding success of Delta Smelt, Striped Bass, Threadfin Shad, Longfin Smelt, Mississippi Silversides, and American Shad. Need Data from this project has been used to inform the Fall Low Salinity Habitat Program (FLaSH), Directed Outflow Project (DOP), and Management, Analysis and Synthesis Team reports, as well as life history models used for the conservation of fish and their habitats. Understanding what prey are utilized for food in the context of available prey, with the associated body-condition of fish, helps clarify the existence and timing of food limitation for young pelagic fish in the estuary. This work began as part of the Pelagic Organism Decline investigations and continued as a contributor to FLaSH investigations during which we in collaborated with the Fish Health Monitoring Project. Recently staff completed Longfin Smelt diet investigations as part element #296 (Longfin Smelt Investigations – in response to a litigation agreement) that will also contribute to the Longfin Smelt Conceptual Model and Synthesis effort (element #320). Finally, we will process Delta Smelt diets from investigations prompted by the Delta Smelt Resilience Strategy, and as part of the DOP. Objectives 1. What are the diets of pelagic fishes (especially Delta Smelt and Longfin Smelt) in the estuary and do they vary regionally or temporally? 2. Is there evidence of reduced feeding success spatially or temporally in the estuary? 3. Is feeding success associated with changes in relative weight or condition of fish? 4. Is there seasonal and regional overlap of diets between species (with a focus on age-0 Delta Smelt, Longfin Smelt, Striped Bass, Prickly Sculpin, Pacific Herring, and Threadfin Shad)?
    Science topics None specified
    Updated April 29, 2022
  • Title

    Aquatic Habitat Sampling Platform: Standardized Fish Community Sampling Across Habitat Types

    Lead U.S. Bureau of Reclamation [USBR]
    Description Description The Aquatic Habitat Sampling Platform (AHSP) is an integrated aquatic species and habitat sampling system that can effectively monitor aquatic organisms and reveal habitat associations while having minimal or no “take” of sensitive species. Further development and deployment of the AHSP will expand data collection to shallow and off-channel habitat, while offering the capability to transition to deeper and open water habitats, providing reliable sampling efficiency estimates (e.g., probability fish detection) and “catch” per unit effort (i.e., number of individual species per volume of water sampled) and improving our knowledge about populations, habitat associations and major stressors of key organisms within the San Francisco Estuary (Estuary). Need Within the Estuary, numerous monitoring techniques are used. However, monitoring weaknesses for determining fish status and trends include: 1) restricted locations available for some techniques;2) limited ability to simultaneously assess zooplankton and fish larvae;and 3) difficulty in estimating fish population size due to lack of gear efficiency information (Honey et al. 2004). Furthermore, past attempts at integrated abundance indices from more than one sampling method have had limited success. Although there continues to be considerable collaborative monitoring and research devoted to understanding Central Valley fish species, coordination among activities has been difficult. Other issues include permitting take of listed species and time-consuming monitoring with extended periods of down time due to sample post-processing of fish and invertebrate species. Identification of key microhabitats for each lifestage and attributes and linking associated physical parameters such as habitat features (e.g., depth, structure, channel type) and water quality is needed. Objectives • Test AHSP operation within the Estuary while providing information highly relevant to pressing Delta management issues (IEP 2016); • Provide detailed information on distribution and approximate abundance of adult Delta Smelt within identified habitat types (Biological Opinion on the Long-Term Operational Criteria and Plan for coordination of the Central Valley Project and State Water Project;https://www.fws.gov/sfbaydelta/documents/SWPCVP_OPs_BO_12-15_final_OCR.pdf);and • Assess habitat associations and diurnal behavior of Delta Smelt and other fishes (Durand 2015).
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Central Valley Salmonid Coordinated Genetic Monitoring [Year 4]

    Lead U.S. Bureau of Reclamation [USBR]
    Description Description This work will include tasks to rapidly identify winter-run Chinook juvenile salmon at the CVP/SWP salvage facilities, process juvenile salmonid tissues from various CVPIA and IEP fish monitoring stations, and support coordination of genetic monitoring across the CVP and SJRRP programs. PIs: Josh Israel (USBR);Scott Blankenship (Cramer Fish Science);Ken Bannister (USFWS);John Carlos Garza (NOAA-Fisheries);Brett Harvey (DWR);Noble Hendrix (QEDA);Rachel Johnson (NOAA-Fisheries);Mariah Meek (UC Davis);Kevin Reece (DWR) Need This study is needed due to the limited accuracy of Lenght at Date stock identification. Inaccurate identification of Chinook salmon is problematic because it compromises the management value of data collected from standard monitoring programs. This project will improve the science and management value of the Central Valley salmon monitoring network, supported through IEP and Central Valley Project Improvement Act (CVPIA) monitoring stations, by accurately determining stock identification of multiple Chinook salmon stocks across their distribution. Classification tables will be developed to characterize monthly and seasonal accuracy between length-at-date and genetic race assignment at IEP and BiOp monitoring locations. This multi-year dataset will be used to evaluate the likelihood of accurate assignment and potential biophysical explanatory variables influencing genetic accuracy. Objectives Improve accuracy of CVPIA and IEP monitoring programs by providing genetic stock identification information for tissues collected from Red Bluff, Knights Landing, DJFMP, salvage facilities and San Joaquin River fish monitoring stations. Samples will be collected from all four runs of Chinook salmon based on length-at-date (i.e., samples will be collected from Chinook of various sizes throughout the sampling period).
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Enhanced Acoustic Tagging, Analysis, and Real-Time Monitoring

    Lead National Oceanic and Atmospheric Administration [NOAA]
    Description Description This project tracks the movement and survival of wild and hatchery juvenile Chinook salmon with a large acoustic receiver network (JSATS), including real-time receivers, and the development of real-time metrics and retrospective modeling of juvenile salmon migration data. Need There is a well-documented need for improved detection and associated modeling of salmon migration and survival in the Central Valley. Understanding salmon survival and movement dynamics in the Delta and its tributaries is critical to the operation of state and federal water projects, recovery of ESA-listed species, and sport and commercial fisheries management. Objectives • Maintain 20 real-time JSATS receivers: will provide information on migrating salmon smolt location and timing of Delta entry and exist, which is key for informing time-sensitive decisions • Deployment of autonomous JSATS receiver array: this will provide fine-scale reach-specific survival and movement rates • Development of new metrics for the real-time data: this will inform key management relevant questions, such how many fish are entrained at critical junctions • Development of real-time website to convey movement and survival rates of acoustic tagged juvenile salmonids at various real-time locations in the Sacramento River and Delta.
    Science topics Salmon migration
    Updated April 29, 2022
  • Title

    Suisun Marsh Salinity Control Gate Study

    Lead California Department of Water Resource [DWR]
    Description Description Suisun Bay and Marsh are a key part of the habitat for Delta Smelt, but during drier periods such as summer, Delta Smelt may be at least partially excluded from Suisun Marsh due to high salinities. The purpose of this proposal is to provide scientific support a management action for Smelt, operation of the Suisun Marsh Salinity Control Gates (SMSCG). This facility is currently to tidally pump water into the Marsh to improve fall and winter habitat conditions for waterfowl, but could also provide a tool to manage aquatic habitat for Delta Smelt in other periods. Specifically, by using the SMSCG to direct more fresh water in Suisun Marsh, our prediction is that reduced salinities will improve habitat conditions for Delta Smelt in the region. Need The status of Delta Smelt is dire. As part of the Resources Agency's Delta Smelt Resiliency Strategy, in August 2018 we conducted pilot operations of the SMSCG to support Delta Smelt , with promising results. Based on this early success, we expect that the SMSCG will be used as a seasonal tool to support Delta Smelt in summer-fall in coming years as part of the coming FWS Biological Opinion and DFW ITP. Neither has been completed, but SMSCG operations for fish are expected to be required in each. Hence, the proposed study is intended to provide a scientific evaluation and guidance for an expected SMSCG action in 2020. Objectives The primary objective of this project is to evaluate the effectiveness of the SMSCG action. Questions to be addressed include: • Did the action improve habitat conditions for Delta Smelt in the Suisun Region? • Does the Suisun Region typically have better habitat and food web conditions than the upstream River Region? • Do Delta Smelt respond favorably to the SMSCG flow action? • Does operation of the SMSCG affect other fishes and clams?
    Science topics Salinity
    Updated April 29, 2022
  • Title

    Physiological and Behavioral Effects of Domestication on Delta Smelt

    Lead California Department of Water Resource [DWR]
    Description Description Due to the continued population decline of Delta Smelt and the threat of extinction, conservation efforts may include future supplementation practices using the refuge population of Delta Smelt at the Fish Conservation and Culture Laboratory (FCCL) in Byron, CA to assist in maintaining the wild population. Prior to any supplementation planning, it is first critical to determine if Delta Smelt with varying levels of domestication indices (i.e. level of hatchery ancestry) respond differently, both physiologically and behaviorally, to various habitat conditions. This project aims to provide a better understanding of the effects of domestication on captive Delta Smelt (Hypomesus transpacificus) by assessing the refuge population at the FCCL. Three studies will be conducted exploring if domestication index (i.e. the level of hatchery ancestry) affects the physiological and behavioral performance of Delta Smelt in response to physical handling and climate change stressors. Need Physiological and behavioral changes of hatchery fish due to domestication could lead to unintended detrimental effects in the wild;therefore, research characterizing the alterations of hatchery Delta Smelt across levels of domestication indices are warranted to understand the effects of captivity and how they might shape future supplementation and conservation strategies. For example, identification of differences among groups of Delta Smelt with varied domestication index may create the need for domestication management and the implementation of altered hatchery practices. This project will provide relevant and timely information for conservation managers and adaptive restoration strategies and dovetail with the recommendations from the 2017 Delta Smelt Supplementation Workshop. As such, this study is included in the supplementation studies work plan which came out of that workshop. Specifically, this project fits within two topics in the IEP Science Strategy: Effects of Climate Change and Extreme Events and Restoring Native Species and Communities. Objectives 1. To characterize domestication effects on hatchery Delta Smelt by synthesizing existing/historical datasets on growth and reproduction of fish at the FCCL since the start of the hatchery program. 2. To identify the impacts of domestication index on the physiological stress response of Delta Smelt following handling stress. 3. To determine the effects of domestication index on individual and group swimming behavior, responses to predation, and responses within the context of climate change factors including warming and increased salinity.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Developing an eDNA metabarcoding protocol to improve fish and mussel monitoring in the San Francisco Estuary

    Lead National Oceanic and Atmospheric Administration [NOAA]
    Description Description We propose to develop an eDNA metabarcoding protocol to complement existing IEP monitoring surveys and assess the effects of management activities such as habitat restoration or flow alteration. We will develop a reference sequence database for native and invasive fish, mussels, and other macroinvertebrates present in the San Francisco Estuary (SFE). We will optimize a molecular and computational pipeline for metabarcoding and ground truth the method against three SFE monitoring efforts, each using different sampling gear. We will investigate the relationship between eDNA sequence read count and fish biomass or abundance (EDSM survey). Finally, we will determine the ability of metabarcoding to detect fish and macroinvertebrate assemblages across large and small spatial scales and over time. Need Our overarching goal is to develop a non-invasive, low cost monitoring tool that can be used in conjunction with existing IEP monitoring programs or used alone to assess biological community composition at locations of interest in the SFE. This proposal is related to the 2020 – 2024 IEP Science Strategy by creating a new monitoring tool that can assist in two main areas: 1) Restoring Bay-Delta native fishes and community interactions and 2) assessing effects of flow alteration on Bay-delta aquatic resources. Broadly, this study will inform management decisions by supporting and augmenting existing monitoring surveys in the SFE. It will also lead to a richer and more complete understanding of SFE ecology. This study is not explicitly required by law or agreement, and to our knowledge is neither a recommended action nor a result from an IEP review or synthesis effort. Objectives Objective 1: Develop robust molecular methods and a computational pipeline for detection of SFE fish and macroinvertebrates by eDNA metabarcoding of water samples. Objective 2: Compare eDNA metabarcoding head-to-head with existing and historical monitoring data from three ongoing ecological surveys using diverse conventional sampling gear and evaluate accuracy of fish abundance and biomass estimates from eDNA metabarcoding data. Objective 3: Evaluate factors that influence eDNA detection of species of interest (e.g. rare or invasive species) and suites of species (e.g. benthic fishes and invertebrates) on two spatial scales, within and between habitats, along with temporal variation.
    Science topics Fish
    Updated April 29, 2022
  • Title

    Predation Dynamics Across Reach-Specific Gradients in Juvenile Salmon Survival

    Lead U.S. Geological Survey [USGS]
    Description Description The overarching goal of this project is to determine if predation by piscivorous fishes is an important explanatory driver of survival of juvenile Chinook Salmon emigrating through the north Delta. To achieve this goal, we seek to determine if variation in reach-specific characteristics of predation dynamics covary with survival of acoustictagged juvenile Chinook Salmon collected during the study period. This will be accomplished by comparing reach-specific characteristics of the piscivore community and its observed and modeled consumption of juvenile Chinook Salmon across a range of environmental conditions. Need This is not a mandated study but it addresses an important research need. Objectives • How does the piscivore community (species composition, size structure, and abundance) vary across specific migratory pathways (river reaches) in the North Delta? • To what extent do environmental conditions (e.g., water temperature, turbidity, and discharge) control the consumption of juvenile Chinook Salmon? • Do characteristics of the predator community explain variation in survival of acoustic tagged salmon collected during the study period?
    Science topics Predation
    Updated April 29, 2022
  • Title

    Directed Field Collections

    Lead California Department of Fish and Wildlife [CDFW]
    Description Description The Direct Field Collections element (-089) provides funding support for expanded field collections, allowing CDFW to provide other, IEP-approved researchers access to research-capable boats and experienced operators, and thus the ability to safely sample the upper San Francisco Estuary. This element most recently facilitated investigations associated with the Fall Low Salinity Habitat (FLaSH) project and the Directed Outflow Project (DOP). Need This element allows CDFW and thus IEP to provide boat and operator time to assist collaborating researchers leading approved IEP projects with “on-the-water” sampling. There is no mandate for this element. Objectives To provide CDFW operational flexibility to assist collaborating researchers leading approved IEP projects with access to CDFW boat operators and boats to complete "onthe-water" sampling.
    Science topics None specified
    Updated April 29, 2022
  • Title

    North Delta Flow Action: Role of Improved Yolo Bypass Flows on Delta Food Web Dynamics

    Lead California Department of Water Resource [DWR]
    Description Description In a collaborative effort between CA Department of Water Resources, US Bureau of Reclamation, CA Department of Fish and Wildlife, United States Geological Survey, San Francisco State University, and UC Davis, this study will investigate the role of augmented summer and fall flows in the Yolo Bypass and North Delta areas on lower trophic food web dynamics and the benefits to listed fish species. Using both continuous and discrete sampling approaches, this study will relate hydrologic patterns to chlorophyll-a, nutrients and primary productivity, plankton densities and composition (phytoplankton and zooplankton), contaminant concentrations, as well as water quality parameters such as electrical conductivity, turbidity, temperature, and dissolved oxygen. In addition, caged hatchery Delta Smelt will be monitored to determine the effects of the managed flow action and increased food web productivity on fish survival, growth, and behavior. Need Due to the food-limited nature of the San Francisco Estuary, it is critical to understand mechanisms that result in successful food web productivity including phytoplankton blooms. Food limitation is one of the primary hypothesized causes of the Pelagic Organism Decline. In 2011 and 2012 there was evidence that a moderate Yolo Bypass flow pulse during fall agricultural drainage periods was followed by phytoplankton blooms in the lower Sacramento River. Managed flow actions in the following years showed an increase in food web productivity could be repeated;however, results varied across years and flow actions indicating more research is warranted to understand correlations between flow and abiotic conditions, and the biological response of the food web. The increases of summer/fall flows in North Delta, has been considered a management strategy as part of complying with USFWS Delta Smelt Biological Opinion Action 4. The augmentation of flows through the Yolo Bypass/North Delta is also included as one of several Delta Smelt Resiliency Strategies by Natural Resources Agency. Objectives • Determine if managed flow actions through the Yolo Bypass stimulate increased primary productivity locally and downstream, and if it is repeatable. • Characterize how nutrients, chlorophyll and plankton (composition and density) in the Toe Drain, Cache Slough Complex, and lower Sacramento River change in response to flow pulses. • Determine if nutrient subsidies of the source water and downstream are limited by abiotic and biotic factors. • Characterize spatial differences and transport of pesticide contaminants in the Yolo Bypass in response to the flow actions. • Determine survival, growth and behavior of caged hatchery Delta Smelt before and after the flow action in the Yolo Bypass.
    Science topics Flows, Water management
    Updated April 29, 2022
  • Title

    Estimating Abundance of Juvenile Winter-run Chinook Salmon Entering and Exiting the Delta [SAIL]

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description Description This is a continuation of a five year project funded by CDWR and CDFW and the Central Valley Project Improvement Act in 2017. The objective of the project is to improve estimates of population abundances for fall, winter and spring run juvenile Chinook Salmon at Sacramento and Chipps Island by improving efficiency estimates using data from releases of coded wire tags (CWT), acoustic tags (AT), and by genetically sampling the trawl catch in 2018. The project will (1) develop statistical models for estimating trawl efficiencies using 2016-2018 data for paired AT-CWT releases of winter run and fall-run Chinook Salmon;(2) use 2018 genetic sampling of trawl catch in combination with efficiency estimates to estimate population abundances of fall, spring and winter run at Sacramento and Chipps Island in 2018;(3) implement trawl efficiency studies for multiple salmon runs in 2018 informed by the 2016 and 2017 results and in coordination with hatcheries for inclusion of AT fish with existing CWT releases;and (4) combine trawl efficiencies with genetic samples of trawl catch to provide estimates of fall, spring and winter-run salmon abundance (with estimated precision) entering and exiting the Delta in 2018. Need There is growing appreciation that a salmon monitoring network that could quantitative estimates of abundance is desirable to improve our knowledge and resolution of life stage success and movement across the landscape (Salmon SAIL conceptual models 2016). Objectives (1) Estimate the population-level status and trends for winter run;and status of spring and fall run;(2) evaluate production estimates for juvenile winter-run Chinook Salmon entering the Delta used in water project take development;(3) provide estimates of winter and fall run-specific freshwater cohort strength to support ocean harvest management decisions;(4) establish a time series of winter, spring and fall run-specific production estimates at key locations for incorporation into life cycle models.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Enhanced Delta Smelt Monitoring [EDSM]

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description Description The Enhanced Delta Smelt Monitoring (EDSM) program is a year-round monitoring program comprised of multiple crews trawling concurrently at multiple sites in predefined strata within the San Francisco Estuary. Post-larval Delta Smelt are targeted approximately April through June using 20mm trawling gear, and Kodiak trawling gear is employed the remainder of the year. Gear efficiency experiments and shallow water sampling elements are incorporated when possible. Need The declining Delta Smelt population has highlighted the need to keep improving the array of information that supports our understanding of the factors affecting Delta Smelt population dynamics and management decisions to minimize adverse effects of water operations on the population. EDSM has biological significance and potential conservation benefit by providing data to resource managers on nearly all life stages of endangered Delta Smelt and near-real-time data on the juvenile and adult life stages. EDSM data is provided to the Smelt Working Group and other managers in near realtime to help inform management decisions during the entrainment season. Objectives • To estimate the total abundance of Delta Smelt, along with standard errors or confidence intervals, on a weekly to bi-weekly basis for various life stages (postlarvae, juveniles, sub-adults, adults) throughout the year; • To estimate the spatial distribution of Delta Smelt at a management relevant temporal and spatial resolution;and • To provide data that support management decisions and address scientific questions to further understanding of sampling efficiency, drivers of Delta Smelt population patterns, and other conservation and management-relevant topics.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Effect of Outflow Alteration upon Delta Smelt Habitat, Condition and Survival

    Lead U.S. Bureau of Reclamation [USBR]
    Description Description The Directed Outflow Project (DOP) is a continuing collaborative effort among a dozen state, federal and non-governmental groups. The DOP will employ a focused spatial and temporal approach to evaluate mechanistic hypotheses directly related to the rationales provided for the summer Delta outflow action and Yolo Bypass Toe Drain action to benefit Delta Smelt, with direct relevance to the fall outflow action. Paired data collections (same location and time) of abiotic and biotic habitat constituents to test specific hypotheses will assist in avoiding prior shortcomings of using data collected for different studies/hypotheses and/or across variable spatial/temporal scales (as discussed in MAST [2015] and elsewhere). Sampling will occur during the Delta Smelt juvenile rearing-stage, a period known to be associated with the location of the low salinity zone (LSZ). Results should strengthen our understanding of the mechanisms and drivers impacting Delta Smelt vital rates and associated habitat features with a focus on outflow conditions. Results should assist in evaluating the benefit and feasibility of future flow augmentation actions for managers and decision makers. Results from this and other related studies will inform evaluations on which particular outflow-related action or group of actions provides the most benefit for Delta Smelt. Need Requests and plans for water management actions related to augmentation of Delta outflow have proceeded and are expected to proceed in the future. However, there is uncertainty and disagreement regarding the mechanistic relationship of Delta outflow during the rearing period to Delta Smelt vital rates and habitat, and the hypothesized benefit of outflow alteration for Delta Smelt. Delta outflow has experienced reductions in recent years, coinciding with the collapse of the Delta Smelt. Reduced outflow has been linked to reductions in habitat suitability in Suisun Bay and Marsh and movement of the LSZ to the Confluence of the Sacramento-San Joaquin River where little connection to shallow open water habitats exists. Objectives The DOP’s main objective will be to evaluate the hypothesized benefit of outflow alteration for Delta Smelt and its habitat in coordination with all stakeholder groups. The following process and product related sub-objectives will facilitate progression toward this evaluation objective. • Test mechanistic hypotheses addressing the rationale behind outflow-based actions to benefit Delta Smelt. • Concurrently sample fish and measure abiotic/biotic habitat conditions at each randomly selected location along the salinity and habitat gradient of the north to western Delta along the Sacramento River during the summer and fall.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Extracting Better Information from Long-Term Monitoring Data: Estimating Occupancy and Abundance of Near-Shore Fishes in the Sacramento-San Joaquin River Delta

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description Description The purpose of this study is to expand IEP monitoring and inference to other dominant near-shore, littoral habitats not sampled by beach seines through the use of boat electrofishing. To accomplish this we will sample key littoral fish species across various near-shore habitats in order to determine how best to estimate abundance, occupancy, capture probabilities, and related environmental drivers. Need Expanding DJFMP sampling to other habitats throughout the Delta will allow our program to detect and monitor fishes and ecological trends through time, alleviating a recognized data gap. Current sampling relies on data collected through non-random fixed point sampling of unobstructed habitats, which limits the utility of our data to inform management decision. Objectives • Design boat electrofishing survey methods to expand DJFMP’s monitoring into habitats and locations not sampled by beach seining. • Design and develop field and data analysis methods for estimating capture probability and abundance using boat electrofishing techniques. • Predict spatio-temporal distribution of habitats occupied by key littoral species.
    Science topics Habitat
    Updated April 29, 2022
  • Title

    Food Temperature Optimization Model for CVP

    Lead U.S. Bureau of Reclamation [USBR]
    Description This study aims to improve understanding of how nutrient and zooplankton exports from CVP reservoirs impact downstream food web productivity.
    Science topics None specified
    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

    Examining the relationship between Longfin Smelt and flow in the San Francisco Bay Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description The overarching goal of this study is to investigate the time-varying effects of flow variation and food availability on longfin smelt population dynamics, via advanced modeling of a diverse set of environmental and ecological monitoring time series. Specifically, this project will:(1) Assess how key environmental drivers (flow, salinity, temperature) have changed over the past 5 decades (1967 to present) across the San Francisco Estuary (SFE); (2) Examine how longfin smelt population dynamics have changed over that time period, and whether/when breakpoints in abundance and trends exist (e.g., periods of 'decline' vs' stability'); (3) Quantify the effects of environmental on driving observed fluctuations in longfin smelt dynamics; (4) Determine whether/how environment-smelt relationships have changed in magnitude or sign over time; and if they changed, whether such changes have been spatially consistent across the SFE. These goals will inform ongoing conservation efforts of longfin smelt by determining the combinations of flow, habitat, and prey availability conditions that lead to stable population dynamics for the species.
    Science topics Fish, Flows, Longfin Smelt, Zooplankton
    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
  • Title

    Impact of Temperature and Contaminants on Chinook salmon survival: A Multi‐Stressor Approach

    Lead National Oceanic and Atmospheric Administration [NOAA]
    Description This project will examine how contaminant exposures at different temperatures impact a number of critical physiological functions and the associated genes that maintain salmon fitness. The project will determine the sensitivity of fall‐run Chinook salmon to a mixture of bifenthrin, a pyrethoid pesticide, and triclosan, an antibacterial added to personal care products, at optimal and high temperatures that Chinook salmon encounter during their outmigration through the Sacramento and San Joaquin rivers. The hypothesis is that these stressors will impact salmon predator and disease susceptibility and will interact, such that the cumulative effect on salmon could not be predicted from multiple single exposures. To test the hypothesis, fall‐run Chinook salmon parr will be exposed to sublethal concentrations of bifenthrin, triclosan, and a mixture of bifenthrin and triclosan at different temperatures. The impacts of these exposures on salmon will be assessed with the following endpoints: (1) predator susceptibility through altered response latencies and escape velocities;  (2) disease susceptibility in response to a disease challenge; and (3) differential gene expression by high‐throughput sequencing of the Chinook salmon transcriptome.
    Science topics Pesticides
    Updated September 28, 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

    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

    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

    Evaluating contributions of hatchery-origin fish to conservation of endangered Sacramento River winter run Chinook salmon during a drought

    Lead University of California - Davis [UC Davis]
    Description Hatchery-reared fish have been used to supplement endangered winter-run Chinook salmon in the upper Sacramento River since 1989. Intense drought in the past five years has led fisheries managers to substantially modify their hatchery protocols, increasing the total number of fish released and using hatchery-origin adults for producing juveniles. However, the impact of these practices is not fully understood. This project evaluated multiple aspects of how hatchery–reared fish contribute to natural production of winter-run Chinook salmon in the upper Sacramento River. The researchers assessed whether hatchery-reared fish are spawning in the wild and producing natural-origin offspring using a novel panel of genetic markers developed during the study. The study also assessed if inadvertent domestication selection was occurring in the hatchery during the drought years and if more highly related hatchery broodstock pairings returned fewer offspring than less related pairs.
    Science topics Drought
    Updated February 1, 2024
  • Title

    In search of refuge: Investigating the thermal life history of Delta Smelt through in-situ oxygen isotope ratio analysis of otoliths.

    Lead University of California - Davis [UC Davis]
    Description The inner ear bones of fish, or otoliths, grow continuously and their chemistry reflects the water conditions that a fish has experienced throughout its life. In this project, researchers used in-situ chemical analysis to determine the oxygen isotopic composition of otoliths, which can reflect the water temperature that a fish has experienced. They applied this method to archived adult Delta Smelt otoliths from multiple different water years spanning the time from before and during the recent drought. Using these data, they investigated the relationship between delta smelt abundance and environmental parameters, such as water temperature. More specifically they investigated whether delta smelt are able to find temperature refuges, even in drought years.
    Science topics Climate change, Delta Smelt, Endangered species, Fish, Temperature
    Updated February 26, 2024
  • Title

    Defining the architecture and recurrence interval for faults in the Sacramento-San Joaquin Delta: Assessing Potential Geohazards

    Lead San Diego State University
    Description This project aimed to create a detailed fault map for the Sacramento-San Joaquin Delta by mapping the faults throughout the Delta waterways. The project began with a review of existing data and reports, then a high-resolution seismic reflection and sidescan sonar survey, and finally, collection/analysis, including radiocarbon dating, of sediment cores to create the first detailed fault maps for the Delta waterways. The project worked to constrain the significant rupture histories of the Kirby Hills and Midland Faults, which is important for understanding the potential of future earthquakes.
    Science topics Landscape change, Seismicity
    Updated March 7, 2024
  • Title

    Revealing the invisible contributors to the diets of larval longfin smelt and striped bass in the San Francisco Estuary.

    Lead San Francisco State University [SFSU]
    Description To better understand why the longfn smelt is threatened, the project compared the diet of larval longfn smelt to a thriving fsh with overlapping natal habitat and of similar size and morphology— the Pacifc herring. Using new genetic analysis methods, the project aimed to elucidate species composition of fsh diets in greater detail than has been done before and to measure diferences in composition and frequency of prey across habitats. In particular, the project aimed to identify prey items that were not previously seen using traditional diet analysis methods and assess whether any prey are indicative of natal habitats
    Science topics Fish, Longfin Smelt
    Updated February 26, 2024