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  • Title

    Operation Baseline Project 1: Conceptual Framework

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

    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

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

    Lead Cramer Fish Sciences
    Description There is a great deal of telemetry data amassed from studies in the Sacramento-San Joaquin Delta. It continues to grow every year with special studies and monitoring efforts. Multiple research priorities surrounding fish ecology in the Delta could be addressed, at least in part, by synthesizing the myriad telemetry data sets that exist; this work would benefit greatly from the centralization and standardization of data workflows surrounding telemetry research. With the guidance of a PIT Advisory Team, we plan to establish a collection of open-source, technology-agnostic, accessible resources to support a reproducible and transparent telemetry data workflow for researchers in the region. The workflow and resources do not invent new procedures, rather improve and standardize those already used by the telemetry research community. This will bring us in closer alignment with centralized, coordinated data workflows that have been successfully implemented in other regions and data communities. The final open-source set of resources will include a design and roadmap for implementing a central telemetry database and workflow, an R package for the preparation, QA/QC, and basic analysis of telemetry data, and a regional workshop offering training programs in the proposed telemetry data workflow.
    Science topics Chinook Salmon, Fish, Other species, Salmon migration, Steelhead Trout, Striped bass, Sturgeon
    Updated August 26, 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

    Perceptions of risk and management of the Delta levee system

    Lead University of California - Santa Cruz [UCSC]
    Description This study of the perceptions of flood risk and management of the levee system in a deltaic region of California illuminates the social, cultural, and psychological complexities of risk assessment. In order to better understand risk tolerance, we included stakeholders from the following groups: agriculture, engineering, boating and recreation industry, local reclamation districts, conservation organizations, water exporters, county government, and state agencies. Methods employed are qualitative and quantitative and include interviews and media analysis. For decades the Sacramento-San Joaquin Delta has been ripe with political controversies stemming from conflicting interests for its natural resources. The results of this study reveal distinct views on the sustainability of the Delta’s levees, the resilience of local communities, and who is accountable for present conditions. The findings of this study also elucidate nuances in the conversations on the viability of mitigation and adaptation as conditions in the Delta change. We conducted this study in two parts. First, we used the Q methodology and found five distinct views that shape stakeholders’ perceptions of risk of flooding from levee failure: fatalistic, skeptical, free market, bio-centric, and human ingenuity. Second, we collected over 500 newspaper articles from 1986 to 2017 to analyze the framing of issue of flooding in the Delta. As opposed to our study with diverse stakeholders, our media analysis show that the issue of flood risk has been framed in the media mostly along the binary lines of unpreventable catastrophe and control through emergency management.
    Science topics Levees
    Updated January 23, 2024
  • Title

    Monitoring Sacramento River winter-run Chinook salmon life history diversity, growth, and habitat use among varying hydroclimatic regimes

    Lead University of California - Berkeley [UC Berkeley]
    Description Sacramento River winter-run Chinook salmon have been endangered since 1994. Historically, the fish spawned during summer in cool tributaries upstream of Sacramento, but dams have limited spawning habitat to a small reach of the river. Today, survival of their offspring is heavily dependent on cool summer water releases from reservoirs, which also provide critical water supplies for irrigation, municipal, and industrial needs, as well as providing flood control and hydropower generation. During drought, this can lead to difficult management decisions. Understanding how winter run Chinook salmon respond to drought and water temperature is therefore vital to the management of this endangered population. This project tackled two outstanding questions about winter-run salmon ecology. The first was how winter-run Chinook use different rearing habitats during drought and non-drought periods, and the second was to explore which habitats provide enhanced growth during drought and non-drought periods. To answer these questions, UC Berkeley post-doc Pedro Morais used isotopic analysis of otoliths, or fish ear bones, which grow continuously throughout their lives and therefore carry a record of their environment and growth. Using otoliths, researchers can reconstruct details of fishes’ lives, including water temperature and migration patterns.
    Science topics None specified
    Updated February 1, 2024
  • Title

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

    Lead San Francisco Estuary Institute [SFEI]
    Description

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

     
    Science topics None specified
    Updated October 10, 2024