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  • Title

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

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

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

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

    Habitat Values of Native SAV [Submerged Aquatic Vegetation] in the Low Salinity Zone of San Francisco Estuary

    Lead San Francisco State University [SFSU]
    Description We will investigate the importance of native submerged aquatic vegetation (SAV) in providing food web support for native fish species in the low salinity zone of the San Francisco Bay-Delta. These SAV beds, composed primarily of Stuckenia pectinata (sago pondweed), are an extensive feature along many of the islands in Suisun Bay and the west Delta, yet almost nothing is known of their seasonal or interannual patterns, their invertebrate communities, or how their physical structure or food resources influence use by native fishes. We hypothesize that the position of these beds in the shallow subtidal zone along the islands increases habitat options adjacent to wetlands and channels for numerous fish species, including species of concern such as delta smelt and chinook salmon. The objectives of this project are to: 1) characterize patterns in habitat structure, community composition, and productivity of SAV beds in four locations in Suisun Bay and the western Delta over a three year period (with comparisons to non-native Egeria densa beds), 2) document the epifaunal invertebrate community composition and abundance in the Stuckenia beds, 3) assess fish use of these beds through seining and acoustic monitoring of hatchery-tagged fish, 4) utilize stable isotope analyses to evaluate food web relationships within and among the beds, and 5) begin preliminary evaluation of the potential to restore native SAV to subsided lands in this region.
    Science topics Chinook Salmon, Green sturgeon, White Sturgeon, Sacramento Splittail, Delta Smelt, Steelhead Trout
    Updated April 29, 2022
  • Title

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

    Lead University of California - Davis [UC Davis]
    Description The proposed project directly addresses priority research detailed by the Delta Science Program to protect native fishes that depend on the Bay-Delta system focusing on adaptations to local habitats and physiological tolerances to key environmental stressors;in delta smelt (Hypomesus transpacificus). Temperature and salinity changes associated with anthropogenic climate change are likely to further exacerbate delta smelt population declines. We hypothesize that delta smelt tolerance to forecasted temperature rises and salinity intrusions into the Bay-Delta system can be assessed at a mechanistic level, and that acclimation thresholds can be established by means of genomic responses. This proposal builds upon successful development of a cDNA microarray for delta smelt containing approximately 2000 individual gene fragments, and the subsequent application of biomarkers for assessing the effects of chemical stressors on larval development with links to swimming behavior. We propose to develop a Next Generation oligonucleotide microarray in delta smelt, with ca. 15K genes, in order to assess mechanistic tolerance to changes in gemperature and salinity. Genomic studies will be conducted integrating effects on energetic activity and swimming performance studies, in an interdisciplinary approach that will permit the establishment of links between tolerance mechanisms and adverse outcomes.
    Science topics Delta Smelt, Water temperature, Salinity, Turbidity
    Updated April 29, 2022