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  • Title

    Monitoring and Evaluation of the North Delta Food Subsidies and Colusa Basin Drain Study

    Lead California Department of Water Resource [DWR]
    Description The North Delta Food Subsidies – Colusa Basin Drain Study monitors and evaluates the effects of the North Delta Flow Action on the Delta food web.
    Science topics Delta Smelt, Fish, Flows, Water management
    Updated June 13, 2024
  • 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

    Monitoring and Assessment of Suisun Marsh Salinity Control Gates Action

    Lead California Department of Water Resource [DWR]
    Description The Suisun Marsh Salinity Control Gates (SMSCGs) have the potential to provide an increase in low-salinity-zone habitat for endangered Delta Smelt. Operation of the SMSCGs in summer and fall to improve Delta Smelt habitat are called for in the Biological Opinion and Incidental Take permit for the Central Valley Project and State Water Project. To support the adaptive management of the action, DWR is planning to monitor the change in water quality, phytoplankton, zooplankton, fishes, and clams resulting from the action.
    Science topics Delta Smelt, Phytoplankton, Salinity
    Updated September 3, 2024
  • Title

    Suisun Marsh Salinity Control Gates Action Pilot Study

    Lead California Department of Water Resource [DWR]
    Description In summer 2018 we used a unique water control structure in the San Francisco Estuary to direct a managed flow pulse into Suisun Marsh. Field monitoring showed that turbidity and chlorophyll were at higher levels in Suisun Marsh, representing better habitat conditions, than the upstream Sacramento River region throughout the study period. Fish monitoring data suggested that small numbers of Delta Smelt colonized Suisun Marsh from the Sacramento River during the 2018 Flow Action.
    Science topics Delta Smelt, Phytoplankton, Salinity
    Updated June 13, 2024
  • 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

    The Effect of Drought on Delta Smelt Vital Rates

    Lead University of California - Davis [UC Davis]
    Description This Project is necessary to obtain a better understanding of the effects of drought and management's response to drought on the Delta Smelt in order to avoid extinction. This study will test predication from other models to evaluate the impact of drought and management measures on Delta Smelt responses in terms of growth, phenotype diversity and survival during the spring and summer, when drought impacts are greatest.
    Science topics Delta Smelt, Drought
    Updated November 18, 2022
  • Title

    The Consequences of Operational Decisions on Water Quality: Reconciling Delta Smelt, Salmon, and Human Needs

    Lead Contra Costa Water District [CCWD]
    Description The purpose of this project is to assess the consequences of actions taken to protect threatened or endangered Chinook salmon species relative to other upstream and in-Delta water management actions that have changed seasonal salinity in the Delta, thus reducing the ability of delta smelt to survive as a species;and, to investigate with modeling scenarios the potential to ameliorate this trade-off with specific operational actions.
    Science topics Delta Smelt, Chinook Salmon
    Updated April 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

    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

    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

    Modeling the Delta Smelt Population of the San Francisco Estuary

    Lead San Francisco State University [SFSU]
    Description The purpose of this project is to develop an individual-based particle-tracking model examining population behavior of Delta smelt under different scenarios.
    Science topics Delta Smelt
    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

    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 June 13, 2024
  • 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

    20-mm Survey [Delta Smelt distribution monitoring]

    Lead California Department of Fish and Wildlife [CDFW]
    Description California Department of Fish and Wildlife (CDFW) conducts the 20-mm Survey annually to monitor the distribution and relative abundance of larval and juvenile Delta Smelt (Hypomesus transpacificus) in the upper San Francisco Bay Estuary. The survey began in 1995 and supplies near real-time catch data to water and fisheries managers as part of an adaptive management strategy to limit the risk of Delta Smelt entrainment during water exports Data collected: temperature, electro-conductivity, water transparency, turbidity, water volume, tidal stage, fish, and zooplankton.
    Science topics Stage, Tides, Other zooplankton, Water temperature, Turbidity, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Benthos
    Updated April 29, 2022
  • Title

    Endangered Species Project

    Lead California Department of Pesticide Regulation [DPR]
    Description In California, DPR has been studying endangered species protection issues with federal funding since 1988. DPR activities include mapping sites occupied by federally listed species, evaluating pesticide exposure risks to inhabited sites, classifying risk and developing protection strategies to minimize risk as needed. There are currently 359 federally listed species in California including federally protected endangered and threatened species, proposed endangered, proposed threatened and Category 1 candidate species (that await only administrative processes to become protected species). Collectively, the federally listed species may occupy about 16 million acres, or about 16 percent of the land area of the state, albeit at very low densities. Of all federally listed species in California, the San Joaquin kit fox has by far the greatest overlap with agricultural areas, accounting for about 10 million acres in 14 counties, mostly in the agriculturally rich southern San Joaquin Valley. Other species that are interspersed with agricultural areas include birds, mammals, reptiles, amphibians, crustaceans and many plants.
    Science topics Agriculture, Urban development, Insecticides, Rodenticides, Herbicides, Fungicides, Chinook Salmon, Delta Smelt, Benthos, Shorebirds, Giant garter snake, California tiger salamander, Insects, Other species, Fish, Mammals, Birds, Amphibians and reptiles
    Updated April 29, 2022
  • Title

    Fall Midwater Trawl Survey [FMWT]

    Lead California Department of Fish and Wildlife [CDFW]
    Description The FMWT was initiated to determine the relative abundance and distribution of age-0 striped bass (Morone saxatilis), delta smelt (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), American shad (Alosa sapidissima), splittail (Pogonichthys macrolepidotus), and threadfin shad (Dorosoma petenense) in the estuary. FMWT has sampled annually since it's inception in 1967, with the exceptions of 1974 and 1979, when sampling was not conducted. The FMWT samples 122 stations each month from September to December and a subset of these data is used to calculate an annual abundance index.
    Science topics Stage, Mysis, Other zooplankton, Water temperature, Turbidity, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail
    Updated April 29, 2022
  • Title

    California Natural Diversity Database [CNDDB]

    Lead California Department of Fish and Wildlife [CDFW]
    Description The California Natural Diversity Database (CNDDB) is an inventory of the status and locations of rare plants and animals in California. CNDDB staff work with partners to maintain current lists of rare species, as well as to maintain an ever-growing database of GIS-mapped locations for these species. The CNDDB is a "natural heritage program" and is part of a nationwide network of similar programs overseen by NatureServe (formerly part of The Nature Conservancy). All natural heritage programs provide location and natural history information on special status plants, animals, and natural communities to the public, other agencies, and conservation organizations. The data help drive conservation decisions, aid in the environmental review of projects and land use changes, and provide baseline data helpful in recovering endangered species and for research projects.
    Science topics Mudflats, Intertidal / transition zones, Above-highwater refugia, Main channels, Sloughs, Backwater, Submerged aquatic vegetation, Floating aquatic vegetation, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Non-forested vegetation, Delta islands, Pacific flyway, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Pelagic fish, Benthos, Salt marsh harvest mouse, Waterfowl, Shorebirds, Gulls, Giant garter snake, California tiger salamander, Insects, Mollusks, Crustaceans, Striped bass, Corbicula/Potamocorbula, Nutria, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Saltwater / freshwater marshes, Habitat, Other species, Fish, Mammals, Birds, Amphibians and reptiles, Invertebrates, Invasive / non native species, Non-resident / overwintering birds
    Updated April 29, 2022
  • Title

    San Francisco Bay Study

    Lead California Department of Fish and Wildlife [CDFW]
    Description The San Francisco Bay Study (Bay Study) was established in 1980 to determine the effects of freshwater outflow on the abundance and distribution of fish and mobile crustaceans in the San Francisco Estuary, primarily downstream of the Sacramento-San Joaquin Delta. Sampling ranges from south of the Dumbarton Bridge in South San Francisco Bay, to just west of Alcatraz Island in Central San Francisco Bay, throughout San Pablo and Suisun bays, north to the confluence Steamboat and Cache sloughs on the Sacramento River, and east to Old River Flats on the San Joaquin River. The open water or boat survey samples 52 stations monthly: 35 original stations, 7 stations added in 1988, 4 stations added in 1991, and 6 stations added in 1994. The study included a beach seine survey, discontinued in 1987, and a shore-based ringnet survey for crabs, discontinued in 1994. The Bay Study uses a 42-foot stern trawler to sample with 2 trawl nets at each open water station. The otter trawl, which samples demersal fishes, shrimp, and crabs, is towed against the current at a standard engine rpm for 5 minutes then retrieved. The midwater trawl, which samples pelagic fishes, is towed with the current at a standard engine rpm for 12 minutes and retrieved obliquely such that all depths are sampled equally. The open water survey included a plankton net that sampled larval fish and crustaceans, but this was discontinued in 1989. Fish, caridean shrimp, and brachyuran crabs are identified, measured, and counted. Shrimp and crabs are also sexed. Sampling effort is quantified (i.e. distance towed, volume of water filtered) and salinity, water temperature, Secchi depth, and station depth are measured;wave height, tide, cloud cover, and tow direction are categorized. The length, catch, and effort data is used to calculate catch-per-unit-effort (CPUE) by species and age class. The CPUE data is used to calculate monthly and annual abundance indices, which are used to track seasonal and annual population trends. Important factors that control or regulate abundance and distribution of fish and mobile crustaceans in the estuary include salinity, temperature, freshwater outflow, ocean temperature, upwelling, and surface currents, primary and secondary productivity, and introduced species. We are interested in how species respond to changes in the physical environment on several temporal scales - seasonal, annual, decadal, and longer. We produce several annual Status and Trends reports that summarize recent changes for the most commonly collected species. These reports are published in the Spring issue of the IEP Newsletter, which can be found at http://iep.water.ca.gov/report/newsletter. The 1999 IEP Technical Report, "Report on the 1980-1995 Fish, Shrimp, and Crab Sampling in the San Francisco Estuary, California", is a good source of basic information. This report is out-of-print, but can be found at www.water.ca.gov/iep/docs/tech_rpts/tech_rprt_63_toc.html. website: https://water.ca.gov/-/media/DWR-Website/Web-Pages/Programs/Environmental-Services/Interagency-Ecological-Program/Files/2019-IEP-Work-Plan_2018-12-11.pdf?la=en&hash=C305D1B1DA7931D95E8676247669F098F26A28FA
    Science topics Water temperature, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Crustaceans, Conductivity, Mammals
    Updated April 29, 2022
  • Title

    Smelt Larva Survey

    Lead California State Water Resources Control Board [SWRCB]
    Description The Smelt Larva Survey provides near real-time distribution data for longfin smelt larvae in the Delta, Suisun Bay and Suisun Marsh. Sampling takes place within the first two weeks in January and repeats every other week through the second week in March. Each 4-day survey consists of a single 10-minute oblique tow conducted at each of the 35 survey locations (see map) using an egg and larva net. The 505-micron mesh net is hung on a rigid frame shaped like an inverted-U, which in turn is attached to skis to prevent it from digging into the bottom when deployed. The net mouth area measures 0.37 m2. The conical net tapers back from the frame 3.35 m to a 1-liter cod-end jar, which collects and concentrates the sample. Immediately after each tow, juvenile fishes are removed, identified, measured and returned to the water immediately, and the remaining larvae are preserved in 10% formalin for later identification in the Lab in Stockton.
    Science topics Stage, Salinity, Water temperature, Turbidity, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Conductivity
    Updated April 29, 2022
  • Title

    Spring Kodiak Trawl Survey

    Lead California Department of Fish and Wildlife [CDFW]
    Description The Spring Kodiak Trawl Survey (SKT) has sampled annually since its inception in 2002. The SKT determines the relative abundance and distribution of spawning delta smelt (Hypomesus transpacificus). The SKT samples 40 stations each month from January to May. These 40 stations range from San Pablo Bay upstream to Stockton on the San Joaquin River, Walnut Grove on the Sacramento River, and the Sacramento Deep Water Ship Channel. Each 'Delta-wide' survey takes approximately 4 - 5 days per month to complete. Historically, 'Delta-wide' surveys were followed by a 'Supplemental' survey two weeks later to intensively sample areas of highest delta smelt concentration to estimate the proportion of male and female delta smelt that were in pre-spawning, spawning and spent maturation stages. Beginning in 2008, in an effort to minimize take of spawning adults, routine 'Supplemental' surveys were discontinued and are now only conducted under the recommendation of the Smelt Working Group and the approval of managers.
    Science topics Stage, Salinity, Water temperature, Turbidity, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Conductivity, Other species
    Updated April 29, 2022
  • Title

    Summer Townet Survey

    Lead California Department of Fish and Wildlife [CDFW]
    Description The Summer Townet (STN) Survey was initiated in 1959 to determine relative distribution and abundance of young of the year (age-0) striped bass (Morone saxatilis) in the Delta. To predict fishery recruitment, the survey calculates an index to measure age-0 striped bass year class strength. This index is based on abundance when age-0 striped bass attain a mean length of 38.1 mm. In contrast, the delta smelt (Hypomesus transpacificus) index is the average of the first two survey indices. The delta smelt index was developed about 1990 in response to declining delta smelt abundance. It has proven valuable in gauging the health of the estuary;delta smelt abundance trend data was used as supporting evidence for their listing as threatened in 1992 under the Federal and State Endangered Species Acts. It appears that zooplankton data are also collected.
    Science topics Mysis, Other zooplankton, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Striped bass, Fish
    Updated April 29, 2022
  • Title

    Suisun Marsh Fish Study

    Lead University of California - Davis [UC Davis]
    Description The University of California, Davis has been involved in fish and wildlife monitoring and research within Suisun Marsh for 35 years and has been instrumental in detecting important trends associated with naturally fluctuating environmental conditions as well as anthropogenic influences. Research has included a 35+ year time series on the fish and invertebrate communities of the slough networks, research on waterfowl nesting patterns and population biology, and research on the demography of salt marsh harvest mouse. The Suisun Marsh Fish Study anchors this effort as it is the longest established survey in Suisun marsh. It will continue the research of Professor Peter Moyle under the direction of John Durand, and will focus upon the detection of changes in the aquatic ecosystem in response to developing stressors in the San Francisco Estuary (SFE). This time series is designed to further our understanding of the ecology and function of the fish community residing within Suisun Marsh and the San Francisco Estuary (SFE), and acts as one of the key surveys with Interagency Ecological Program's monitoring effort.
    Science topics Stage, Tides, Salinity, Water temperature, Dissolved oxygen, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Pelagic fish, Benthos, Salt marsh harvest mouse, Mollusks, Crustaceans, Striped bass, Corbicula/Potamocorbula, Conductivity, Environmental drivers, Other species, Fish, Invertebrates
    Updated April 29, 2022
  • Title

    Fish Salvage and Genetic Analysis

    Lead U.S. Bureau of Reclamation [USBR]
    Description The State Water Project (SWP), operated by the California Department of Water Resources (DWR), and the Central Valley Project (CVP), operated by the U.S. Bureau of Reclamation, export water out of the San Francisco Bay Delta for urban and agricultural use in California. Salvage of fish at both facilities is conducted 24 hours a day, seven days a week at regular intervals. Since 1957, the U.S. Bureau of Reclamation (USBR) has salvaged fish at the Tracy Fish Collection Facility (TFCF). CDFW's Fish Facilities Unit, in cooperation with DWR, began salvaging fish at the Skinner Delta Fish Protective Facility (SDFPF) in 1968. Fish salvage and loss rates are used to determine the need for changes in operations in response to National Marine Fisheries Service (NMFS) regulatory requirements. Salvage and loss monitoring includes daily monitoring and reporting of estimated loss of salvaged fish, as well as monitoring and reporting of salvaged Coded Wired Tagged (CWT) hatchery fish. This information is widely used by West Coast fisheries agencies to collect information on natural and hatchery-reared stocks of salmon and steelhead. Our state-of-the-art genetic analysis techniques are used to quantify salvage rates of listed runs of California's Central Valley juvenile Chinook Salmon. We also utilize advanced genetic analysis techniques to identify different populations of Central Valley juvenile Chinook Salmon, and actively participate in development of new analysis methods.
    Science topics Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Striped bass, Fish, Invasive / non native species
    Updated April 29, 2022
  • Title

    Yolo Bypass Fish Monitoring

    Lead California Department of Water Resource [DWR]
    Description California Department of Water Resources (DWR) has operated a fisheries monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: (1) collect baseline data on lower trophic levels (phytoplankton, zooplankton, and aquatic insects), juvenile fish and adult fish, hydrology, and water quality parameters;(2) investigation of the temporal and seasonal patterns in chlorophyll-a concentrations, including whether high concentrations are exported from the Bypass during agricultural and natural flow events and the possibility of manipulating bypass flows to benefit listed species like Delta Smelt (Hypomesus transpacificus) and Chinook salmon (Oncorhynchus tshawytscha). The YBFMP operates a rotary screw trap and fyke trap, and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts.
    Science topics Chinook Salmon, Chlorophyll A / B, Conductivity, Delta Smelt, Direction, Dissolved oxygen, Endangered species, Fish, Flood, Food webs, Green sturgeon, Habitat, Habitat restoration, Insects, Intertidal / transition zones, Invasive / non native species, Invertebrates, Longfin Smelt, Main channels, Nitrogen, Nitrogen / ammonia, Nutrients, Other species, Other zooplankton, Pelagic fish, pH, Phytoplankton, Primary production, Sacramento Splittail, Salmon migration, Salmon rearing, Saltwater / freshwater marshes, SAV/FAV, Seasonally flooded, Solar irradiance, Stage, Steelhead Trout, Striped bass, Sturgeon, Submerged aquatic vegetation, Surface water / flow, Tides, Turbidity, Velocity, Water, Water temperature, Wetlands, White Sturgeon, Zooplankton
    Updated August 28, 2024
  • Title

    Enhanced Delta Smelt Monitoring [EDSM] Program

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description The Enhanced Delta Smelt Monitoring (EDSM) Program is conducted year-round by the U.S. Fish and Wildlife Service Lodi Office. This survey conducts high-frequency sampling in both the entrainment and entrainment-reference zones on a weekly basis. The survey will allow us to estimate the abundance of Delta Smelt in each zone to determine proportional entrainment and the relative risk of water operations to the population.
    Science topics Water temperature, Turbidity, Main channels, Sloughs, Delta Smelt, Conductivity
    Updated April 29, 2022
  • Title

    Fish Restoration Program Monitoring

    Lead California Department of Fish and Wildlife [CDFW]
    Description The Fish Restoration Program (FRP), an inter-agency agreement between the California Department of Fish and Wildlife (CDFW) and the California Department of Water Resources (DWR), will restore at least 8,000 acres of tidal wetlands in the Sacramento-San Joaquin Delta (Delta) and Suisun Marsh pursuant to requirements in federal Biological Opinions and the California Incidental Take Permit for operation of the State Water Project and Central Valley Project. The rationale for restoration is that state or federally listed fish species, Delta Smelt Hypomesus transpacificus, spring-run and winter-run Central Valley Chinook Salmon Oncorhynchus tshawytscha, and Longfin Smelt Spirinchus thaleichthys will benefit from increased availability of habitat and food web resources. The CDFW FRP Monitoring Team is responsible for monitoring the biological effectiveness of individual FRP tidal wetland restoration projects. Fish catch, invertebrate catch, and water quality data have been collected as baseline monitoring data and to determine the most efficient methods for monitoring wetland restoration efforts.
    Science topics Nitrogen / ammonia, Phosphorous, Carbon, Chlorophyll A / B, Phytoplankton, Other zooplankton, Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Submerged aquatic vegetation, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Insects, Mollusks, Crustaceans, Invertebrates
    Updated April 29, 2022
  • Title

    FCCL Conservation Hatchery Operation for Delta Smelt Refuge Population Maintenance and Research Support

    Lead U.S. Bureau of Reclamation [USBR]
    Description This facility houses the Delta Smelt Refuge population and produces Delta Smelt for release into the Delta. It is also responsible for the genetic management of the captive population and support of studies on supplementation.
    Science topics Delta Smelt
    Updated April 29, 2022
  • 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

    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

    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

    Feasibility of Acoustic Telemetry in Delta Smelt

    Lead University of California - Davis [UC Davis]
    Description

    This project aims to test the feasibility of using novel acoustic transmitters to track Delta smelt in the San Francisco Bay-Delta. Successful utilization of acoustic telemetry to track Delta smelt can provide researchers and resource managers with information about the species’ habitat preferences, the effects of water-management practices on Delta smelt movement and distribution, and the success of ongoing supplemental release efforts. The assessment of feasibility will include a comprehensive analysis of both the lethal and sublethal effects of surgical tag implantation on Delta smelt, as well as the development of a species-specific tagging protocol.
    Science topics Delta Smelt
    Updated October 15, 2024