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1,613 results for “SANS”
San Francisco Estuary Institute Phytoplankton eDNA and Toxin Monitoring, San Francisco Bay, CA, 2014-2023
From late 2014-present, San Francisco Estuary Institute has conducted molecular monitoring of phytoplankton in partnership with the US Geological Survey from several stations stretching from Rio Vista in the North Delta to the Lower South Bay, past the Dumbarton Bridge. These samples have been analyzed for 18S eDNA data in partnership with Timothy Otten at Bend Genetics, targeting the V7 region. The included dataset covers the 2014-2023 period, including data up to 2022, conducted with an Illumina MISEQ platform, and from 2022-2023 using a NEXTSEQ platform, which enabled much greater sampling depth. Two sets of taxonomic assignments are included in this data release, one using the Silva database, and the other using the PR2 database, two of the leading sources of phytoplankton taxonomic data aiding in assignments of OTUs to taxa. Raw sequence data will also be uploaded to NCBI for comparison. Data collection continues and this release will be updated as new time periods are added.
CVPIA Predation Contact Point Study - 2021: Impacts of Water Diversions in the Sacramento – San Joaquin Delta
The Central Valley Project Improvement Act (CVPIA) has led to the implementation of a Decision Support Model (DSM) to assist in the prioritization of CVPIA restoration actions. The fall-run Chinook salmon (Oncorhynchus tshawytscha) DSM depends on a coarse-resolution salmon life-cycle model to predict the population benefits of different restoration actions and scenarios. One critical element of the life-cycle model is how to incorporate predation mortality during the juvenile rearing and outmigration portion of the salmon life-cycle in the Sacramento-San Joaquin Delta (the Delta). Of particular importance to potential restoration activities, is the predation mortality that occurs in proximity to, and as a result of contact points between predator and prey fishes. Water diversions that support agricultural and municipal use result in fish mortality through entrainment and impingement. Additionally, this infrastructure may attract both predators and prey fishes, thereby increasing predation rates and prey mortality near these anthropogenic contact points. Throughout the spring of 2021, we used ARIS (adaptive resolution imaging sonar; Sound Metrics) sonars to compare piscivore abundance at 30 small water diversions in the north Delta to adjacent shorelines. We used predation event recorders (PERs) to assess the predation risk of juvenile salmonids with linear distance (m) from diversions and other predation drivers in the north Delta. Finally, we used a boat electrofishing survey to determine the piscivore community structure and compare spatial trends in black bass (Micropterus spp.) CPUE and relative abundance throughout these waterways. Piscivore abundance was greater near small water diversions than at adjacent shorelines and the predation risk of juvenile salmonids increased with proximity to diversions. Additionally, predation risk increased with increasing piscivore abundance and decreasing water depth. The north Delta predator community was dominated by black b
Interagency Ecological Program: Integrated Dataset of Phytoplankton Enumeration Data in the San Francisco Estuary, 1992-2024
Phytoplankton community composition is an important driver of zooplankton productivity and food supply for higher trophic levels in the San Francisco Estuary. Various monitoring surveys throughout the region collect phytoplankton enumeration data dating back to the 1990s. These include surveys from the CA Department of Water Resources (CADWR), CA Department of Fish and Wildlife (CDFW), the US Bureau of Reclamation (USBR), and the US Geological Survey (USGS). These surveys collect data via various sampling and laboratory methods which are not always directly comparable. This integrated dataset includes both enumeration counts and well-documented metadata to allow for informed decision-making in the integration of these data. It also standardizes taxonomic names between groups via a key list. Note that, in this dataset, we make conservative decisions about taxonomic resolution to ensure maximum compatibility between groups. For more detailed metadata and higher taxonomic resolution, refer to individual surveys’ publications or reach out to their primary contact.
CVPIA Predation Contact Point Study - 2019: Impacts of Artificial Light At Night in the Sacramento – San Joaquin Delta
The Central Valley Project Improvement Act (CVPIA) has led to the implementation of a Decision Support Model (DSM) to assist in the prioritization of CVPIA restoration actions. The fall-run Chinook salmon DSM depends on a coarse-resolution salmon life-cycle model to predict the population benefits of different restoration actions and scenarios. One critical element of the life-cycle model is how to incorporate predation mortality during the juvenile rearing and outmigration portion of the salmon life-cycle in the Sacramento-San Joaquin Delta. Of particular importance to potential restoration activities, is the predation mortality that occurs in proximity to, and as a result of contact points between predator and prey fishes. A recent Literature review and meta-analysis of potential contact points in the Sacramento-San Joaquin Delta identified artificial lighting at night (ALAN) and submerged aquatic vegetation (SAV) as two contact points that have been found to influence predation elsewhere and warrant further study in this river delta (Lehman et al. 2019). Other contact points identified in this review that may affect predation of fall-run Chinook salmon juveniles included water diversions, docks, piers, scour holes, and rip rap; however, the literature on predator prey interactions associated with these contact points is lacking (Lehman et al. 2019). These datasets cover two different experiments in the Sacramento-San Joaquin Delta during spring 2019 from April - June. One experiment focused on artificial illumination and was a paired control impact study where new artificial illumination sources were introduced into the ecosystem. The other experiment relied on existing physical contact points (SAV, docks, pilings, bridges, and diversions) and assessed predation risk as a function of proximity to these points. Both experiments used predation event recorders to quantify relative predation risk and the ALAN experiment used Adaptive Resolution Imaging Sonar (ARIS) t
Mohler Restoration Snorkel Surveys on the Stanislaus River, San Joaquin County, CA, 2024-2025
The East Stanislaus Conservation District, Cramer Fish Sciences, and cbec, inc. ecoengineering, funded by a Bureau of Reclamation Central Valley Project Improvement Act program grant, are designing, constructing, and monitoring the Mohler Salmonid Habitat Restoration project, aimed at improving juvenile rearing and outmigration habitat on the lower Stanislaus River. The project is located approximately 20 km upstream from the confluence with the San Joaquin River, an area where little habitat restoration has been done. The project has the potential to create approximately 5.8 acres of seasonally inundated rearing and outmigration habitat for Central Valley fall-run Chinook Salmon ( Oncorhynchus tshawytscha ) and steelhead ( O. mykiss ) . The project is anticipated to be constructed in 2025 or 2026 with two year of post-project monitoring following. This work supports effectiveness monitoring of the project via rearing (snorkel) surveys and is ongoing.
Data from “Larval and juvenile Longfin Smelt diets as a function of fish size and prey density in the San Francisco Estuary”
This publication includes the raw data from the manuscript: Lojkovic Burris, Z. P., R. D. Baxter, and C. E. Burdi. 2022. Larval and juvenile Longfin Smelt diets as a function of fish size and prey density in the San Francisco Estuary. California Fish and Wildlife Journal 108:e11. http://www.doi.org/10.51492/cfwj.108.11 Data includes the diets of larval and juvenile Longfin Smelt in the San Francisco Estuary from 2005 to 2008 in the form of diet by number, diet by weight, macroinvertebrate prey lengths, prey length-weight equations, and prey weight conversions.
Interagency Ecological Program and US Fish and Wildlife Service: San Francisco Estuary Enhanced Delta Smelt Monitoring Program Data, 2016-2024
The Enhanced Delta Smelt Monitoring Program (EDSM) was initiated by the U.S. Fish and Wildlife Service in 2016. The main purpose of EDSM is to provide information about endemic Delta Smelt (Hypomesus transpacificus) population sizes and distributions within the upper San Francisco Estuary. To track the life cycle of this annual species, larval trawling with a fine-mesh (20 mm) net is conducted during the spring months, and Kodiak trawling for juveniles and adults occurs during the summer, fall, and winter months. Sampling sites are chosen via a stratified random sampling design. A minimum of two tows are conducted at each site, and field staff typically sample between 18 and 41 sites weekly. All fish collected are identified and enumerated, and a subset are measured for body length. Environmental data (water temperature, conductivity, dissolved oxygen, turbidity, depth) are also measured. In addition to Hypomesus spp., this long-term monitoring dataset can also be useful in evaluating the status and trends of other species of interest, especially pelagic fishes. For more information: https://www.fws.gov/office/lodi-fish-and-wildlife
Interagency Ecological Program: Zooplankton abundance in the Upper San Francisco Estuary from 1972-2021, an integration of 7 long-term monitoring programs
The upper San Francisco Estuary is an inland inverse delta formed by the confluence of 5 major rivers that drain 40% of the land in California (USA). It is a central hub of water delivery in California and home to a number of commercially important and endangered fish, such as Chinook Salmon, Green Sturgeon, and Delta Smelt. To monitor the environmental impacts of water exports from this system, extensive ecological monitoring has been conducted since the 1960s. To track lower trophic levels, zooplankton abundance has been monitored from 1972 to present. Starting with just one survey (the CA Department of Water Resources’ [CDWR] and California Department of Fish and Wildlife’s [CDFW] Environmental Monitoring Program) in 1972, the suite of zooplankton surveys gradually expanded with time. Several surveys traditionally focused on monitoring fish abundance added zooplankton nets to their sampling programs. The CDFW 20-mm larval fish survey added zooplankton sampling in 1995, the CDWR Yolo Bypass Fish Monitoring Program add zooplankton in 1999, the CDFW Summer Townet Survey added zooplankton in 2005, and the Fall Midwater Trawl added zooplankton in 2007. Two new sampling programs, the Fish Restoration Program and Directed Outflow Project, began in 2015 and 2017, respectively. All sampling programs continue today. Each survey samples once or twice monthly at set of fixed or random stations that varies across surveys depending on their objectives. While the Environmental Monitoring Program samples year-round, the other surveys are mostly seasonal, although additional months were sampled in some years. Most surveys target open channels although the Fish Restoration Program samples in or near shallow tidal wetlands. Three size classes of zooplankton are targeted by these sampling programs with different net mesh sizes: micro zooplankton (copepods and rotifers) are targeted with a 43 µm mesh net, meso zooplankton (copepods and cladocerans) are targeted with 150 - 160 µm mesh
Detecting repeating earthquakes on the San Andreas Fault with unsupervised machine-learning of spectrograms (supplementary material)
<p>Supplementary material for Sawi et al., 2023, <i>Detecting repeating earthquakes on the San Andreas Fault with unsupervised machine-learning of spectrograms </i>(The Seismic Record). Catalog of repeating earthquakes in sequences on a 10-km long segment of the San Andreas Fault in California from 1984-2019. </p><p> </p><p><strong>Catalog Header</strong></p><p>YR/MO/DY...........Date of event</p><p>HR/MN/SC...........Time of event</p><p>LAT/LON/DEP........Location of event</p><p>EX/EY/EZ...........Relative location uncertainty (in m)</p><p>MAG................NCSN magnitude</p><p>evID.................NCSN event ID</p><p>seqID................Repeating earthquake sequence ID</p><p>isRESp............Is quasi-periodic RES (bool)</p><p> </p><p><strong>References: </strong></p><p>Sawi T., Waldhauser F., Holtzman B. K., Groebner, N. (2023) Detecting repeating earthquakes on the San Andreas Fault with unsupervised machine-learning of spectrograms. The Seismic Record. </p><p>Waldhauser, F., and Schaff, D. P. (2021). A Comprehensive Search for Repeating Earthquakes in Northern California: Implications for Fault Creep, Slip Rates, Slip Partitioning, and Transient Stress. J Geophys Res B Solid Earth, 126(11), 1–22. <a href="https://doi.org/10.1029/2021JB022495">https://doi.org/10.1029/2021JB022495</a></p>
Snow Water Equivalent Dataset for the South Fork of the San Joaquin River (2018/2021) and Senales (2019/2021)
<p>The dataset is related to: Premier, V., Marin, C., Bertoldi, G., Barella, R., Notarnicola, C., & Bruzzone, L. (2022). Exploring the Use of Multi-source High-Resolution Satellite Data for Snow Water Equivalent Reconstruction over Mountainous Catchments. <em>The Cryosphere Discussions</em>, 1-42.</p> <p>It contains three hydrological seasons - from 1st of October 2018 to 30th of September 2021 - of snow water equivalent (SWE) for the South Fork of the San Joaquin river in California (USA) and two hydrological seasons - from 1st of October 2019 to 30th of September 2021 - for the Schnals/Senales basin in South Tyrol (Italy). The product is daily and with a spatial resolution of 25 m. SWE values are in mm. Snow cover area (SCA) can be derived from the same by thresholding pixel containing SWE greater than 0 mm. Further information about the reference system is contained in the attributes of the netcdf files. Please, contact the authors for further questions. Information about the methodology and the input data for producing these time series is contained in the related article.</p>
Efficacy and fate of fluridone applications for control of invasive submersed aquatic vegetation in the estuarine environment of the Sacramento-San Joaquin Delta
We conducted a study in the Sacramento-San Joaquin Delta to determine efficacy of the widely used herbicide fluridone in an estuarine ecosystem. The primary goal of SAV removal was restoration of open water habitat for endangered Hypomesus transpacificus (Delta Smelt). Over 18 months and multiple sets of multi-week fluridone applications, we monitored concentrations of fluridone and responses by SAV across pairs of treated and reference sites. Fluridone concentrations in the water were generally below the 2-5 parts per billion required for SAV control. Monitoring demonstrated these low water concentrations were likely due to dissipation by tides, despite use of pelleted fluridone formulations marketed for flowing water environments. Fluridone did, however, accumulate in sediment at concentrations hundreds of times higher than those measured in the water. Nonetheless, we did not observe lasting reductions in SAV abundance or changes in SAV community composition. By demonstrating lack of efficacy of one of the few herbicides permitted for use in this estuary, this study highlights the need for development of SAV management tools tailored to the challenges of hydrologically complex environments like estuaries.
Environmental and biological data associated with captive-reared Delta Smelt Study, Sacramento-San Joaquin Delta, CA, January-March 2019
The endangered Delta Smelt Hypomesus transpacificus is an osmerid fish endemic to the upper San Francisco Estuary. A captive breeding program for the species led by the Fish Culture and Conservation Laboratory (FCCL), University of California, Davis, began in 1996 to create a refuge population. In order to better understand how captive Delta Smelt would fare in conditions outside of the hatchery, we placed captive-reared fish in enclosures in the Sacramento San-Joaquin Delta, and evaluated their ability to survive, feed, and maintain condition. Fish were acclimated in the hatchery at FCCL, tagged, swabbed, weighed, measured, and transferred to enclosures in the field. There were three types of enclosures (n=2 for each type), varying in mesh size and wrap condition. In January 2019, 384 adult Delta Smelt (243 days post hatch) were transferred to enclosures in Rio Vista. In February 2019, 360 adult Delta Smelt (278 days post hatch) were transferred to enclosures in the Deepwater Shipping Channel. For each deployment, fish remained in enclosures for approximately one month, then were retrieved from enclosures, euthanized, identified, weighed and measured. A subset were also analyzed for diet contents. During the one-month long deployments, cages were checked for biofouling, damage, and dead fish, and water quality measurements and zooplankton samples were collected.
Fish Facilities Salvage Data, San Francisco, California, 1993-2024
The Bureau of Reclamation’s (Reclamation) Central Valley Project (CVP) and the California Department of Water Resource’s (DWR) State Water Project (SWP) deliver millions of acre-feet of water annually for agricultural, municipal, industrial, and environmental needs in California from the Sacramento-San Joaquin River Delta (Delta) through the C.W. “Bill” Jones Pumping Plant (JPP) and Banks Pumping Plant. Since 1957, a Reclamation operated fish salvage facility, the Tracy Fish Collection Facility (TFCF), is located upstream of the JPP and functions to salvage fish entrained in exported water (Bates and Vinsonhaler 1957). Additionally, the John E. Skinner Delta Fish Protective Facility (SDFPF) was added by the California Department of Water Resources in 1968 to salvage fishes diverted by the SWP. The salvage process involves fish collection, counting, handling and transportation back to the Delta. To prevent fish loss, CVP and SWP fish facilities were constructed at Old river, where fish are diverted to the fish facilities for counting and reporting. After counting, the fish are collected in storage tanks and taken to several release locations in the Delta via fish-haul tank trucks. Millions of fishes from 69 species are salvaged through this process by the two fish facilities. Data collected includes species collected, fish lengths, water flow, export amounts, and water quality. Fishes listed (Endangered Species Act (ESA) or California Endangered Species Act (CESA)) were Chinook Salmon, Delta Smelt, steelhead trout, Longfin Smelt, and Green Sturgeon. The California Department of Fish and Wildlife monitors fish salvage and manages the data collected from the fish facilities in addition to data collected and managed by DWR and Reclamation.
Harmful algal bloom and aquatic weeds data from the Sacramento-San Joaquin Delta, collected to evaluate the impact of the 2021 Temporary Urgency Change Order and Emergency Drought Barrier
Condition 8 of the June 2021 Temporary Urgency Change Order for the Central Valley Project (CVP) and State Water Project (SWP) requires a special study of harmful algal blooms (HABs) in the Sacramento–San Joaquin Delta (Delta) and the spread of submersed aquatic vegetation (SAV), and floating aquatic vegetation (FAV), also referred to as “aquatic weeds”. A report on the study was submitted to the State Water Resources Control Board on June 1, 2022. This data package contains all publicly available data used in the report, including visual cyanobacteria reports, cyanotoxin data, water quality, nutrients, flow/hydrodynamics, chlorophyll-a concentrations, temperature, coverage of SAV and FAV, use of herbicides, and human populations. Many of these data were derived from other datasets, though some were collected specifically for this study
Near-surface, soil, and air temperature data acquired across multiple locations on the San Joaquin Experimental Range, California, 2011-2017
These temperature records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These temperature records are for studies at the San Joaquin Experimental Range (Lat 37.083, Long -119.716, elevation 210-520 m, www.fs.fed.us/psw/ef/san_joaquin/). Temperature sensors were located at 23 sites across the landscape. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges, and valleys. To characterize surface temperature variation within a site, 21 sensors were arranged in an identical pattern around and in six, 5x5 m experimental gardens. An additional 18 sensors were placed along three transects over the landscape running E-W. They were placed strategically to sample topographic inflection points (hill tops and valley bottoms) as well as north and south facing slopes. Temperatures were recorded on a 10 or 20-minute interval, depending on the sensor, using HOBO (Onset, www.onsetcomp.com) devices.
Weather station data acquired across multiple locations on the San Joaquin Experimental Range, California, 2011-2017
These weather station records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These weather station records are for studies at the San Joaquin Experimental Range (Lat 37.083, Long -119.716, elevation 210-520 m, www.fs.fed.us/psw/ef/san_joaquin/). Weather stations were located at six sites across the landscape. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges, and valleys. Three full weather stations (north slope, south slope, and valley floor) monitored precipitation, wind, insolation, temperature, relative humidity, and soil moisture. Three micro stations (west slope, east slope, and ridge) measured soil moisture at -20 cm. Data was recorded on a 10-minute interval using HOBO (Onset, www.onsetcomp.com) devices.
California Department of Fish and Wildlife Adult Sturgeon Study, Sacramento-San Joaquin Watershed, 1954-2022
The Sacramento-San Joaquin Watershed, located in Central and Northern California, drains approximately 43,000 square miles and terminates at the Golden Gate Bridge. This watershed hosts numerous species of ecological, cultural, and recreational importance, including White (Acipenser transmontanus) and Green Sturgeon (Acipenser medirostris). Sturgeon were severely overfished in the late 1800s and early 1900s, prompting a closure of the recreational and commercial sturgeon fishery in 1917 by the California Department of Fish and Game (CDFG; Now California Department of Fish and Wildlife, CDFW). The fishery remained closed until 1954, when a recreational fishery was once again allowed by the CDFG. A single year of surveying was conducted by the CDFG in 1954 to monitor the new fishery and a semi-regular survey was established in 1967. Since then, CDFW has systematically surveyed subadult and adult White and Green Sturgeon as part of the Adult Sturgeon Study, with annual surveys conducted between 2005 and 2022. Capturing adult sturgeon using 3.7m deep drifted trammel nets in areas including Suisun Bay, Grizzly Bay, and San Pablo Bay, these efforts have been supplemented by angler-contributed data, collected through mail returns and river/bay creel surveys. Tagging practices involve individually coded ½” Petersen-disk tags, with reward values introduced in 1974 to encourage angler cooperation and enhance tag return rate accuracy. The adoption of PIT (Passive Integrated Transponder) tags began in 2007 and has been consistently employed since 2019. These data provide insights into tag return rates, recaptures, and mortalities, supporting the estimation of abundance and harvest rates. This comprehensive dataset enriches our understanding of sturgeon population dynamics and is crucial for monitoring California sturgeon.
Discrete water temperature, flow, solar radiation, chlorophyll-a and inundation, Sacramento-San Joaquin Delta, CA, 1999-2019
The objective of our study is to better understand the factors affecting chlorophyll-a production within a floodplain and its transport downstream to determine how lateral connectivity influences longitudinal connectivity. The Yolo Bypass is an engineered floodplain of the Sacramento River that inundates during periods of high outflow via overtopping weirs. Water traveling through the Yolo Bypass flows parallel to the Sacramento River and re-connects to the mainstem at the southern extent of the floodplain. Several monitoring programs in the Sacramento San-Joaquin Delta and Yolo Bypass collect discrete and continuous water quality data, including chlorophyll measurements. For this study, we synthesized available flow, water temperature, chlorophyll and inundation data between March 1999 to December 2019 and modeled the effects of environmental variables and inundation on chlorophyll-a production in the floodplain, the mainstem, and downstream of the floodplain/mainstem.
USFWS Adult White Sturgeon Monitoring, San Joaquin River, 2012-2025
Overview The Central Valley Project Improvement Act (CVPIA) funds habitat improvement work and associated monitoring in the Central Valley of California to increase salmonid populations in furtherance of meeting CVPIA fish doubling goals. This data package contains three datasets for adult White Sturgeon (Acipenser transmontanus) monitoring in the San Joaquin River (SJR) conducted by the US Fish and Wildlife Service, Lodi Fish and Wildlife Office. The primary purpose for this sampling was to capture White Sturgeon and implant acoustic telemetry tags for a tracking project. Therefore, the data are useful for determining when and where White Sturgeon were captured, but they should not be used to determine actual distribution or abundance. SJR_Adult_WST_Set Data This dataset contains data from a sampling program using various methods to catch adult White Sturgeon in the San Joaquin River. Sets were made at targeted locations primarily from March-May in 2012-2024 (other dates were occasionally sampled). SJR_Adult_WST_Catch Data This dataset contains data for individual fish caught via gillnets, trammel nets, setlines, or angling in the San Joaquin River. Species and fork length were recorded for all fish. For White Sturgeon, girth, maturation, tag, and surgery information are provided. SJR_Fish_Taxonomy Data This dataset contains data for fish codes used in the Catch datafile. For each species that was captured, the Species codes are listed with the corresponding Interagency Ecological Program code, common name, taxonomy (Phylum, Class, Order, Family, Genus, and Species), and whether or not the species is native to the region.
Sacramento-San Joaquin Bay-Delta Continuous (15 minute) Water Quality Monitoring: South Delta Region, collected by the North Central Region Office, DWR, 1999 – ongoing
The Department of Water Resources (DWR) Water Quality Evaluation Section (WQES) provides technical expertise and program support for regulatory compliance, water operations, emergency response, and environmental restoration. Wireless telemetry is used to transmit real-time provisional data to the California Data Exchange Center (CDEC), making the data publicly available. The published dataset is quality controlled and quality assured providing detailed information at 15-minute intervals from 18 monitoring stations, using Xylem’s YSI EXO2 and YSI 6600 multiparameter sondes to document individual water quality measurements of multiple water quality parameters. The dataset informs operations for the California State Water Project and supports water quality monitoring required by Water Right Decision D-1641, the Delta Compliance Program, the South Delta Temporary Barriers and the South Delta Improvement Program. It is important to note that the start dates and subsequent equipment upgrades vary between stations and equipment leading to discrepancies in the dataset’s date ranges.
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