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Historical methyl mercury in San Francisco Bay San Francisco Bay, California is considered a mercury-impaired watershed. Elevated concentrations of mercury are found in water and sediment as well as fish and estuarine birds. Sources of mercury to the watershed since 1845 include sediment-associated mercury from mercury mining, mercury losses from gold amalgamation activities in mines of the Sierra Nevada, aerial deposition of mercury from global and regional emissions to air, and the direct discharge of mercury to Bay waters associated with the urbanization and industrialization of the estuary. We assessed historical trends in mercury bioaccumulation by measuring mercury concentrations in feathers of the endangered California Ridgway’s rail (formerly California... Categories: Data; Tags: California Ridgway's Rail, Feathers, Ice Cores, Lake Tahoe, Mercury, All tags... San Francisco Bay, Sediment, Structural Equation Model, USGS Science Data Catalog (SDC), Wyoming, Fewer tags The Effects of Heterospecifics and Climatic Conditions on Incubation Behavior within a Mixed-Species Colony This U.S. Geological Survey Data Release contains the data and metadata associated with the journal article. Parental incubation behavior largely influences nest survival, a critical demographic process in avian population dynamics, and behaviors vary across species with different life history breeding strategies. Although research has identified nest survival advantages of mixing colonies, behavioral mechanisms that might explain these effects is largely lacking. We examined parental incubation behavior using video-monitoring techniques on Alcatraz Island, California, of black-crowned night-heron Nycticorax nycticorax (hereinafter, night-heron) in a mixed-species colony with California gulls Larus californicus... Types: Citation; Tags: Alcatraz Island, Black-crowned night herons, San Francisco Bay, USGS Science Data Catalog (SDC), incubation behavior, All tags... video monitoring, Fewer tags LEAN-corrected San Francisco Bay Digital Elevation Model, 2018 Lidar-derived digital elevation models often contain a vertical bias due to vegetation. In areas with tidal influence the amount of bias can be ecologically significant, for example, by decreasing the expected inundation frequency. We generated a corrected digital elevation mode (DEM) for tidal marsh areas around San Francisco Bay using the Lidar Elevation Adjustment with NDVI (LEAN) technique (Buffington et al. 2016). Survey-grade GPS survey data (6614 points), NAIP-derived Normalized Difference Vegetation Index, and original 1 m lidar DEM from 2010 were used to generate a model of predicted bias across tidal marsh areas. The predicted bias was then subtracted from the original lidar DEM and merged with the NOAA... Categories: Data; Types: ArcGIS REST Map Service, ArcGIS Service Definition, Downloadable, GeoTIFF, Map Service, Raster; Tags: Remote Sensing, San Francisco Bay, USGS Science Data Catalog (SDC), biota, digital elevation models, All tags... estuary, lidar, wetlands, Fewer tags A Century of Landscape Disturbance and Urbanization of the San Francisco Bay Region affects the Present-day Genetic Diversity of the California Ridgway’s Rail (Rallus obsoletus obsoletus) Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail ( Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11... Categories: Data; Types: Citation, Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: Clapper Rail, Fragmentation, Microsatellites, Population declines, Ridgway’s rail, All tags... San Francisco Bay, USGS Science Data Catalog (SDC), Fewer tags Breeding Waterbird Populations in South San Francisco Bay 2005-2019 The dataset includes three separate excel spreadsheets which provides waterbird (and predator) observations within individual survey units during the May 2019 breeding waterbird survey of south San Francisco Bay (2019WaterbirdSurveyFullData.xlsx), the total number of American avocets, black-necked stilts, and Forster's terns within each pond unit surveyed during the May 2019 survey (2019WaterbirdSurveyPondModel.xlsx), and the annual total number of nests for American avocets, black-necked stilts, and Forster's terns in south San Francisco between 2005 and 2019 (SouthBayWaterbirdNests2005-2019.xlsx). These data support the following publication: Hartman, C.A., Ackerman, J.T., Schacter, C.R., Herzog, M.P., Tarjan,... Categories: Data; Tags: San Francisco Bay, USGS Science Data Catalog (SDC), Wildlife Biology, biota, birds, All tags... estuarine ecosystems, land use change, long-term ecological monitoring, migratory species, population dynamics, wetland ecosystems, Fewer tags Tidal Wetland Habitat Projections with Sea-level Rise Across Sites in the San Francisco Bay Estuary (2020-2100) Habitat projections from the WARMER-2 model for four tidal wetland sites in San Francisco Bay estuary under the constant sediment scenario, plus 0.2 ppt per decade salinity scenario, and the community transition organic productivity function under a 99 cm by 2100 sea-level rise scenario. Results are the average from one hundred Monte Carlo simulations. Tags: Brackish Marsh, Emergent Tidal Marsh, Emergent Wetland, San Francisco Bay, biota, All tags... climate change, numerical modeling, sea-level change, wetland, Fewer tags Small Mammal Surveys from Northern San Francisco Bay: 1998-2014 This datasets summarizes small mammal trapping efforts that USGS San Francisco Bay Estuary Field Station has led, co-led, or supervised, to detect and monitor the endangered salt marsh harvest mouse (Reithrodontomys raviventris) in the northern reaches of San Francisco Bay from 1998-2014. As the salt marsh harvest mouse is listed as endangered under the Endangered Species Act, sensitive location information can be made available upon request by contacting the dataset point of contact. These data support the following publication: Marcot, B.G., Woo, I., Thorne, K.M., Freeman, C.M., and Guntenspergen, G.R., 2020. Habitat of the endangered salt marsh harvest mouse (Reithrodontomys raviventris) in San Francisco Bay.... Categories: Data; Tags: San Francisco Bay, San Pablo Bay, USGS Science Data Catalog (SDC), Wildlife Biology, biota, All tags... capturing (animals), endangered species, habitat use, habitats, mammals, small mammal assemblage, vegetation, wildlife, Fewer tags San Francisco Bay Tidal Marsh Avian Predator Surveys, 2010 This dataset contains avian survey observations across four tidal marsh areas around San Francisco Bay. Multiple surveys were conducted around both high and low tides during the winter of 2010/11. Each survey alternated between scan and focals. During scans, all observable birds were counted. During focals, the behavior of a single, randomly selected bird was observed. Water level data was collected concurrently at each site and is provided with the avian survey data. These data support the following publication: Thorne, K.M., Spragens, K.A., Buffington, K.J., Rosencranz, J.A. and Takekawa, J., 2019. Flooding regimes increase avian predation on wildlife prey in tidal marsh ecosystems. Ecology and evolution, 9(3),... Categories: Data; Tags: Ecology, Emergent Tidal Marsh, Petaluma River, San Francisco Bay, USGS Science Data Catalog (SDC), All tags... Wildlife Biology, biota, birds, carnivores, flooding, sea-level change, Fewer tags Sediment Deposition and Accretion Data from a Tidal Salt Marsh in South San Francisco Bay, California 2021-2022 The U.S. Geological Survey, Western Ecological Research Center collected sediment and accretion data at a wave-exposed tidal salt marsh in South San Francisco Bay, California. Sediment traps and feldspar marker horizons (MH) were deployed along transects of increasing distance from the sediment source, at primary, secondary and tertiary marsh channels/bay. Data were collected bi-monthly over two month periods in summer 2021 and winter 2021/2022. Included here are trap and MH plot locations, calculated sediment fluxes at each station by deployment period, annual accretion rates, and covariates associated with sediment deposition and accretion including vegetation structure and elevation. This project aimed to assess... Categories: Data; Tags: Ecology, Eden Landing Ecological Reserve, High Salt Marsh, Land Use Change, San Francisco Bay, All tags... Sedimentology, USGS Science Data Catalog (SDC), accretion, biota, blue carbon, carbon, sea-level change, sediment transport, surface deposition, wetland ecosystems, Fewer tags Sediment Biogeochemistry and Mercury Measurements from Wetlands of the San Francisco Bay, CA. Habitat biogeochemistry was assessed by measuring 31 variables in sediments, porewater, and surface waters related to mercury content, organic matter, sediment characteristics, and microbial rates of sulfate reduction, iron reduction, and methanogenesis. Fifty-six composite surface (0-2 cm) sediment cores and 32 surface water samples were collected in three wetlands in the spring and summer of 2005 and 2006. Categories: Data; Tags: Arachnids, Birds, Crustaceans, Insects, San Francisco Bay, All tags... bioaccumulation, biota, coastal ecosystems, ecotoxicology, food web, wetland ecosystems, Fewer tags Western sandpiper diet composition in south San Francisco Bay, CA Diet composition can be influenced by age- and sex-related factors including an individual’s morphology, social status, and acquired skills; however, specialization may only be necessary when competition is intensified by high population densities or increased energetic demands. The western sandpiper is a small (22-35 grams) migratory shorebird that exhibits female-biased sexual size dimorphism with a 5 percent greater body size and a 15 percent longer bill in females compared to males. It is considered a generalist with a diverse diet that includes benthic invertebrates and biofilm – a thin layer of microphytobenthos, bacteria, and detritus encased in a polysaccharide-rich matrix of extracellular polymeric substances... Categories: Data; Tags: San Francisco Bay, USGS Science Data Catalog (SDC), Wildlife Biology, ecology, food web, All tags... wildlife, Fewer tags Prey fish returned to Forster’s tern colonies in South San Francisco Bay during 2005-2015 Prey fish were collected at 17 Forster’s tern breeding colonies during colony visits from 2005-2015. Prey fish were identified to the lowest taxonomic category. We present relative abundances by colony and year for each of the 10 major species groups. Unidentified fish species or rarely observed species were combined into an “Other” category. We calculated an arithmetic mean, standard deviation (sd), 25th quantile, and 75th quantile for dry standard length (SL; mm) and dry mass (g) for each fish species at each colony. These data support the following publication: Peterson SH, Ackerman JT, Eagles-Smith CA, Herzog MP, Hartman CA (2018) Prey fish returned to Forster’s tern colonies suggest spatial and temporal differences... Tags: San Francisco Bay, South San Francisco Bay, USGS Science Data Catalog (SDC), biota, dietary coomposition, All tags... dropped fish, foraging, migratory species AND fish, prey selection, seabird, Fewer tags Surface Elevation Table Measurements at Five Tidal Marshes Across the San Francisco Bay-Delta (2016-2019) Surface elevation tables with marker horizons (SET-MH) measure millimeter-scale changes in elevation over time. A combination of pin measurements (elevation change) and surface deposition measurements (marker horizon) is used to distinguish elevation changes due to belowground and aboveground processes. SET-MHs were installed in 2016 and were measured quarterly across five tidal marshes (Petaluma marsh, San Pablo Bay National Wildlife Refuge, Rush Ranch, Browns Island, and Miners Slough). These data support the following publication: Thorne, K., Jones, S., Freeman, C., Buffington, K., Janousek, C., and Guntenspergen, G. 2022. Atmospheric river storm flooding influences tidal marsh elevation building processes.... Categories: Data; Tags: Ecology, San Francisco Bay, USGS Science Data Catalog (SDC), Wetland Ecosystems, environment, All tags... shoreline accretion, Fewer tags Sediment Biogeochemistry and Subsequent Mercury Biomagnification in Wetland Food Webs of the San Francisco Bay, CA (ver. 2.0, December 2023) Methylmercury (MeHg) is a globally pervasive contaminant that biomagnifies in food webs and can reach toxic concentrations in consumers at higher trophic levels, including wildlife and humans. The production of MeHg, and its subsequent entry and biomagnification in food webs, is governed by a complex suite of biogeochemical, physical, and ecological processes, resulting in spatial variation in the distribution of MeHg. To better understand the link between MeHg production in sediments and MeHg bioaccumulation in biota, we evaluated the effects of habitat biogeochemistry, food web structure, and diet composition on bioaccumulation in the wetland-obligate California black rail (Laterallus jamaicensis coturniculus)... Tags: Arachnids, Birds, Crustaceans, Insects, San Francisco Bay, All tags... USGS Science Data Catalog (SDC), bioaccumulation, biota, coastal ecosystems, ecotoxicology, food web, wetland ecosystems, Fewer tags Tidal Wetland Elevation Projections for Five San Francisco Bay Delta Regions Using WARMER-2, 2000-2100 Projections of marsh elevation change with WARMER-2 across five regions of the San Francisco Bay Delta (Cache Yolo, South Delta, North Delta, Central Delta, and Suisun). The model was run across a range of initial elevations for each region and for scenarios of sea-level rise (30, 61, 91, 122, 152, 183, 305 cm by 2100), sediment availability (historic, constant, declining, and increase), and with and without a temporally dynamic tidal range. Results from the Delta Simulation Model 2 hydrodynamic model were used to calculate rates of tide range increase with sea-level rise. WARMER-2 was calibrated using soil cores from Callaway et al 2012 (Rush Ranch and Browns Island cores), and a soil core from Miners Slough. ... Categories: Data; Tags: Brackish Marsh, Delta, Emergent Tidal Marsh, Freshwater Tidal Marsh, San Francisco Bay, All tags... USGS Science Data Catalog (SDC), biota, numerical modeling, sea-level change, wetland, Fewer tags Mercury Concentrations and Stable Isotope Ratios for California Black Rails and their Invertebrate Prey from Wetlands of the San Francisco Bay, CA Methylmercury concentrations and stable isotope ratios were measured from back feathers of California black rails (Laterallus jamaicensis coturniculus) and six taxa of their invertebrate prey (Amphipoda, Arachnida, Coleoptera, Diptera, Gastropoda, and Hemiptera). Samples were collected from three wetlands in the spring and summer of 2005 and 2006. Categories: Data; Tags: Arachnids, Birds, Crustaceans, Insects, San Francisco Bay, All tags... bioaccumulation, biota, coastal ecosystems, ecotoxicology, food web, wetland ecosystems, Fewer tags Marsh Vegetation Surveys Across the San Francisco Bay Estuary, 2008-2018 Fifty-one tidal marsh sites across five regions (sub-embayments) were surveyed in the Delta, Suisun Bay, San Pablo Bay, central San Francisco Bay, and South San Francisco Bay. Vegetation surveys spanned ten years, from July 2008 to January 2018. A total of 5,112 plots were surveyed. Plots were positioned on transects along an elevation gradient and evenly distributed across each site, where possible, to capture spatial variability along elevation and distance gradients. At each plot, percent cover of all plant species, bare ground, and litter as well as average height was visually assessed within a 0.25 m2 quadrat. Total plant cover in a plot could exceed 100 percent due to vegetation layering. Bare ground and litter... Categories: Data; Tags: Botany, Ecology, Ecology, Emergent Tidal Marsh, Freshwater and Brackish Tidal Aquatic Vegetation, All tags... Salinity, San Francisco Bay, San Joaquin Delta, San Pablo Bay, Suisun Bay, USGS Science Data Catalog (SDC), bays, biodiversity, biogeography, community ecology, elevation, estuary, plants (organisms), salinity, species diversity, vegetation, wetland, wetland ecosystems, wetlands, Fewer tags