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In 2010 the U.S. Geological Survey (USGS), Coastal and Marine Geology Program completed three cruises to map the bathymetry of the main channel and shallow intertidal mudflats in the southernmost part of south San Francisco Bay. The three surveys were merged to generate comprehensive maps of Coyote Creek (from Calaveras Point east to the railroad bridge) and Alviso Slough (from the bay to the town of Alviso) to establish baseline bathymetry prior to the breaching of levees adjacent to Alviso and Guadalupe Sloughs as part of the South Bay Salt Pond Restoration Project (http://www.southbayrestoration.org). Since 2010 we have conducted four additional surveys to monitor bathymetric change in this region as restoration...
The aim of this USGS program is to provide site specific sea-level rise predictions to land managers through the intensive collection of field data and innovative predictive modeling. In 2009 and 2010, thousands of elevation and vegetation survey points were collected in salt marsh at 12 sites surrounding San Francisco Bay. The elevation data was synthesized into a continuous elevation model for each site, providing land owners valuable baseline data. This site hosts the project report, pages describing each of the 12 marshes visited in this study, and maps and GIS data for all of the marshes including high-resolution digital elevation models.
Coastal ecosystems have been identified by the International Panel on Climate Change (2007) as areasthat will be disproportionally affected by climate change. Recent sea-level rise projections range from 0.57to 1.1 m (Jevrejeva et al. 2012) or 0.75 to 1.9 m by Grinsted et al. (2010) and Vermeer and Rahmstorf(2009) by 2100, which are contingent upon the ambient temperature conditions and CO2 emissions. Sealevelrise projections for San Francisco Bay are 1.24 m by 2100 (Cayan et al. 2008). The expectedaccelerated rate of sea-level rise through the 21st century will put many coastal ecosystems at risk,especially those in topographically low-gradient areas.Sea-level rise response modeling was conducted at 12 tidal salt...
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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...
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Tracklines and associated observations were mapped and analyzed using ArcMap (ESRI, Redlands, CA). GPS data were recorded in NAD27 map datum and projected to an USGS Albers Equal Area Conic map projection for presentation and subsequent density analyses. Concatenated GPS and observation data were then used to generate point and line coverages in ArcMap (ESRI, Redlands, CA). We designed a custom analytic tool using ArcMap Model Builder that allows for the construction and export of user-specified and effort-adjusted spatial binning of species observations along continuous trackines. For the purposes of this report, we calculated seabird density estimates and marine mammal counts along continuous 3.0-kilometer and...
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This data set contains decomposition rates for litter of Salicornia pacifica, Distichlis spicata, and Deschampsia cespitosa buried at 7 tidal marsh sites in 2015. Sediment organic matter values were collected at a subset of sites. These data support the following publication: Janousek, C.N., Buffington, K.J., Guntenspergen, G.R. et al. Ecosystems (2017). doi:10.1007/s10021-017-0111-6. http://link.springer.com/article/10.1007/s10021-017-0111-6
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This data table contains mean decomposition rates and mean carbon:nitrogen ratios for different litter types buried in 7 marshes during 2015. Note that C:N data are repeated for low and high marsh areas at each site in the table. These data support the following publication: Janousek, C.N., Buffington, K.J., Guntenspergen, G.R. et al. Ecosystems (2017). doi:10.1007/s10021-017-0111-6. http://link.springer.com/article/10.1007/s10021-017-0111-6
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This data table contains results for the 2014 mesocosm tests of inundation effects on decomposition. These data support the following publication: Janousek, C.N., Buffington, K.J., Guntenspergen, G.R. et al. Ecosystems (2017). doi:10.1007/s10021-017-0111-6. http://link.springer.com/article/10.1007/s10021-017-0111-6
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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...
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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 Suisun marsh using a modification of the Lidar Elevation Adjustment with NDVI (LEAN) technique (Buffington et al. 2016). GPS survey data (6912 points, collected across public and private land in 2018), Normalized Difference Vegetation Index (NDVI) derived from an airborne multispectral image (June 2018), a 1 m lidar DEM from September 2018, and a 1 m canopy surface model were used to generate models of predicted bias across the...
The papers in this special issue feature state-of-the-art approaches to understanding the physical processes related to sediment transport and geomorphology of complex coastal–estuarine systems. Here we focus on the San Francisco Bay Coastal System, extending from the lower San Joaquin–Sacramento Delta, through the Bay, and along the adjacent outer Pacific Coast. San Francisco Bay is an urbanized estuary that is impacted by numerous anthropogenic activities common to many large estuaries, including a mining legacy, channel dredging, aggregate mining, reservoirs, freshwater diversion, watershed modifications, urban run-off, ship traffic, exotic species introductions, land reclamation, and wetland restoration. The...
We evaluated the biogeomorphic processes of a large (309 ha) tidal salt marsh and examined factors that influence its ability to keep pace with relative sea-level rise (SLR). Detailed elevation data from 1995 and 2008 were compared with digital elevation models (DEMs) to assess marsh surface elevation change during this time. Overall, 37 % (113 ha) of the marsh increased in elevation at a rate that exceeded SLR, whereas 63 % (196 ha) of the area did not keep pace with SLR. Of the total area, 55 % (169 ha) subsided during the study period, but subsidence varied spatially across the marsh surface. To determine which biogeomorphic and spatial factors contributed to measured elevation change, we collected soil cores...
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Information about these images can be found in the Final Report for Sea-level Rise Response Modeling for San Francisco Bay Estuary Tidal Marshes. Site-specific data are available by request. Contact: Dr. John Y. Takekawa, USGS Western Ecological Research Center, San Francisco Bay Estuary Field Station, 505 Azuar Dr. Vallejo, Calif. 94592, 707-562-2000
This project evaluates the effects of global climate change and sea level rise on estuarine intertidal habitat in the San Francisco Bay and the Pacific Flyway migratory waterbirds that rely on this habitat. Phase 2 of this project is a continuation of work to evaluate the effects of global climate change and sea level rise (SLR) on intertidal shoals in the San Francisco Bay Estuary and the migratory waterbirds that rely on this critically important resource in the Pacific Flyway. The primary objectives are to: 1) use downscaled global climate change models to translate SLR and climate scenarios into habitat quantity predictions through Delft3D and Dflow-FM (unstructured grid) geomorphic modeling; 2) model the response...
This set of elevation models was developed to understand current (2010) conditions of San Francisco salt marshes and for input into sea-level rise prediction models. These elevation models were built by interpolating surveyed elevation points. The elevation surveys were conducted with a Leica RX1230 Real-Time Kinematic GPS which is capable of < 2 cm vertical accuracy.
Coastal areas are high-risk zones subject to the impacts of global climate change, with significant increases in the frequencies of extreme weather and storm events, and sea-level rise forecast by 2100. These physical processes are expected to alter estuaries, resulting in loss of intertidal wetlands and their component wildlife species. In particular, impacts to salt marshes and their wildlife will vary both temporally and spatially and may be irreversible and severe. Synergistic effects caused by combining stressors with anthropogenic land-use patterns could create areas of significant biodiversity loss and extinction, especially in urbanized estuaries that are already heavily degraded. In this paper, we discuss...
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This data table contains summary data for temperature time series in near-surface sediments in high and low tidal marsh at 7 sites during 2015. These data support the following publication: Janousek, C.N., Buffington, K.J., Guntenspergen, G.R. et al. Ecosystems (2017). doi:10.1007/s10021-017-0111-6. http://link.springer.com/article/10.1007/s10021-017-0111-6
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This table contains data on dry mass remaining in a subset of Salicornia pacifica and Deschampsia cespitosa litter bags removed over a series of time points spanning 6 months. These data support the following publication: Janousek, C.N., Buffington, K.J., Guntenspergen, G.R. et al. Ecosystems (2017). doi:10.1007/s10021-017-0111-6. http://link.springer.com/article/10.1007/s10021-017-0111-6
These datasets provide information on plant alpha, beta, and gamma diversity, and plant species abundance at several spatial scales for tidal wetlands along a salinity gradient in the San Francisco Bay-Delta and an impounded brackish wetland complex in Suisun Marsh, California. Files include diversity metrics calculated at the patch, site, and region scales, average percent cover of wetland dominant plants at the patch scale, and average percent cover of all wetland plants at the site scale. These data support the following paper: Jones, S.F., Janousek, C.N., Casazza, M.L., Takekawa, J.Y. and Thorne, K.M., 2021. Seasonal impoundment alters patterns of tidal wetland plant diversity across spatial scales. Ecosphere,...
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This data provides county level occurrence information for all individuals used in modelling potential exposure and spread of highly pathogenic avian influenza (HPAIv) from the 2021-2022 North American outbreak. The data set contains individual identifiers and taxa information, an indicator of exposure, exposure status (Susceptible, Exposed by HPAIv detection in the county, or Exposed by secondary contact with an exposed bird), and date of first occurrence of each individual bird and that bird's exposure status within each visited county. Herein, county refers to any county, parish, borough, census area, or geographic region identified in the associated geospatial data US_CAN_AI.shp (ESRI shapefile format). Occurrence...


map background search result map search result map Historical methyl mercury in San Francisco Bay 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) Bird Density and Marine Mammal Counts Based on 7700 Meter Bins in Southern California, 1999-2002 Inundation Experiments, 2014 Decomposition rates and carbon:nitrogen ratios for different litter types, 2015 Litter Decomposition Rates, 2015 Sediment Temperature, 2015 Linear loss of litter over time, 2015 LEAN-Corrected DEM for Suisun Marsh Impounded and tidal wetland plant diversity and composition across spatial scales, San Francisco Bay-Delta, California, USA (2016-2018) Timing of Occurrence of Waterfowl in U.S. Counties and Canadian Counties, Boroughs, Census Districts, and Other Populated Area Designations with Modeled Exposure Status to Highly Pathogenic Avian Influenza Virus in 2021-2022 LEAN-Corrected DEM for Suisun Marsh Impounded and tidal wetland plant diversity and composition across spatial scales, San Francisco Bay-Delta, California, USA (2016-2018) Bird Density and Marine Mammal Counts Based on 7700 Meter Bins in Southern California, 1999-2002 Inundation Experiments, 2014 Decomposition rates and carbon:nitrogen ratios for different litter types, 2015 Litter Decomposition Rates, 2015 Sediment Temperature, 2015 Linear loss of litter over time, 2015 Historical methyl mercury in San Francisco Bay Timing of Occurrence of Waterfowl in U.S. Counties and Canadian Counties, Boroughs, Census Districts, and Other Populated Area Designations with Modeled Exposure Status to Highly Pathogenic Avian Influenza Virus in 2021-2022