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Chromium in San Francisco Bay: inorganic speciation, distribution, and geochemical processes, University of California: Santa Cruz.1994.
Spatial and Temporal Variability in the Aquatic Cycling of Chromium. SFEI Contribution No. 220. University of California: Santa Cruz, CA.1998.
San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants - 2016 Data Summary. U.S. Geological Survey: Dixon, CA. p 19 pp.2016.
As part of the Regional Monitoring Program (RMP) and the USGS’s long-term Wildlife Contaminants Program, the USGS samples double-crested cormorant (Phalacrocorax auritus) and Forster’s tern (Sterna forsteri) eggs throughout the San Francisco Bay Estuary approximately every three years to assess temporal trends in contaminant concentrations. This sampling has been carried out in 2006, 2009, and 2012. Although RMP sampling was scheduled to take place in 2015, it was delayed until 2016. This document summarizes egg collections for 2016, as well as mercury concentrations in Forster’s tern eggs on an individual egg basis.
Integrating Toxicity Risk in Bird Eggs and Chicks: Using Chick Down Feathers To Estimate Mercury Concentrations in Eggs. Environmental Science and Technology 43, 2166-2172.2009.
San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants, California—2018. U.S. Geological Survey: Reston, Virginia.2019.
2010 Annual Monitoring Results. San Francisco Estuary Institute: Richmond, CA.2012.
Contaminants of Emerging Concern in the San Francisco Estuary: Carbamazepine. SFEI Contribution No. 658. SFEI: Richmond, CA. p 14.2012.
Estimated Atmospheric Deposition Fluxes of Dioxins in the San Francisco Estuary. SFEI Contribution No. 661. SFEI: Richmond, CA.2012.
Relationship Between Sediment Toxicity and Contamination in San Francisco Bay (Abstract). Marine Environmental Research 285-309 . SFEI Contribution No. 332.1999.
Relationship Between Sediment Toxicity and Contamination in San Francisco Bay. SFEI Contribution No. 27. San Francisco Estuary Institute: Oakland, CA. pp 285-309.1997.
Patterns and trends in sediment toxicity in the San Francisco Estuary. Environmental Research 105 (1), 145-155 . SFEI Contribution No. 496.2007.
Relationships Between Sediment Toxicity and Contamination in San Francisco Bay. Marine Environmental Research 48, 285-309 . SFEI Contribution No. 27.1999.
The effects of kaolin clay on the amphipod Eohaustorius estuarius: Part Two. SFEI Contribution No. 822.2017.
The Effects of Kaolin Clay on the Amphipod Eohaustorius estuarius. SFEI Contribution No. 755. Department of Environmental Toxicology, University of California, Davis: Davis, CA.2015.
Several lines of evidence from the Regional Monitoring Program and other studies have suggested that sediment grain size characteristics influence amphipod (Eohaustorius estuarius) survival in 10 day toxicity tests. Two workshops were convened to address the influence of non-contaminant factors on amphipod toxicity tests, and the current project was prioritized based on the recommendations of experts participating in these workshops. The study was designed to investigate the effects of kaolin clay on amphipod survival since this is the dominant clay type in Francisco Estuary sediments. In these experiments reference sand was spiked with increasing concentrations of kaolin to determine whether there was a dose-based relationship between amphipod mortality and increasing concentrations of this type of clay. Wild-caught E. estuarius were collected from Beaver Creek Beach (Oregon) and supplied by Northwest Aquatic Sciences. The initial experiment did not demonstrate a dose-response relationship: E. estuarius survival in all concentrations from 10% to 100% kaolin was lower than in the sand control, and survival in the clay spiked sand was also highly variable. This experiment exposed a mixture of amphipod size classes representative of those typically provided by the amphipod supplier. Reasoning that variable response to clay was related to variable tolerances by the different amphipod size classes, a follow-up experiment was conducted to investigate this relationship. Amphipods were separated into small, medium and large size classes and these were exposed to 100% kaolin. These results showed survival in 100% clay was 86%, 82% and 66% by small, medium and large amphipods, respectively. To further investigate size-related responses to clay, small, medium and large amphipods were exposed to concentrations of sand spiked with clay from 0 to 100%. The results of this experiment showed that smaller amphipods tolerated high clay concentrations better than larger animals, but there was not a strict monotonic dose-response relationship. Conclusions based on this experiment were constrained by an inability to sort amphipods into three distinct size classes, because there were not enough of the largest animals present at the Oregon collection site. In addition, grain size analysis of the sand spiked clay suggested that the clay tended to flocculate in the treatments above 70% kaolin. This experiment was repeated when three distinct size classes were present in December 2014. The results of this experiment also showed that smaller amphipods tolerated high kaolin better than larger amphipods. As in the previous experiment, there was not a monotonic response to clay, especially at the higher kaolin concentrations, and the grain size analysis also showed flocculation occurred in the highest clay treatments. Despite these inconsistencies, the results of this experiment suggest that tolerance of E. estuarius to clay varies with amphipod size. Average survival was 81%, 79%, and 65% for small, medium and large amphipods, respectively in concentrations > 50% clay. Possible mechanisms for size specific clay effects on this amphipod species include lower survival related to reduced energy reserves in larger animals, inhibition of gill function, and inhibition of feeding and locomotion through clogging of amphipod setae. The results suggest that use of smaller amphipods in routine monitoring of high clay sediments will reduce the influence of this factor on test results. Additional experiments with high clay reference site sediments from San Francisco Bay are recommended to confirm the size related response with field sediments.
Aqueous Speciation and 1-Octanol-Water Partitioning of Tributyl- and Triphenyltin: Effect of pH and Ion Composition. Environmental Science and Technology 31 (9), 2596-2602.1997.
East Contra Costa Historical Ecology Study GIS data, GIS data produced for the East Contra Costa County Historical Ecology Study.2011.
Annotated Bibliography for Sycamore Alluvial Woodland Habitat Mapping and Regeneration Studies Project.. 2017.
One component of the Sycamore Alluvial Woodland Habitat Mapping and Regeneration Studies Project is this annotated bibliography of existing scientific literature pertaining to California sycamore ecology. This annotated bibliography is a product of an extensive review into documents, mapping efforts, and personal communications, and presents sources that have been determined to be relevant to understanding the factors that influence California sycamore health and regeneration in central California. The annotated bibliography is divided into the following sections by topic: General Ecology; Historical and Present Distribution; Restoration Ecology and Management; Wildlife Ecology; Geomorphology; Hydrology and Soils; and Health and Regeneration. Each item is briefly summarized and its relevance to the project is described. References that fall under multiple categories are cross-referenced within the document. Similarly, key words are indicated or each reference to highlight various subtopics affecting California sycamore ecology.
Trends in Suspended Sediment Input to the San Francisco Bay for Local Tributaries Watersheds. San Francisco Estuary Institute.. 2005.
Effect of salinity on the olfactory toxicity of dissolved copper in juvenile salmon. SFEI Contribution No. 733.2015.
Sediment transport in the San Francisco Bay Coastal System: An overview. Marine Geology Special Issue: A multi-discipline approach for understanding sediment transport and geomorphic evolution in an estuarine-coastal system.2013.
Historical Ecology and Landscape Change in the Central Laguna de Santa Rosa. SFEI Contribution No. 820. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.2017.
This study synthesizes a diverse array of data to examine the ecological patterns, ecosystem functions, and hydrology that characterized a central portion of the Laguna de Santa Rosa during the mid-19th century, and to analyze landscape changes over the past 150 years. The primary purpose of this study was to help guide restoration actions and other measures aimed at reducing nutrient loads within this portion of the Laguna de Santa Rosa watershed.
Mt. Wanda Historical Ecology Investigation. SFEI Contribution No. 743. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 51.2015.
Re-Oaking North Bay. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.2020.
Petaluma Valley Historical Hydrology and Ecology Study. SFEI Contribution No. 861. San Francisco Estuary Institute: Richmond, CA.2018.
This study reconstructs the historical landscape of the Petaluma River watershed and documents the major landscape changes that have taken place within the watershed over the past two centuries. Prior to Spanish and American settlement of the region, the Petaluma River watershed supported a dynamic and interconnected network of streams, riparian forests, freshwater wetlands, and tidal marshes. These habitats were utilized by a wide range of plant and animal species, including a number of species that are today listed as threatened or endangered such as Ridgway’s Rail, Black Rail, salt marsh harvest mouse, California red-legged frog, Central California Coast steelhead, and soft bird’s beak (CNDDB 2012, SRCD 2015). Agricultural and urban development beginning in the mid-1800s has significantly altered the landscape, degrading habitat for fish and wildlife and contributing to contemporary management challenges such as flooding, pollutant loading, erosion, and sedimentation. While many natural areas and remnant wetlands still exist throughout the watershed—most notably the Petaluma Marsh—their ecological function is in many cases seriously impaired and their long-term fate jeopardized by climate change and other stressors. Multi-benefit wetland restoration strategies, guided by a thorough understanding of landscape history, can simultaneously address a range of chronic management issues while improving the ecological health of the watershed, making it a better place to live for both people and wildlife.
Application of Gene Expression Analysis for Sediment Toxicity Stressor Identification. SFEI Contribution No. 659.2012.
Observational Study of Sycamore Regeneration at two sites in Santa Clara County after the 2016-2017 Water Year. SFEI Contribution No. 874.2018.
Landscape Scale Management Strategies for Arroyo Mocho and Arroyo Las Positas: Process-Based Approaches for Dynamic, Multi-Benefit Urban Channels. SFEI Contribution No. 714. San Francisco Estuary Institute: Richmond, CA.2014.
San Francisco Bay Shoreline Adaptation Atlas: Working with Nature to Plan for Sea Level Rise Using Operational Landscape Units. SFEI Contribution No. 915. SFEI & SPUR: Richmond, CA. p 255.. 2019.
As the climate continues to change, San Francisco Bay shoreline communities will need to adapt in order to build social and ecological resilience to rising sea levels. Given the complex and varied nature of the Bay shore, a science-based framework is essential to identify effective adaptation strategies that are appropriate for their particular settings and that take advantage of natural processes. This report proposes such a framework—Operational Landscape Units for San Francisco Bay.
Sycamore Alluvial Woodland: Habitat Mapping and Regeneration Study. SFEI Contribution No. 816.2017.
This study investigates the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW), representing managed and natural settings. Using an array of ecological and geomorphic field analyses, we discuss site characteristics favorable to SAW health and regeneration, make recommendations for restoration and management, and identify next steps. Findings from this study will contribute to the acquisition, restoration, and improved management of SAW as part of the Santa Clara Valley Habitat Plan (VHP).
Landscape Patterns and Processes of the McCormack-Williamson Tract and Surrounding Area: A framework for restoring a resilient and functional landscape. SFEI Contribution No. 674. SFEI-ASC: Richmond, CA.2013.
Shifting Shores: Marsh Expansion and Retreat in San Pablo Bay. SFEI Contribution No. 751.2015.
As sea level rise accelerates, our shores will be increasingly vulnerable to erosion. Particular concern centers around the potential loss of San Francisco Bay’s much-valued tidal marshes, which provide natural flood protection to our shorelines, habitat for native wildlife, and many other ecosystem services. Addressing this concern, this study is the first systematic analysis of the rates of marsh retreat and expansion over time for San Pablo Bay, located in the northern part of San Francisco Bay.
• Over the past two decades, more of the marshes in San Pablo Bay have expanded (35% by length) than retreated (6%).
• Some areas have been expanding for over 150 years.
• Some marsh edges that appear to be retreating are in fact expanding rapidly at rates of up to 8 m/yr.
• Marsh edge change may be a useful indicator of resilience, identifying favorable sites for marsh persistence.
• These data can provide a foundation for understanding drivers of marsh edge expansion and retreat such as wind direction, wave energy, watershed sediment supply, and mudflat shape.
• This understanding of system dynamics will help inform management decisions about marsh restoration and protection.
• This study provides a baseline and method for tracking marsh edge response to current and future conditions, particularly anticipated changes in sea level, wave energy, and sediment supply.
Recommended next steps:
• This pilot study for San Pablo Bay marshes should be extended to other marshes in San Francisco Bay.
• These initial marsh expansion and retreat findings should be further analyzed and interpreted to improve our understanding of system drivers and identify management responses.
• A program for repeated assessment should be developed to identify and track changes in shoreline position, a leading indicator of the likelihood marsh survival.
Sycamore Alluvial Woodland Planting Guide. SFEI Contribution No. 901.2018.
Futures Past: Exploring California Landscapes with SFEI. Boom: A Journal of California 4 (3), 24.2014.
Northern San Diego County Lagoons Historical Ecology Investigation. SFEI Contribution No. 722. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 215.2014.
From past patterns to future potential: using historical ecology to inform river restoration on an intermittent California river. Landscape Ecology 31 (3), 20.2016.
Context Effective river restoration requires understanding a system’s potential to support desired functions. This can be challenging to discern in the modern landscape, where natural complexity and heterogeneity are often heavily suppressed or modified. Historical analysis is therefore a valuable tool to provide the long-term perspective on riverine patterns, processes, and ecosystem change needed to set appropriate environmental management goals and strategies.
Objective In this study, we reconstructed historical (early 1800s) riparian conditions, river corridor extent, and dry-season flow on the lower Santa Clara River in southern California, with the goal of using this enhanced understanding to inform restoration and management activities.
Method Hundreds of cartographic, textual, and visual accounts were integrated into a GIS database of historical river characteristics.
Results We found that the river was characterized by an extremely broad river corridor and a diverse mosaic of riparian communities that varied by reach, from extensive ([100 ha) willow-cottonwood forests to xeric scrublands. Reach-scale ecological heterogeneity was linked to local variations in dry-season water availability, which was in turn underpinned by regional geophysical controls on groundwater and surface flow.
Conclusions Although human actions have greatly impacted the river’s extent, baseflow hydrology, and riparian habitats, many ecological attributes persist in more limited form, in large part facilitated by these fundamental hydrogeological controls. By drawing on a heretofore untapped dataset of spatially explicit and long-term environmental data, these findings improve our understanding of the river’s historical and current conditions and allow the derivation of reach-differentiated restoration and management opportunities that take advantage of local potential.
An Assessment of the South Bay Historical Tidal-Terrestrial Transition Zone. SFEI Contribution No. 693. San Francisco Estuary Institute: Richmond, CA.2013.
Landscape Resilience Framework: Operationalizing Ecological Resilience at the Landscape Scale. SFEI Contribution No. 752. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.. 2015.
Building Ecological Resilience in Highly Modified Landscapes.2018.
Ecological resilience is a powerful heuristic for ecosystem management in the context of rapid environmental change. Significant efforts are underway to improve the resilience of biodiversity and ecological function to extreme events and directional change across all types of landscapes, from intact natural systems to highly modified landscapes such as cities and agricultural regions. However, identifying management strategies likely to promote ecological resilience remains a challenge. In this article, we present seven core dimensions to guide long-term and large-scale resilience planning in highly modified landscapes, with the objective of providing a structure and shared vocabulary for recognizing opportunities and actions likely to increase resilience across the whole landscape. We illustrate application of our approach to landscape-scale ecosystem management through case studies from two highly modified California landscapes, Silicon Valley and the Sacramento–San Joaquin Delta. We propose that resilience-based management is best implemented at large spatial scales and through collaborative, cross-sector partnerships.
Futures Past Exploring California landscapes with the San Francisco Estuary Institute. Boom: The Journal of California . pp 4-27.2014.
Historical Ecology Reconnaissance for the Lower Salinas River. SFEI Contribution No. 581. San Francisco Estuary Institute: Richmond. p 32.2009.
Historical Ecology of the lower Santa Clara River, Ventura River, and Oxnard Plain: an analysis of terrestrial, riverine, and coastal habitats. SFEI Contribution No. 641. SFEI: Oakland.2011.
Upper Penitencia Creek Historical Ecology Assessment. SFEI Contribution No. 664. SFEI: Richmond, CA.2012.
Report of the 2003 Program Review. SFEI Contribution No. 303. San Franciso Estuary Institute: Oakland.2004.
Dry Creek Watershed Sediment Source Reconnaissance Technical Memorandum. SFEI Contribution No. 595. San Francisco Estuary Institute: Oakland,Ca.2009.
A Sediment Budget for Two Reaches of Alameda Creek. SFEI Contribution No. 550. San Francisco Estuary Institute.2008.
San Francisco Bay Microplastics Project: Science-Supported Solutions and Policy Recommendations. SFEI Contribution No. 955. 5 Gyres: Los Angeles, CA.2019.
Plastics in our waterways and in the ocean, and more specifically microplastics (plastic particles less than 5 mm in size), have gained global attention as a pervasive and preventable threat to marine ecosystem health. The San Francisco Bay Microplastics Project was designed to provide critical data on microplastics in the Bay Area. The project also engaged multiple stakeholders in both science and policy discussions. Finally, the project was designed to generate scientifically supported regional and statewide policy recommendations for solutions to plastic pollution.
Land Grant Research and the Pictorial Collection. In Exploring the Bancroft Library. Exploring the Bancroft Library. The Bancroft Library/Signature Books. Vol. In Faulhab, p 196.2006.
Short-term biogeochemical influence of a diatom bloom on the nutrient and trace metal concentrations in a South San Francisco Bay microcosm experiment. Estuaries . SFEI Contribution No. 240.2002.
Tracing Ni, Cu and Zn kinetics and equilibrium partitioning between dissolved and particulate phases in South San Francisco Bay, CA, using stable isotopes and HR-ICPMS. Geochimica Cosmochimica Acta 66, 3062-3082 . SFEI Contribution No. 255.2002.
Determination of dissolved manganese (II) in estuarine and coastal waters, by differential pulse cathodic stripping voltammetry. Analytica Chimica Acta 344, 175-180 . SFEI Contribution No. 217.1997.
Trace metal exchange in solution by the fungicides Ziram and Maneb (dithiocarbamates) and subsequent uptake of the lipophilic organic Zn, Cu and Pb complexes into phytoplankton cells. Environmental Toxicology and Chemistry 16, 2046-2053 . SFEI Contribution No. 213.1997.
Competitive equilibration techniques for determining transition metal speciation in natural waters: Evaluation using model data. Analytica Chimica Acta 343, 161-181 . SFEI Contribution No. 211.1997.
Effects of diethyldithiocarbamate and 8-hydroxyquinoline additions on algal uptake of ambient. Estuaries 20, 66-76 . SFEI Contribution No. 212.1997.
Analysis for Cd, Cu, Ni, Zn and Mn in estuarine water by inductively coupled plasma mass spectrometry coupled with an automated flow injection system. Analytica Chimica Acta 455, 11-22 . SFEI Contribution No. 239.2002.
Biogeochemistry of arsenic in natural waters: The importance of methylated species. Environmental Science & Technology 25, 420-427 . SFEI Contribution No. 160.1991.
Speciation of dissolved copper and nickel in South San Francisco Bay: A Multi-method approach. Analytica Chimica Acta 284, 557-572 . SFEI Contribution No. 176.1994.
Determination of copper speciation in marine waters by competitive ligand equilibration/liquid-liquid extraction: An evaluation of the technique. Analytica Chimica Acta 284, 573-586 . SFEI Contribution No. 178.1994.
Uptake of lipophilic organic Cu, Cd, and Pb complexes in the coastal diatom, Thalassiosira Weissflogii. Environmental Science and Technology 28, 1781-1790 . SFEI Contribution No. 179.1994.
Organic speciation of silver in marine waters. Environmental Science and Technology 29, 2616-2621 . SFEI Contribution No. 186.1995.
Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2000. SFEI Contribution No. 242. US Geological Survey Open-File Report. pp 96-591.2002.
Sediment Toxicity Identification Evaluations San Francisco Bay Regional Monitoring Program for Trace Substances. SFEI Contribution No. 243. San Francisco Estauary Institute: Richmond, CA.2002.
Summary of Suspended-Solids Concentration Data, San Francisco Bay, California, Water Year 1995. SFEI Contribution No. 13. US Geological Survey Open-File Report. pp 96-591.1996.
Summary of Suspended-Solids Concentration Data, San Francisco Bay, California, Water Year 1994. SFEI Contribution No. 14. US Geological Survey Open-File report. pp 95-776.1996.
Neonicotinoids and Their Degradates in San Francisco Bay Water. SFEI Contribution No. 1002. San Francisco Estuary Institute: Richmond, CA.2020.
In the summer of 2017, open Bay water samples were collected during the RMP Status and Trends Water Cruise. Samples were analyzed for 19 neonicotinoids and metabolites. The only neonicotinoid detected was imidacloprid, an active ingredient used in both urban and agricultural applications. Imidacloprid was detected at a single site above the method detection limits (2.2-2.6 ng/L) in Lower South Bay at a level of 4.2 ng/L. This value is within the range of concentrations found in a separate RMP study in water samples collected from the South and Lower South Bay margins in 2017. Imidacloprid was detected at 3 of 12 of the margin sites at levels between 3.9 and 11 ng/L; no other neonicotinoids were detected. Of note, these RMP studies appear to represent the first evaluation of ambient neonicotinoid concentrations in an estuarine environment in the nation.
2019 RMP North Bay Selenium Monitoring Sampling and Analysis Plan. SFEI Contribution No. 969. San Francisco Estuary Institute: Richmond, CA.2020.
The goal of monitoring for selenium in the North Bay tissue and water is to identify leading indicators of change to allow prompt management response to signs of increasing impairment. At the 2016 technical workshop, participants reached a consensus that monitoring sturgeon, clams, and water are all needed to answer management questions. Recommendations for long-term monitoring of these three matrices are detailed in the North Bay Monitoring Design document (Grieb et al. 2018). The purpose of this Sampling and Analysis Plan is to clearly document the sampling design, methods, and responsibilities; and to facilitate coordination among project partners.
2019 Sport Fish Monitoring Sampling and Analysis Plan. SFEI Contribution No. 970. San Francisco Estuary Institute: Richmond, CA.2020.
The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) monitors concentrations of contaminants in fish tissue as indicators of bioaccumulation of contaminants in the Bay. In 2019, the RMP will conduct its eighth round of sport fish monitoring by collecting sport fish samples from various locations in the Bay as a part of routine Status and Trends Monitoring. Add-ons to the routine Status and Trends sport fish monitoring design will include archiving for microplastics and fipronil, as well as additional collections of shiner surfperch in Priority Margin Unit areas (PMUs).