Library
Our library features many hundreds of entries.
To search among them, click "Search" below to pull down options, including filtering by document type, author, year, and keyword.
Find these options under "Show only items where." Or you can also sort by author, title, type, and year clicking the headings below.
The biological deserts fallacy: Cities in their landscapes contribute more than we think to regional biodiversity. BioScience 71 (2) . SFEI Contribution No. 1031.
2021. (781.56 KB)Cities are both embedded within and ecologically linked to their surrounding landscapes. Although urbanization poses a substantial threat to biodiversity, cities also support many species, some of which have larger populations, faster growth rates, and higher productivity in cities than outside of them. Despite this fact, surprisingly little attention has been paid to the potentially beneficial links between cities and their surroundings.
We identify five pathways by which cities can benefit regional ecosystems by releasing species from threats in the larger landscape, increasing regional habitat heterogeneity and genetic diversity, acting as migratory stopovers, preadapting species to climate change, and enhancing public engagement and environmental stewardship. Increasing recognition of these pathways could help cities identify effective strategies for supporting regional biodiversity conservation and could provide a science-based platform for incorporating biodiversity alongside other urban greening goals.
A biogeographic pattern in sparrow bill morphology: parallel adaptation to tidal marshes. Evolution 59, 1588-1595 . SFEI Contribution No. 447.
2005. Biogeochemistry of arsenic in natural waters: The importance of methylated species. Environmental Science & Technology 25, 420-427 . SFEI Contribution No. 160.
1991. The biogeochemical cycling of manganese in San Francisco Bay: Temporal and spatial variations. SFEI Contribution No. 52. Vol. 54, pp 227-239.
2002. The Bioavailability of Toxic Contaminants in the San Francisco Bay-Delta: Proceedings of a Two-Day Seminar Series. SFEI Contribution No. 142. San Francisco Bay - Delta Aquatic Habitat Institute, Richmond, CA: Berkeley, CA.
1988. The Bioavailability of Toxic Contaminants in the San Francisco Bay-Delta - Proceedings of a Two Day Seminar Series. SFEI Contribution No. 154. San Francisco Estuary Institiute: Richmond, CA. p 182.
. 1989. (11.24 MB)Bioaccumulation of Contaminants by Transplanted Bivalves in the San Francisco Estuary: Status and Trends. SFEI Contribution No. 191. San Francisco Estuary Institute: Richmond, CA. p 80.
1996. Bioaccumulation of contaminants by transplanted bivalves in the San Francisco Estuary: A summary of status and trends with emphasis on Local Effects Monitoring Programs. SFEI Contribution No. 11. (Bay Area Dischargers Association) San Francisco Estuary Institute: Richmond, CA. pp 171-175.
1997. Bioaccumulation of contaminants by bivalve molluscs in the vicinity of municipal wastewater discharges to San Francisco Bay: Wet season results, 1991/1992. SFEI Contribution No. 170. Aquatic Habitat Institute: Richmond, CA.
1992. Best Management Practices in Stone Fruit Project. San Francisco Estuary Institite: Oakland, Ca.
2009. (2.07 MB)Benthic macrofaunal assemblages of the San Francisco Estuary and Delta, USA. Environmental Monitoring Assessment.
2013. (642.77 KB)Benthic lead fluxes in San Francisco Bay, California, USA. Geochimica et Cosmochimica Acta 58, 3307-3313 . SFEI Contribution No. 180.
1994. Benthic fluxes of silver in San Francisco Bay. Marine Chemistry 56, 15-26 . SFEI Contribution No. 214.
1997. Bay Science: A Report to the Science Content Committee of The Bay Center. San Francisco Estuary Institute.
2005. Baylands Vegetation Mapping Protocol (Version 1.0). SFEI Contribution No. 304. San Francisco Estuary Institute: Oakland, CA.
2004. (450.49 KB)Baylands Resilience Framework for San Francisco Bay: Wildlife Support. SFEI Contribution No. 1115. San Francisco Estuary Institute: Richmond, CA.
2023. (10.03 MB)BAYLANDS ECOSYSTEM HABITAT GOALS: REPORT ON THE PROCESS TO SET REGIONAL GOALS FOR WETLANDS RESTORATION IN THE SAN FRANCISCO BAY AREA. SFEI Contribution No. 227. San Francisco Estuary Institute: Richmond, CA.
1998. (3.12 KB)Baylands Ecosystem Habitat Goals. SFEI Contribution No. 330. U. S. Environmental Protection Agency, San Francisco, Calif./S.F. Bay Regional Water Quality Control Board, Oakland, Calif. p 328.
1999. (7.11 MB)2015. The Baylands and Climate Change: What We Can Do. Baylands Ecosystem Habitat Goals Science Update 2015. California State Coastal Conservancy: Oakland, CA.
(31.68 MB)Bay Area Wetlands Regional Monitoring Program (Abstract, SOE 2001). San Francisco Estuary Institute: Richmond, CA.
2001. (6.46 KB)Bay Area Wetlands Ecosystem Goals Project: Key Baylands Species. SFEI Contribution No. 121. San Francisco Estuary Institute.
1998. (25.65 KB)Bay Area Wetlands Ecosystem Goals Project: Key Baylands Habitats. SFEI Contribution No. 122. San Francisco Estuary Institute.
1998. (35.49 KB)Bay Area Wetlands Ecosystem Goals Project: Draft Functional Correspondence between Past and Present Key Habitats. SFEI Contribution No. 123. San Francisco Estuary Institute.
1998. (23.63 KB)Bay Area Green Infrastructure Water Quality Synthesis. SFEI Contribution No. 922. San Francisco Estuary Institute : Richmond, CA.
2018. (2.31 MB) (1.95 MB)2009. Bay Area Base Map.
(1.27 MB)Bay Area Aquatic Resources Inventory (BAARI) . SFEI Contribution No. 746. p 79.
. 2011. (41.31 MB)Bay 2017 Bay RMP Field Sampling Report. SFEI Contribution No. 849. San Francisco Estuary Institute : Richmond, CA.
2018. (7.01 MB)Bathymetric change analysis in San Francisco Bay, California, from 1971 to 2020. United States Geological Survey Pacific Coastal and Marine Science Center: Santa Cruz, CA.
2023. This data release provides bathymetric change grids of four geographic areas of San Francisco Bay, California, comparing digital elevation models (DEMs) created from bathymetric data collected in the 1970s and 1980s with DEMs created from bathymetric data collected in the 2010s and 2020. These types of change analyses can provide information on the quantities and patterns of erosion and deposition in San Francisco Bay over the 9 to 47 years between surveys, and they reveals that the bay floor lost about 34 million cubic meters of sediment between the intervening time period. Results from this study can be used to assess how San Francisco Bay has responded to changes in the system such as sea-level rise and variation in sediment supply from the Sacramento-San Joaquin Delta and local tributaries, and supports the creation of a new, system-wide sediment budget. These bathymetric change grids can also provide data to ecosystem managers about the quantities and patterns of sediment volume change in San Francisco Bay to assist in decision-making for a variety of sediment-related issues, including restoration of tidal marshes, exposure of legacy contaminated sediment, and strategies for the beneficial use of dredged sediment.
Bathymetric change analysis in San Francisco Bay, California, from 1971 to 2020. United States Geological Survey.
2023. This data release provides bathymetric change grids of four geographic areas of San Francisco Bay, California, comparing digital elevation models (DEMs) created from bathymetric data collected in the 1970s and 1980s with DEMs created from bathymetric data collected in the 2010s and 2020. These types of change analyses can provide information on the quantities and patterns of erosion and deposition in San Francisco Bay over the 9 to 47 years between surveys, and they reveals that the bay floor lost about 34 million cubic meters of sediment between the intervening time period. Results from this study can be used to assess how San Francisco Bay has responded to changes in the system such as sea-level rise and variation in sediment supply from the Sacramento-San Joaquin Delta and local tributaries, and supports the creation of a new, system-wide sediment budget. These bathymetric change grids can also provide data to ecosystem managers about the quantities and patterns of sediment volume change in San Francisco Bay to assist in decision-making for a variety of sediment-related issues, including restoration of tidal marshes, exposure of legacy contaminated sediment, and strategies for the beneficial use of dredged sediment.
Basic Regional Spatial Analysis of Non - Indigenous Invasive Species (NIS) Spartina Invasions in the San Francisco Estuary. SFEI Contribution No. 372. San Francisco Estuary Institute: Richmond, Ca.
2001. (429.92 KB)BACWA Polychlorinated Biphenyls in Municipal Wastewater Effluent Study. SFEI Contribution No. 79. San Francisco Estuary Institute.
2002. Atmospheric Deposition of Trace Metals in San Francisco Bay. SFEI Contribution No. 278. San Francisco Estuary Institute: Richmond, CA.
2002. Atmospheric Concentrations and Fluxes of Organic Compounds in the Northern San Francisco Estuary. Environmental Science and Technology 36 (22), 4741-4747 . SFEI Contribution No. 474.
2002. Atlas of Sediment Contamination, Toxicity, and Benthic Assemblages in San Francisco Bay. SFEI Contribution No. 38. San Francisco Estuary Institute: Richmond, CA.
1999. An Assesssment of the Loading of Toxic Contaminants to the San Francisco Bay-Delta. SFEI Contribution No. 137. San Francisco Estuary Institute: Richmond. p 330.
1987. An Assessment of the South Bay Historical Tidal-Terrestrial Transition Zone. SFEI Contribution No. 693. San Francisco Estuary Institute: Richmond, CA.
2013. (7.87 MB)An Assessment of The Loading of Toxic Contaminants to The San Francisco-Bay Delta: Full Report. SFEI Contribution No. 143. AHI: Richmond, CA. p 360.
1987. (14.59 MB)An Assessment of The Loading of Toxic Contaminants to The San Francisco-Bay Delta: Executive Summary. SFEI Contribution No. 144. AHI: Richmond, CA. p 26.
1987. (1.89 MB)Assessment of Potential Aquatic Herbicide Impacts to California Aquatic Ecosystems. Archives of Environmental Contamination and Toxicology . SFEI Contribution No. 539.
2008. (330.69 KB)Assessment of Nutrient Status and Trends in the Delta in 2001–2016: Effects of drought on ambient concentrations and trends. SFEI Contribution No. 865. Aquatic Science Center: Richmond, CA.
2018. (8.33 MB)Nutrients and the effects of nutrients on water quality in the Sacramento-San Joaquin Delta is a priority focus area for the Delta Regional Monitoring Program (Delta RMP). The Program’s first assessment question regarding nutrients is: “How do concentrations of nutrients (and nutrient-associated parameters) vary spatially and temporally?” In this analysis, we confirmed previously reported declining trends in the San Joaquin River for nutrient concentrations at Vernalis and chlorophyll-a concentrations at Buckley Cove and Disappointment Slough. A slight increasing trend for dissolved oxygen at Buckley Cove was also detected which could be confirmation that management actions for the San Joaquin River Dissolved Control Program are having the desired effect. Finally, at stations in Suisun Bay, the Confluence region, and Franks Tract, chlorophyll-a showed modest increasing trends, which were not evident in previous analyses. The new analyses presented in this report and the findings from earlier reports constitute encouraging early progress toward answering the Delta RMP’s assessment questions. Specifically, due to the existence of long-term data sets and synthesis efforts, spatial and temporal trends in the concentrations of nutrients and nutrient-related parameters are reasonably well understood and so are the magnitudes of the most important sources of nutrients from outside the Delta. However, additional synthesis work could be done to understand the factors behind these trends. Large knowledge gaps remain about nutrient sinks, sources, and processes within the Delta. The mechanistic, water quality-hydrodynamic models being developed for the Delta may be able to address these questions in the future.
Assessment of Macrobenthos Response to Sediment Contamination in the San Francisco Estuary (published in Environmental Toxicology and Chemistry). Environmental Toxicology and Chemistry 23, 2178.
2004. Assessment of macrobenthos resonse to sediment contamination in the San Francisco Estuary, USA. Environmental Toxicology and Chemistry 23 . SFEI Contribution No. 60.
2004. (213.18 KB)Assessment of Long-Chain Polyethoxylate Surfactants in Wastewater Effluent, Stormwater Runoff, and Ambient Water of San Francisco Bay, CA. SFEI Contribution No. 1126. American Chemical Society.
2023. Ethoxylated surfactants are ubiquitous organic environmental contaminants that have received continued attention over the past several decades, particularly as manufacturing rates increase worldwide and as toxicity concerns grow regarding alcohol ethoxylates. Presence of these compounds in surface water has been considered primarily the result of contaminated wastewater effluent by ethoxylated surfactant degradates; as a result, monitoring has focused on the small subset of short-chain ethoxylates in wastewater effluent and receiving waters. This study quantified long-chain alcohol and alkylphenol ethoxylated surfactants in San Francisco Bay area stormwater runoff, wastewater effluent, and ambient Bay water to determine concentrations and inform potential pathways of contamination. We employed high-performance liquid chromatography coupled to high-resolution mass spectrometry to quantitate long-chain polyethoxylates, which are rarely monitored in ethoxylated surfactant studies. Similar total ethoxylated surfactant concentrations were observed in stormwater runoff (0.004–4.7 μg/L) and wastewater effluent (0.003–4.8 μg/L, outlier of 45 μg/L). Ambient Bay water contamination (0.0001–0.71 μg/L) was likely the result of both stormwater and wastewater inputs to San Francisco Bay. These results suggest that a broader focus including long-chain compounds and stormwater pathways may be needed to fully characterize the occurrence and impacts of ethoxylated surfactants in urban surface waters.
An assessment of future tidal marsh resilience in the San Francisco Estuary through modeling and quantifiable metrics of sustainability. Frontiers in Environmental Science 10.
2022. Quantitative, broadly applicable metrics of resilience are needed to effectively manage tidal marshes into the future. Here we quantified three metrics of temporal marsh resilience: time to marsh drowning, time to marsh tipping point, and the probability of a regime shift, defined as the conditional probability of a transition to an alternative super-optimal, suboptimal, or drowned state. We used organic matter content (loss on ignition, LOI) and peat age combined with the Coastal Wetland Equilibrium Model (CWEM) to track wetland development and resilience under different sea-level rise scenarios in the Sacramento-San Joaquin Delta (Delta) of California. A 100-year hindcast of the model showed excellent agreement (R2 = 0.96) between observed (2.86 mm/year) and predicted vertical accretion rates (2.98 mm/year) and correctly predicted a recovery in LOI (R2 = 0.76) after the California Gold Rush. Vertical accretion in the tidal freshwater marshes of the Delta is dominated by organic production. The large elevation range of the vegetation combined with high relative marsh elevation provides Delta marshes with resilience and elevation capital sufficiently great to tolerate centenary sea-level rise (CLSR) as high as 200 cm. The initial relative elevation of a marsh was a strong determinant of marsh survival time and tipping point. For a Delta marsh of average elevation, the tipping point at which vertical accretion no longer keeps up with the rate of sea-level rise is 50 years or more. Simulated, triennial additions of 6 mm of sediment via episodic atmospheric rivers increased the proportion of marshes surviving from 51% to 72% and decreased the proportion drowning from 49% to 28%. Our temporal metrics provide critical time frames for adaptively managing marshes, restoring marshes with the best chance of survival, and seizing opportunities for establishing migration corridors, which are all essential for safeguarding future habitats for sensitive species.
Assessment of emerging polar organic pollutants linked to contaminant pathways within an urban estuary using non-targeted analysis. SFEI Contribution No. 1107. Environmental Sciences: Processes and Impacts.
2021. A comprehensive, non-targeted analysis of polar organic pollutants using high resolution/accurate mass (HR/AM) mass spectrometry approaches has been applied to water samples from San Francisco (SF) Bay, a major urban estuary on the western coast of the United States, to assess occurrence of emerging contaminants and inform future monitoring and management activities. Polar Organic Chemical Integrative Samplers (POCIS) were deployed selectively to evaluate the influence of three contaminant pathways: urban stormwater runoff (San Leandro Bay), wastewater effluent (Coyote Creek, Lower South Bay), and agricultural runoff (Napa River). Grab samples were collected before and after deployment of the passive samplers to provide a quantitative snapshot of contaminants for comparison. Composite samples of wastewater effluent (24 hours) were also collected from several wastewater dischargers. Samples were analyzed using liquid-chromatography coupled to high resolution mass spectrometry. Resulting data were analyzed using a customized workflow designed for high-fidelity detection, prioritization, identification, and semi-quantitation of detected molecular features. Approximately 6350 compounds were detected in the combined data set, with 424 of those compounds tentatively identified through high quality spectral library match scores. Compounds identified included ethoxylated surfactants, pesticide and pharmaceutical transformation products, polymer additives, and rubber vulcanization agents. Compounds identified in samples were reflective of the apparent sources and pathways of organic pollutant inputs, with stormwater-influenced samples dominated by additive chemicals likely derived from plastics and vehicle tires, as well as ethoxylated surfactants.
Assessment Framework as a Tool for Integrating and Communicating Watershed Health Indicators for the San Francisco Estuary. SFEI Contribution No. 634. San Francisco Estuary Institute: Oakland, CA.
2011. (2.14 MB)Assessing the Impact of Periodic Dredging on Macroinvertebrate-Prey Availability for Benthic Foraging Fishes: Final Study Plan and Preliminary Pilot Study Results. SFEI Contribution No. 833. U.S. Geological Survey: Vallejo, CA.
2017. (1.88 MB)Assessing Historic Mercury Concentrations in Sediments, San Francisco Bay Estuary. . SFEI Contribution No. 124.
2004. Asian Kelp Undaria pinnatifida in the northeastern Pacific Ocean. Biological Invasions 4, 333-338 . SFEI Contribution No. 417.
2002. (110.59 KB)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. (194.19 KB)Aquatics Herbicides: Overview of Usage, Fate and Transport, Potential Environmental Risk, and Future Recommendations for the Sacramento-San Joaquin Delta and Central Valley. SFEI Contribution No. 414. San Francisco Estuary Institute.
2005. (633.6 KB)Aquatic Pesticides Monitoring Program Quality Assurance Program Plan. SFEI Contribution No. 302.
2004. (588.8 KB)Aquatic Pesticides Monitoring Program Phase 3 (2005) Bioassessment of Waterbodies Treated With Aquatic Pesticides. SFEI Contribution No. 393. San Francisco Estuary Institute: Oakland, CA.
2005. (1.22 MB)Aquatic Pesticides Monitoring Program Phase 3 (2004) Monitoring Project Report. SFEI Contribution No. 391. San Francisco Estuary Institute: Oakland, CA.
2004. (1.15 MB)Aquatic Pesticides Monitoring Program Phase 2 (2003) Monitoring Project Report. SFEI Contribution No. 108. San Francisco Estuary Institute: Oakland, CA.
2004. (1.06 MB)Aquatic Pesticides Monitoring Program Phase 1 (2002) Project Report. SFEI Contribution No. 103.
2003. Aquatic Pesticides Monitoring Program Nonchemical Alternatives Year 3 Final Report. SFEI Contribution No. 390. San Francisco Estuary Institute.
2005. (4.49 MB)Aquatic Pesticides Monitoring Program Monitoring Project Final Report. SFEI Contribution No. 392. San Francisco Estuary Institute: Oakland, CA.
2005. (905.48 KB)Aquatic Pesticide Monitoring Program Modeling Workgroup Final Report. SFEI Contribution No. 104.
2003. (950.69 KB)Aquatic Pesticide Monitoring Program Literature Review. SFEI Contribution No. 71. San Francisco Estuary Institute: Oakland, CA.
2003. (5.45 MB)Aquatic bioinvasions in the San Francisco Estuary. Berkeley Society for Conservation Biology Annual Meeting.
1999. 2005. Approaches to presenting the science of the San Francisco Bay/Delta Estuary. SFEI Contribution No. 459.
Approaches to presenting the science of the San Francisco Bay/Delta estuary. SFEI Contribution No. 514. San Francisco Estuary Institute: Oakland, CA.
2005. Applying Sediment Quality Objective Assessments to San Francisco Bay Samples from 2008-2012. San Francisco Estuary Institute and Southern California Coastal Water Research Project: Richmond, CA.
2013. (2.9 MB)Applying Sediment Quality Objective Assessment Protocols to Two San Francisco Bay 303(d)-Listed Sites. Final Report. San Francisco Estuary Institute: Richmond.
2013. (1.34 MB)Applied Aquatic Science: A Business Plan for EcoAtlas. San Francisco Estuary Institue: Richmond, CA.
2017. (1.69 MB) (323.4 KB) (214.45 KB)The following plan is intended to ensure the continued vitality of the toolset. The plan’s success will depend upon the continued collaboration of the public agencies that have supported the toolset thus far, but it must also integrate principles of resilience as it accounts for the tensions that arise as organizations move in different strategic directions.
Application of Gene Expression Analysis for Sediment Toxicity Stressor Identification. SFEI Contribution No. 659.
2012. (3.21 MB)Appendix 1: All Deliverables Submitted for the Critical Coastal Areas Program, Phase I. San Francisco Estuary Institute.
2007. (14.83 MB)Apparent Tolerance of Common Tern (Sterna hirundo) Embryos to a Pentabrominated Diphenyl Ether Mixture (DE-71). USGS-Patuxent Wildlife Research Center: Beltsville, Maryland.
2011. (1.57 MB)2005. APMP Phase 3 Bioassesment Report. SFEI Contribution No. 462.
APMP Alternatives Program Executive Summary. SFEI Contribution No. 118. San Francisco Estuary Institute: Oakland, CA.
2004. (325.38 KB)Anthropogenic sources of lead in the Sacramento and San Joaquin drainage basins. Environmental Science and Technology . SFEI Contribution No. 289.
2003. . 2010.