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Historical Changes in Channel Alignment along Lower Laguna de Santa Rosa and Mark West Creek. SFEI: Richmond, CA.
2014. ![application/pdf](/modules/file/icons/application-pdf.png)
Mt. Wanda Historical Ecology Investigation. SFEI Contribution No. 743. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 51.
2015. ![application/pdf](/modules/file/icons/application-pdf.png)
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Ecological Horticulture at the Presidio. . SFEI Contribution No. 1080. San Francisco Estuary Institute: Richmond, Ca.
2022. The Presidio of San Francisco—the nation’s largest urban national park—is located in an area of exceptional ecological diversity. Historically, many different habitat types thrived in the mix of windswept dunes, riparian forests, and curious dwarf oak woodlands that characterized this landscape. Many of these habitat types are rare today (and some were even rare in the region historically), and together they harbor a host of unique plants and animals.
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Reconnecting Riverside with its River: Integrating Historical and Urban Ecology for a Healthier Future. SFEI Contribution No. 1133. San Francisco Estuary Institute: Richmond, Ca.
2023. ![application/pdf](/modules/file/icons/application-pdf.png)
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Re-Oaking North Bay. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.
2020. ![application/pdf](/modules/file/icons/application-pdf.png)
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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.
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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. Effect of salinity on the olfactory toxicity of dissolved copper in juvenile salmon. SFEI Contribution No. 733.
2015. ![application/pdf](/modules/file/icons/application-pdf.png)
Optimizing Chemicals Management in the United States and Canada through the Essential-Use Approach. Environmental Science & Technology 57 (4).
2023. Chemicals have improved the functionality and convenience of industrial and consumer products, but sometimes at the expense of human or ecological health. Existing regulatory systems have proven to be inadequate for assessing and managing the tens of thousands of chemicals in commerce. A different approach is urgently needed to minimize ongoing production, use, and exposures to hazardous chemicals. The premise of the essential-use approach is that chemicals of concern should be used only in cases in which their function in specific products is necessary for health, safety, or the functioning of society and when feasible alternatives are unavailable. To optimize the essential-use approach for broader implementation in the United States and Canada, we recommend that governments and businesses (1) identify chemicals of concern for essentiality assessments based on a broad range of hazard traits, going beyond toxicity; (2) expedite decision-making by avoiding unnecessary assessments and strategically asking up to three questions to determine whether the use of the chemical in the product is essential; (3) apply the essential-use approach as early as possible in the process of developing and assessing chemicals; and (4) engage diverse experts in identifying chemical uses and functions, assessing alternatives, and making essentiality determinations and share such information broadly. If optimized and expanded into regulatory systems in the United States and Canada, other policymaking bodies, and businesses, the essential-use approach can improve chemicals management and shift the market toward safer chemistries that benefit human and ecological health.
Modeling Stormwater Loads of Contaminants of Emerging Concern: Literature Review and Recommendations. SFEI Contribution No. 1131. San Francisco Estuary Institute: Richmond, CA.
2024. ![application/pdf](/modules/file/icons/application-pdf.png)
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.
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Trends in Suspended Sediment Input to the San Francisco Bay for Local Tributaries Watersheds. San Francisco Estuary Institute.
. 2005. ![application/pdf](/modules/file/icons/application-pdf.png)
East Contra Costa Historical Ecology Study GIS data, GIS data produced for the East Contra Costa County Historical Ecology Study.
2011. ![application/zip](/modules/file/icons/package-x-generic.png)
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2009.
Quaternary Ammonium Compounds: A Chemical Class of Emerging Concern. Environmental Science & Technology 57 (20), 7645-7665.
2023. Quaternary ammonium compounds (QACs), a large class of chemicals that includes high production volume substances, have been used for decades as antimicrobials, preservatives, and antistatic agents and for other functions in cleaning, disinfecting, personal care products, and durable consumer goods. QAC use has accelerated in response to the COVID-19 pandemic and the banning of 19 antimicrobials from several personal care products by the US Food and Drug Administration in 2016. Studies conducted before and after the onset of the pandemic indicate increased human exposure to QACs. Environmental releases of these chemicals have also increased. Emerging information on adverse environmental and human health impacts of QACs is motivating a reconsideration of the risks and benefits across the life cycle of their production, use, and disposal. This work presents a critical review of the literature and scientific perspective developed by a multidisciplinary, multi-institutional team of authors from academia, governmental, and nonprofit organizations. The review evaluates currently available information on the ecological and human health profile of QACs and identifies multiple areas of potential concern. Adverse ecological effects include acute and chronic toxicity to susceptible aquatic organisms, with concentrations of some QACs approaching levels of concern. Suspected or known adverse health outcomes include dermal and respiratory effects, developmental and reproductive toxicity, disruption of metabolic function such as lipid homeostasis, and impairment of mitochondrial function. QACs’ role in antimicrobial resistance has also been demonstrated. In the US regulatory system, how a QAC is managed depends on how it is used, for example in pesticides or personal care products. This can result in the same QACs receiving different degrees of scrutiny depending on the use and the agency regulating it. Further, the US Environmental Protection Agency’s current method of grouping QACs based on structure, first proposed in 1988, is insufficient to address the wide range of QAC chemistries, potential toxicities, and exposure scenarios. Consequently, exposures to common mixtures of QACs and from multiple sources remain largely unassessed. Some restrictions on the use of QACs have been implemented in the US and elsewhere, primarily focused on personal care products. Assessing the risks posed by QACs is hampered by their vast structural diversity and a lack of quantitative data on exposure and toxicity for the majority of these compounds. This review identifies important data gaps and provides research and policy recommendations for preserving the utility of QAC chemistries while also seeking to limit adverse environmental and human health effects.
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. ![application/pdf](/modules/file/icons/application-pdf.png)
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.
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Relationship Between Sediment Toxicity and Contamination in San Francisco Bay. SFEI Contribution No. 27. San Francisco Estuary Institute: Oakland, CA. pp 285-309.
1997. Relationships Between Sediment Toxicity and Contamination in San Francisco Bay. Marine Environmental Research 48, 285-309 . SFEI Contribution No. 27.
1999. Relationship Between Sediment Toxicity and Contamination in San Francisco Bay (Abstract). Marine Environmental Research 285-309 . SFEI Contribution No. 332.
1999. Patterns and trends in sediment toxicity in the San Francisco Estuary. Environmental Research 105 (1), 145-155 . SFEI Contribution No. 496.
2007. The effects of kaolin clay on the amphipod Eohaustorius estuarius: Part Two. SFEI Contribution No. 822.
2017. ![application/pdf](/modules/file/icons/application-pdf.png)
Contaminants of Emerging Concern in the San Francisco Estuary: Carbamazepine. SFEI Contribution No. 658. SFEI: Richmond, CA. p 14.
2012. ![application/pdf](/modules/file/icons/application-pdf.png)
Estimated Atmospheric Deposition Fluxes of Dioxins in the San Francisco Estuary. SFEI Contribution No. 661. SFEI: Richmond, CA.
2012. ![application/pdf](/modules/file/icons/application-pdf.png)
2010 Annual Monitoring Results. San Francisco Estuary Institute: Richmond, CA.
2012. ![application/pdf](/modules/file/icons/application-pdf.png)
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Hydrodynamic, sediment transport, and sediment flocculation data from south San Francisco Bay, California, summer 2020. United Sates Geological Survey.
2021. The U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center collected hydrodynamic and suspended sediment flocculation data at channel and shallow water sites in south San Francisco Bay in July 2020. The data were used to determine water column stratification, turbulence profiles, and floc size evolution. The goal of this project was to bound the controls on floc size and floc settling velocity to improve estimates of sediment fluxes and consider error in numerical models of sediment transport in San Francisco Bay. This data release includes hydrodynamic, sediment concentration, and particle size timeseries during July 2020, as well as sediment bed properties, water column particle size distributions, and CTD profiles collected on four days in July 2020 at both sites. Details on station location, instrumentation, and measured variables are included on pages for each data type. These data were collected as part of a collaborative project with the USGS California Water Science Center. Funding was provided by the San Francisco Estuary Institute.
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.
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San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants, California—2018. U.S. Geological Survey: Reston, Virginia.
2019. ![application/pdf](/modules/file/icons/application-pdf.png)
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. ![application/pdf](/modules/file/icons/application-pdf.png)
Spatial and Temporal Variability in the Aquatic Cycling of Chromium. SFEI Contribution No. 220. University of California: Santa Cruz, CA.
1998. Chromium in San Francisco Bay: inorganic speciation, distribution, and geochemical processes, University of California: Santa Cruz.
1994.