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Neonicotinoids and Their Degradates in San Francisco Bay Water. SFEI Contribution No. 1002. San Francisco Estuary Institute: Richmond, CA.
2020. (1.8 MB)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 Sport Fish Monitoring Sampling and Analysis Plan. SFEI Contribution No. 970. San Francisco Estuary Institute: Richmond, CA.
2020. (628 KB)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).
Contaminant Concentrations in Sport Fish from San Francisco Bay: 2019. SFEI Contribution No. 1036. San Francisco Estuary Institute: Richmond, CA.
2021. (5.15 MB)2019 RMP North Bay Selenium Monitoring Sampling and Analysis Plan. SFEI Contribution No. 969. San Francisco Estuary Institute: Richmond, CA.
2020. (2.08 MB)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.
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-Sediment Concentration Data, San Francisco Bay, California, Water Year 2000. SFEI Contribution No. 242. US Geological Survey Open-File Report. pp 96-591.
2002. 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. 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. Biogeochemistry of arsenic in natural waters: The importance of methylated species. Environmental Science & Technology 25, 420-427 . SFEI Contribution No. 160.
1991. 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. 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. 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. 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. 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. 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. Organic speciation of silver in marine waters. Environmental Science and Technology 29, 2616-2621 . SFEI Contribution No. 186.
1995. 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. 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. Sampling and Quality Assurance and Quality Control: A Guide for Scientists Investigating the Occurrence of Microplastics Across Matrices. Applied Spectroscopy 74 (9) . SFEI Contribution No. 1012.
2020. Plastic pollution is a defining environmental contaminant and is considered to be one of the greatest environmental threats of the Anthropocene, with its presence documented across aquatic and terrestrial ecosystems. The majority of this plastic debris falls into the micro (1 lm–5 mm) or nano (1–1000 nm) size range and comes from primary and secondary sources. Its small size makes it cumbersome to isolate and analyze reproducibly, and its ubiquitous distribution creates numerous challenges when controlling for background contamination across matrices (e.g., sediment, tissue, water, air). Although research on microplastics represents a relatively nascent subfield, burgeoning interest in questions surrounding the fate and effects of these debris items creates a pressing need for harmonized sampling protocols and quality control approaches. For results across laboratories to be reproducible and comparable, it is imperative that guidelines based on vetted protocols be readily available to research groups, many of which are either new to plastics research or, as with any new subfield, have arrived at current approaches through a process of trial-and-error rather than in consultation with the greater scientific community. The goals of this manuscript are to (i) outline the steps necessary to conduct general as
well as matrix-specific quality assurance and quality control based on sample type and associated constraints, (ii) briefly review current findings across matrices, and (iii) provide guidance for the design of sampling regimes. Specific attention is paid to the source of microplastic pollution as well as the pathway by which contamination occurs, with details provided regarding each step in the process from generating appropriate questions to sampling design and collection.
San Francisco Bay Microplastics Project: Science-Supported Solutions and Policy Recommendations. SFEI Contribution No. 955. 5 Gyres: Los Angeles, CA.
2019. (17.53 MB)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.
Dry Creek Watershed Sediment Source Reconnaissance Technical Memorandum. SFEI Contribution No. 595. San Francisco Estuary Institute: Oakland,Ca.
2009. (3.06 MB) (27.1 MB)A Sediment Budget for Two Reaches of Alameda Creek. SFEI Contribution No. 550. San Francisco Estuary Institute.
2008. (26.45 MB)Decentralized Wastewater Discharges and Multiple Benefit Natural Infrastructure: Preliminary Analysis and Next Steps (Final Project Report). East Bay Dischargers Authority .
2015. (7.78 MB)Report of the 2003 Program Review. SFEI Contribution No. 303. San Franciso Estuary Institute: Oakland.
2004. (1023.38 KB)Futures Past Exploring California landscapes with the San Francisco Estuary Institute. Boom: The Journal of California . pp 4-27.
2014. 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)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. (17.09 MB) (201.86 MB)Historical Ecology Reconnaissance for the Lower Salinas River. SFEI Contribution No. 581. San Francisco Estuary Institute: Richmond. p 32.
2009. (44 MB)Historical Vegetation and Drainage Patterns of Western Santa Clara Valley: A technical memorandum describing landscape ecology in Lower Peninsula, West Valley, and Guadalupe Watershed Management Areas. SFEI Contribution No. 622. SFEI: Oakland.
2010. (43.77 MB) (1.29 MB)Upper Penitencia Creek Historical Ecology Assessment. SFEI Contribution No. 664. SFEI: Richmond, CA.
2012. (16.48 MB)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.
Building Ecological Resilience in Highly Modified Landscapes.
2018. (4.93 MB)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.
Landscape Resilience Framework: Operationalizing Ecological Resilience at the Landscape Scale. SFEI Contribution No. 752. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
. 2015. (5.18 MB)Northern San Diego County Lagoons Historical Ecology Investigation. SFEI Contribution No. 722. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 215.
2014. (305.02 MB) (50.9 MB)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. (259.64 MB) (84.6 MB) (20.93 MB)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.
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. (45.32 MB)Shifting Shores: Marsh Expansion and Retreat in San Pablo Bay. SFEI Contribution No. 751.
2015. (93.2 MB) (31.73 MB)EXECUTIVE SUMMARY
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.
Key findings:
• 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.
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. (21.34 MB)Sycamore Alluvial Woodland Planting Guide. SFEI Contribution No. 901.
2018. (1.22 MB)Observational Study of Sycamore Regeneration at two sites in Santa Clara County after the 2016-2017 Water Year. SFEI Contribution No. 874.
2018. (8.44 MB)Sycamore Alluvial Woodland: Habitat Mapping and Regeneration Study. SFEI Contribution No. 816.
2017. (53.95 MB) (21.31 MB)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).
Integrating Planning with Nature: Building climate resilience across the urban-to-rural gradient. SFEI Contribution No. 1013.
2020. (6.35 MB) (88.2 MB)Application of Gene Expression Analysis for Sediment Toxicity Stressor Identification. SFEI Contribution No. 659.
2012. (3.21 MB)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. (65.92 MB) (8.46 MB)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. (94.51 MB) (39.07 MB)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.
Petaluma Valley Historical Hydrology and Ecology Study. SFEI Contribution No. 861. San Francisco Estuary Institute: Richmond, CA.
2018. (121.7 MB) (43.68 MB)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.
Re-Oaking North Bay. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.
2020. (20.51 MB) (1.83 MB)Historical Changes in Channel Alignment along Lower Laguna de Santa Rosa and Mark West Creek. SFEI: Richmond, CA.
2014. (9.78 MB)Peninsula Watershed Historical Ecology Study. SFEI Contribution No. 1029. San Francisco Estuary Institute: Richmond, Ca.
2021. (204.95 MB) (21.97 MB)Mt. Wanda Historical Ecology Investigation. SFEI Contribution No. 743. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 51.
2015. (20.92 MB) (57.9 MB)Ecological Horticulture at the Presidio. . SFEI Contribution No. 1080. San Francisco Estuary Institute: Richmond, Ca.
2022. (52.48 MB) (3.06 MB)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.
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. (1.02 MB)Optimizing Chemicals Management in the United States and Canada through the Essential-Use Approach. Environmental Science & Technology 57 (4).
2023. (2.72 MB)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.