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Spotswood, E.; Grossinger, R.; Hagerty, S.; Bazo, M.; Benjamin, M.; Beller, E.; Grenier, L.; Askevold, R. A. 2019. Making Nature's City. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.

Cities will face many challenges over the coming decades, from adapting to a changing climate to accommodating rapid population growth. A related suite of challenges threatens global biodiversity, resulting in many species facing extinction. While urban planners and conservationists have long treated these issues as distinct, there is growing evidence that cities not only harbor a significant fraction of the world’s biodiversity, but also that they can also be made more livable and resilient for people, plants, and animals through nature-friendly urban design. 

Urban ecological science can provide a powerful tool to guide cities towards more biodiversity-friendly design. However, current research remains scattered across thousands of journal articles and is largely inaccessible to practitioners. Our report Making Nature’s City addresses these issues, synthesizing global research to develop a science-based approach for supporting nature in cities. 

Using the framework outlined in the report, urban designers and local residents can work together to connect, improve, and expand upon city greenspaces to better support biodiversity while making cities better places to live. As we envision healthier and more resilient cities, Making Nature’s City provides practical guidance for the many actors who together will shape the nature of cities.

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Spotswood, E.; Grossinger, R. M.; Hagerty, S.; Beller, E. E.; Grenier, J. Letitia; Askevold, R. A. 2017. Re-Oaking Silicon Valley: Building Vibrant Cities with Nature. SFEI Contribution No. 825. San Francisco Estuary Institute: Richmond, CA.

In this report, we investigate how re-integrating components of oak woodlands into developed landscapes — “re-oaking” — can provide an array of valuable functions for both wildlife and people. Re-oaking can increase the biodiversity and ecological resilience of urban ecosystems, improve critical urban forest functions such as shade and carbon storage, and enhance the capacity of cities to adapt to a changing climate. We focus on Silicon Valley, where oak woodland replacement by agriculture and urbanization tells a story that has occurred in many other cities in California. We highlight how the history and ecology of the Silicon Valley landscape can be used as a guide to plan more ecologically-resilient cities in the Bay Area, within the region and elsewhere in California. We see re-oaking as part of, and not a substitute for, the important and broader oak woodland conservation efforts taking place throughout the state.

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Spotswood, E.; Beller, E. E.; Grossinger, R. M.; Grenier, L.; Heller, N.; Aronson, M. 2021. The biological deserts fallacy: Cities in their landscapes contribute more than we think to regional biodiversity. BioScience 71 (2) . SFEI Contribution No. 1031.

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.

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Spotswood, E.; Benjamin, M.; Stoneburner, L.; Wheeler, M. 2021. Nature inequity and higher COVID-19 case rates in less green neighbourhoods in the United States. Nature Sustainability 4 (10).

Nature inequity and higher COVID-19 case rates in less green neighbourhoods in the United StatesUrban nature—such as greenness and parks—can alleviate distress and provide space for safe recreation during the COVID-19 pandemic. However, nature is often less available in low-income populations and communities of colour—the same communities hardest hit by COVID-19. In analyses of two datasets, we quantified inequity in greenness and park proximity across all urbanized areas in the United States and linked greenness and park access to COVID-19 case rates for ZIP codes in 17 states. Areas with majority persons of colour had both higher case rates and less greenness. Furthermore, when controlling for sociodemographic variables, an increase of 0.1 in the Normalized Difference Vegetation Index was associated with a 4.1% decrease in COVID-19 incidence rates (95% confidence interval: 0.9–6.8%). Across the United States, block groups with lower-income and majority persons of colour are less green and have fewer parks. Our results demonstrate that the communities most impacted by COVID-19 also have the least nature nearby. Given that urban nature is associated with both human health and biodiversity, these results have far-reaching implications both during and beyond the pandemic.

Related data: https://www.sfei.org/data/nature-equity-covid-2021

 

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Sowers, J. M.; Salomon, M. N.; Ticci, M.; Beller, E. E.; Grossinger, R. M. 2012. Watching Our Watersheds: Santa Clara Valley Past, Google Earth KMZ files: Santa Clara Valley historical points of interest, stream courses and habitats.
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Sonoma Land Trust and partners. 2020. Sonoma Creek Baylands Strategy. Prepared by Sonoma Land Trust, San Francisco Estuary Institute, Point Blue Conservation Science, Environmental Science Associates, Ducks Unlimited, U.S. Fish and Wildlife Service.
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Sonoma Land Trust and partners. 2023. Petaluma River Baylands Strategy. Prepared by San Francisco Estuary Institute, Sonoma Land Trust, Point Blue Conservation Science, Ducks Unlimited, and Sonoma Resource Conservation District. Funded by the Wildlife Conservation Board.
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Sommers, F.; Mudrock, E.; Labenia, J.; Baldwin, D. 2016. Effects of salinity on olfactory toxicity and behavioral responses of juvenile salmonids from copper. Aquatic Toxicology 175.

Dissolved copper is one of the more pervasive and toxic constituents of stormwater runoff and is commonly found in stream, estuary, and coastal marine habitats of juvenile salmon. While stormwater runoff does not usually carry copper concentrations high enough to result in acute lethality, they are of concern because sublethal concentrations of copper exposure have been shown to both impair olfactory function and alter behavior in various species in freshwater. To compare these results to other environments that salmon are likely to encounter, experiments were conducted to evaluate the effects of salinity on the impairment of olfactory function and avoidance of copper. Copper concentrations well within the range of those found in urban watersheds, have been shown to diminish or eliminate the olfactory response to the amino acid, l-serine in freshwater using electro-olfactogram (EOG) techniques. The olfactory responses of both freshwater-phase and seawater-phase coho and seawater-phase Chinook salmon, were tested in freshwater or seawater, depending on phase, and freshwater-phase coho at an intermediate salinity of 10‰. Both 10‰ salinity and full strength seawater protected against the effects of 50μg copper/L. In addition to impairing olfactory response, copper has also been shown to alter salmon behavior by causing an avoidance response. To determine whether copper will cause avoidance behavior at different salinities, experiments were conducted using a multi-chambered experimental tank. The circular tank was divided into six segments by water currents so that copper could be contained within one segment yet fish could move freely between them. The presence of individual fish in each of the segments was counted before and after introduction of dissolved copper (<20μg/L) to one of the segments in both freshwater and seawater. To address whether use of preferred habitat is altered by the presence of copper, experiments were also conducted with a submerged structural element. The presence of sub-lethal levels of dissolved copper altered the behavior of juvenile Chinook salmon by inducing an avoidance response in both freshwater and seawater. While increased salinity is protective against loss of olfactory function from dissolved copper, avoidance could potentially affect behaviors beneficial to growth, survival and reproductive success.

Soberón, F. Sánchez; Sutton, R.; Sedlak, M.; Yee, D.; Schuhmacher, M.; Park, J. - S. 2020. Multi-box mass balance model of PFOA and PFOS in different regions of San Francisco Bay. Chemosphere 252 . SFEI Contribution No. 986.

We present a model to predict the long-term distribution and concentrations of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) in estuaries comprising multiple intercommunicated sub-embayments. To that end, a mass balance model including rate constants and time-varying water inputs was designed to calculate levels of these compounds in water and sediment for every sub-embayment. Subsequently, outflows and tidal water exchanges were used to interconnect the different regions of the estuary. To calculate plausible risks to population, outputs of the model were used as inputs in a previously designed model to simulate concentrations of PFOA and PFOS in a sport fish species (Cymatogaster aggregata). The performance of the model was evaluated by applying it to the specific case of San Francisco Bay, (California, USA), using 2009 sediment and water sampled concentrations of PFOA and PFOS in North, Central and South regions. Concentrations of these compounds in the Bay displayed exponential decreasing trends, but with different shapes depending on region, compound, and compartment assessed. Nearly stable PFOA concentrations were reached after 50 years, while PFOS needed close to 500 years to stabilize in sediment and fish. Afterwards, concentrations stabilize between 4 and 23 pg/g in sediment, between 0.02 and 44 pg/L in water, and between 7 and 104 pg/g wet weight in fish, depending on compound and region. South Bay had the greatest final concentrations of pollutants, regardless of compartment. Fish consumption is safe for most scenarios, but due to model uncertainty, limitations in monthly intake could be established for North and South Bay catches.

Smith, R.; Thompson, B. 1994. Towards an Optimal Sampling Design for the RMP. SFEI Contribution No. 6. San Francisco Estuary Institute: Richmond, CA.
Smith, R.; Riege, L. 1996. DOD Sediment Criteria Project Ambient Analysis Draft Interim Report. SFEI Contribution No. 9. San Francisco Regional Water Quality Control Board: Oakland, CA.
Slotton, D. G.; Jones, A. B. 1996. Mercury Effects, Sources, and Control Measures. SFEI Contribution No. 20. San Francisco Estuary Institute: Richmond, CA.
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Sigala, M. 2019. 2019 RMP Contaminant Concentrations in San Francisco Bay Sportfish Cruise Report. SFEI Contribution No. 968. Marine Pollution Studies Laboratory, Moss Landing Marine Laboratories: Moss Landing, CA.

This report contains information on the spring and summer field sampling efforts conducted by the Marine Pollution Studies Laboratory at Moss Landing Marine Labs (MPSL-MLML). The purpose of this field effort was to collect sportfish for an eighth season of data (in support of 1994, 1997, 2000, 2003, 2006, 2009, and 2014 surveys) in the ongoing study of Contamination in San Francisco Bay Sportfish. The work was contracted through the San Francisco Estuary Institute (SFEI) for the Regional Monitoring Program (RMP) for Water Quality. 

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Siemering, G. 2005. Aquatic Pesticides Monitoring Program Monitoring Project Final Report. SFEI Contribution No. 392. San Francisco Estuary Institute: Oakland, CA.
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Siemering, G.; David, N.; Franz, A.; Malamud-Roam, F.; Hayworth, J. 2003. Aquatic Pesticide Monitoring Program Literature Review. SFEI Contribution No. 71. San Francisco Estuary Institute: Oakland, CA.
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Siemering, G. 2004. Aquatic Pesticides Monitoring Program Phase 2 (2003) Monitoring Project Report. SFEI Contribution No. 108. San Francisco Estuary Institute: Oakland, CA.
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Siegel, S.; Callaway, J. 2002. Data Collection Protocol Sedimentation- Erosion Tables (SET's). SFEI Contribution No. 244. University of San Francisco, Wetlands and Water Resources: San Francisco, CASan Rafael, CA.
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Shimabuku, I.; Trowbridge, P.; Sun, J. 2018. Bay 2017 Bay RMP Field Sampling Report. SFEI Contribution No. 849. San Francisco Estuary Institute : Richmond, CA.
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Shimabuku, I.; Trowbridge, P.; Salop, P.; Franz, A. 2018. 2018 RMP Bivalve Retrieval Cruise Plan. SFEI Contribution No. 893. San Francisco Estuary Institute : Richmond, CA.
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Shimabuku, I.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Bivalve Deployment Cruise Plan. SFEI Contribution No. 892. San Francisco Estuary Institute: Richmond, CA.
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Shimabuku, I.; Pearce, S.; Trowbridge, P.; Franz, A.; Yee, D.; Salop, P. 2018. Field Operations Manual for the Regional Monitoring Program. SFEI Contribution No. 902. San Francisco Estuary Institute: Richmond, CA.
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Shimabuku, I.; Chen, D.; Wu, Y.; Miller, E.; Sun, J.; Sutton, R. 2022. Occurrence and risk assessment of organophosphate esters and bisphenols in San Francisco Bay, California, USA. Science of the Total Environment 813 . SFEI Contribution No. 982.

Organophosphate esters (OPEs) and bisphenols are two classes of industrial chemicals that are ubiquitously detected in environmental matrices due to high global production and widespread use, particularly in the manufacture of plastic products. In 2017, water samples collected throughout the highly urbanized San Francisco Bay were analyzed for 22 OPEs and 16 bisphenols using liquid chromatography-electrospray ionization-Q Trap-mass spectrometry. Fifteen of the 22 OPEs were detected, with highest median concentrations in the order TCPP (42 ng/L) > TPhP (9.5 ng/L) > TBOEP (7.6 ng/L) > TnBP (7.5 ng/L) > TEP (6.7 ng/L) > TDCIPP (6.2 ng/L). In contrast, only two of 16 bisphenols, BPA and BPS, were quantified, with concentrations ranging from <0.7–35 ng/L and <1–120 ng/L, respectively. BPA and a few OPEs (EHDPP and TEHP) were primarily present in the particulate phase, while BPS and all other observed OPEs were predominantly found in the dissolved phase. Pairwise correlation analysis revealed several strong, positive correlations among OPEs, and few weak, negative correlations between OPEs and BPA, suggesting differences between the two classes with respect to their sources, pathways, and/or fate in the environment. Concentrations of OPEs and bisphenols observed in this study were generally consistent with reported concentrations in other estuarine and marine settings globally. TDCIPP exceeded existing predicted no-effect concentrations (PNECs) at some sites, and six other compounds (TCrP, IDDPP, EHDPP, TPhP, TBOEP, and BPA) were observed at levels approaching individual compound PNECs (not considering mixture effects), indicating potential risks to Bay biota. These results emphasize the need to control releases of these contaminants in order to protect the ecosystem. Periodic monitoring can be used to maintain vigilance in the face of potential regrettable substitutions.

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Shimabuku, I.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Bivalve Retrieval Cruise Plan. SFEI Contribution No. 893. San Francisco Estuary Institute: Richmond, CA.
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SFEI. 2016. 2015 Annual Monitoring Report. SFEI Contribution No. 775. San Francisco Estuary Institute: Richmond, CA.
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SFEI. 2017. The Pulse of the Bay: The 25th Anniversary of the RMP. SFEI Contribution No. 841. San Francisco Estuary Institute: Richmond, CA.
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SFEI. 2021. Ecotone levees and wildlife connectivity: A technical update to the Adaptation Atlas. SFEI Contribution No. 1037. San Francisco Estuary Institute: Richmond, CA.
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SFEI. 2003. 2003 Pulse of the Estuary: Monitoring & Managing Contamination in the San Francisco Estuary. SFEI Contribution No. 74. San Francisco Estuary Institute : Oakland, CA.
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SFEI. 2004. 2004 Pulse of the Estuary: Monitoring & Managing Contamination in the San Francisco Estuary. SFEI Contribution No. 401. San Francisco Estuary Institute : Oakland, CA.
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SFEI. 2005. 2005 Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary. SFEI Contribution No. 78. San Francisco Estuary Institute: Oakland, CA. p 84.
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SFEI. 2006. The 2004 to 2005 RMP Annual Monitoring Results. Regional Monitoring Program for Water Quality in the San Francisco Estuary (RMP). SFEI Contribution No. 519. San Francisco Estuary Institute. p 220.
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SFEI. 2016. 2016 RMP Sturgeon Derby Study Sampling & Analysis Plan. San Francisco Estuary Institute : Richmond, CA.
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SFEI. 2019. The Pulse of the Bay 2019: Pollutant Pathways. SFEI Contribution No. 954. San Francisco Estuary Institute: Richmond, CA.
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SFEI. 2015. 2015 Sturgeon Muscle Plug Study Sampling & Analysis Plan. San Francisco Estuary Institute : Richmond, CA.
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SFEI. 2012. 2011 Pulse of the Estuary: Pollutant Effects on Aquatic Life. SFEI Contribution No. 660. San Francisco Estuary Institute : Richmond, CA. p 104.
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SFEI. 2015. 2015 Pulse of the Bay: The State of Bay Water Quality - 2015 and 2065. SFEI Contribution No. 759. San Francisco Estuary Institute: Richmond, CA.
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SFEI. 2013. 2013 Pulse of the Bay: Contaminants of Emerging Concern. San Francisco Estuary Institute : Richmond, CA. p 102.
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SFEI. 2009. 2009 Pulse of the Estuary: Bay Sediments - Past a Tipping Point. SFEI Contribution No. 583. San Francisco Estuary Institute: Oakland, CA. p 92.
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SFEI. 2008. 2008 Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary. SFEI Contribution No. 559. San Francisco Estuary Institute: Oakland, CA.
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SFEI. 2007. 2007 Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary. SFEI Contribution No. 532. San Francisco Estuary Institute: Oakland, CA. p 88.
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SFEI; ESA,; Baye, P. 2023. Growing Resilience: Recommendations for Dune Management at North Ocean Beach. SFEI Contribution No. 1155. San Francisco Estuary Institute: Richmond, CA.
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SFEI. 2001. 1993 - 1999 Pulse of the Estuary: Monitoring and Managing Contamination in the San Francisco Estuary. SFEI Contribution No. 101. San Francisco Estuary Institute: Oakland, CA.
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SFEI; CDHS,. 2001. The San Francisco Bay Seafood Consumption Study Report. SFEI Contribution No. 369. San Francisco Estuary Institute: Oakland, CA.
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SFEI. 2023. Landscape Scenario Planning Tool User Guide v2.2.0. San Francisco Estuary Institute: Richmond, Calif.
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SFEI; Safran, S. M. 2014. Natural Flow Hydrodynamic Modeling Technology Support Phase 1 Technical Memorandum.

This technical memorandum summarizes the work to date carried out by the San Francisco Estuary Institute (SFEI) to generate a bathymetric-topographic digital elevation model (DEM) of the historical Sacramento-San Joaquin Delta (representative of early 1800s conditions). The historical DEM described in this document is an interim/draft product completed for Phase I of the Bay-Delta Natural Flow Hydrodynamics and Salinity Transport modeling project. It is expected that the product and methods described here will be refined during a second phase of the project.

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SFEI. 2010. 2010 Pulse of the Estuary: Linking the Watersheds and the Bay. SFEI Contribution No. 618. San Francisco Estuary Institute : Oakland, CA. p 96.
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2020. 2019-20 RMP North Bay Selenium Study. 2019-20 RMP North Bay Selenium Study. SFEI Contribution No. 1051. San Francisco Estuary Institute: Richmond, CA.

This report details activities associated with the Regional Monitoring Program North Bay Selenium Study. The  study was designed to monitor two sites for selenium (Se) in clam tissues and water six times between June  2019 and February 2020. This report outlines the sampling activities, personnel, and site locations monitored for  the project. 

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2021. 2020-21 RMP North Bay Selenium Study. SFEI Contribution No. 1052. San Francisco Estuary Institute: Richmond, CA.

This report details activities associated with the Regional Monitoring Program North Bay Selenium Study in 2020 and 2021. The study was designed to monitor two sites for selenium (Se) in water and clam tissue six times annually between June and February. Due to the COVID pandemic, however, four sample collection events were completed. This report outlines the sampling activities, personnel, and site locations monitored for the project.

 

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Senn, D. B.; Novick, E. 2014. Suisun Bay Ammonium Synthesis. SFEI Contribution No. 706. San Francisco Estuary Institute: Richmond, CA. p 191.
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Senn, D.; Trowbridge, P. 2016. San Francisco Bay Nutrient Management Strategy Observation Program. SFEI Contribution No. 877. San Francisco Estuary Institute: Richmond, CA.
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Senn, D.; Novick, E. 2016. Nutrient Management Strategy Science Plan Report. SFEI Contribution No. 878. San Francisco Estuary Institute: Richmond, CA.
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Sedlak, M.; Sutton, R.; Miller, L.; Lin, D. 2019. Microplastic Strategy Update. SFEI Contribution No. 951. San Francisco Estuary Institute: Richmond, CA.

Based on the detection of microplastics in San Francisco Bay surface water and Bay Area wastewater effluent in 2015, the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) convened a Microplastic Workgroup (MPWG) in 2016 to discuss the issue, identify management information needs and management questions (MQs), and prioritize studies to provide information to answer these management questions. The MPWG meets annually to review on-going microplastic projects and to conduct strategic long-term planning in response to new information in this rapidly evolving field.


In this nascent field with new findings published almost daily, the Strategy is designed to be a living document that is updated periodically. This Strategy Update includes a short summary of recent findings from the San Francisco Bay Microplastics Project - a major monitoring effort in the Bay - and an updated multi-year plan based on the newly acquired knowledge and current management needs.

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Sedlak, M.; Greig, D. 2012. Perfluoroalkyl compounds (PFCs) in wildlife from an urban estuary. Journal of Environmental Monitoring 14, 146-154.
Sedlak, M.; Sutton, R.; Wong, A.; Lin, D. 2018. Per and Polyfluoroalkyl Substances (PFAS) in San Francisco Bay: Synthesis and Strategy. SFEI Contribution No. 867. San Francisco Estuary Institute : Richmond, CA.
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RMP Lead Scientist. 2015. 2015 RMP Artesian Slough Sampling & Analysis Plan. San Francisco Estuary Institute: Richmond, CA.
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