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Cohen, A. N. 2008. Zebra & quagga mussel invasions in the western US. International Association of Great Lakes Research (IAGLR).
Cohen, A. N.; Weinstein, A. 2001. Zebra Mussel's Calcium Threshold and Implications for its Potential Distribution in North America. SFEI Contribution No. 356. San Francisco Estuary Institute: Richmond CA.
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Cohen, A. N.; Nordby, J. C. 2005. Year-end Report to the National Science Foundation. SFEI Contribution No. 456. San Francisco Estuary Institute: Oakland, CA.
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Williams, M.; Cayce, K. 2009. WRMP Factsheet — Wetland and Riparian Base Map. San Francisco Estuary Institute: Oakland, Ca.
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Grosso, C.; Lowe, S.; Pearce, S.; O'Connor, K.; Teunis, L.; Stein, E. D.; Siu, J.; Scianni, M. 2023. WRAMP Training and Outreach Plan. SFEI Contribution No. 1136. p 39.

The goal of this Training and Outreach Plan is to increase the overall awareness and use  of the WRAMP datasets and tools in support of wetland resource planning,  management, and project performance tracking in California. Specifically, a near-term  goal is to develop modular training sessions that can be linked together in different  ways to customize how the datasets, monitoring methods, and online tools might be  used for different purposes. 

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King, A. 2019. Wind Over San Francisco Bay and the Sacramento-San Joaquin River Delta: Forcing for Hydrodynamic Models. SFEI Contribution No. 937. San Francisco Estuary Institute: Richmond, CA.
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Panlasigui, S.; Pearce, S.; Hegstad, R.; Quinn, M.; Whipple, A. 2020. Wildlife Habitat and Water Quality Enhancement Opportunities at Castlewood Country Club. SFEI Contribution No. 1003. San Francisco Estuary Institute: Richmond, CA.

Meeting human and ecological needs within San Francisco Bay’s watersheds is increasingly challenged by flooding, water quality degradation, and habitat loss, exacerbated by intensified urbanization and climate change. Addressing these challenges requires implementing multi-benefit strategies through new partnerships and increased coordination across the region’s diverse landscapes. Actions to improve water quality and enhance habitat for biodiversity in our highly developed and managed landscapes can help the region as a whole to build resilience to withstand current pressures and future change. The EPA-funded project, “Preparing for the Storm,” aims to address these challenges at the site- and landscape-scale through studies and implementation projects in the Livermore-Amador Valley. As part of this larger project, this technical report presents a synthesis of water quality and habitat improvement opportunities for a golf course of Castlewood Country Club.

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Iknayan, K.; Wheeler, M.; Safran, S. M.; Young, J. S.; Spotswood, E. 2021. What makes urban parks good for California quail? Evaluating park suitability, species persistence, and the potential for reintroduction into a large urban national park. Journal of Applied Ecology.

  1. Preserving and restoring wildlife in urban areas benefits both urban ecosystems and the well-being of urban residents. While urban wildlife conservation is a rapidly developing field, the majority of conservation research has been performed in wildland areas. Understanding the applicability of wildland science to urban populations and the relative importance of factors limiting species persistence are of critical importance to identifying prescriptive management strategies for restoring wildlife to urban parks.
  2. We evaluated how habitat fragmentation, habitat quality and mortality threats influence species occupancy and persistence in urban parks. We chose California quail Callipepla californica as a representative species with potential to respond to urban conservation. We used publicly available eBird data to construct occupancy models of quail in urban parks across their native range, and present an application using focal parks interested in exploring quail reintroduction.
  3. Urban parks had a 0.23 ± 0.02 probability of quail occupancy, with greater occupancy in larger parks that were less isolated from potential source populations, had higher shrub cover and had lower impervious cover. Less isolated parks had higher colonization rates, while larger parks had lower extinction rates. These results align with findings across urban ecology showing greater biodiversity in larger and more highly connected habitat patches.
  4. A case study highlighted that interventions to increase effective park size and improve connectivity would be most influential for two highly urban focal parks, while changes to internal land cover would have a relatively small impact. Low joint extinction probability in the parks (0.010 ± 0.013) indicated reintroduced populations could persist for some time.
  5. Synthesis and applications. We show how eBird data can be harnessed to evaluate the responsiveness of wildlife to urban parks of variable size, connectivity and habitat quality, highlighting what management actions are most needed. Using California quail as an example, we found park size, park isolation and presence of coyotes are all important drivers of whether quail can colonize and persist in parks. Our results suggest reintroducing quail to parks could be successful provided parks are large enough to support quail, and management actions are taken to enhance regional connectivity or periodic assisted colonization is used to supplement local populations.
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Stein, E. D.; Cayce, K.; Salomon, M. N.; Bram, D. L.; De Mello, D.; Grossinger, R. M.; Dark, S. 2014. Wetlands of the Southern California Coast: Historical Extent and Change Over Time. SFEI Contribution No. 720. Southern California Coastal watershed Research Project (SCCWRP), San Francisco Estuary Institute (SFEI), CSU Northridge Center for Geographical Studies: Costa Mesa, Richmond, Northridge.
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Lowe, S. 2019. West Valley Watershed Assessment 2018: Baseline Ecological Condition Assessment of Southwest San Francisco Bay Creeks in Santa Clara County; Calabazas, San Tomas Aquino, Saratoga, Sunnyvale East and West. Salomon, M., Pearce, S., Josh Collins, Titus, D., Eds.. SFEI Contribution No. 944. San Francisco Estuary Institute: Richmond.

This report describes baseline information about the amount and distribution of aquatic resources, and evaluates the overall ecological conditions of streams using the California Rapid Assessment Method (CRAM), for the West Valley watershed in Santa Clara County; consisting of Sunnyvale East and West Channels, Calabazas Creek, San Tomas Aquino and Saratoga creeks, and many smaller tributaries.

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Cohen, A. N. 1992. Weeding the Garden. Atlantic Monthly 270, 76-86.
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Cohen, A. N. 2000. Weeding the garden. In Preserving Wildlife: An International Perspective. Michael, M. A., Ed.. Preserving Wildlife: An International Perspective. Prometheus Books: Amherst NY. pp 84-92.
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Kleckner, A.; Sutton, R.; Yee, D.; Gilbreath, A.; Trinh, M. 2023. Water Year 2023 RMP Near-Field Water Sampling and Analysis Plan. SFEI Contribution No. 1142. San Francisco Estuary Institute: Richmond, CA.

This report details plans associated with the pilot near-field water sampling for the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). The RMP recently reviewed the Status & Trends (S&T) Program and added a pilot effort to quantify contaminants of emerging concern (CECs) in Bay water in areas near (“near-field” of) expected loading pathways during or shortly after storm events and during the dry season. For the first year of the pilot (Water Year 2022), the near-field design included three targeted, near-field stations and four ambient Bay stations. Subsequent years added a fourth near-field station. Samples will be collected at these stations during or shortly after two storm events, and once in the dry season. The analytes that are being measured include bisphenols, organophosphate esters (OPEs), PFAS, and a suite of stormwater CECs.

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Hoenicke, R.; Hayworth, J. 2005. A Watershed Monitoring Strategy for Napa County. SFEI Contribution No. 428. San Francisco Estuary Institute: Napa,. p 34.
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Hoenicke, R.; Bleier, C. 2007. Watershed Management and Land Use. CCMP Implementation Committee.
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Lowe, S.; Pearce, S.; Collins, J. 2017. A Watershed Approach to Restoration and Mitigation Planning, Monitoring, and Assessment Based on the Wetland and Riparian Area Monitoring Plan (WRAMP): Addendum to the Upper Pajaro River Watershed Assessment 2015. SFEI Contribution No. 818. San Francisco Estuary Institute: Richmond. CA. p 30.

This report demonstrates a possible watershed-based approach to evaluating mitigation sites using the California Rapid Assessment Method (CRAM). The Santa Clara Valley Water District (Valley Water) is leading the Llagas Creek Flood Control Project in the upper Pajaro River watershed, Santa Clara County, CA. Mitigation for the Project involves enhancing riverine wetlands on-site (within the flood control channel) and restoring riverine wetlands and enhancing depressional wetlands at Lake Silveira, in the Llagas Creek watershed. Valley Water is incorporating CRAM into its planning and assessment of mitigation efforts and Valley Water's Priority D.5 Project's Pajaro River Watershed ambient stream condition survey (2015) provided the watershed context for evaluating project conditions against the general ecological conditions of streams within the watershed - employing CRAM. This WRAMP demonstration compared pre-project ecological condition assessments (employing CRAM) from the project's impact and mitigation sites to ambient watershed conditions and estimated the amount of ecological lift expected in the future as a result of the planned mitigation and restoration efforts.

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Cohen, A. N.; Gottleib, R. 1991. Water and GrowthL Restructuring the Relationship. Public Officials for Water and Environmental Reform: Sacramento, CA.
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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Werbowski, L. M.; Gilbreath, A.; Munno, K.; Zhu, X.; Grbic, J.; Wu, T.; Sutton, R.; Sedlak, M.; Deshpande, A. D.; Rochman, C. M. 2021. Urban Stormwater Runoff: A Major Pathway for Anthropogenic Particles, Black Rubbery Fragments, and Other Types of Microplastics to Urban Receiving Waters. Environmental Science and Technology Water . SFEI Contribution No. 1040.

Stormwater runoff has been suggested to be a significant pathway of microplastics to aquatic habitats; yet, few studies have quantified microplastics in stormwater. Here, we quantify and characterize urban stormwater runoff from 12 watersheds surrounding San Francisco Bay for anthropogenic debris, including microplastics. Depth-integrated samples were collected during wet weather events. All stormwater runoff contained anthropogenic microparticles, including microplastics, with concentrations ranging from 1.1 to 24.6 particles/L. These concentrations are much higher than those in wastewater treatment plant effluent, suggesting urban stormwater runoff is a major source of anthropogenic debris, including microplastics, to aquatic habitats. Fibers and black rubbery fragments (potentially tire and road wear particles) were the most frequently occurring morphologies, comprising ∼85% of all particles across all samples. This suggests that mitigation strategies for stormwater should be prioritized. As a case study, we sampled stormwater from the inlet and outlet of a rain garden during three storm events to measure how effectively rain gardens capture microplastics and prevent it from contaminating aquatic ecosystems. We found that the rain garden successfully removed 96% of anthropogenic debris on average and 100% of black rubbery fragments, suggesting rain gardens should be further explored as a mitigation strategy for microplastic pollution.

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Wheeler, M.; Stoneburner, L.; Spotswood, E.; Grossinger, R.; Barar, D.; Randisi, C. 2022. An Urban Forest Master Plan for East Palo Alto. SFEI Contribution No. 1071. San Francisco Estuary Institute: Richmond, CA.
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Hagerty, S.; Spotswood, E.; McKnight, K.; Grossinger, R. M. 2019. Urban Ecological Planning Guide for Santa Clara Valley. SFEI Contribution No. 941. San Francisco Estuary Institute: Richmond, CA.

This document provides some of the scientific foundation needed to guide planning for urban biodiversity in the Santa Clara Valley region, grounded in an understanding of landscape history, urban ecology and local setting. It can be used to envision the ecological potential for individual urban greening projects, and to guide their siting, design and implementation. It also can be used to guide coordination of projects across the landscape, with the cooperation of a group of stakeholders (such as multiple agencies, cities and counties). Users of this report may include a wide range of entities, such as local nonprofits, public agencies, city planners, and applicants to the Open Space Authority’s Urban Open Space Grant Program.
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Bruland, K. W.; Phinney, J. T. 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.
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Lowe, S.; Salomon, M.; Pearce, S.; Josh Collins; Titus, D. 2016. Upper Pajaro River Watershed Condition Assessment 2015. Technical memorandum prepared for the Santa Clara Valley Water District - Priority D5 Project. SFEI Contribution No. 810. San Francisco Estuary Institute: Richmond, CA. p 60.

In 2015 The Santa Clara Valley Water District and it's consultants conducted a watershed wide survey to characterize the distribution and abundance of the aquatic resources within the upper Pajaro River watershed wtihin Santa Clara County, CA based on available GIS datasets, and to assess the overall ecological condition of streams within the watershed based on a statistically based random sample design and the California Rapid Assessment Method for streams (CRAM).

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Sutton, R.; Lin, D.; Sedlak, M.; Box, C.; Gilbreath, A.; Holleman, R.; Miller, L.; Wong, A.; Munno, K.; Zhu, X.; et al. 2019. Understanding Microplastic Levels, Pathways, and Transport in the San Francisco Bay Region. SFEI Contribution No. 950. San Francisco Estuary Institute: Richmond, CA.

Microplastics (particles less than 5 mm) are ubiquitous and persistent pollutants in the ocean and a pervasive and preventable threat to the health of marine ecosystems. Microplastics come in a wide variety of shapes, sizes, and plastic types, each with unique physical and chemical properties and toxicological impacts. Understanding the magnitude of the microplastics problem and determining the highest priorities for mitigation require accurate measures of microplastic occurrence in the environment and identification of likely sources.

To develop critical baseline data and inform solutions, the San Francisco Estuary Institute and the 5 Gyres Institute have completed the first comprehensive regional study of microplastic pollution in a major estuary. This project supported multiple scientific components to develop improved knowledge about and characterization of microparticles and microplastics in San Francisco Bay and adjacent National Marine Sanctuaries, with the following objectives:

  1. Contribute to the development and standardization of sample collection and analysis methodology for microplastic transportation research.
  2. Determine a baseline for future monitoring of microplastics in San Francisco Bay surface water, sediment, and fish, and in ocean waters outside the Golden Gate.
  3. Characterize pathways by which microplastics enter the Bay, including urban stormwater and treated wastewater effluent.
  4. Investigate the contribution of Bay microplastics to the adjacent National Marine Sanctuaries through computer simulations.
  5. Communicate findings to regional stakeholders and the general public through meetings and educational materials.
  6. Facilitate evaluation of policy options for San Francisco Bay, with recommendations on source reduction.

This document presents the findings of this three-year project. A companion document, “San Francisco Bay Microplastics Project: Science-Supported Solutions and Policy Recommendations,” has been developed by 5 Gyres using the findings of this study (Box and Cummins, 2019).

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