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Bruland, K. W.; Anderson, L. A. 1991. Biogeochemistry of arsenic in natural waters: The importance of methylated species. Environmental Science & Technology 25, 420-427 . SFEI Contribution No. 160.
Buchanan, P. A.; Schoellhamer, D. H. 1996. 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.
Buchanan, P. A.; Ganju, N. K. 2002. 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.
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Buzby, N.; Lin, D.; Sutton, R. 2020. Neonicotinoids and Their Degradates in San Francisco Bay Water. SFEI Contribution No. 1002. San Francisco Estuary Institute: Richmond, CA.

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.

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Buzby, N.; Yee, D.; Salop, P.; Foley, M. 2020. 2019 RMP North Bay Selenium Monitoring Sampling and Analysis Plan. SFEI Contribution No. 969. San Francisco Estuary Institute: Richmond, CA.

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.

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Buzby, N.; Yee, D.; Foley, M.; David, J.; Sigala, M.; Bonnema, A. 2020. 2019 Sport Fish Monitoring Sampling and Analysis Plan. SFEI Contribution No. 970. San Francisco Estuary Institute: Richmond, CA.

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).

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Carlton, J. T. 1996. The Invaded estuary (abstract). In In: Third Biennial State of the Estuary Conf.. In: Third Biennial State of the Estuary Conf. San Francisco, CA.
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Chang, D.; Richardot, W.; Miller, E.; Dodder, N.; Sedlak, M.; Hoh, E.; Sutton, R. 2021. Framework for nontargeted investigation of contaminants released by wildfires into stormwater runoff: Case study in the northern San Francisco Bay area. Integrated Environmental Assessment and Management . SFEI Contribution No. 1044.

Wildfires can be extremely destructive to communities and ecosystems. However, the full scope of the ecological damage is often hard to assess, in part due to limited information on the types of chemicals introduced to affected landscapes and waterways. The objective of this study was to establish a sampling, analytical, and interpretive framework to effectively identify and monitor contaminants of emerging concern in environmental water samples impacted by wildfire runoff. A nontargeted analysis consisting of comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC × GC/TOF-MS) was conducted on stormwater samples from watersheds in the City of Santa Rosa and Sonoma and Napa Counties, USA, after the three most destructive fires during the October 2017 Northern California firestorm. Chemicals potentially related to wildfires were selected from the thousands of chromatographic features detected through a screening method that compared samples from fire-impacted sites versus unburned reference sites. This screening led to high confidence identifications of 76 potentially fire-related compounds. Authentic standards were available for 48 of these analytes, and 46 were confirmed by matching mass spectra and GC × GC retention times. Of these 46 compounds, 37 had known commercial and industrial uses as intermediates or ingredients in plastics, personal care products, pesticides, and as food additives. Nine compounds had no known uses or sources and may be oxidation products resulting from burning of natural or anthropogenic materials. Preliminary examination of potential toxicity associated with the 46 compounds, conducted via online databases and literature review, indicated limited data availability. Regional comparison suggested that more structural damage may yield a greater number of unique, potentially wildfire-related compounds. We recommend further study of post-wildfire runoff using the framework described here, which includes hypothesis-driven site selection and nontargeted analysis, to uncover potentially significant stormwater contaminants not routinely monitored after wildfires and inform risk assessment. 

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Clark, S.; Bailey, H. C.; Davis, J. A. 1995. The Effects of Toxic Contaminants in Waters of the San Francisco Bay and Delta. SFEI Contribution No. 184. Prepared for Bay/Delta Oversight Council: Sacramento, CA. p 125 pp.
Cloern, J. E.; Barnard, P. L.; Beller, E. E.; Callaway, J.; Grenier, J. Letitia; Grossinger, R. M.; Whipple, A.; Mooney, H.; Zavaleta, E. 2016. Estuaries: Life on the edge. In Ecosystems of California. Ecosystems of California. University of California Press: Berkeley, CA. pp 359-388.
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Cloern, J. E.; Safran, S. M.; Vaughn, L. Smith; Robinson, A.; Whipple, A.; Boyer, K. E.; Drexler, J. Z.; Naiman, R. J.; Pinckney, J. L.; Howe, E. R.; et al. 2021. On the human appropriation of wetland primary production. Science of the Total Environment 785.

Humans are changing the Earth's surface at an accelerating pace, with significant consequences for ecosystems and their biodiversity. Landscape transformation has far-reaching implications including reduced net primary production (NPP) available to support ecosystems, reduced energy supplies to consumers, and disruption of ecosystem services such as carbon storage. Anthropogenic activities have reduced global NPP available to terrestrial ecosystems by nearly 25%, but the loss of NPP from wetland ecosystems is unknown. We used a simple approach to estimate aquatic NPP from measured habitat areas and habitat-specific areal productivity in the largest wetland complex on the USA west coast, comparing historical and modern landscapes and a scenario of wetland restoration. Results show that a 77% loss of wetland habitats (primarily marshes) has reduced ecosystem NPP by 94%, C (energy) flow to herbivores by 89%, and detritus production by 94%. Our results also show that attainment of habitat restoration goals could recover 12% of lost NPP and measurably increase carbon flow to consumers, including at-risk species and their food resources. This case study illustrates how a simple approach for quantifying the loss of NPP from measured habitat losses can guide wetland conservation plans by establishing historical baselines, projecting functional outcomes of different restoration scenarios, and establishing performance metrics to gauge success.

Cloern, J. E.; Robinson, A.; Richey, A.; Grenier, J. Letitia; Grossinger, R. M.; Boyer, K. E.; Burau, J.; Canuel, E.; DeGeorge, J. F.; Drexler, J. Z.; et al. 2016. Primary Production in the Delta: Then and Now. San Francisco Estuary and Watershed Science 14 (3).

To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it is unclear whether this was always the case. Recent analyses from the Historical Ecology Team and Delta Landscapes Project provide quantitative comparisons of the areal extent of 14 habitat types in the modern Delta versus the historical Delta (pre-1850). Here we describe an approach for using these metrics of land use change to: (1) produce the first quantitative estimates of how Delta primary production and the relative contributions from five different producer groups have been altered by large-scale drainage and conversion to agriculture; (2) convert these production estimates into a common currency so the contributions of each producer group reflect their food quality and efficiency of transfer to consumers; and (3) use simple models to discover how tidal exchange between marshes and open water influences primary production and its consumption. Application of this approach could inform Delta management in two ways. First, it would provide a quantitative estimate of how large-scale conversion to agriculture has altered the Delta's capacity to produce food for native biota. Second, it would provide restoration practitioners with a new approach—based on ecosystem function—to evaluate the success of restoration projects and gauge the trajectory of ecological recovery in the Delta region.

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Cloern, J. E.; Cole, B. E.; Jassby, A. D. 1997. The design of sampling transects for characterizing water quality in estuaries. Estuarine, Coastal and Shelf Science 45, 285-302 . SFEI Contribution No. 23.
Cohen, A. N. 2003. Introduction to the San Francisco Estuary. San Francisco Estuary Institute, Save the Bay and San Francisco Estuary Project: Oakland,CA.
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Cohen, A. N. 1998. Biological invasions in the San Francisco Estuary. In Marine and Aquatic Nonindigenous Species in California: An Assessment of Current Status and Research Needs. Olin, P. G., Cassell, J. L., Eds.. Marine and Aquatic Nonindigenous Species in California: An Assessment of Current Status and Research Needs. California Sea Grant College System, University of California: La Jolla, CA. pp 7-8.
Cohen, A. N.; Schaeffer, K.; McGourty, K.; Cosentino-Manning, N.; De La Cruz, S. E. Wainwri; Elliot, M.; Allen, S. 2007. Introduction for Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. In Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. NOAA National Marine Fisheries Service. p 35.
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Cohen, A. N. 2002. Dispersal Ecology. Blackwell Publishing: Oxford.
Cohen, A. N. 1999. Breifing Paper on a Monitoring Plan for Nonindigenous Organisms in the San Francisco Bay/Delta Estuary. A report for CALFED and the California Urban Water Agencies. San Francisco Estuary Institute. p Richmond CA.
Cohen, A. N. 1998. Monitoring for Non-indigenous Organisms. SFEI Contribution No. 385. San Francisco Estuary Institute: Oakland, CA.
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Cohen, A. N. 1996. Biological invasions of the San Francisco Bay and Delta. Summary of comments. In U. S. Fish and Wildlife Service Directorate Meeting. U. S. Fish and Wildlife Service Directorate Meeting. Ogunquit ME, June 12, 1996.
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Cohen, A. N. 1995. Place Invaders. Energy and Resources News 4, 1-3.
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Cohen, A. N. 2003. On Mitten Crabs and Lung Flukes. In IEP Newsletter. IEP Newsletter. Vol. 16, pp 48-51.
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Cohen, A. N. 1996. Environmental Review and Mitigation of a Water Supply Project in California. A report for the Japanese Ministry of Construction, Tokyo.
Cohen, A. N.; Gollasch, S.; Galil, B. S. 2006. Bridging Divides: Maritime Canals as Invasion Corridors. Monographiae Biologicae 83. Kluwer Academic Publishing: Dordrecht, The Netherlands.
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Cohen, A. N. 2000. "Case studies" on exotic species transported with oyster and marine baitworm shipments. In Toolkit on Best Practices for Prevention and Management. Toolkit on Best Practices for Prevention and Management. UN Global Invasive Species Programme.
Cohen, A. N.; Weinstein, A.; Carlton, J. T. 1999. Aquatic bioinvasions in the San Francisco Estuary. Berkeley Society for Conservation Biology Annual Meeting.
Cohen, A. N. 2004. An Exotic Species Detection Program for Puget Sound. SFEI Contribution No. 380. San Francisco Estuary Institute: Oakland.
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Cohen, A. N. 1994. Storming the Bay. Terrain 24, 4,7.
Cohen, A. N. 2004. An Exotic Species Detection Program for the Lower Columbia River Estuary. SFEI Contribution No. 381. San Francisco Estuary Institute: Oakland.
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Cohen, A. N. 2004. Invasions in the sea. SFEI Contribution No. 312. Vol. 22, pp 37-41.
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Cohen, A. N. 2001. Impacts from the Asian clam Potamocorbula amurensis. In National Management Plan. National Management Plan. National Invasive Species Council: Washington DC.
Cohen, A. N.; McGann, M.; Sloan, D. 1996. Documenting the intorduction of estuarine foraminifers: a San Francisco Bay Study. Ann. Mtg., Geological Society of America, Denver, CO, Oct. 1996 (abstract).
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Cohen, A. N. 2005. A review of Zebra Mussels' Environmental Requirements. Resources, C. A. Department, Ed.. SFEI Contribution No. 420. San Francisco Estuary Institute: Sacramento, CA.
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Cohen, A. N.; Zabin, C. J. 2009. Oyster shells as vectors for exotic species. Journal of Shellfish Research 28 (1), 163-167 . SFEI Contribution No. 709.
Cohen, A. N. 1996. Stopping ballast water invaders. Native Species Network 1, 1.
Cohen, A. N. 1988. Recalculating the Tule Factor. A report for The Bay Institute of San Francisco: Sausalito, CA.
Cohen, A. N. 1998. Biological invasions in the San Francisco Estuary. Olin, P. G., Cassell, J. L., Eds.. California Sea Grant College System, University of California, La Jolla CA. pp 7-8.
Cohen, A. N. 1996. Gateway to the Inland Coast: The Story of the Carquinez Strait. California State Lands Commission: Sacramento CA.
Cohen, A. N. 1988. Subsides in the Central Utah Project: Whose CUP is Running over?. Report for the Natural Resources Defense Council: San Francisco, CA.
Cohen, A. N. 2002. The highly invaded ecosystem of San Francisco Bay. Cawthron Institute, Nelson, New Zealand.
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Cohen, A. N. 1997. Green crabs disrupting fisheries worldwide. p 7 . SFEI Contribution No. 199.
Cohen, A. N. 2001. Invasions in the San Francisco Estuary. In National Management Plan. National Management Plan. National Invasive Species Council: Washington DC.
Cohen, A. N. 1989. Threatened in the nest. Pacific Discovery (Calif. Acad. Sci.) 42, 6-13.
Cohen, A. N.; Schaeffer, K.; Cosentino-Manning, N. 2007. Shellfish Beds in Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. In Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. NOAA National Marine Fisheries Service: Santa Rosa, CA. pp 50-55.
Cohen, A. N. 2001. Success factors in human-dispersed organisms. Dispersal, Annual Symposium of the British Ecological Society, Page 8.
Cohen, A. N. 2005. Overview of 2004/05 Rapid Assessment Shore and Channel Surveys for Exotic Species in San Francisco Bay. SFEI Contribution No. 452. San Francisco Estuary Institute: Oakland, CA.
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Cohen, A. N. 2001. Case study: hitchhikers in or on marine baitworms and their packing material. In Toolkit for Managing Invasive Species. Toolkit for Managing Invasive Species. United Nations Global Invasive Species Program.
Cohen, A. N. 2001. Case Study 2.5: Petition for U.S. federal action on the green seaweed Caulerpa taxifolia. Wittenberg, R., Cock, M. J. W., Eds.. United Nations Global Invasive Species Program. CAB International, Wallingford, Oxon, UK. p 31.
Cohen, A. N. 2002. Exotic organisms in southern California Bays and Harbors. Marine Bioinvasions Conference . SFEI Contribution No. 481.