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Lowe, J.; Plane, E.; Gonzalez, J.; Salomon, M. 2021. Guidance for Restoration of Natural and Nature-Based Features in the Wetland-Upland Transition Zone. San Francisco Estuary Institute, California State Coastal Conservancy: Richmond, CA.
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Jahn, A. 2018. Gut Contents Analysis of Four Fish Species Collected in the San Leandro Bay RMP PCB Study in August 2016. SFEI Contribution No. 900. San Francisco Estuary Institute: Richmond, CA.
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Cohen, A. N. 1997. Have claw, will travel. Aquatic Nuisance Species Digest 2, 1, 16-17. . SFEI Contribution No. 200.
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Cohen, A. N. 1994. The hidden costs of California's water. In Life on the Edge: A Resource Guide to California's Endangered Wildlife. Life on the Edge: A Resource Guide to California's Endangered Wildlife. Biosystems Books: Santa Cruz, CA. pp 288-302.
Cohen, A. N. 2002. The highly invaded ecosystem of San Francisco Bay. Cawthron Institute, Nelson, New Zealand.
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Baumgarten, S.; Grossinger, R. M.; Beller, E. E.; Trowbridge, W.; Askevold, R. A. 2017. 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.

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.

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Program, H. Ecology. 2012. Historical Ecology of the McCormack-Williamson Tract: A Landscape Framework for Restoration. SFEI Contribution No. 674. Aquatic Science Center / San Francisco Estuary: Richmond, CA.
Safran, S. M.; Baumgarten, S. A.; Beller, E. E.; Bram, D. L.; Crooks, J. A.; Dark, S. J.; Grossinger, R. M.; Longcore, T. R.; Lorda, J.; Stein, E. D. 2018. The Historical Ecology of the Tijuana Estuary & River Valley (Restore America's Estuaries 2018 Conference Presentation).

This talk was given at the 2018 Restore America's Estuary Conference in Long Beach, CA as part of a special session titled "Restoration Perspectives from the Tijuana River National Estuarine Research Reserve." It is based on information from the Tijuana River Valley Historical Ecology Investigation, a report published in 2017.

Though many areas of the binational Tijuana River watershed remain relatively undeveloped, land and water use changes over the past 200 years have resulted in significant ecological impacts, particularly in the more urbanized areas of the lower watershed. Drawing upon a diverse set of historical data, we reconstructed the ecological and hydrogeomorphic conditions of the lower Tijuana River valley prior to major Euro-American modification (ca. 1850) and documented major changes in habitat distribution and physical processes over this time. The river corridor, which was historically dominated by riparian scrub, today instead supports dense stands of riparian forest. The valley bottom surrounding the river corridor, which historically supported extensive seasonal wetlands, has largely been converted to drier habitat types and agricultural uses. The estuary, which historically supported large expanses of salt marsh and mudflat as well as seasonally dry salt flats, has retained much of its former extent and character, but has been altered by increased sediment input and other factors. The new information about the historical landscape presented here is relevant to a number of issues scientists and managers are dealing with today, including the conservation of endangered species, the fate of the valley’s riparian habitats after the recent invasion of invasive shot-hole borer beetles, and the effects on groundwater levels on native plant communities. We will also draw from other historical ecology studies conducted in Southern California to illustrate how the information about the past has been utilized to improve the functioning and resilience of nearby coastal ecosystems.

Presentation recording: available here.

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Beller, E. E.; Grossinger, R. M.; Whipple, A. 2009. Historical Ecology Reconnaissance for the Lower Salinas River. SFEI Contribution No. 581. San Francisco Estuary Institute: Richmond. p 32.
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2005. Historical Landscape Analysis (full title to come from Robin). SFEI Contribution No. 396. San Francisco Estuary Institute.
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Zhu, X.; Munno, K.; Grbic, J.; Werbowski, L. M.; Bikker, J.; Ho, A.; Guo, E.; Sedlak, M.; Sutton, R.; Box, C.; et al. 2021. Holistic Assessment of Microplastics and Other Anthropogenic Microdebris in an Urban Bay Sheds Light on Their Sources and Fate. Environmental Science and Technology Water . SFEI Contribution No. 1060.

The physical and chemical properties of microplastics and their environmental distributions may provide clues about their sources and inform their fate. We demonstrate the value of extensive monitoring of microplastics in an urban bay, San Francisco Bay. Surface water, fish, sediment, stormwater runoff, and treated wastewater were sampled across the bay and adjacent national marine sanctuaries (NMS). We found microplastics and other anthropogenic microdebris (“microdebris”) in all sample types. Concentrations were higher in the bay than in the NMS, and within the bay, concentrations were higher during the wet season than during the dry season. The fate of microdebris varied depending on their morphologies and densities: fibers were dominant in fish, black rubbery fragments were common in sediment, as were fibers, while buoyant fragments and fibers were widely observed in surface waters. Notably, we found large amounts of black rubbery fragments, an emerging contaminant, in stormwater. Moreover, stormwater was a significant pathway of microdebris, with concentrations roughly 140 times greater than those found in wastewater, which was dominated by fibers. Overall, we demonstrate the value of multimatrix regional monitoring to evaluate the sources and fate of microplastics, which can inform effective mitigation for other urban bays around the world.


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Dusterhoff, S. D.; Doehring, C.; Shusterman, G. 2014. How Creeks Meet the Bay: Changing Interfaces (Interactive web map).

San Francisco Bay’s connections to local creeks are integral to its health. These fluvial-tidal (F-T) interfaces are the points of delivery for freshwater, sediment, contaminants, and nutrients. The ways in which the F-T interface has changed affect flooding dynamics, ecosystem functioning, and resilience to a changing climate. As the historical baylands have been altered, the majority of contemporary F-T interface types have changed leading to additional F-T interface types within the present-day landscape. Illustrations of each F-T interface type and methods for classification are available here

This project is part of Flood Control 2.0. For further information please visit this project page

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.

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Ferreira, J. C. T.; Lacy, J. R.; Mcgill, S. C.; WinklerPrins, L. T.; Nowacki, D. J.; Stevens, A. W.; Tan, A. C. 2023. Hydrodynamic and sediment transport data from Whale's Tail marsh and adjacent waters in South San Francisco Bay, California 2021-2022. United States Geological Survey.

The U.S. Geological Survey Pacific Coastal and Marine Science Center collected hydrodynamic and sediment-transport data at shallow water sites in South San Francisco Bay and in the Whale's Tail South marsh in Eden Landing Ecological Reserve in Alameda County, CA in 2021 and 2022. This data release includes hydrodynamic and sediment transport time-series data spanning from June 2021 to January 2022, as well as sediment bed properties and water column suspended-sediment concentrations Details on station location, instrumentation, and measured variables are included in sections for each data type. The data were collected to determine sediment supply and sediment delivery to marshes, both in the bay and in tidal creeks as well as across the bay-marsh interface during varying tidal and wave conditions. The goal of the project was to more accurately predict the fate of marshes and to optimize management actions. They were collected as part of a collaborative study with the USGS Western Ecological Research Center. These data are intended for science researchers, students, policy makers, and the general public.

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Allen, R. M.; Lacy, J. R.; McGill, S. C.; Ferreira, J. C. T. 2021. Hydrodynamic, sediment transport, and sediment flocculation data from south San Francisco Bay, California, summer 2020. United Sates Geological Survey.

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.

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David, N.; Oros, D. R. 2002. Identification and evaluation of unidentified organic contaminants in the San Francisco Estuary. SFEI Contribution No. 45. San Francisco Estuary Institute: Oakland, CA.
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Cohen, A. N.; Nordby, J. C.; Beissinger, S. R. 2002. The impact of an invasive Atlantic cordgrass (Spartina alterniflora) on San Francisco Bay Song Sparrow populations: direct and indirect influence. In Terrestrial Vertebrates of Tidal Marshes: Evolution, Ecology and Conservation. Terrestrial Vertebrates of Tidal Marshes: Evolution, Ecology and Conservation. Silver Spring, MD.
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. 1994. Impacts of invasions in the Bay and Delta. Abs. Proc. 75th Ann. Mtg., Pac. Div. Amer. Assoc. Adv. Sci..
Fiorillo, J. T. 1994. Implementation Manual for the San Leandro Creek Watershed Awareness Program, 1993-1994. SFEI Contribution No. 177. San Francisco Estuary Institute: Richmond, Ca. p 75.
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Hatje, V.; Bruland, K. W.; A. Flegal, R. 2016. Increases in Anthropogenic Gadolinium Anomalies and Rare Earth Element Concentrations in San Francisco Bay over a 20 Year Record. Environ. Sci. Technol. 50 (8).

We evaluated both the spatial distribution of gadolinium (Gd) and other rare earth elements (REE) in surface waters collected in a transect of San Francisco Bay (SFB) and their temporal variations within the Bay over two decades. The REE were preconcentrated using the NOBIAS PA-1 resin prior to analysis by high-resolution inductively coupled plasma mass spectrometry. Measurements revealed a temporal increase in the Gd anomaly in SFB from the early 1990s to the present. The highest Gd anomalies were observed in the southern reach of SFB, which is surrounded by several hospitals and research centers that use Gd-based contrast agents for magnetic resonance imaging. Recent increases in that usage presumably contributed to the order of magnitude increase in anthropogenic Gd concentrations in SFB, from 8.27 to 112 pmol kg–1 over the past two decades, and reach the northeast Pacific coastal waters. These measurements (i) show that “exotic” trace elements used in new high-tech applications, such as Gd, are emerging contaminants in San Francisco Bay and that anthropogenic Gd concentrations increased substantially over a 20 year period; (ii) substantiate proposals that REE may be used as tracers of wastewater discharges and hydrological processes; and (iii) suggest that new public policies and the development of more effective treatment technologies may be necessary to control sources and minimize future contamination by REE that are critical for the development of new technologies, which now overwhelm natural REE anomalies.

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