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2017
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Wu, Y.; Tan, H.; Sutton, R.; Chen, D. 2017. From Sediment to Top Predators: Broad Exposure of Polyhalogenated Carbazoles in San Francisco Bay (U.S.A.). Environmental Science and Technology 51, 2038-2046.

The present study provides the first comprehensive investigation of polyhalogenated carbazoles (PHCZ) contamination in an aquatic ecosystem. PHCZs have been found in soil and aquatic sediment from several different regions, but knowledge of their bioaccumulation and trophodynamics is extremely scarce. This work investigated a suite of 11 PHCZ congeners in San Francisco Bay (United States) sediment and organisms, including bivalves (n = 6 composites), sport fish (n = 12 composites), harbor seal blubber (n = 18), and bird eggs (n = 8 composites). The most detectable congeners included 3,6-dichlorocarbazole (36-CCZ), 3,6-dibromocarbazole (36-BCZ), 1,3,6-tribromocarbazole (136-BCZ), 1,3,6,8-tetrabromocarbazole (1368-BCZ), and 1,8-dibromo-3,6-dichlorocarbazole (18-B-36-CCZ). The median concentrations of ΣPHCZs were 9.3 ng/g dry weight in sediment and ranged from 33.7 to 164 ng/g lipid weight in various species. Biomagnification was observed from fish to harbor seal and was mainly driven by chlorinated carbazoles, particularly 36-CCZ. Congener compositions of PHCZs differed among species, suggesting that individual congeners may be subject to different bioaccumulation or metabolism in species occupying various trophic levels in the studied aquatic system. Toxic equivalent (TEQ) values of PHCZs were determined based on their relative effect potencies (REP) compared to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The median TEQ was 1.2 pg TEQ/g dry weight in sediment and 4.8 – 19.5 pg TEQ/g lipid weight in biological tissues. Our study demonstrated the broad exposure of PHCZs in San Francisco Bay and their characteristics of bioaccumulation and biomagnification along with dioxin-like effects. These findings raise the need for additional research to better elucidate their sources, environmental behavior, and fate in global environments.

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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Sutton, R.; Sedlak, M. 2017. Microplastic Monitoring and Science Strategy for San Francisco Bay. SFEI Contribution No. 798. San Francisco Estuary Institute: Richmond, Calif.
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Holleman, R.; MacVean, L.; Mckibben, M.; Sylvester, Z.; Wren, I.; Senn, D. 2017. Nutrient Management Strategy Science Program. SFEI Contribution No. 879. San Francisco Estuary Institute: Richmond, CA.
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Sadaria, A. M.; Sutton, R.; Moran, K. D.; Teerlink, J.; Brown, J. V.; Halden, R. U. 2017. Passage of fiproles and imidacloprid from urban pest control uses through wastewater treatment plants in northern California. Environmental Toxicology and Chemistry 36, 1473-1482 . SFEI Contribution No. 783.

Urban pest control insecticides, specifically fipronil and its four major degradates (fipronil sulfone, sulfide, desulfinyl, and amide) and imidacloprid, were monitored during drought conditions in eight San Francisco Bay wastewater treatment plants (WWTPs). In influent and effluent, ubiquitous detections were obtained in units of ng/L for fipronil (13-88), fipronil sulfone (1-28), fipronil sulfide (1-5) and imidacloprid (58-306). In influent, 100% of imidacloprid and 62 ± 9% of total fiproles (fipronil and degradates) were present in the dissolved state, with the balance being bound to filter-removable particulates. Targeted insecticides persisted during wastewater treatment, regardless of treatment technology utilized (imidacloprid: 93 ± 17%; total fiproles: 65 ± 11%), with partitioning into sludge (3.7-151.1 μg/kg dry weight as fipronil) accounting for minor losses of total fiproles entering WWTPs. The load of total fiproles was fairly consistent across the facilities but fiprole speciation varied. This first regional study on fiprole and imidacloprid occurrences in raw and treated California sewage revealed ubiquity and marked persistence to conventional treatment of both phenylpyrazole and neonicotinoid compounds. Flea and tick control agents for pets are identified as potential sources of pesticides in sewage meriting further investigation and inclusion in chemical-specific risk assessments. 

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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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Wu, J.; Gilbreath, A.; McKee, L. J. 2017. Regional Watershed Spreadsheet Model (RWSM): Year 6 Progress Report. SFEI Contribution No. 811. San Francisco Estuary Institute: Richmond, CA.
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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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Sun, J.; Pearce, S.; Trowbridge, P. 2017. RMP Field Sampling Report 2016. SFEI Contribution No. 826. San Francisco Estuary Institute: Richmond, CA.
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Yee, D.; Ross, J. 2017. San Francisco Bay California Toxics Rule Priority Pollutant Ambient Water Monitoring Report. SFEI Contribution No. 814. San Francisco Estuary Institute: Richmond.
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Holleman, R.; Nuss, E.; Senn, D. 2017. San Francisco Bay Interim Model Validation Report. SFEI Contribution No. 850. San Francisco Estuary Institute: Richmond, CA.
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Davis, J.; Yee, D.; Fairey, R.; Sigala, M. 2017. San Leandro Bay PCB Study Data Report. SFEI Contribution No. 855. San Francisco Estuary Institute: Richmond, CA.
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Beagle, J.; Richey, A.; Hagerty, S.; Salomon, M.; Askevold, R. A.; Grossinger, R. M.; Reynolds, P.; McClain, C.; Spangler, W.; Quinn, M.; et al. 2017. Sycamore Alluvial Woodland: Habitat Mapping and Regeneration Study. SFEI Contribution No. 816.

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).

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Safran, S. M.; Baumgarten, S. A.; Beller, E. E.; Crooks, J. A.; Grossinger, R. M.; Lorda, J.; Longcore, T. R.; Bram, D. L.; Dark, S. J.; Stein, E. D.; et al. 2017. Tijuana River Valley Historical Ecology Investigation. Prepared for the State Coastal Conservancy. A Report of SFEI-ASC’s Resilient Landscapes Program. SFEI Contribution No. 760. San Francisco Estuary Institute - Aquatic Science Center : Richmond, CA. p 230.

The Tijuana River Valley Historical Ecology Investigation addresses a regional data gap by reconstructing the landscape and ecosystem characteristics of the river valley prior to the major modifications of the late 19th and 20th centuries. The research presented here, funded by the California State Coastal Conservancy, supplies foundational information at the regional and system scale about how the Tijuana Estuary, River, and valley looked and functioned in the recent past, as well as how they have changed over time. The ultimate goal of this study is to provide a new tool and framework that, in combination with contemporary research and future projections, can support and guide ongoing restoration design, planning, and management efforts in the valley.

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2016
SFEI. 2016. 2015 Annual Monitoring Report. SFEI Contribution No. 775. San Francisco Estuary Institute: Richmond, CA.
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San Francisco Estuary Institute (SFEI). 2016. 2016 Regional Monitoring Program Update. SFEI Contribution No. 790. San Francisco Estuary Institute: Richmond, CA.
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RMP. 2016. 2016 RMP Detailed Workplan and Budget. San Francisco Estuary Institue: Richmond, CA.
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RMP. 2016. 2016 RMP Multi-Year Plan. San Francisco Estuary Institute: Richmond, CA.
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SFEI. 2016. 2016 RMP Sturgeon Derby Study Sampling & Analysis Plan. San Francisco Estuary Institute : Richmond, CA.
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Robinson, A.; Safran, S. M.; Beagle, J.; Grenier, J. Letitia; Grossinger, R. M.; Spotswood, E.; Dusterhoff, S. D.; Richey, A. 2016. A Delta Renewed: A Guide to Science-Based Ecological Restoration in the Sacramento-San Joaquin Delta. Delta Landscapes Project. Prepared for the California Department of Fish and Wildlife and Ecosystem Restoration Program. A Report of SFEI-ASC’s Resilient Landscapes Program. SFEI Contribution No. 799. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.

This report offers guidance for creating and maintaining landscapes in the Sacramento-San Joaquin Delta that support desired ecological functions, while retaining the overall agricultural character and water-supply service of the region. Based on extensive research into how the Delta functioned historically, how it has changed, and how it is likely to evolve, we discuss where and how to re-establish the dynamic natural processes that can sustain native Delta habitats and wildlife into the future. The approach, building on work others have piloted and championed, is to restore or emulate natural processes where possible, establish an appropriate mosaic of habitat types at the landscape scale, use multi-benefit management strategies to increase support for native species in agricultural and urban areas, and allow the Delta to adapt to future uncertainties of climate change, levee failure, and human population growth. With this approach, it will be critical to integrate ecological improvements with the human landscape: a robust agricultural economy, water infrastructure and diversions, and urbanized areas. Strategic restoration that builds on the history and ecology of the region can contribute to the strong sense of place and recreational value of the Delta.

Printed copies of the report are available for purchase.

 

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Safran, S. M.; Grenier, J. Letitia; Grossinger, R. M. 2016. Ecological implications of modeled hydrodynamic changes in the upper San Francisco Estuary: Phase II Technical Memorandum. SFEI Contribution No. 786.

The physical and ecological environment of the upper San Francisco Estuary has been profoundly altered since the early 1800s. Recent efforts have utilized maps of the upper estuary’s historical habitat types to infer associated changes in desired ecosystem processes and functions. The work presented in this memo builds on these previous efforts, but utilizes a new tool for evaluating change over time: a 3D hydrodynamic model of the pre-development estuary. This model was constructed by Resource Management Associates (RMA) using a new digital elevation model of the pre-development upper estuary generated by SFEI and UC Davis (UCD) and “natural” boundary flows calculated by the California Department of Water Resources (CDWR).


Once completed and calibrated, the pre-development model was paired with a similar model of the contemporary system in order to analyze hydrodynamic changes in the upper estuary. These analyses are presented in a technical memorandum published by RMA (2015). This memorandum takes these analyses and considers the ecological implications of modeled changes (see the “Results” section). Hydrodynamic analyses include analyzing changes in tidal prism, isohaline positions, low-salinity zone habitat, channel velocity, and source water distribution.


 In addition to describing the ecological implications of modeled hydrodynamic changes, this memorandum summarizes major ongoing questions about estuarine hydrodynamics that might be explored using these models, including changes in water residence time, temperature, transport pathways, and the connectivity of aquatic and semi-aquatic habitats. Understanding changes in these and other factors would greatly improve our understanding of the desirable ecosystem functions provided by the historical system and, as a result, improve our ability to recover these functions now and into the future.

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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.

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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.
Josh Collins; Lowe, S. 2016. Framework to coordinate water quality improvement and wildlife habitat conservation to protect California streams, wetlands, and riparian areas.

Project funded by an USEPA Wetland Program Development Grant (Region 9) #99T05901: Framework for Coordinated Assessment of CA Wildlife Habitat and Aquatic Resource Areas

. SFEI Contribution No. 776. San Francisco Estuary Institute: Richmond, CA. p 89.

The emergence of comparable landscape approaches to wildlife conservation and water quality improvement through federal and California state regulatory and management programs provides an opportunity for their coordination to better protect California’s aquatic resources, especially streams, wetlands, and riparian areas. Such coordination is patently desirable.  A framework has been developed to help coordinate restoration and compensatory mitigation across policies governing wildlife conservation and water quality in the landscape context. The framework is based on the Wetland and Riparian Area Monitoring Plan (WRAMP) of the California Wetland Monitoring Workgroup (CWMW) of the Water Quality Monitoring Council. The framework presented in this memorandum is a version of the standard WRAMP framework. It only differs from the standard framework to better accommodate wildlife conservation planning, assessment and reporting. To distinguish this version from the standard version, it is termed the 'WRAMP for wildlife'.

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Beller, E. E.; Downs, P. W.; Grossinger, R. M.; Orr, B. K.; Salomon, M. 2016. From past patterns to future potential: using historical ecology to inform river restoration on an intermittent California river. Landscape Ecology 31 (3), 20.

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.

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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.

Hale, T.; Grosso, C. 2016. An Introduction to EcoAtlas: Applied Aquatic Science. San Francisco Estuary Institute: Richmond, CA. p 16 pages.

This memo was developed by SFEI to introduce the EcoAtlas tools, their intended (target) user community, and the short- and long-term intended applications. 

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Lowe, S.; Salomon, M.; Pearce, S. 2016. Lower Peninsula Watershed Condition Assessment 2016. Technical memorandum prepared for the Santa Clara Valley Water District - Priority D5 Project. SFEI Contribution No. 809. San Francisco Estuary Institute: Richmond, CA. p 49.

In 2016 The Santa Clara Valley Water District and its consultants conducted a watershed wide survey to characterize the distribution and abundance of the aquatic resources within the Lower Peninsula watershed wtihin Santa Clara County, CA based on available GIS data, 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. 2016. Microplastic Contamination in San Francisco Bay - Fact Sheet. 2015, Revised 2016. SFEI Contribution No. 770.
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Sutton, R.; Mason, S. A.; Stanek, S. K.; Willis-Norton, E.; Wren, I. F.; Box, C. 2016. Microplastic contamination in the San Francisco Bay, California, USA. Marine Pollution Bulletin 109 . SFEI Contribution No. 769.

Despite widespread detection of microplastic pollution in marine environments, data describing microplastic abundance in urban estuaries and microplastic discharge via treated municipal wastewater are limited. This study presents information on abundance, distribution, and composition of microplastic at nine sites in San Francisco Bay, California, USA. Also presented are characterizations of microplastic in final effluent from eight wastewater treatment plants, employing varying treatment technologies, that discharge to the Bay. With an average microplastic abundance of 700,000 particles/km2, Bay surface water appears to have higher microplastic levels than other urban waterbodies sampled in North America. Moreover, treated wastewater from facilities that discharge into the Bay contains considerable microplastic contamination. Facilities employing tertiary filtration did not show lower levels of contamination than those using secondary treatment. As textile-derived fibers were more abundant in wastewater, higher levels of fragments in surface water suggest additional pathways of microplastic pollution, such as stormwater runoff.

Mason, S. A.; Garneau, D.; Sutton, R.; Chu, Y.; Ehmann, K.; Barnes, J.; Papazissimos, D.; Rogers, D. L. 2016. Microplastic pollution is widely detected in US municipal wastewater treatment plant effluent. Environmental Pollution 218, 1045-1054.

Municipal wastewater effluent has been proposed as one pathway for microplastics to enter the aquatic environment. Here we present a broad study of municipal wastewater treatment plant effluent as a pathway for microplastic pollution to enter receiving waters. A total of 90 samples were analyzed from 17 different facilities across the United States. Averaging all facilities and sampling dates, 0.05 ± 0.024 microparticles were found per liter of effluent. Though a small value on a per liter basis, even minor municipal wastewater treatment facilities process millions of liters of wastewater each day, yielding daily discharges that ranged from ∼50,000 up to nearly 15 million particles. Averaging across the 17 facilities tested, our results indicate that wastewater treatment facilities are releasing over 4 million microparticles per facility per day. Fibers and fragments were found to be the most common type of particle within the effluent; however, some fibers may be derived from non-plastic sources. Considerable inter- and intra-facility variation in discharge concentrations, as well as the relative proportions of particle types, was observed. Statistical analysis suggested facilities serving larger populations discharged more particles. Results did not suggest tertiary filtration treatments were an effective means of reducing discharge. Assuming that fragments and pellets found in the effluent arise from the 'microbeads' found in many cosmetics and personal care products, it is estimated that between 3 and 23 billion (with an average of 13 billion) of these microplastic particles are being released into US waterways every day via municipal wastewater. This estimate can be used to evaluate the contribution of microbeads to microplastic pollution relative to other sources (e.g., plastic litter and debris) and pathways (e.g., stormwater) of discharge.

Safran, S. M.; Clark, E.; Beller, E. E.; Grossinger, R. M. 2016. Mission Bay Historical Ecology Reconnaissance Study: Data Collection Summary (Technical Report). SFEI Contribution No. 777.

The goals of the Mission Bay Historical Ecology Reconnaissance Study were to collect and compile high-priority historical
data about the Mission Bay landscape, identify sources that could help to develop a deeper understanding of early
ecological conditions, and to identify future possible research directions based on the available data. This technical
memorandum is intended to document the archives consulted during the reconnaissance study, summarize the collected
and compiled data, and to identify potential next steps. A separate technical presentation to project staff and advisors will
summarize the preliminary findings and questions generated from a review of the historical dataset. Ultimately, this
research is intended to support the San Diego Audubon Society’s Mission Bay Wetlands Conceptual Restoration Plan (CRP)
and the ReWild Mission Bay project.

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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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Jabusch, T. W.; Trowbridge, P. 2016. Nutrient Monitoring Planning Workshop - Summary of Existing Nutrient Monitoring Programs, Data Gaps, and Potential Delta RMP “No Regrets” Monitoring Activities. Aquatic Science Center: Richmond, CA.

This report was prepared as a briefing document for a September 2016 workshop held in Sacramento by the Delta Regional Monitoring Program. The purpose of the workshop was to plan how to invest in nutrients-related studies in order to inform better management of Delta waterways. First, the report compiles information about the major existing nutrient monitoring programs in the Sacramento-San Joaquin Delta. Next, it outline options for “no regrets” actions for workshop participants to review. The report summarizes interviews with representatives of Delta monitoring and resource management programs, describes current monitoring efforts in the Delta, and presents the conclusions and recommendations from recently completed data syntheses.

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Houtz, E. F.; Sutton, R.; Park, J. - S.; Sedlak, M. 2016. Poly- and perfluoroalkyl substances in wastewater: Significance of unknown precursors, manufacturing shifts, and likely AFFF impacts. Water Research . SFEI Contribution No. 780.

In late 2014, wastewater effluent samples were collected from eight treatment plants that discharge to San Francisco (SF) Bay in order to assess poly- and perfluoroalkyl substances (PFASs) currently released from municipal and industrial sources. In addition to direct measurement of twenty specific PFAS analytes, the total concentration of perfluoroalkyl acid (PFAA) precursors was also indirectly measured by adapting a previously developed oxidation assay. Effluent from six municipal treatment plants contained similar amounts of total PFASs, with highest median concentrations of PFHxA (24 ng/L), followed by PFOA (23 ng/L), PFBA (19 ng/L), and PFOS (15 ng/L). Compared to SF Bay municipal wastewater samples collected in 2009, the short chain perfluorinated carboxylates PFBA and PFHxA rose significantly in concentration. Effluent samples from two treatment plants contained much higher levels of PFASs: over two samplings, wastewater from one municipal plant contained an average of 420 ng/L PFOS and wastewater from an airport industrial treatment plant contained 560 ng/L PFOS, 390 ng/L 6:2 FtS, 570 ng/L PFPeA, and 500 ng/L PFHxA. The elevated levels observed in effluent samples from these two plants are likely related to aqueous film forming foam (AFFF) sources impacting their influent; PFASs attributable to both current use and discontinued AFFF formulations were observed. Indirectly measured PFAA precursor compounds accounted for 33%–63% of the total molar concentration of PFASs across all effluent samples and the PFAA precursors indicated by the oxidation assay were predominately short-chained. PFAS levels in SF Bay effluent samples reflect the manufacturing shifts towards shorter chained PFASs while also demonstrating significant impacts from localized usage of AFFF.

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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Trowbridge, P. R.; Davis, J. A.; Mumley, T.; Taberski, K.; Feger, N.; Valiela, L.; Ervin, J.; Arsem, N.; Olivieri, A.; Carroll, P.; et al. 2016. The Regional Monitoring Program for Water Quality in San Francisco Bay, California, USA: Science in support of managing water quality. Regional Studies in Marine Science 4.

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is a novel partnership between regulatory agencies and the regulated community to provide the scientific foundation to manage water quality in the largest Pacific estuary in the Americas. The RMP monitors water quality, sediment quality and bioaccumulation of priority pollutants in fish, bivalves and birds. To improve monitoring measurements or the interpretation of data, the RMP also regularly funds special studies. The success of the RMP stems from collaborative governance, clear objectives, and long-term institutional and monetary commitments. Over the past 22 years, high quality data and special studies from the RMP have guided dozens of important decisions about Bay water quality management. Moreover, the governing structure and the collaborative nature of the RMP have created an environment that allowed it to stay relevant as new issues emerged. With diverse participation, a foundation in scientific principles and a continual commitment to adaptation, the RMP is a model water quality monitoring program. This paper describes the characteristics of the RMP that have allowed it to grow and adapt over two decades and some of the ways in which it has influenced water quality management decisions for this important ecosystem.

Schiff, K.; Trowbridge, P. R.; Sherwood, E. T.; Tango, P.; Batiuk, R. A. 2016. Regional monitoring programs in the United States: Synthesis of four case studies from Pacific, Atlantic, and Gulf Coasts. Regional Studies in Marine Science 4.

Water quality monitoring is a cornerstone of environmental protection and ambient monitoring provides managers with the critical data they need to take informed action. Unlike site-specific monitoring that is at the heart of regulatory permit compliance, regional monitoring can provide an integrated, holistic view of the environment, allowing managers to obtain a more complete picture of natural variability and cumulative impacts, and more effectively prioritize management actions. By reviewing four long-standing regional monitoring programs that cover portions of all three coasts in the United States–Chesapeake Bay, Tampa Bay, Southern California Bight, and San Francisco Bay–important insights can be gleaned about the benefits that regional monitoring provides to managers. These insights include the underlying reasons that make regional monitoring programs successful, the challenges to maintain relevance and viability in the face of ever-changing technology, competing demands and shifting management priorities. The lessons learned can help other managers achieve similar successes as they seek to establish and reinvigorate their own monitoring programs.

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Dusterhoff, S. D.; Doehring, C.; Baumgarten, S.; Grossinger, R. M.; Askevold, R. A. 2016. Resilient Landscape Vision for Lower Walnut Creek: Baseline Information and Management Strategies. Flood Control 2.0. An SFEI-ASC Resilient Landscape Program report developed in cooperation with the Flood Control 2.0 Regional Science Advisors and Contra Costa County Flood Control and Water Conservation District. SFEI Contribution No. 782. San Francisco Estuary Institute-Aquatic Science Center: Richmond, CA.

Lower Walnut Creek (Contra Costa County, CA) and its surrounding landscape have undergone considerable land reclamation and development since the mid-nineteenth century. In 1965, the lower 22 miles of Walnut Creek and the lower reaches of major tributaries were converted to flood control channels to protect the surrounding developed land. In the recent past, sediment was periodically removed from the lower Walnut Creek Flood Control Channel to provide flow capacity and necessary flood protection. Due to the wildlife impacts and costs associated with this practice, the Contra Costa County Flood Control and Water Conservation District (District) is now seeking a new channel management approach that works with natural processes and benefits people and wildlife in a cost-effective manner. Flood Control 2.0 project scientists and a Regional Science Advisory Team (RSAT) worked with the District to develop a long-term management Vision for lower Walnut Creek that could result in a multi-benefit landscape that restores lost habitat and is resilient under a changing climate.

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Hunt, J.; Trowbridge, P.; Yee, D.; Franz, A.; Davis, J. 2016. Sampling and Analysis Plan for 2016 RMP Status and Trends Bird Egg Monitoring. SFEI Contribution No. 827. San Francisco Estuary Institute: Richmond, CA. p 31 pp.
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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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Doehring, C.; Beagle, J.; Lowe, J.; Grossinger, R. M.; Salomon, M.; Kauhanen, P.; Nakata, S.; Askevold, R. A.; Bezalel, S. N. 2016. San Francisco Bay Shore Inventory: Mapping for Sea Level Rise Planning. SFEI Contribution No. 779. San Francisco Estuary Institute: Richmond, CA.

With rising sea levels and the increased likelihood of extreme weather events, it is important for regional agencies and local municipalities in the San Francisco Bay Area to have a clear understanding of the status, composition, condition, and elevation of our current Bay shore, including both natural features and built infrastructure.


The purpose of this Bay shore inventory is to create a comprehensive and consistent picture of today’s Bay shore features to inform regional planning. This dataset includes both structures engineered expressly for flood risk management (such as accredited levees) and features that affect flooding at the shore but are not designed or maintained for this purpose (such as berms, road embankments, and marshes). This mapping covers as much of the ‘real world’ influence on flooding and flood routing as possible, including the large number of non-accredited structures.
This information is needed to:

  1. identify areas vulnerable to flooding.
  2. identify adaptation constraints due to present Bay shore alignments; and
  3. suggest opportunities where beaches, wetlands, and floodplains can be maintained or restored and integrated into flood risk management strategies.

The primary focus of the project is therefore to inform regional planners and managers of Bay shore characteristics and vulnerabilities. The mapping presented here is neither to inform FEMA flood designation nor is it a replacement for site-specific analysis and design.


The mapping consists of two main elements:

  1. Mapping of Bay shore features (levees, berms, roads, railroads, embankments, etc.) which could affect flooding and flood routing.
  2. Attributing Bay shore features with additional information including elevations, armoring, ownership (when known), among others.

SFEI delineated and characterized the Bay shore inland to 3 meters (10ft) above mean higher high water (MHHW) to accommodate observed extreme water levels and the commonly used range of future sea level rise (SLR) scenarios. Elevated Bay shore features were mapped and classified as engineered levees, berms, embankments, transportation structures, wetlands, natural shoreline, channel openings, or water control structures. Mapped features were also attributed with elevation (vertical accuracy of <5cm reported in 30 meter (100ft) segments from LiDAR derived digital elevation models (DEMs), FEMA accreditation status, fortification (e.g., riprap, buttressing), frontage (e.g., whether a feature was fronted by a wetland or beach), ownership, and entity responsible for maintenance. Water control structures, ownership, and maintenance attributes were captured where data was available (not complete for entire dataset). The dataset was extensively reviewed and corrected by city, county, and natural resource agency staff in each county around the Bay. This report provides further description of the Bay shore inventory and methods used for developing the dataset. The result is a publicly accessible GIS spatial database.

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Ackerman, J.; Hartman, A.; Herzog, M. P.; Toney, M. 2016. San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants - 2016 Data Summary. U.S. Geological Survey: Dixon, CA. p 19 pp.

As part of the Regional Monitoring Program (RMP) and the USGS’s long-term Wildlife Contaminants Program, the USGS samples double-crested cormorant (Phalacrocorax auritus) and Forster’s tern (Sterna forsteri) eggs throughout the San Francisco Bay Estuary approximately every three years to assess temporal trends in contaminant concentrations. This sampling has been carried out in 2006, 2009, and 2012. Although RMP sampling was scheduled to take place in 2015, it was delayed until 2016. This document summarizes egg collections for 2016, as well as mercury concentrations in Forster’s tern eggs on an individual egg basis.

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Salomon, M.; Dusterhoff, S. D.; Askevold, R. A.; Grossinger, R. M. 2016. San Francisquito Creek Baylands: Landscape Change Metrics Analysis. Flood Control 2.0. SFEI Contribution No. 784. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 12.

Major Findings
Over the past 150 years, lower San Francisquito Creek and the adjacent baylands have been modified for the sake of land reclamation and flood control. This study focused on developing an understanding of the magnitude of habitat change since the mid-19th century through comparisons of key historical and contemporary landscape-scale habitat features, as well as several key landscape metrics that relate to ecological functions and landscape resilience. The major findings from the analyses conducted for this study are as follows:
• Historically, the San Francisquito Creek Baylands included a mosaic of habitat types, including an extensive tidal marsh plain with salt pannes and an expansive tidal channel network, a broad bay flat, and a relatively wide contiguous low-gradient tidal-terrestrial transition zone.
• Since the late 19th century, a combination of land reclamation and the inland migration of the shoreline has resulted in a 55% decrease in tidal marsh area, a 67% decrease in total tidal channel length, a 40% reduction in channel flat area, a 20% increase in bay flat area, and a 95% decrease in tidal-terrestrial transition zone length.
• Land reclamation has also resulted in the creation of new features that did not exist in the area historically including tidal lagoons, non-tidal open water features, and non-tidal wetlands.
 

Recommendations
The findings from this study provide insight into the drivers for and magnitude of habitat change within the San Francisquito Creek Baylands, and can therefore help inform climate-resilient approaches for regaining some of the lost landscape features and ecological functions. Specific management recommendations developed from the study findings are as follows:
• The dramatic decrease in tidal marsh area and associated tidal channel length since the mid-1800s make tidal marsh restoration a high priority. To make restored areas sustainable over the long-term, restoration should include reestablishing regular tidal inundation as well as reestablishing a connection with San Francisquito Creek and the delivery of freshwater and fine sediment. Restoration efforts should focus on large contiguous areas with minimal infrastructure and should ideally be done sometime over the next decade to ensure the restored areas will have a chance of surviving the sharp increase in the rate of sea level rise that is predicted to occur around 2030 (Goals Update 2015).
• Similarly, the dramatic decrease in the tidal-terrestrial transition zone makes it a high priority for any restoration vision for this area. The transition zone provides distinct ecological services and marsh migration space, and is in need of restoration throughout the South Bay. Since most of the upland land along the historical tidal-terrestrial transition zone is currently developed, near-term restoration efforts should focus on creating transition zone habitats on the bayside of flood risk management levees (Goals Update 2015).
• The landscape metrics used in this study (tidal habitat area, tidal channel length, and tidal-terrestrial interface length) can be used to help design resilient landscape restoration and adaptation strategies around the mouth of San Francisquito Creek. Specifically, the metrics can be used to assess the long-term ecological benefit associated with various processes-based restoration approaches (i.e., approaches that create habitat features and establish physical processes required for habitat resilience). Additional useful landscape metrics are being developed as part of the Resilient Silicon Valley project (see Robinson et al. 2015).

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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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2015
San Francisco Estuary Institute. 2015. 2013-2014 Annual Monitoring Results. SFEI Contribution No. 758. San Francisco Estuary Institute: Richmond, CA.
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Yee, D. 2015. 2013 RMP Water Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
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