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Conceptual Understanding of Fine Sediment Transport in San Francisco Bay. SFEI Contribution No. 1114. San Francisco Estuary Institute: Richmond, CA.2023.
Sediment is a lifeblood of San Francisco Bay (Bay). It serves three key
Sediment is a lifeblood of San Francisco Bay (Bay). It serves three key
functions: (1) create and maintain tidal marshes and mudflats, (2) transport
nutrients and contaminants, and (3) reduce impacts from excessive human-derived
nutrients in the Bay. Because of these important roles, we need a
detailed understanding of sediment processes in the Bay.
This report offers a conceptual understanding of how fine-grained sediment
(i.e. silt and finer, henceforth called fine sediment) moves around at different
scales within the Bay, now and into the future, to synthesize current knowledge
and identify critical knowledge gaps. This information can be used to support
Bay sediment management efforts and help prioritize funding for research
and monitoring. In particular, this conceptual understanding is designed to
inform future San Francisco Bay Regional Monitoring Program (RMP) work
under the guidance of the Sediment Workgroup of the RMP for Water Quality
in San Francisco Bay, which brings together experts who have worked on
many different components of the landscape, including watersheds and
tributaries, marshes and mudflats, beaches, and the open Bay. This report
describes sediment at two scales: a conceptual understanding of open-Bay
sediment processes at the Bay and subembayment scale (Chapter 2); and
a conceptual understanding of sediment processes at the baylands scale
(Chapter 3). Chapter 4 summarizes the key knowledge gaps and provides
recommendations for future studies.
Managing Open Space in Support of Net Zero: Carbon sequestration opportunities and tradeoffs in the Alameda Watershed. San Francisco Estuary Institute: Richmond, CA. p 120.2023.
Shoreline Resilience Framework for San Francisco Bay: Wildlife Support. SFEI Contribution No. 1115. San Francisco Estuary Institute: Richmond, CA.2023.
Delta Wetland Futures: Blue Carbon and Elevation Change. SFEI Contribution No. 1105. San Francisco Estuary Institute: Richmond, CA.2022.
Delta Wetland Futures: Tidal Marsh Resilience to Sea Level Rise. SFEI Contribution No. 1106. San Francisco Estuary Institute: Richmond, CA.2022.
Leveraging Wetlands for a Better Climate Future: Incorporating Blue Carbon into California's Climate Planning. SFEI Contribution No. 1084. San Francisco Estuary Institute: Richmond, CA. p 31.2022.
The 2022 update to California’s climate change Scoping Plan incorporates management actions in the state’s forests, shrublands/chaparral, grasslands, croplands, developed lands, deltaic wetlands, and sparsely vegetated lands. Missing from this list are the tidally-influenced coastal ecosystems outside the Sacramento-San Joaquin Delta. These blue carbon ecosystems support high rates of carbon storage and sequestration while providing many co-benefits that can enhance coastal climate change resilience. With sufficient data and robust modeling approaches, California has the opportunity to incorporate blue carbon in future Scoping Plan updates and set actionable targets for restoration, migration space conservation, and other management activities that promote long-term survival of the state’s coastal wetlands. To support this goal, this report offers a high-level overview of the state of the science for blue carbon quantification in California. This summary, which covers datasets and quantification approaches, key focus areas for additional science investment, and example scenarios for coastal wetland restoration, is intended to facilitate broader inclusion of blue carbon in future Scoping Plan updates and other state-level climate-planning documents.
RESILIENT STATEN ISLAND: Landscape Scenario Analysis Pilot Application. SFEI Contribution No. 1083. San Francisco Estuary Institute: Richmond, Ca.2022.
A central motivating question for the Sacramento-San Joaquin Delta science and management community is what should be done, where and when, to support future Delta landscapes that are ecologically and economically viable and resilient to change. Actions must be taken that have the greatest potential for achieving multiple benefits. This is especially important given the urgency to rapidly transition Delta landscapes to address biodiversity loss, erosion of ecosystem resilience, flood risk, water supply reliability, and cultural and economic sustainability. Landscape-scale planning is needed to examine how individual actions add up to meaningful change. Such planning involves figuring out how different areas can provide different functions at different times and helps show how choices made now can help shift trajectories toward desired outcomes. Too often, land use and management decisions are made based on a limited set of objectives or at the site scale, resulting in missed opportunities. Actions (or inaction) should not foreclose on critical opportunities. Moving forward, there is great need to more effectively compare possible future scenarios across a range of ecological and economic factors. This scenario analysis for Staten Island — a large Delta island managed for multiple uses and facing challenges similar to elsewhere in the Delta — provides an approach to help address this need.
The biological deserts fallacy: Cities in their landscapes contribute more than we think to regional biodiversity. BioScience 71 (2) . SFEI Contribution No. 1031.2021.
Cities are both embedded within and ecologically linked to their surrounding landscapes. Although urbanization poses a substantial threat to biodiversity, cities also support many species, some of which have larger populations, faster growth rates, and higher productivity in cities than outside of them. Despite this fact, surprisingly little attention has been paid to the potentially beneficial links between cities and their surroundings.
We identify five pathways by which cities can benefit regional ecosystems by releasing species from threats in the larger landscape, increasing regional habitat heterogeneity and genetic diversity, acting as migratory stopovers, preadapting species to climate change, and enhancing public engagement and environmental stewardship. Increasing recognition of these pathways could help cities identify effective strategies for supporting regional biodiversity conservation and could provide a science-based platform for incorporating biodiversity alongside other urban greening goals.
On the human appropriation of wetland primary production. Science of the Total Environment 785.2021.
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.
Sediment for Survival: A Strategy for the Resilience of Bay Wetlands in the Lower San Francisco Estuary. SFEI Contribution No. 1015. San Francisco Estuary Institute: Richmond, CA.2021.
This report analyses current data and climate projections to determine how much natural sediment may be available for tidal marshes and mudflats and how much supplemental sediment may be needed under different future scenarios. These sediment supply and demand estimates are combined with scientific knowledge of natural physical and biological processes to offer a strategy for sediment delivery that will allow these wetlands to survive a changing climate and provide benefits to people and nature for many decades to come. The approach developed in this report may also be useful beyond San Francisco Bay because shoreline protection, flood risk-management, and looming sediment deficits are common issues facing coastal communities around the world.
The resilience of San Francisco Bay shore habitats, such as tidal marshes and mudflats, is essential to all who live in the Bay Area. Tidal marshes and tidal flats (also known as mudflats) are key components of the shore habitats, collectively called baylands, which protect billions of dollars of bay-front housing and infrastructure (including neighborhoods, business parks, highways, sewage treatment plants, and landfills). They purify the Bay’s water, support endangered wildlife, nurture fisheries, and provide people access to nature within the urban environment. Bay Area residents showed their commitment to restoring these critical habitats when they voted for a property tax to pay for large-scale tidal marsh restoration. However, climate change poses a great threat, because there may not be enough natural sediment supply for tidal marshes and mudflats to gain elevation fast enough to keep pace with sea-level rise.
Trees and Hydrology in Urban Landscapes. SFEI Contribution No. 1034. San Francisco Estuary Institute: Richmond, CA.2021.
Effective implementation of urban greening strategies is needed to address legacies of landscape change and environmental degradation, ongoing development pressures, and the urgency of the climate crisis. With limited space and resources, these challenges will not be met through single-issue or individual-sector management and planning. Increasingly, local governments, regulatory agencies, and other urban planning organizations in the San Francisco Bay Area are expanding upon the holistic, portfolio-based, and multi-benefit approaches.
This effort, presented in the Trees and Hydrology in Urban Landscapes report, seeks to build links between stormwater management and urban ecological improvements by evaluating how complementary urban greening activities, including green stormwater infrastructure (GSI) and urban tree canopy, can be integrated and improved to reduce runoff and contaminant loads in stormwater systems. This work expands the capacity for evaluating engineered GSI and non-engineered urban greening within a modeling and analysis framework, with a primary focus on evaluating the hydrologic benefit of urban trees. Insights can inform stormwater management policy and planning.
Delta Landscapes Primary Production: Past, Present, Future. SFEI Contribution No. 988. San Francisco Estuary Institute: Richmond, CA.2020.
This report describes the Delta Landscapes Primary Production project, which quantifies how landscape change in the Delta has altered the quantity and character of primary production. Combining historical and modern maps with simple models of production for five dominant plant and algae groups, we estimate primary production across the hydrologically connected Delta. We evaluate changes in primary production over time (between the early 1800s and early 2000s), between wet and dry years, and with future targets for landscape-scale restoration. For managers in the Delta, restoring historical patterns of primary productivity is a means to better support native fish and other wildlife. To better equip decision makers in managing for improved primary production, this study offers historical context and the best available science on the relative production value of habitat types and their configurations.
Integrating Planning with Nature: Building climate resilience across the urban-to-rural gradient. SFEI Contribution No. 1013.2020.
Making Nature's City. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.2019.
Cities will face many challenges over the coming decades, from adapting to a changing climate to accommodating rapid population growth. A related suite of challenges threatens global biodiversity, resulting in many species facing extinction. While urban planners and conservationists have long treated these issues as distinct, there is growing evidence that cities not only harbor a significant fraction of the world’s biodiversity, but also that they can also be made more livable and resilient for people, plants, and animals through nature-friendly urban design.
Urban ecological science can provide a powerful tool to guide cities towards more biodiversity-friendly design. However, current research remains scattered across thousands of journal articles and is largely inaccessible to practitioners. Our report Making Nature’s City addresses these issues, synthesizing global research to develop a science-based approach for supporting nature in cities.
Using the framework outlined in the report, urban designers and local residents can work together to connect, improve, and expand upon city greenspaces to better support biodiversity while making cities better places to live. As we envision healthier and more resilient cities, Making Nature’s City provides practical guidance for the many actors who together will shape the nature of cities.
Building Ecological Resilience in Highly Modified Landscapes.2018.
Ecological resilience is a powerful heuristic for ecosystem management in the context of rapid environmental change. Significant efforts are underway to improve the resilience of biodiversity and ecological function to extreme events and directional change across all types of landscapes, from intact natural systems to highly modified landscapes such as cities and agricultural regions. However, identifying management strategies likely to promote ecological resilience remains a challenge. In this article, we present seven core dimensions to guide long-term and large-scale resilience planning in highly modified landscapes, with the objective of providing a structure and shared vocabulary for recognizing opportunities and actions likely to increase resilience across the whole landscape. We illustrate application of our approach to landscape-scale ecosystem management through case studies from two highly modified California landscapes, Silicon Valley and the Sacramento–San Joaquin Delta. We propose that resilience-based management is best implemented at large spatial scales and through collaborative, cross-sector partnerships.
Sediment Supply to San Francisco Bay. SFEI Contribution No. 842. San Francisco Estuary Institute : Richmond, CA.2018.
Translating Science-Based Restoration Strategies into Spatially-Explicit Restoration Opportunities in the Delta (2018 Bay-Delta Science Conference Presentation).2018.
In a previous report titled “A Delta Renewed” we offered a collection of guidelines for science-based ecological restoration in the Sacramento-San Joaquin Delta that emphasized restoring or emulating natural processes, anticipating future changes associated with climate change, establishing appropriate configurations of habitat types at the landscape scale, and utilizing a variety multi-benefit management strategies. In this talk, we present on our recent work to support regional restoration planning efforts by developing a repeatable process for using these guidelines to identify spatially-explicit restoration opportunities. The process is largely GIS-based and utilizes spatial data on existing land cover and conservation status, habitat configuration (including patch sizes and distances), surface elevations (including depth of subsidence), and future changes in tidal elevations associated with sea-level rise. By distilling generalized guidelines into spatially-explicit opportunities, we hope to provide a practical tool for incorporating science into planning. To that end, these new methods are currently being piloted through planning efforts focused on the Central Delta Corridor and the McCormack Williamson Tract, and are also being used to assist with the quantification of ecological restoration potential in the Delta Plan Ecosystem Amendment.
Presentation recording: available here.
Delta Landscapes: A Delta Renewed User Guide. SFEI Contribution No. 854.2017.
A Delta Renewed User Guide aims to increase the accessibility of the technical findings in A Delta Renewed for easier application to restoration and conservation efforts across the Delta. The recommendations in A Delta Renewed focus on landscape-scale ecological guidance. We present three examples of how the information in A Delta Renewed might be used to address different management and restoration questions. Because of the complexity of the Delta system, this guide does not address all possible questions and does not replace the need for detailed, site-specific data and expertise. Rather, it shows how the information in A Delta Renewed might provide a common foundation for restoration planning.
The User Guide was written for a broad audience, including restoration practitioners, landowners, and local, state and federal agencies. The guide provides a step-by-step path through A Delta Renewed; a user is walked through how to apply the findings of the report via a series of steps to address each of the three restoration and management questions. This process is intended to help the user access regionally-specific recommendations and strategies to plan and manage future Delta landscapes that can support desired ecological functions over the long term.
The goal of A Delta Renewed and this guide is not to recreate the Delta of the past. Rather, the objective is to understand how we can re-establish or mimic important natural processes and patterns within this altered system to support desirable ecological functions (such as healthy native fish populations, a productive food web, and support for endangered species), now and into the future.
Delta Landscapes Executive Summary. SFEI Contribution No. 853.2017.
Re-Oaking Silicon Valley: Building Vibrant Cities with Nature. SFEI Contribution No. 825. San Francisco Estuary Institute: Richmond, CA.2017.
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.
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.2016.
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.
Ecological implications of modeled hydrodynamic changes in the upper San Francisco Estuary: Phase II Technical Memorandum. SFEI Contribution No. 786.2016.
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.
Estuaries: Life on the edge. In Ecosystems of California. Ecosystems of California. University of California Press: Berkeley, CA. pp 359-388.2016.
Primary Production in the Delta: Then and Now. San Francisco Estuary and Watershed Science 14 (3).2016.
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.
Landscape Resilience Framework: Operationalizing Ecological Resilience at the Landscape Scale. SFEI Contribution No. 752. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.. 2015.
Vision for a Resilient Silicon Valley Landscape. SFEI Contribution No. 753.. 2015.
A Delta Transformed: Ecological Functions, Spatial Metrics, and Landscape Change in the Sacramento-San Joaquin Delta. SFEI Contribution No. 729. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.2014.
Reducing Methylmercury Accumulation in the Food Webs of San Francisco Bay and Its Local Watersheds. SFEI Contribution No. 707. San Francisco Estuary Institute: Richmond, CA.2014.
Seasonal and annual trends in forage fish mercury concentrations, San Francisco Bay. Science of the Total Environment 444, 591-601.2013.
Seasonal and annual trends in forage fish mercury concentrations, San Francisco Bay. Science of the Total Environment 444, 591-601.2013.
Reducing methylmercury accumulation in the food webs of San Francisco Bay and its local watersheds. Environmental Research 119, 3-26.2012.
Water Quality in South San Francisco Bay, California: Current Condition and Potential Issues for the South Bay Salt Pond Restoration Project. Reviews of Environmental Contamination and Toxicology 206, 115-147 . SFEI Contribution No. 610.2010.
Spatial trends and impairment assessment of mercury in sport fish in the Sacramento-San Joaquin Delta Watershed. Environmental Pollution . SFEI Contribution No. 575.2009.
Mercury and Methylmercury Processes in North San Francisco Bay Tidal Wetland Ecosystems. SFEI Contribution No. 449. San Francisco Estuary Institute: Oakland, CA.2008.
California Bay-Delta Authority Fish Mercury Project, Year 2 (2006) Annual Report. Sport Fish Sampling and Analysis. SFEI Contribution No. 535. San Francisco Estuary Institute.2007.
Ecological Connections between Baylands and Uplands: Examples from Marin County. SFEI Contribution No. 521.2007.
The Relationship between Landscape Features and Sport Fish Mercury in the Sacramento-San Joaquin Delta Watershed. SFEI Contribution No. 534. San Francisco Estuary Institute.2007.
Environmental threats to tidal marsh vertebrates of the San Francisco Bay Estuary. Studies in Avian Biology 32, 176-339 . SFEI Contribution No. 489.2006.
First evidence of conspecific brood parasitism in song sparrows with comments on methods sufficient to document this behavior. Condor . SFEI Contribution No. 490.2006.
Mercury in biosentinel fish in San Francisco Bay: First-year project report. SFEI Contribution No. 520.2006.
Trophic adaptations in sparrows and other vertebrates of tidal marshes. Studies in Avian Biology . SFEI Contribution No. 500.2006.
A biogeographic pattern in sparrow bill morphology: parallel adaptation to tidal marshes. Evolution 59, 1588-1595 . SFEI Contribution No. 447.2005.
Mercury and Methylmercury Processes in North San Francisco Bay Tidal Wetland Ecosystems. CalFed with San Francisco Estuary Institute as primary contractor.2005.
The tidal marsh food web. SFEI Contribution No. 472. University of California: Berkeley, CA. p 12 pp.. 2002.