San Francisco Estuary and Watershed Science

Abstracts are not associated with Essays. —the SFEWS Editors

Conservation efforts and other land-management decisions are often intended to provide multiple benefits, but real or perceived trade-offs between goals can increase conflict and limit the practice of Multiple-Benefit Conservation. To support decision-making, policy, and management in the Sacramento–San Joaquin River Delta of California, where multiple potentially conflicting goals and values have been identified, we developed a flexible framework for quantifying the benefits and trade-offs that result from landscape change, implemented as an open-source R package. Integrating multiple data sets and methods, we developed metrics that represent (1) agricultural livelihoods, (2) water quality, (3) climate-change resilience, and (4) biodiversity support benefits and then projected the net effects on each metric of three alternative Delta landscapes. Each alternative represented changes that could result by 2050 from meeting habitat-restoration targets in the Delta Plan for riparian and non-tidal wetlands, the continued expansion of perennial crops, or a combination of the two. We found that habitat restoration would provide significant biodiversity support benefits and some climate-change resilience and water-quality benefits without significant trade-offs for agricultural livelihoods, while the continued expansion of perennial crops would provide significant benefits to agricultural livelihoods with simultaneous trade-offs to climate-change resilience and a mix of benefits and trade-offs for water-quality metrics. The combined alternative illustrated the interaction between restoration and perennial crop expansion, with still significant but reduced benefits to both agricultural livelihoods and biodiversity support. Our results provide insights into the effects of each of these drivers of landscape change, alone and in combination, with implications for policy and management to support the practice of Multiple-Benefit Conservation in the Sacramento–San Joaquin River Delta. Our framework serves as a foundation for future collaborative development among scientists, managers, policy-makers, and other interested parties to facilitate evaluation of a more comprehensive set of metrics across new alternative landscapes.

Increases in water temperature caused by climate change will challenge the management of water and species in the San Francisco Estuary. Our goals were to describe spatial and seasonal patterns in water temperature across the upper estuary, and evaluate how temperature stress and suitability vary across the aquatic ecosystem. We synthesized 10 years of continuous water-temperature data at 75 stations across six regions of the estuary between 2010 and 2019. We identified stressful temperature thresholds for species of interest using published physiological limits and observed distributions, including Endangered Species Act-listed native fishes (e.g., osmerids, salmonids), native fishes (e.g., cyprinids), non-native species (e.g., centrarchids, bivalves), and nuisance species such as invasive aquatic vegetation, and harmful cyanobacteria. We then quantified thermal stress across varying spatial and temporal scales and metrics. Analyses indicated there were detectable regional temperature differences, and that Suisun Bay was the only region to provide regular thermal refuge during the warmer parts of the year, though portions of the confluence and Suisun Marsh also provided potential thermal refuge during summer/fall and during cooler parts of the day. Meanwhile, the Central and South Delta experienced the warmest temperatures, exceeding thresholds for listed species throughout summer and early fall. We found that listed species such as juvenile salmonids and osmerids experience more thermal stress across a number of metrics. Fishes with higher heat tolerance (including non-natives and select natives), aquatic vegetation, and Microcystis (a harmful cyanobacteria) had the lowest average number of thermal stress days. This study demonstrates that the estuary is already exhibiting stressful conditions for species of concern, and thermal stress will only increase with climate change. We identify at what times of year and where the estuary may provide refuge from thermal stress conditions across a variety of species, which has important implications for restoration prioritization, design, and species management.

Climate change is having widespread negative effects on freshwater environments, including an increasing frequency and severity of droughts. Drought conditions present unique challenges for the federally listed Central Valley Chinook Salmon (Oncorhynchus tshawytscha), which use the already limited floodplain in the Central Valley as rearing habitat. In this study, we examined how differing hydrologic conditions influence the run composition of juvenile Chinook Salmon in the floodplain (Yolo Bypass) versus the mainstem of the Sacramento River. Juvenile Chinook Salmon from the Yolo Bypass and areas along the Sacramento River were identified to the genetically distinct runs (fall, late fall, winter, and spring) from 2013-2019. We found overwhelmingly that Length at Date methods are misclassifying fish, particularly late fall and spring run fish, and winter-run fish in the bypass. Using this genetic run-timing, we found that the abundances of endangered runs (spring and winter) are reduced during low flow periods in both the bypass and Sacramento River. Even during drought conditions, juvenile Chinook Salmon rearing in the Yolo Bypass attained significantly larger sizes than those in the Sacramento River. When comparing fish growth across time, during wet years fish in the bypass start smaller and get significantly larger over the course of the year as compared to drought years, while during both wet and dry years fish in the Sacramento River largely attain a smaller size than the Yolo Bypass fish. This suggests that floodplain habitat is critical to maintaining diversity in juvenile Chinook Salmon.

Emergent tidal wetlands are declining globally as a result of sea level rise and land use change. This habitat loss can keenly affect rare plant species within wetlands, and may require restoration to meet species recovery goals related to retaining populations throughout species' ranges. Soft salty bird’s-beak (Chloropyron molle ssp. molle) is a federally- and state-endangered hemi-parasitic plant that occurs at the upper marsh transition zone in the San Francisco Bay–Delta, California, USA. We combined field surveys to document habitat associations and trends in abundance with genomic surveys to understand patterns of genetic structure in this rare endemic. We found that C. molle ssp. molle persisted at nine previously occupied marsh sites, although four sites (Hill Slough, MOTCO East, Fagan Marsh, and Joice Island) were smaller in population size than when surveyed in the 1990s. Additionally, twelve sites contained plots with suitable but unoccupied habitat that could be further assessed for restoration. Genomic analysis of over 40,000 single-nucleotide polymorphisms (SNPs) and 253 individuals grouped C. molle ssp. molle into six to seven regional genetic clusters with isolation by distance, and confirmed that C. molle ssp. molle is genetically distinct from adjacent populations of its closest relative (C. molle ssp. hispidum). The western-most C. molle ssp. molle sites of Point Pinole and Fagan Marsh were the most genetically and geographically isolated and had the lowest genome-wide diversity. Heterozygosity in sets of genes associated with tidal elevation, salinity, and annual and summer precipitation varied independently across populations. Overall, these genomic patterns indicate that selecting donor sites with similar environmental conditions and utilizing composite seeding approaches from multiple sites could allow for local adaptation to a range of possible environmental conditions. This comprehensive survey of habitat and genomic patterns can allow for the development of restoration actions and build climate-adaptation planning to help prevent the loss of a rare plant.

Deposition of inorganic sediment is essential for the sustainability of tidal salt marshes. Understanding variability in sediment sources and the processes of sediment delivery to salt marshes are high priorities for decision-makers responsible for managing sediment and conserving and restoring marshes. Research on sediment transport to marshes is published in technical journals, but these scientific findings must be translated and communicated to inform critical decisions related to managing sediment in estuaries. We convened a diverse group of collaborators—including natural-resource managers, regulators, scientists, and restoration planners and practitioners—to review and interpret the results of previously published field investigations on and around the salt marsh at China Camp State Park in Marin County, California. We discussed and translated key results of those studies using new graphics and more accessible language. Here, we present a general introduction to the topic of sediment delivery to salt marshes, background descriptions of the China Camp marsh and the physical processes that we characterized there, key scientific conclusions, and proposed management implications. Key conclusions include (1) bay shallows are an important but variable source of marsh sediment, (2) flood tides and waves move sediment across the bay–marsh edge, (3) tidal creeks may not always import sediment to the marsh platform, and (4) protective effects of marsh vegetation depend on species and season. China Camp marsh is one of the last remaining pre-colonial salt marshes in the San Francisco Estuary and is unique in being relatively unmodified by humans and in retaining an unimpeded transition into natural uplands. Additional studies in a variety of marshes with different attributes and sediment regimes will broaden understanding of how best to conserve, manage, and restore tidal marshes that provide numerous ecosystem services to for humans and wildlife.