San Francisco Estuary and Watershed Science

A robust monitoring network that provides quantitative information about the status of imperiled species at key life stages and geographic locations over time is fundamental for sustainable management of fisheries resources. For anadromous species, management actions in one geographic domain can substantially affect abundance of subsequent life stages that span broad geographic regions. Quantitative metrics (e.g., abundance, movement, survival, life history diversity, and condition) at multiple life stages are needed to inform how management actions (e.g., hatcheries, harvest, hydrology, and habitat restoration) influence salmon population dynamics. The existing monitoring network for endangered Sacramento River winter-run Chinook Salmon (SRWRC, Oncorhynchus tshawytscha) in California’s Central Valley was compared to conceptual models developed for each life stage and geographic region of the life cycle to identify relevant SRWRC metrics. We concluded that the current monitoring network was insufficient to diagnose when (life stage) and where (geographic domain) chronic or episodic reductions in SRWRC cohorts occur, precluding within- and among-year comparisons. The strongest quantitative data exist in the Upper Sacramento River, where abundance estimates are generated for adult spawners and emigrating juveniles. However, once SRWRC leave the upper river, our knowledge of their identity, abundance, and condition diminishes, despite the juvenile monitoring enterprise. We identified six system-wide recommended actions to strengthen the value of data generated from the existing monitoring network to assess resource management actions: (1) incorporate genetic run identification; (2) develop juvenile abundance estimates; (3) collect data for life history diversity metrics at multiple life stages; (4) expand and enhance real-time fish survival and movement monitoring; (5) collect fish condition data; and (6) provide timely public access to monitoring data in open data formats. To illustrate how updated technologies can enhance the existing monitoring to provide quantitative data on SRWRC, we provide examples of how each recommendation can address specific management issues

We quantified the greenhouse-gas (GHG) emission and economic implications of alternative crop and wetland mosaics on a Sacramento–San Joaquin Delta island: Staten Island. Using existing GHG fluxes measurements for the Delta and biogeochemical models, we estimated GHG emissions for a range of scenarios, including the status quo, modified groundwater management, and incorporating rice and managed wetlands. For current land uses, emissions were predicted to vary greatly (48,000 to 105,000 t CO₂-e yr^{− 1}) with varying groundwater depth. GHG emissions were highest when water depth was 120 cm, the typical depth for a Delta island, and lowest if water table depth was shallowest (60 cm). In the alternate land-use scenarios, we simulated wetlands and rice cultivation in areas of highest organic-matter soils, greatest subsidence, and GHG emissions. For each scenario, we analyzed economic implications for the land-owner by determining profit changes relative to the status quo. We spatially assigned areas for rice and wetlands, and then allowed the Delta Agricultural Production (DAP) model to optimize the allocation of other crops to maximize profit. The scenario that included wetlands decreased profits 79% relative to the status quo but reduced GHG emissions by 43,000 t CO₂-e yr^{− 1} (57% reduction). When mixtures of rice and wetlands were introduced, farm profits decreased 16%, and the GHG emission reduction was 33,000 t CO₂-e yr^{− 1} (44% reduction). When rice was cultivated on 38% of the island, profit increased 12% and emissions were 22,000 t CO₂-e yr^{− 1} lower than baseline emissions (30% reduction). Conversion to a mosaic of wetlands and crops including rice could substantially reduce overall GHG emissions of cultivated lands in the Delta without greatly affecting profitability.

Current legislation and plans for the Sacramento–San Joaquin Delta (Delta) call for large-scale restoration of aquatic and terrestrial habitats, which will require significant changes in waterways, land uses, and cultural patterns. These re-made landscapes will be subject to a variety of new human uses, which Delta planning and adaptive management literature has yet to adequately consider. Failing to account for human uses and evolving place values can lead to diminished performance and public support for Delta restoration efforts.

Our empirical study examined restored and naturalized Delta landscapes using an integrative landscape approach that seeks to reconcile multiple goals and land-use agendas that span ecological, social, economic, and political domains. The research design consisted of six overlapping methods that included a planning, policy, and law review specific to the Delta; surveys and interviews with approximately 100 land managers, scientists, land-owners, law-enforcement personnel, agency representatives, and Delta residents; nine case studies of restored and naturalized delta landscapes; GIS mapping; and extensive field work.

Findings derived from the synthesis of these methods show that human uses of the Delta’s re-wilded landscapes are diverse and pervasive. Given the infrastructural and urbanized context of the region, these environments are subject to multiple and sometimes conflicting uses, perceptions, and place values. Though these myriad uses cannot be fully predicted or controlled (nor should they be), findings showed that more proactive and inclusive planning for human uses can encourage or discourage particular uses while also building constituency, support, and active engagement in ecological restoration efforts. We conclude that reconciling human uses with ecological recovery in the Delta will require a more localized, multi-functional, and creative approach to designing and adaptively managing these emergent landscapes. We recommend that more resources and experimental prototyping be dedicated to such work.

Fucus distichus, a rockweed common to the mid-intertidal shoreline within the San Francisco Estuary (previously known as F. gardneri), was injured during the Cosco Busan oil spill in November 2007 and subsequent clean-up actions. Restoration planning activities are underway to help recover F. distichus at sites within central San Francisco Bay where damage occurred. As a first step, we conducted shoreline surveys during the summers of 2012–2013 to map the occurrence of this rockweed. Of the 151.73 km of rocky shoreline within the central bay, F. distichus covered 32.16 km of shoreline. The alga generally occurred in narrow bands but formed expansive beds at locations with natural, flat bedrock benches. We also observed F. distichus on artificial substrata such as seawalls and riprap, but not on pilings. Samples of F. distichus from 11 sites throughout the central / east San Francisco Bay were genetically analyzed (microsatellite genotyping). The populations analyzed (1) had low genetic diversity, (2) the frequency of homozygotes was higher than expected (suggesting high inbreeding), and (3) also displayed geographic population structure, in part driven by very small differences in the midst of extremely low within-population genetic diversity. However, these genetic data do not raise concerns for restoration methods in terms of choosing donor populations and mixing F. distichus from different sites within the central bay. The choice of donor populations should be based on practical criteria for effective restoration; individuals will nonetheless be taken from locations as nearby to donor sites as possible. Various locations throughout the central San Francisco Bay are composed of cobble or small riprap that are populated with F. distichus, which could provide efficient means of translocating rockweed for future restoration activities.