San Francisco Estuary and Watershed Science

This two-part special issue reviews the basic ecology of tidal wetlands in the San Francisco Estuary. Several articles highlight the well-preserved tracts of historic tidal marsh found at China Camp State Park and Rush Ranch Open Space Preserve. These two protected areas serve as important reference sites for wetland restoration and conservation and also comprise San Francisco Bay National Estuarine Research Reserve (SF Bay NERR). SF Bay NERR is part of the National Oceanic and Atmospheric Administration’s nationwide network of 28 estuarine research reserves (http://www.nerrs.noaa.gov) that all share common goals: (1) conducting standardized long-term monitoring, (2) supporting applied environmental research, (3) providing stewardship of estuarine natural resources, and (4) linking science with decision making in pursuit of effective solutions to coastal management problems.

Early restoration efforts in San Francisco Bay focused primarily on establishing appropriate elevations for plant recruitment, based on plant distributions in natural wetlands. Sites were graded and planted, and tidal connections were re-established with the expectation that restored wetlands would quickly resemble natural ecosystems. Over time, restoration efforts have evolved, with the realization that natural development of restoration sites is preferable, including a dense channel network and the accumulation of soils of appropriate texture. Bay restoration efforts also have grown substantially in size and scope. Whereas projects of 50 hectares were considered large in the 1980s, now many projects are 100s of hectares. Larger projects are on the scale of 1000s of hectares, with the largest approximately 6000 hectares (the South Bay Salt Pond Restoration Project). This massive increase in scale has brought enormous restoration opportunities, but it also has increased the complexity of restoration projects and highlighted the necessity of large-scale public involvement. Awareness of non-native plants at restoration sites is just one example of factors that have increased restoration complexity. Potential impacts of climate change also have moved to the forefront of restoration design, as sea-level rise and potential shifts in salinity are critical factors for long-term restoration planning.

Climate change will affect tidal wetlands with higher rates of sea-level rise and higher concentrations of salt in brackish and freshwater tidal systems, in addition to causing increases in atmospheric CO2 concentration, warmer temperatures, and shifts in precipitation. In the San Francisco Bay–Delta, the areas most likely to be affected—brackish and freshwater tidal wetlands—are also the sites with the majority of endemic plant species and the greater biodiversity and productivity. Effects on the San Francisco Bay– Delta estuary are complex and difficult to predict, but a few things are clear. Biodiversity of the tidal wetland system in the San Francisco Bay–Delta region will decline, with subsequent effects on ecosystem functioning and services. Altered plant production, physiological tolerances, and shifts in rates of mortality will modify wetland plant communities in ways not yet predictable. Lower ecosystem productivity from salinity increases will affect both primary and detrital-based food webs. Such changes will cascade via the food webs into invertebrate, bird, and pelagic systems. Tidal wetlands are especially sensitive to processes that climate change will alter. Several of these altered processes are exacerbated by water diversions from the Delta.

The San Francisco Bay estuary is highly urbanized, but it supports the largest remaining extent of tidal salt marshes on the west coast of North America as well as a diverse native bird community. San Francisco Bay tidal marshes are occupied by more than 113 bird species that represent 31 families, including five subspecies from three families that we denote as tidal-marsh obligates. To better identify the niche of bird species in tidal marshes, we present a review of functional groups based on foraging guilds and habitat associations. Foraging guilds describe the method by which species obtain food from tidal marshes, while habitat associations describe broad areas within the marsh that have similar environmental conditions. For example, the ubiquitous song sparrows (Alameda Melospiza melodia pusillula, Suisun M. m. maxillaris, and San Pablo M. m. samuelis) are surface-feeding generalists that consume prey from vegetation and the ground, and they are found across the entire marsh plain into the upland–marsh transition. In contrast, surface-feeding California black rails (Laterallus jamaicensis coturniculus) are cryptic, and generally restricted in their distribution to the mid- and high-marsh plain. Although in the same family, the endangered California clapper rail (Rallus longirostris obsoletus) has become highly specialized, foraging primarily on benthic fauna within marsh channels when they are exposed at low tide. Shorebirds such as the black-necked stilt (Himantopus mexicanus) typically probe in mud flats to consume macroinvertebrate prey, and are generally restricted to foraging on salt pans within the marsh plain, in ponds, or on mud flats during transitional stages of marsh evolution. The abundance and distribution of birds varies widely with changing water depths and vegetation colonization during different stages of restoration. Thus, tidal-marsh birds represent a rich and diverse community in bay marshes, with niches that may be distinguished by the food resources they consume and the habitats that they occupy along the tidal gradient.

The distribution of macroinvertebrates across a tidal gradient is described froma study of invertebrate distribution across tidal marsh sub-habitats, a non-quantitative survey of epifauna on intertidal rocky substrate, and a few additional observations and records from China Camp State Park, Marin County, California. In the tidal marsh study, invertebrates were sampled from distinct sub-habitat types: high-order channels, low-order channels, vegetated marsh plain, and natural levees adjacent to channels. Invertebrates were collected using a variety of trapping methods to account for capture biases associated with any one method. All common invertebrate taxa were significantly more abundant in a particular sub-habitat, and within each trapping method a few species accounted for most of the biomass. On intertidal rocks, 79% of the taxa identified to species or genus were exotic, but a few native species were common.

The Rush Ranch Open Space Preserve (Rush Ranch) is located at the northwestern edge of the Potrero Hills and includes the largest remaining undiked tidal wetland within the Suisun Marsh region of the San Francisco Estuary. The brackish tidal wetlands grade into the transitional vegetation and undeveloped grasslands of the Potrero Hills, and we describe diverse vegetation that reflects the estuarine position, land use history, and hydrogeomorphic complexity of the site.

We present a useful framework for future study of vegetation at this San Francisco Bay National Estuarine Research Reserve site. Rush Ranch includes four major estuarine geomorphic units that are widely distributed in the region and support vegetation: subtidal channel beds, fringing tidal marsh, tidal marsh plain and tidal marsh–terrestrial ecotone. These are distinguished by small variations in hydrology and elevation, as noted and described through field observations and historic vegetation-mapping data. We discuss vegetation within each of these landforms, considering each vegetation community as a function of changing physical environment and biological interactions. Past land use and exotic plant species invasions have substantially altered Rush Ranch's tidal marsh vegetation patterns. Our results indicate 27% of the current estuarine wetland-associated flora at Rush Ranch are exotic species, and several are highly invasive. Despite these influences, Rush Ranch’s position in the landscape provides important and increasingly rare habitat linkages between the tidal marsh and upland grasslands, which allows great potential for restoration and enhancement. We present a detailed flora and vegetation analysis by hydrogeomorphic setting to provide an ecological framework for future monitoring, research, and adaptive conservation management at Rush Ranch.