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Map interpretation and processing were completed in August of 2003 and 9 separate digital habitat maps were constructed. Approximately 90 km2 of archived multibeam data and 50 km2 of sidescan sonar data were interpreted for habitat characterization. Ninety-one distinct estuarine benthic habitat types were identified and Bay-floor samples, collected by the USGS and NOS, were used to document substrate type and “groundtruth” habitat interpretations. Additionally, generalized habitat descriptions and codes were developed by MLML and NOAA to aid in development of habitat/fish associations. The defined habitats typically range between 10 and 30 m of water depth and deepen to approximately 50 m at the northern extent of the survey area. Modern sedimentation from fluvial input and tidal scouring has resulted in a dynamic and complex Bay-floor. Strong currents have produced large sediment wave fields, rippled sediment patches, and scoured channel floors and walls. Soft habitats composed primarily of mud and/or sand dominate the region while hard rocky and mixed habitats are relatively rare and occur mainly in shallow areas adjacent to peninsulas and islands. Anthropogenic effects such as debris fields and dredging are distinctly displayed in the data and delineated on the habitat maps. Among geophysical data sets, the sidescan sonar data provided the best textural information while the multibeam bathymetry provided the best Bay-floor relief information and imaged the dynamic bedforms and scoured features especially well.
In addition to this habitat mapping effort, and because eelgrass had been identified as a significant subtidal habitat, the Eelgrass Pilot Recovery Project was initiated in the Spring of 2003. This pilot project was designed to fill in critical information gaps and was integrated with a larger Bay-wide Eelgrass Research Project coordinated by NMFS. The purpose of the pilot recovery project was to provide recovery rate data for planning of restoration projects, which provides the basis for computation of interim lost resource services and restoration planning. The population ecology portion of the project expanded the investigation into previously identified annual and perennial growth forms of eelgrass over large areas of the Bay. This fact is important since an unusually high prevalence of annuals would dramatically alter options for restoration and expectations for management as west coast restoration strategies have heretofore been based on perennial growth strategies. In addition to this field work a literature review eelgrass research in San Francisco Bay was compiled.
For a more detailed description of these projects please see the following reports:
- Greene, H.G., J. J. Bizzarro. Moss Landing Marine Laboratories. Benthic Habitat Maps of San Francisco Bay Interpreted from Multibeam Bathymetric Images and Side-scan Sonar Mosaics. October 1, 2003.
- Wyllie-Echeverria, S., M. Fonseca. Eelgrass (Zostera marina L.) research in San Francisco Bay, California from 1920 to the present. February 2003.
- Fonseca, M., S. Wyllie-Echeverria, C. Addison, T. Wyllie-Echeverria. NOAA Joint Pilot Project on Eelgrass (Zostera marina L.) Recovery in San Francisco Bay. September 30, 2003.
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Significant Habitats
Below you will find brief descriptions of some subtidal habitats within San Francisco Bay. It is not intended to be a complete listing of all significant subtidal habitats within the Bay, rather it represents the current focus areas of the NOS partnership project and areas that could be impacted by development and maintenance of an expanding commercial infrastructure within the Bay. Various habitat data layers and themes are featured in the ArcView portion of this project in an effort to better focus subtidal management goals. As more data resources become available this chapter will be expanded to include additional subtidal habitats of significant interest to NOAA and its regional partners.
Eelgrass
Eelgrass is a flowering plant that grows underwater in estuaries and in shallow coastal areas. In San Francisco Bay, eelgrass beds are considered to be a valuable shallow-water habitat, providing shelter, feeding, or breeding habitat for many species of invertebrates, fishes, and some waterfowl. Eelgrass beds supply organic material to nearshore environments, and their root systems stabilize area sediments. These plants grow in relatively few locations within the Bay and require special conditions to flourish. Cultivation of eelgrass is difficult and efforts to grow eelgrass in San Francisco Bay thus far have not succeeded.
Threats to Eelgrass Beds:
- Dredging is one of the greatest threats to eelgrass. Not only are the plants removed, but the entire physical, biological, and chemical structure of the ecosystem is changed. Plumes of silt bury plants, smother animals and reduce light penetration.
- Shoreline or over-water construction changes the shoreline in ways that can alter the absorption of wave energy, erode the bottom, or increase turbidity. Structures built over the water also prevent eelgrass from getting enough sunlight.
- Pollution causes increased nutrient-loading, which causes excessive epiphyte growth on eelgrass blades, blocking out light; herbicide run-off can kill or damage eelgrass plants.
- Oil spills cause eelgrass plants to lose their leaves.
- Species invasion by plants introduced from other areas by humans will crowd and displace native plants.
- Electricity plants and other power generators that use seawater as a coolant, pump warm water back into the sea where it can kill eelgrass.
- Logging, particularly clearcutting in watersheds increases sedimentation and turbidity in estuaries far downstream.
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Oyster Reefs
The small native oyster (Ostrea lurida) was once abundant in many estuaries along the west coast, including a large population in San Francisco Bay. Loss of habitat, overharvesting, and degraded water quality have almost completely depleted the Bay's native oyster population; reducing a once-dominant local fishery resource to a few scattered, remnant populations. Because oyster reefs function as essential bottom communities in the Bay, this oyster decline led to the loss of extensive three-dimensional habitat important to a myriad of fish and invertebrates. The loss of oyster reefs caused a cascading series of impacts to Bay food webs. Also lost was the ecological role oysters play as filter feeders, transferring phytoplankton and other suspended solids from the water column to the sediments and enabling nutrient transfer and increased water clarity.
For information on oyster reef restoration, visit Save The Bay's Native Oyster Project. This is a highly collaborative effort, combining environmental nonprofit organizations, university researchers, and Bay area residents. Partners include Restore America's Estuaries, the NOAA Community-Based Restoration Program, NOAA Fisheries, San Francisco State University, and the California Department of Fish and Game.
NOAA Restoration Center Oyster Restoration Projects (pdf)
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Rocky Reefs, Ledges and Pinnacles
Rocky reefs, ledges and pinnacles can be found throughout San Francisco Bay. Rocky reefs are mainly concentrated at the entrance to the Bay; rock walls and ledges are found in the North and Central Bay; and rocky pinnacles are found just inside the Golden Gate Bridge, off Richmond, and in San Rafael Bay. The rocky reefs, ledges, and pinnacles support dense populations of algae and invertebrates and concentrations of rockfish, striped bass, and bait fish such as the Northern anchovy and topsmelt. One of the Bay's most productive areas, and the most popular site among sport fishermen, is a series of four submerged rocks located between the Golden Gate Bridge and Alcatraz Island. The Bay Rocks (Blossom Rock, Harding Rock, Arch Rock, and Shag Rocks) are bedrock outcrops that extend above 40' elevation, as referenced to mean lower low water (MLLW) vertical datum. The Harbor Safety Committee and the U.S. Army Corps of Engineers (ACOE) considers these rocks a hazard to navigation and have recommended that these rocks be either lowered or removed. However, very little is known about the implications that the removal of this habitat may have on fish and other wildlife.
Shifting Shoals and Shattered Rocks–How Man Has Transformed the Floor of West-Central San Francisco Bay. 2004. By John L. Chin, Florence L. Wong, and Paul R. Carlson
Multibeam Data and Socio-Economic Issues in West-Central San Francisco Bay
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