Phytoplankton blooms are prominent features of biological variability in shallow coastal ecosystems such as estuaries, lagoons, bays, and tidal rivers. Long-term observation and research in San Francisco Bay illustrates some patterns of phytoplankton spatial and temporal variability and the underlying mechanisms of this variability. Blooms are events of rapid production and accumulation of phytoplankton biomass that are usually responses to changing physical forcings originating in the coastal ocean (e.g., tides), the atmosphere (wind), or on the land surface (precipitation and river runoff). These physical forcings have different timescales of variability, so algal blooms can be short-term episodic events, recurrent seasonal phenomena, or rare events associated with exceptional climatic or hydrologic conditions. The biogeochemical role of phytoplankton primary production is to transform and incorporate reactive inorganic elements into organic forms, and these transformations are rapid and lead to measurable geochemical change during blooms. Examples include the depletion of inorganic nutrients (N, P, Si), supersaturation of oxygen and removal of carbon dioxide, shifts in the isotopic composition of reactive elements (C, N), production of climatically active trace gases (methyl bromide, dimethylsulfide), changes in the chemical form and toxicity of trace metals (As, Cd, Ni, Zn), changes in the biochemical composition and reactivity of the suspended particulate matter, and synthesis of organic matter required for the reproduction and growth of heterotrophs, including bacteria, zooplankton, and benthic consumer animals. Some classes of phytoplankton play special roles in the cycling of elements or synthesis of specific organic molecules, but we have only rudimentary understanding of the forces that select for and promote blooms of these species. Mounting evidence suggests that the natural cycles of bloom variability are being altered on a global scale by human activities including the input of toxic contaminants and nutrients, manipulation of river flows, and translocation of species. This hypothesis will be a key component of our effort to understand global change at the land-sea interface. Pursuit of this hypothesis will require creative approaches for distinguishing natural and anthropogenic sources of phytoplankton population variability, as well as recognition that the modes of human disturbance of coastal bloom cycles operate interactively and cannot be studied as isolated processes.

Phytoplankton bloom dynamics in coastal ecosystems: A review with some general lessons from sustained investigation of San Francisco Bay, California

Populations of native and introduced aquatic organisms in the San Francisco Bay/Sacramento- San Joaquin Delta Estuary ("BayJDelta") have undergone significant declines over the past two decades. De- creased river inflow due to drought and increased freshwater diversion have contributed to the decline of at least some populations. Effective management of the estuary's biological resources requires a sensitive indicator of the response to freshwater inflow that has ecological significance, can be measured accurately and easily, and could be used as a "policy" variable to set standards for managing freshwater inflow. Positioning of the 27~0 (grams of salt per kilogram of seawater) bottom salinity value along the axis of the estuary was examined for this purpose. The 2% bottom salinity position (denoted by X,) has simple and significant statistical relationships with annual measures of many estuarine resources, including the supply of phytoplankton and phytoplankton-derived detritus from local production and river loading; benthic macroinvertebrates (molluscs); mysids and shrimp; larval fish survival; and the abundance of planktivorous, piscivorous, and bottom-foraging fish. The actual mechanisms are understood for only a few of these populations. X, also satisfies other recognized requirements for a habitat indicator and probably can be measured with greater accuracy and precision than alternative habitat indicators such as net freshwater inflow into the estuary. The 2%~ value may not have special ecological significance for other estuaries (in the BayJDelta, it marks the locations of an estuarine turbidity maximum and peaks in the abundance of several estuarine organisms), but the concept of using near-bottom isohaline position as a habitat indicator should be widely applicable. Although X, is a sensitive index of the estuarine community's response to net freshwater inflow, other hydraulic features of the estuary also determine population abundances and resource levels. In particular, di - version of water for export from or consumption within the estuary can have a direct effect on population abundance independent of its effect on X,. The need to consider diversion, in addition to X,, for managing certain estuarine resources is illustrated using striped bass survival as an example. The striped bass survival data were also used to illustrate a related important point: incorporating additional explanatory variables may decrease the prediction error for a population or process, but it can increase the uncertainty in parameter estimates and management strategies based on these estimates. Even in cases where the uncertainty is currently too large to guide management decisions, an uncertainty analysis can identify the most practical direction for future data acquisition.

https://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/deltaflow/docs/exhibits/swrcb/swrcb_jassby1995.pdf

Isohaline Position as a Habitat Indicator for Estuarine Populations

The North Atlantic portunid crab Carcinus maenas (Linnaeus, 1758) has invaded the North Pacific Ocean following more than two centuries of global dispersal due to human activities. C. maenas was first collected in San Francisco Bay, California, in 1989–1990, where its distribution and prey selectivity were investigated in 1992–1994. It has become abundant in shallow, warm lagoons (which as favorable and retentive microhabitats may have served as invasion incubators) and spread throughout the north, central and south bays. It may have arrived in ballast water, on fouled ships, amongst algae with imported live bait or lobsters, or by intentional release; genetic comparisons of the Bay population with possible source populations may aid in defining the transport mechanism. C. maenas' eurytopic nature, its high breeding potential, and its diet and feeding behavior suggest the potential for extensive ecosystem alterations through predator-prey interactions, competition, disturbance, and indirect effects. Although both negative economic impacts through reduction or disruption of fisheries and positive impacts of providing bait and human-food fisheries have been documented in a few regions, the potential economic impacts in San Francisco Bay remain largely unknown.

Introduction, dispersal and potential impacts of the green crab Carcinus maenas in San Francisco Bay, California

Estimating suspended solids concentrations from backscatter intensity measured by acoustic Doppler current profiler in San Francisco Bay, California

Multiple indicators (Chl a, C : N ratios, [6L3C]POC, and two classes of lipid biomarker compounds- sterols and phospholipid ester-linked fatty acids) were used to evaluate spatial and temporal variations in the origin of particulate organic matter (POM) in the San Francisco Bay (SFB) estuary. Comparisons were made between the northern and southern subestuaries of SFB, as well as along the salinity gradient of northern SFB. Two sample types were collected-seston, which was used to characterize the bulk POM, and tissues of the suspension-feeding bivalve Potamocorbula amurensis -in order to evaluate the assimilable portion of the POM. Samples were collected around biological and physical events (phytoplankton blooms and freshwater inflow) thought to be the primary mechanisms controlling temporal variability in organic matter sources. Seston samples indicate that phytoplankton sources of POM are important throughout the entire SFB system, with additional inputs of organic matter from bacterial and terrestrial vascular plant sources delivered to the northern region. Analysis of biomarker compounds in- P. amurensis tissues indicates that phytoplankton supply a large fraction of the assimilable carbon to clams throughout SFB, although isotopic analysis of clam tissues suggests that the origin of this reactive carbon varies spatially and that freshwater algae are an important source of reactive organic matter to clams living in northern SFB.

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1995.40.1.0067

Molecular and isotopic tracers used to examine sources of organic matter and its incorporation into the food webs of San Francisco Bay

San Francisco Bay, the largest bay on the California coast, is a broad, shallow, turbid estuary comprising two geographically and hydrologically distinct subestuaries: the northern reach lying between the connection to the Pacific Ocean at the Golden Gate and the confluence of the Sacramento-San Joaquin River system, and the southern reach (herein called South Bay) between the Golden Gate and the southern terminus of the bay. The northern reach is a partially mixed estuary dominated by seasonally varying river inflow, and the South Bay is a tidally oscillating lagoon-type estuary. Freshwater inflows, highest during winter, generate strong estuarine circulation and largely determine water residence times. They also bring large volumes of dissolved and particulate materials to the estuary. Tidal currents, generated by mixed semidiurnal and diurnal tides, mix the water column and, together with river inflow and basin geometry, determine circulation patterns. Winds, which are strongest during summer and during winter storms, exert stress on the bay’s water surface, thereby creating large waves that resuspend sediment from the shallow bay bottom and, together with the tidal currents, contribute markedly to the transport of water masses throughout the shallow estuary.

J. W. Gartner

Papers

Environmental setting of San Francisco Bay