The recent invasion of San Francisco Bay by the suspension-feeding clam Putamocorbula amurensis has provided an opportunity to document the ecological consequences of a major biological disturbance. Previous work over the last two decades has shown that phytoplankton biomass in the upper estuary is low (2-3 mg Chl a m-3) during seasonal periods of high river flow and short residence time, and it is usually high (peak > 30 mg Chl a m-3) during the summer-autumn seasons of low river flow and long residence time. However since P. amurensis became widespread and abundant in 1987, the summer phytoplankton biomass maximum has disappeared, presumably because of increased grazing pressure by this newly introduced species. For the period 1977-l 990, mean estimated primary production was only 39 g C mm2 yr-' during years when bivalve suspension feeders were abundant (>2,000 mm2), compared to 106 g C m-2 yr-' when bivalves were absent or present in low numbers. These observations support the hypothesis that seasonal and interannual fluctuations in estuarine phytoplankton biomass and primary production can be regulated jointly by direct physical effects (e.g. river-driven transport) and trophic interactions (episodes of enhanced grazing pressure by immigrant populations of benthic suspension feeders).

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San Francisco Bay has a high degree of spatial variability in physical properties (e.g. suspended sediment concentrations, water depths, vertical mixing rates) that affect biologcal processes. We used this setting to test the hypothesis that light avdability is the primary control of phytoplankton growth in this turbid nutrient-rich estuary. In situ incubations (24 h), designed to simulate vertical mixing over the water column at 2 rates, were done at 4 sites. The photic depth to mixed depth ratio (G:&,,) at the 4 sites ranged from 0.12 to 1.1. Phytoplankton growth rates were esbmated by 14c assimilation and by changes in cell number. Growth rates were highest (approximately 2 divisions d-l) where the photic depth was large relative to the mixed depth, and small or negative where Zp:& was small. Growth rate increased with total daily light exposure and fit a hyperbolic funcbon that predicts maximum specific growth rate of about 2 &visions d-' and a compensation irradiance of about 1.4 Einst. m-' d-'.

Detailed surveys throughout San Francisco Bay over an annual cycle (1980) show that seasonal variations of phytoplankton biomass, community composition, and productivity can differ markedly among estuarine habitat types. For example, in the river-dominated northern reach (Suisun Bay) phytoplankton seasonality is characterized by a prolonged summer bloom of netplanktonic diatoms that results from the accumulation of suspended particulates at the convergence of nontidal currents (i.e. where residence time is long). Here turbidity is persistently high such that phytoplankton growth and productivity are severely limited by light availability, the phytoplankton population turns over slowly, and biological processes appear to be less important mechanisms of temporal change than physical processes associated with freshwater inflow and turbulent mixing. The South Bay, in contrast, is a lagoon-type estuary less directly coupled to the influence of river discharge. Residence time is long (months) in this estuary, turbidity is'lower and estimated rates of population growth are high (up to l-2 doublings d-r), but the rapid production of phytoplankton biomass is presumably balanced by grazing losses to benthic herbivores. Exceptions occur for brief intervals (days to weeks) during spring when the water column stratifies so that algae retained in the surface layer are uncoupled from benthic grazing, and phytoplankton blooms develop. The degree of stratification varies over the neap-spring tidal cycle, so the South Bay represents an estuary where (1) biological processes (growth, grazing) and a physical process (vertical mixing) interact to cause temporal variability of phytoplankton biomass, and (2) temporal variability is highly dynamic because of the short-term variability of tides. Other mechanisms of temporal variability in estuarine phytoplankton include: zooplankton grazing, exchanges of microalgae between the sediment and water column, and horizontal dispersion which transports phytoplankton from regions of high productivity (shallows) to regions of low productivity (deep channels).Multi-year records of phytoplankton biomass show that large deviations from the typical annual cycles observed in 1980 can occur, and that interannual variability is driven by variability of annual precipitation and river discharge. Here, too, the nature of this variability differs among estuary types. Blooms occur only in the northern reach when river discharge falls within a narrow range, and the summer biomass increase was absent during years of extreme drought (1977) or years of exceptionally high discharge (1982). In South Bay, however, there is a direct relationship between phytoplankton biomass and river discharge. As discharge increases so does the buoyancy input required for density stratification, and wet years are characterized by persistent and intense spring blooms.