THERMAL DYNAMICS OF ESTUARINE PHYTOPLANKTON: 
A CASE STUDY OF SAN FRANCISCO BAY 
James E. Cloern, Brian E. Cole, Raymond L.J. Wong 
and Andrea E. Alpine 
U.S. Geological Survey 
Abstract 
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 persis¬ 
tently high, such that phytoplankton growth and productivity are 
severely limited by light availability, the phytoplankton popula¬ 
tion turns over slowly, and biological processes appear to be 
less important mechanisms of temporal change than physical pro¬ 
cesses associated with freshwater inflow and turbulent mixing. 
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 is high (up to 1-2 doublings d” 1 ) 
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 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 vari¬ 
ability is highly dynamic because of the short-term variability 
of tides. Other mechanisms of temporal variability in estuarine 
phytoplankton include zooplankton grazing, exchanges of micro¬ 
algae 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 
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