Although nutrient supply often underlies long-term changes in aquatic primary production, other regulatory processes can be important. The Sacramento-San Joaquin River Delta, a complex of tidal waterways forming the landward portion of the San Francisco Estuary, has ample nutrient supplies, enabling us to examine alternate regulatory mechanisms over a 21-yr period. Delta-wide primary productivity was reconstructed from historical water quality data for 1975-1995. Annual primary production averaged 70 g C m Ϫ2 , but it varied by over a factor of five among years. At least four processes contributed to this variability: (1) invasion of the clam Potamocorbula amurensis led to a persistent decrease in phytoplankton biomass (chlorophyll a) after 1986; (2) a long-term decline in total suspended solids-probably at least partly because of upstream dam construction-increased water transparency and phytoplankton growth rate; (3) river inflow, reflecting climate variability, affected biomass through fluctuations in flushing and growth rates through fluctuations in total suspended solids; and (4) an additional pathway manifesting as a long-term decline in winter phytoplankton biomass has been identified, but its genesis is uncertain. Overall, the Delta lost 43% in annual primary production during the period. Given the evidence for food limitation of primary consumers, these findings provide a partial explanation for widespread Delta species declines over the past few decades. Turbid nutrient-rich systems such as the Delta may be inherently more variable than other tidal systems because certain compensatory processes are absent. Comparisons among systems, however, can be tenuous because conclusions about the magnitude and mechanisms of variability are dependent on length of data record.Phytoplankton primary productivity in lakes, estuaries, and the ocean plays an essential role in element cycling, water quality, and food supply to heterotrophs (Cloern 1996). Although we implicitly recognize primary productivity as a time-varying process, much of our effort to measure and understand this variability has focused on time scales of 1 yr or less. How much does annual primary production vary from year to year or over periods of decades, and what are the underlying mechanisms of variability at these longer time scales? These time scales are of particular interest from a practical viewpoint: they span the period over which we must separate anthropogenic influences from natural variability in order to understand the effects of our current use of water resources. Long-term studies of annual primary production in individual systems can also help us to understand

Primary productivity was measured monthly at 6 sites within San Francisco Bay, USA, throughout 1980. The 6 sites were chosen to represent a range of estuarine environments with respect to salinity, phytoplankton community composition, turbidity, and water depth. Annual net production over the photic zone ranged from 95 to 150 g C m-2, and was highest in regions of lowest turbidity. Daily photic zone net productivity PN,, ranged from 0.05 to 2.2 g C m-2 d-', and was significantly correlated with the composite parameter B I,/& (where B = phytoplankton biomass; I, = daily surface insolation; E = attenuation coefficient). Lnear regression of PN,, against B Io/€ indicated that most (82 %) of the spatio-temporal variability in primary productivity within this estuary is explained by variations in light availability and phytoplankton biomass. We also calculated annual water-column net productivity PN, as a fraction of annual gross productivity PGx The ratio PN,, : PG, was inversely related to the ratio of water depth H to annual mean photic depth Z,. This linear relation indicates that the watercolumn of San Francisco Bay is a net photosynthetic source of organic carbon only when the ratio H : Z, < 6. In deep turbid habitats, where H : Tp > 6 , respiratory loss exceeds productivity. Thus, 2 empirical formulations allow us to estimate productivity over the photic zone and water column from simple properties that are easily measured.

We have previously shown that primary productivity in San Francisco Bay, USA, is highly correlated with phytoplankton biomass B (chlorophyll a concentration) and an index of light avallability in the photic zone, 2, I, (photic depth times surface irradiance). To test the generality of this relation, we compiled data from San Francisco Bay and 5 other USA estuarine systems (Neuse and South Rivers, Puget Sound, Delaware Bay and Hudson River Plume), and regressed daily produclvity J ' P (mg C m-2 d-') against the composite parameter B Z, I,. Regressions for each estuary were significant and typically over 80 % of the varialon in P was correlated with variations in B Z,I,. Moreover, the pooled data (n = 211) from 4 estuaries where methodologies were comparable fell along one regression line ( r 2 = 0.82), indicating that primary productivity can be estimated in a diversity of estuarine waters from simple measures of phytoplankton biomass and hght availability. This implies that physiological variabhty (e. g. responses to variations in nutrient availabhty, temperature, sahnity, photoperiod) is a secondary control on phytoplankton production in nutrient-rich estuaries, and that one empirical function can be used to estimate seasonal variations in productivity or to map productivity along estuarine gradients of phytoplankton biomass and turbidity.

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