The role of ammonium and nitrate in spring bloom development in San Francisco Bay

The substantial inventory of nitrate (NO3) in San Francisco Bay (SFB) is unavailable to the resident phytoplankton most of the year due to the presence of ammonium (NH4) at inhibitory concentrations that prevents NO3 uptake. Low annual primary productivity in this turbid estuary is generally attributed to the poor irradiance conditions. However, this may not be the only cause; spring phytoplankton blooms occur irregularly in north SFB only when NH4 concentrations are low, <4 μmol L−1 and NO3 uptake by phytoplankton occurs. Field measurements and enclosure experiments confirm the NH4 inhibition process to be the cause of low NO3 utilization most of the year. Detailed analysis of spring blooms in three embayments of SFB over 3 years shows a consistent sequence of events that result in bursts of chlorophyll. The first requirement is improved irradiance conditions through stabilization of the water column by stratification or reduced tidal activity. Second, NH4 concentrations must be reduced to a critical range, 1 to 4 μmol L−1 through dilution by precipitation and by phytoplankton uptake. This enables rapid uptake of NO3 and subsequent increase in chlorophyll. The resulting bloom is due to both the initial uptake of NH4 and the subsequent uptake of NO3. The NO3 uptake step is crucial since it is the larger nitrogen source and uptake occurs at higher rates than that for NH4 at the concentrations that occur in SFB. Existing models of light-limited, non-nutrient limited productivity in SFB require modification to include the NH4 inhibition effect. From measured NH4 uptake rates and initial concentrations, calculations can be made to predict the length of time that favorable irradiance conditions are required for the phytoplankton population to reduce ambient NH4 concentrations to non-inhibiting concentrations and allow bloom formation to begin. For Suisun Bay, the time required is so long that blooms are unlikely in any season. For San Pablo and Central Bays, these times are too long in summer but sufficiently short in spring to allow bloom development, depending on the ambient NH4 concentration prior to the productivity season. NH4 sources to SFB are primarily anthropogenic, from agricultural drainage and sewage treatment plants, and if not sufficiently diluted by runoff and precipitation can prevent development of the spring phytoplankton bloom. Attention should be paid to the form of N making up dissolved inorganic nitrogen (DIN) in nutrient-rich estuaries.