Limnol. Oceanogr., 44(2), 1999, 295–308

Bacterioplankton abundance and metabolic characteristics were observed in northern San Francisco Bay, California, during spring and summer 1996 at three sites: Central Bay, Suisun Bay, and the Sacramento River. These sites spanned a salinity gradient from marine to freshwater, and sampling occurred during a period of seasonally declining river flow. The microbial measures included radio-labeled amino acid uptake (L-leucine, L-proline, Lserine), ectoenzyme activity (aminopeptidase and b-D-glucosidase), and bacterial abundance using 1-mm filters to separate free from particle-associated bacteria. A seasonal decline in all bacterial metabolic measures was observed at all stations, suggesting that a system-wide variable may be important in controlling bacterial activity. One such variable is freshwater flow into the Bay (as a proxy for organic matter flux), which positively covaried with all metabolic measures. A sharp decline in particle-associated bacteria was also observed in Suisun Bay and the Sacramento River between July and August. This decline may have been due to combined effects of declining nutritive value of the aging particles and increasing grazing pressure by benthic filter feeders. Aminopeptidase activity was positively related with increasing salinity, and b-D-glucosidase was negatively correlated with increasing salinity, indicating a gradient in the relative quality of organic matter from carbohydrate-rich riverine to proteinrich oceanic material. Overall, Suisun Bay had the highest mean proportion of particle-associated bacteria (49%), followed by Sacramento River (36%) and Central Bay (11%). Particles were the sites of enhanced ectoenzyme activity but not amino acid incorporation. Bacteria may be actively dissolving the particulate organic matter, but their growth rates on particles are not significantly enhanced. Estuaries are important sites for the bacterial degradation of terrestrial and riverine organic carbon (Lee and Wakeham 1988). In estuarine systems with low primary production and hence low in situ sources of organic carbon, this allochthonous carbon can also be important in supporting the estuarine food web via bacterial secondary production and trophic transfers in the microbial loop. Within an estuary, there are primarily four fates of this organic carbon: respiratory loss, incorporation into biomass, advection out of the system, and burial. A better understanding of the flow of carbon in es1 Present address: US EPA, Gulf Ecology Division, 1 Sabine Island Dr., Gulf Breeze, Florida 32561.