In estuarine environments, the sources and microbial processing of organic carbon affect the structure of biological communities within the estuary, and ultimately the quality and quantity of material delivered to the coastal ocean. The setting for this study is northern San Francisco Bay, a turbid estuary on the West Coast of North America. The first chapter examines the trophic role of microzooplankton (heterotrophic protozoans less than 200 micrometers) using the dilution method. The results suggest that microzooplankton do not control prey abundance. I speculated that an introduced clam, Potamocorbula amurensis, might disrupt this microbial loop by consuming microzooplankton, their prey, or both. Alternatively, the theoretical model, upon which the dilution method is based, may be inappropriate to describe grazing dynamics in particle-rich environments such as San Francisco Bay. Specifically, bacteria associated with particles may experience different grazing pressures than free-living bacteria.

This latter conclusion led me to step down a trophic level to quantify the abundance and metabolic activity of free-living and particle-associated bacteria during a spring-summer period. I found striking seasonal variability in bulk microbial activity and the partitioning of this activity suggesting that bacterioplankton are dependent on organic material delivered to the system via freshwater flow.

The third chapter describes organic matter distributions along the estuarine gradient during this same period. Dissolved constituents normalized to salinity suggest that mixing is mainly conservative. However when the reactive and non-reactive components are compared, a pattern emerges suggesting organic matter is of terrestrial origin in the upper estuary and of oceanic origin in the lower estuary.

The fourth chapter describes the abundance and sizes of suspended particles during this same period. Particle volume distributions were peaked (mode: 10 um diameter) while particle surface area distributions were skewed towards the smaller size classes (2 um diameter), suggesting that much of the habitat available for bacterial attachment was contained on very small particles.

In summary, these results give us a clearer picture of the sources and sinks of bacterioplankton production in this estuary and underscore the importance of terrestrial carbon sources, as opposed to those derived from in situ primary production.