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We used denatunng gradient gel electrophoresis (DGGE) of 1 6 s rDNA PCR amphcons to analyze the composition of Bacterla communities in samples collected during the summer, low flow season from northern San Francisco Bay, California. There were clear compositional differences in communities sampled at different locations in the Bay and at different times of the year. Particle-associated (attached) and free-living (free) bacteria in a given sample were generally more s u n~l a r than communities in different samples. At times, the attached and free communities in a sample appeared ~dentical, suggesting a fairly rapid exchange between them. The free-living community tended to be richer (more operational taxonomic units [OTU] per sample) than the attached comn~unity; however, the difference was not statistically significant. Richness declined through the summer. The richest samples were collected on the J u n e cruise (51 OTU sample-') while the least rich samples were collected on the September crulse (21 OTU sample-'). The number of distinct OTUs encountered in all samples from a cruise ranged from 61 (April) to 45 (October). The greatest number of unique OTUs (26) was found in April samples while the fewest (3) was found in September There was no consistent hierarchy of richness between samples. Sample groups representing location and size fractions contained from 55 to 61 d~fferent OTUs and from 8 to 18 unique (found only once) OTUs. An average of 23% of the OTUs from a given station and size fraction were unlque whlle an average of 5.5% were found on all cruises. Ubiquitous OTUs (found at all stations) ranged from 34 % (free-living, J u n e ) to 7 % (free-living, August) of the distlnct OTUs encountered on a given crulse. Our results suggest little difference in the biogeochemical role played by attached versus free bacteria in San Francisco Bay, particularly in the estuarine turb~dity maximum These results are generally consistent with our analyses of the metabolic potential of these communities.

Abstract. The Louisiana shelf, in the northern Gulf of Mexico, receives large amounts of freshwater and nutrients from the Mississippi–Atchafalaya river system. These river inputs contribute to widespread bottom-water hypoxia every summer. In this study, we use a physical–biogeochemical model that explicitly simulates oxygen sources and sinks on the Louisiana shelf to identify the key mechanisms controlling hypoxia development. First, we validate the model simulation against observed dissolved oxygen concentrations, primary production, water column respiration, and sediment oxygen consumption. In the model simulation, heterotrophy is prevalent in shelf waters throughout the year, except near the mouths of the Mississippi and Atchafalaya rivers, where primary production exceeds respiratory oxygen consumption during June and July. During this time, efflux of oxygen to the atmosphere, driven by photosynthesis and surface warming, becomes a significant oxygen sink. A substantial fraction of primary production occurs below the pycnocline in summer. We investigate whether this primary production below the pycnocline is mitigating the development of hypoxic conditions with the help of a sensitivity experiment where we disable biological processes in the water column (i.e., primary production and water column respiration). With this experiment we show that below-pycnocline primary production reduces the spatial extent of hypoxic bottom waters only slightly. Our results suggest that the combination of physical processes (advection and vertical diffusion) and sediment oxygen consumption largely determine the spatial extent and dynamics of hypoxia on the Louisiana shelf.

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