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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.
Hollibaugh et al. (Sat,) studied this question.