Similarity of particle-associated and free-living bacterial communities in northern San Francisco Bay, California

We used denaturing gradient gel electrophoresis (DGGE) of 16S rDNA PCR amplicons to analyze the composition of Bacteria 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 similar than communities in different samples. At times, the attached and free communities in a sample appeared identical, 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 community; however, the difference was not statistically significant. Richness declined through the summer. The richest samples were collected on the June cruise (51 OTU sample(-1)) while the least rich samples were collected on the September cruise (21 OTU sample(-1)). 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 different 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 unique while an average of 5.5% were found on all cruises. Ubiquitous OTUs (found at all stations) ranged from 34 % (free-living, June) to 7 % (free-living, August) of the distinct OTUs encountered on a given cruise. Our results suggest Little difference in the biogeochemical role played by attached versus free bacteria in San Francisco Bay, particularly in the estuarine turbidity maximum. These results are generally consistent with our analyses of the metabolic potential of these communities.