Bacterial populations in replicate marine enrichment cultures:: assessing variability in abundance using 16S rRNA-based probes

Most studies of marine bacterial communities focus on functional attributes of the community, rather than on population or community structure, at least in part, because of the difficulty in enumerating individual species within complex communities. Here, we describe a study in which populations of three bacterial species were followed over time in replicate marine enrichment cultures using 16S rRNA-based oligonucleotide probes. Three identical enrichment microcosms were established with lignin-rich pulp mill waste as a sole carbon source, inoculated with coastal seawater, and transferred at two-week intervals. Population levels were assessed throughout a six-week period using species-specific 16S rRNA-based oligonucleotide probes directed toward three bacterial species that were numerically important (and culturable) members of the enrichments. Substantial differences in the population levels of each bacterial species were found among the triplicate incubations, despite the fact that the enrichments were inoculated and treated identically. Stochastic differences in the composition of the inoculum and/or ecological interactions within the enrichment replicates may have been important in determining final population levels. Functional ability, assessed as rates of degradation of a synthetic lignin preparation, were fairly similar among the three replicate enrichments (within 70%), despite the substantial differences in population levels of the representative lignin-degrading species.