Research Product

One critical area relating to the release of genetically engineered microorganisms is the response of the resident community. Can an exogenous species perturb indigenous communities of bacteria, altering the ecological processes they execute? Assessment of this requires some fundamental advances in microbial ecology. These include the ability to describe complex microbial communities in detail, an understanding of the relationship between the community composition and the ecological processes mediated by the community, and sensitive methods to monitor and characterize subtle shifts in community composition. The tradition of community studies in microbial ecology is one of isolating and characterizing pure cultures of bacteria obtained from the environment. However, it is recognized that only about 10% of direct bacterial counts in an environmental sample can be brought into culture. Once in culture, the isolates are often difficult to unambiguously identify. The ribosomal RNAs, particularly 16S rRNA, provide an avenue which can circumvent these limitations. 16S rRNA can be extracted directly from natural microbial communities and the sequence information contained therein related to the 16S rRNA sequences of known, well characterized bacterial strains. We have been developing a 16S rRNA-based assessment that utilizes hybridization probes and comparative sequencing to describe specific phylogenetic assemblages within natural microbial communities. The research has focused on the characterization of two complex microbial communities whose members are difficult to isolate and characterize; the bacterial communities of the bovine rumen and the sulfate-reducing bacteria in anaerobic marine sediments.