Characterization of Biofilm Community Structure by Ribosomal RNA sequences
1989
Stahl, David A.
The general objectives of this project are to develop molecular techniques, based upon comparative ribosomal RNA sequencing, for the explicit identification and localization of individual microorganisms in natural biofilms. As model systems sulfidogenic and methanogenic fixed-bed bioreactors have been established. Sampling protocols for microscopic and molecular analyses of, and methods for measuring methane production and sulfate reduction within, these bioreactor systems were developed. The use of fluorescent-oligonucleotide probes for visualizing individual sulfate-reducing bacteria within complex biofilms was demonstrated. The polymerase chain reaction as used for the selective amplification of 16S rRNAs from defined physiological assemblages of organisms (methanogens and sulfate-reducing bacteria). The cloning and sequencing of these amplified products has provided an outline of the microbial diversity within the sulfidogenic and methanogenic bioreactors. Comparative sequencing of additional strains of marine and freshwater caulobacters has been completed in association with ONR investigator John Smit. The use of flow cytometry to enumerate a target organism, in a defined mixture of cells, using a genus-specific fluorescent probe was demonstrated.
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