The use of ribosomal RNA (rRNA) probe technology for the characterization of complex microbial communities is reviewed and illustrated by discussing the results of a long-term study of four anaerobic fixed-bed biofilm reactors. Two distinct approaches were used to characterize the microbial community structure in these biofilm reactors. The first used a collection of phylogenetically defined oligonucleotide rRNA probes for methanogens and sulfate-reducing bacteria (SRB) to quantify their populations. Population abundance was linked to the functional behavior of the biofilm reactor community by determining the effluent concentrations of the substrates, intermediates, and final products of microbial metabolism. This analysis indicated that the presence of SRB (especially Desulfovibrio-species) was not dependent upon the presence of sulfate. Methanobacteriales-species were the major competitors for hydrogen with these SRB in the absence of sulfate. The second approach involved selective amplification, cloning, sequencing, and whole cell hybridization to identify, visualize, and isolate a biofilm community member (strain PT-2). Subsequently, it was determined that the growth rate of strain PT-2 was significantly higher in young biofilms than in established biofilms.

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