Community analysis of biofilters using fluorescence in situ hybridization including a new probe for the Xanthomonas branch of the class Proteobacteria

Domain-, class-, and subclass-specific rRNA-targeted probes were applied to investigate the microbial communities of three industrial and three labora tory-scale biofilters, The set of probes also included a new probe (named X AN818) specific for the Xanthomonas branch of the class Proteobacteria; thi s probe is described in this study, The members of the Xanthomonas branch d o not hybridize with previously developed rRNA-targeted oligonucleotide pro bes for the alpha-, beta-, and gamma-Proteobacteria, Bacteria of the Xantho monas branch accounted for up; to 4.5% of total direct counts obtained with 4',6-diamidino-2-phenylindole. In biofilter samples, the relative abundanc e of these bacteria was similar to that of the gamma-Proteobacteria, Actino bacteria (gram-positive bacteria with a high G+C DNA content) and alpha-Pro teobacteria were the most dominant groups. Detection rates obtained with pr obe EUB338 varied between about 40 and 70%, For samples with high contents of gram-positive bacteria, these percentages were substantially improved wh en the calculations were corrected for the reduced permeability of gram-pos itive bacteria when formaldehyde was used as a fixative, The set of applied bacterial class- and subclass-specific probes yielded, on average, 58.5% ( +/- a standard deviation of 23.0%) of the corrected eubacterial detection r ates, thus indicating the necessity of additional probes for studies of bio filter communities. The Xanthomonas-specific probe presented here may serve as an efficient tool for identifying potential phytopathogens, In situ hyb ridization proved to be a practical tool for microbiological studies of bio filtration systems.