title: Community analysis of biofilters using fluorescence in situ hybridization including a new probe for the Xanthomonas branch of the class Proteobacteria.
abstract: Domain-, class-, and subclass-specific rRNA-targeted probes were applied to investigate the microbial communities of three industrial and three laboratory-scale biofilters. The set of probes also included a new probe (named XAN818) specific for the Xanthomonas branch of the class Proteobacteria; this probe is described in this study. The members of the Xanthomonas branch do not hybridize with previously developed rRNA-targeted oligonucleotide probes for the alpha-, beta-, and gamma-Proteobacteria. Bacteria of the Xanthomonas branch accounted for up to 4.5% of total direct counts obtained with 4',6-diamidino-2-phenylindole. In biofilter samples, the relative abundance of these bacteria was similar to that of the gamma-Proteobacteria. Actinobacteria (gram-positive bacteria with a high G+C DNA content) and alpha-Proteobacteria were the most dominant groups. Detection rates obtained with probe EUB338 varied between about 40 and 70%. For samples with high contents of gram-positive bacteria, these percentages were substantially improved when the calculations were corrected for the reduced permeability of gram-positive 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 rates, thus indicating the necessity of additional probes for studies of biofilter communities. The Xanthomonas-specific probe presented here may serve as an efficient tool for identifying potential phytopathogens. In situ hybridization proved to be a practical tool for microbiological studies of biofiltration systems.
authors.affiliation: Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, Germany.
authors.forename: U
authors.initials: U
authors.lastname: Friedrich
authors.forename: M M
authors.initials: MM
authors.lastname: Naismith
authors.forename: K
authors.initials: K
authors.lastname: Altendorf
authors.forename: A
authors.initials: A
authors.lastname: Lipski
mesh_terms: D000393:Air Pollutants / Q000378:metabolism; D001431:Bacteriological Techniques; D001483:Base Sequence; D001673:Biodegradation, Environmental; D015342:DNA Probes / Q000235:genetics; D017753:Ecosystem; D005374:Filtration / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D014974:Xanthomonas / Q000235:genetics* / Q000302:isolation & purification* / Q000378:metabolism
chemical_list: D000393:Air Pollutants; D015342:DNA Probes; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S