title: Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria.
abstract: A hierarchical set of five 16S rRNA-targeted oligonucleotide DNA probes for phylogenetically defined groups of autotrophic ammonia- and nitrite-oxidizing bacteria was developed for environmental and determinative studies. Hybridization conditions were established for each probe by using temperature dissociation profiles of target and closely related nontarget organisms to document specificity. Environmental application was demonstrated by quantitative slot blot hybridization and whole-cell hybridization of nitrifying activated sludge and biofilm samples. Results obtained with both techniques suggested the occurrence of novel populations of ammonia oxidizers. In situ hybridization experiments revealed that Nitrobacter and Nitrosomonas species occurred in clusters and frequently were in contact with each other within sludge flocs.
authors.affiliation: Department of Civil Engineering, Northwestern University, Evanston, Illinois 60208-3109, USA.
authors.forename: B K
authors.initials: BK
authors.lastname: Mobarry
authors.forename: M
authors.initials: M
authors.lastname: Wagner
authors.forename: V
authors.initials: V
authors.lastname: Urbain
authors.forename: B E
authors.initials: BE
authors.lastname: Rittmann
authors.forename: D A
authors.initials: DA
authors.lastname: Stahl
mesh_terms: D000641:Ammonia / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D001483:Base Sequence; D015342:DNA Probes / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004783:Environmental Microbiology; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D009573:Nitrites / Q000378:metabolism; D009586:Nitrogen Fixation; D010084:Oxidation-Reduction; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D015342:DNA Probes; D004269:DNA, Bacterial; D009573:Nitrites; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D000641:Ammonia