title: The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis.
abstract: Strains of Nitrobacter mediate the second step in the nitrification process by oxidizing nitrite to nitrate. The phylogenetic diversity of the genus is currently not well investigated. In this study, a rep-PCR profile and the nearly complete 16S rRNA gene sequence of 30 strains, comprising a wide physiological as well as ecological diversity and encompassing representatives of the four species, were determined. The sequence diversity of the 16S rRNA gene between different species was low, indicating the need for additional phylogenetic markers. Therefore, primers were developed for amplifying the complete nxrX gene and a 380bp fragment of the nxrB1 gene, which are both genes involved in the nitrite oxidation process. These genes confirmed the division into phylogenetic groups revealed by the 16S rRNA gene but showed a better discriminatory power. They can be a valuable additional tool for phylogenetic analysis within the genus Nitrobacter and can assist in the identification of new Nitrobacter isolates.
authors.affiliation: Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium. bram.vanparys@ugent.be
authors.forename: Bram
authors.initials: B
authors.lastname: Vanparys
authors.forename: Eva
authors.initials: E
authors.lastname: Spieck
authors.forename: Kim
authors.initials: K
authors.lastname: Heylen
authors.forename: Lieven
authors.initials: L
authors.lastname: Wittebolle
authors.forename: Joke
authors.initials: J
authors.lastname: Geets
authors.forename: Nico
authors.initials: N
authors.lastname: Boon
authors.forename: Paul
authors.initials: P
authors.lastname: De Vos
mesh_terms: D000349:Africa; D000569:Americas; D001208:Asia; D001426:Bacterial Proteins / Q000235:genetics*; D004783:Environmental Microbiology; D005060:Europe; D005798:Genes, Bacterial / Q000235:genetics; D014644:Genetic Variation; D009572:Nitrite Reductases / Q000235:genetics* / Q000378:metabolism; D009576:Nitrobacter / Q000145:classification / Q000235:genetics*; D010084:Oxidation-Reduction; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D020539:Sequence Analysis, Protein; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D009572:Nitrite Reductases