The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis

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 ph...

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Bibliographic Details
Published in:Systematic and applied microbiology 2007-06, Vol.30 (4), p.297-308
Main Authors: Vanparys, Bram, Spieck, Eva, Heylen, Kim, Wittebolle, Lieven, Geets, Joke, Boon, Nico, De Vos, Paul
Format: Article
Language:English
Subjects:
16S rRNA
Africa
Americas
Asia
Bacterial Proteins - genetics
Bacteriology
Biological and medical sciences
Environmental Microbiology
Europe
Fundamental and applied biological sciences. Psychology
Genes, Bacterial - genetics
Genetic Variation
Microbiology
Nitrite oxidoreductase
nitrite reductase
Nitrite Reductases - genetics
Nitrite Reductases - metabolism
Nitrobacter
Nitrobacter - classification
Nitrobacter - genetics
nxrA
nxrB
nxrX
Oxidation-Reduction
Phylogenetic diversity
Phylogeny
Polymerase Chain Reaction
Rep-PCR
ribosomal RNA
RNA, Bacterial - genetics
RNA, Ribosomal, 16S - genetics
sequence analysis
Sequence Analysis, Protein
Species Specificity
Systematics
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Summary: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 380 bp 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.
ISSN:0723-2020
1618-0984
DOI:10.1016/j.syapm.2006.11.006