UNIGE document Scientific Article
previous document  unige:19882  next document
add to browser collection
Title

Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon

Authors
Junier, Pilar
Kim, Ok-Sun
Ahn, Tae-Seok
Imhoff, Johannes F.
Witzel, Karl-Paul
Published in Applied Microbiology and Biotechnology. 2009, vol. 83, no. 1, p. 175-188
Abstract The genes and intergenic regions of the amoCAB operon were analyzed to establish their potential as molecular markers for analyzing ammonia-oxidizing betaproteobacterial (beta-AOB) communities. Initially, sequence similarity for related taxa, evolutionary rates from linear regressions, and the presence of conserved and variable regions were analyzed for all available sequences of the complete amoCAB operon. The gene amoB showed the highest sequence variability of the three amo genes, suggesting that it might be a better molecular marker than the most frequently used amoA to resolve closely related AOB species. To test the suitability of using the amoCAB genes for community studies, a strategy involving nested PCR was employed. Primers to amplify the whole amoCAB operon and each individual gene were tested. The specificity of the products generated was analyzed by denaturing gradient gel electrophoresis, cloning, and sequencing. The fragments obtained showed different grades of sequence identity to amoCAB sequences in the GenBank database. The nested PCR approach provides a possibility to increase the sensitivity of detection of amo genes in samples with low abundance of AOB. It also allows the amplification of the almost complete amoA gene, with about 300 bp more sequence information than the previous approaches. The coupled study of all three amo genes and the intergenic spacer regions that are under different selection pressure might allow a more detailed analysis of the evolutionary processes, which are responsible for the differentiation of AOB communities in different habitats.
Keywords Ammonia/*metabolismBetaproteobacteria/*classification/*genetics/isolation & purification*BiodiversityCluster AnalysisDNA, Bacterial/chemistry/*geneticsDNA, IntergenicMolecular Sequence Data*OperonOxidation-ReductionPhylogenyPolymerase Chain Reaction/methods*Polymorphism, GeneticSensitivity and SpecificitySequence Analysis, DNA
Identifiers
PMID: 19274459
Full text
Structures
Citation
(ISO format)
JUNIER, Pilar et al. Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon. In: Applied Microbiology and Biotechnology, 2009, vol. 83, n° 1, p. 175-188. https://archive-ouverte.unige.ch/unige:19882

233 hits

0 download

Update

Deposited on : 2012-04-23

Export document
Format :
Citation style :