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

Junier, Pilar ; Kim, Ok-Sun ; Junier, Thomas ; Ahn, Tae-Seok ; Imhoff, Johannes ; Witzel, Karl-Paul

In: Applied Microbiology and Biotechnology, 2009, vol. 83, no. 1, p. 175-188

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    Titre
    • Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon
    Auteur
    • Junier, Pilar. Ecole Polytechnique Fédérale de Lausanne (EPFL ENAC ISTE EML), CE 1 644 (Centre Est), Station 6, 1015, Lausanne, Switzerland
    • Kim, Ok-Sun. Max-Planck Institute for Evolutionary Biology, 24306, Plön, Germany
    • Junier, Thomas. University of Geneva, 1211, Geneva, Switzerland
    • Ahn, Tae-Seok. Department of Environmental Science, Kangwon National University, 200-701, Chuncheon, South Korea
    • Imhoff, Johannes. Leibniz-Institute of Marine Sciences, University of Kiel, 24105, Kiel, Germany
    • Witzel, Karl-Paul. Max-Planck Institute for Evolutionary Biology, 24306, Plön, Germany
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Applied Microbiology and Biotechnology, 2009, vol. 83, no. 1, p. 175-188. Springer-Verlag
    Autre version électronique
    Identifiant OAI-PMH
    • oai:doc.rero.ch:318304
    Summary
    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 300bp 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