First exploration of Nitrobacter diversity in soils by a PCR cloning-sequencing approach targeting functional gene nxrA

Authors

  • Franck Poly,

    1. Laboratoire d'Ecologie Microbienne, CNRS, UMR, Villeurbanne, France
    2. Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, Villeurbanne, France
    3. Laboratoire d'Ecologie Microbienne, INRA, USC, Villeurbanne, France
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  • Sophie Wertz,

    1. Laboratoire d'Ecologie Microbienne, CNRS, UMR, Villeurbanne, France
    2. Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, Villeurbanne, France
    3. Laboratoire d'Ecologie Microbienne, INRA, USC, Villeurbanne, France
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  • Elisabeth Brothier,

    1. Laboratoire d'Ecologie Microbienne, CNRS, UMR, Villeurbanne, France
    2. Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, Villeurbanne, France
    3. Laboratoire d'Ecologie Microbienne, INRA, USC, Villeurbanne, France
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  • Valérie Degrange

    1. Laboratoire d'Ecologie Microbienne, CNRS, UMR, Villeurbanne, France
    2. Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, Villeurbanne, France
    3. Laboratoire d'Ecologie Microbienne, INRA, USC, Villeurbanne, France
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  • Editor: Michael Wagner

Correspondence: Franck Poly, Laboratoire d'Ecologie Microbienne, CNRS, UMR 5557, bât. G. Mendel, 43 bd du 11 Novembre 1918, 69100 Villeurbanne, France. Tel.: +33 4 72 43 13 79; fax: +33 4 26 23 44 68; e-mail: poly@biomserv.univ-lyon1.fr

Abstract

Nitrite oxidoreductase (NXR) is the key enzyme responsible for the oxidation of NO2 to NO3 in nitrite-oxidizing bacteria. For the first time a molecular approach for targeting the nxrA gene was developed, encoding the catalytic subunit of the NXR, to study diversity of Nitrobacter-like organisms based on the phylogeny of nxrA gene sequences in soils. NxrA sequences of the Nitrobacter strains analysed (Nitrobacter hamburgensis, Nitrobacter vulgaris, Nitrobacter winogradskyi, Nitrobacter alkalicus) by PCR, cloning and sequencing revealed the occurrence of multiple copies of nxrA genes in these strains. The copy number and similarity varied among strains. The diversity of Nitrobacter-like nxrA sequences was explored in three soils (a French permanent pasture soil, a French fallow soil, and an African savannah soil) using a cloning and sequencing approach. Most nxrA sequences found in these soils (84%) differed from nxrA sequences obtained from Nitrobacter strains. Moreover, the phylogenetic distribution and richness of nxrA-like sequences was extremely variable depending on soil type. This nxrA tool extends the panel of functional genes available for studying bacteria involved in the nitrogen cycle.

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