Community analysis of ammonia-oxidising bacteria, in relation to oxygen availability in soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridisation

Authors

  • George A. Kowalchuk,

    Corresponding author
    1. Department of Plant-Microorganism Interactions, Netherlands Institute of Ecology, Centre for Terrestrial Ecology, Boterhoeksestraat 22, P.O. Box 40, 6666 ZG Heteren, The Netherlands
      *Corresponding author. Tel.: +31 (26) 479 1314; Fax: +31 (26) 472 3227; E-mail: gkowal@cto.nioo.knaw.nl
    Search for more papers by this author
  • Paul L.E. Bodelier,

    1. Department of Plant-Microorganism Interactions, Netherlands Institute of Ecology, Centre for Terrestrial Ecology, Boterhoeksestraat 22, P.O. Box 40, 6666 ZG Heteren, The Netherlands
    Search for more papers by this author
  • G.Hans J. Heilig,

    1. Department of Plant-Microorganism Interactions, Netherlands Institute of Ecology, Centre for Terrestrial Ecology, Boterhoeksestraat 22, P.O. Box 40, 6666 ZG Heteren, The Netherlands
    Search for more papers by this author
  • John R. Stephen,

    1. Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
    Search for more papers by this author
  • Hendrikus J. Laanbroek

    1. Department of Microbial Ecology, Netherlands Institute of Ecology, Centre for Limnology, Rijksstraatweg 6, 3631 AC Nieuwersluis, The Netherlands
    Search for more papers by this author

*Corresponding author. Tel.: +31 (26) 479 1314; Fax: +31 (26) 472 3227; E-mail: gkowal@cto.nioo.knaw.nl

Abstract

The rhizosphere of oxygen-releasing wetland plants provides a niche for oxygen-consuming microorganisms such as chemolithotrophic ammonia-oxidising bacteria. These bacteria are adapted to oxygen limitation with respect to their affinity for oxygen, ability to survive periods of anoxia, and immediate response to the appearance of oxygen. In this study the techniques of specific amplification of ammonia oxidiser 16S rDNA fragments by PCR, separation of mixed PCR samples by denaturing gradient gel electrophoresis (DGGE), and band identification by specific hybridisation with oligonucleotide probes were combined to allow for the comparison of the community composition of multiple samples over space and time. DGGE bands of interest were also excised for DNA isolation, reamplification, sequence determination and phylogenetic analysis. We compared monthly samples from both the root zone and the bare sediment of a shallow lake inhabited by the emergent macrophyte Glyceria maxima to determine the seasonal effects that the plant roots and the oxygen availability might have on the β-subgroup ammonia-oxidiser populations present. Similarly, five soil or sediment samples, varying in oxygen availability, from different locations in the Netherlands were compared. Although the presence of two previously defined Nitrosospira sequence clusters could be differentially detected in the samples examined, there was no evidence for a particular group which was specific to periodically anoxic environments.

Ancillary