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PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa

  1. Nicole Weinert1,
  2. Yvette Piceno2,
  3. Guo-Chun Ding1,
  4. Remo Meincke3,
  5. Holger Heuer1,
  6. Gabriele Berg3,
  7. Michael Schloter4,
  8. Gary Andersen2,
  9. Kornelia Smalla1

Article first published online: 11 JAN 2011

DOI: 10.1111/j.1574-6941.2010.01025.x

Issue

FEMS Microbiology Ecology

FEMS Microbiology Ecology

Volume 75, Issue 3, pages 497–506, March 2011

Additional Information

How to Cite

Weinert, N., Piceno, Y., Ding, G.-C., Meincke, R., Heuer, H., Berg, G., Schloter, M., Andersen, G. and Smalla, K. (2011), PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiology Ecology, 75: 497–506. doi: 10.1111/j.1574-6941.2010.01025.x

Author Information

  1. 1

    Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany

  2. 2

    Lawrence Berkeley National Laboratory, Berkeley, CA, USA

  3. 3

    Graz University of Technology, Environmental Biotechnology, Graz, Austria

  4. 4

    Helmholtz Zentrum München, Department for Terrestrial Ecogenetics, Oberschleissheim, Germany

*Correspondence: Kornelia Smalla, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, D-38104 Braunschweig, Germany. Tel.: +49 531 299 3814; fax: +49 531 299 3013; e-mail: kornelia.smalla@jki.bund.de

  1. Editor: Max Häggblom

Publication History

  1. Issue published online: 24 JAN 2011
  2. Article first published online: 11 JAN 2011
  3. Accepted manuscript online: 1 DEC 2010 06:54AM EST
  4. Received 22 September 2010; revised 22 November 2010; accepted 22 November 2010., Final version published online 11 January 2011.

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Keywords:

  • 16S rRNA genes;
  • community DNA;
  • clone library;
  • PhyloChip;
  • potato rhizosphere

Abstract

The phylogenetic composition of bacterial communities in the rhizosphere of three potato cultivars grown at two distant field sites was analysed. Ribosomal gene fragments amplified from total community DNA were hybridized to PhyloChips. A total of 2432 operational taxonomic units (OTUs) were detected by the PhyloChips, of which 65% were found in the rhizosphere of all cultivars at both field sites. From all detected OTUs, 9% revealed a cultivar-dependent abundance at the one or the other field site and 4% at both sites. Differential abundance on the three cultivars was mainly observed for OTUs belonging to the Pseudomonadales, Actinomycetales and Enterobacteriales. More than 40% of OTUs belonging to Bradyrhizobiales, Sphingomonadales, Burkholderiales, Rhodocyclales, Xanthomonadales and Actinomycetales differed significantly in their abundance between the sites. A sequence analysis of six 16S rRNA gene clone libraries corresponded well with the taxonomic community structure evidenced by the PhyloChip hybridization. Most ribotypes matched OTUs detected by the PhyloChip. Those OTUs that responded to the potato cultivar at both field sites might be of interest in view of cultivar-specific effects on bacterial biocontrol strains and pathogens.

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