108. Unraveling the Rhizosphere Using the cpn 60 Genomic Marker and Pyrosequencing

  1. Frans J. de Bruijn
  1. George Lazarovits1,
  2. Amy L. Turnbull1,
  3. Brenda Haug2,
  4. Matthew G. Links3,
  5. Janet E. Hill4 and
  6. Sean M. Hemmingsen2

Published Online: 18 MAR 2013

DOI: 10.1002/9781118297674.ch108

Molecular Microbial Ecology of the Rhizosphere: Volume 1 & 2

Molecular Microbial Ecology of the Rhizosphere: Volume 1 & 2

How to Cite

Lazarovits, G., Turnbull, A. L., Haug, B., Links, M. G., Hill, J. E. and Hemmingsen, S. M. (2013) Unraveling the Rhizosphere Using the cpn 60 Genomic Marker and Pyrosequencing, in Molecular Microbial Ecology of the Rhizosphere: Volume 1 & 2 (ed F. J. de Bruijn), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118297674.ch108

Editor Information

  1. INRA-CNRS Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441-2594 BP52627, F-31320 Castanet-Tolosan, France

Author Information

  1. 1

    A&L Biologicals, Agroecology Research Services, London, Ontario, N5V 3P5 Canada

  2. 2

    National Research Council Canada, Plant Biotechnology Institute, Saskatoon, Saskatchewan, S7N 0W9 Canada

  3. 3

    Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, S7N 0X2 Canada

  4. 4

    Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5B4 Canada

Publication History

  1. Published Online: 18 MAR 2013
  2. Published Print: 3 MAY 2013

ISBN Information

Print ISBN: 9781118296172

Online ISBN: 9781118297674



  • potato;
  • rhizosphere;
  • pyrosequencing;
  • bacteria;
  • fungi;
  • Rhizobium


The microbial communities of two distinct soils and of the rhizosphere, tuber-associated soil, and washed roots of potato plants grown in each soil were profiled by cpn60 gene-targeted metagenomics. DNA samples extracted from these sources were used as templates for PCR amplification of the cpn60 universal target regions present in each metagenomic sample. The cpn60 amplicons were analyzed by pyrosequencing. The 914,932 sequence reads obtained were aligned and assembled into unique cpn60 nucleotide sequences in an autonomous process that did not refer to a database of known cpn60 sequences. This process identified 27,222 unique nucleotide sequences, corresponding to 21,396 unique peptide sequences. The closest matches for each of these sequences in a database of cpn60 sequences, cpnDB, were determined. Bulk soil microbial richness [i.e., total number of unique operational taxonomic units (OTU)] was much greater than that of the plant-associated samples, as expected. The richness of the microbial communities associated with the plant samples ranged from 13% to 44% of that of the bulk soil in which it was grown. When only distinct peptide sequences derived from the nucleotide sequence OTU) were included, the apparent richness was reduced for all samples. If only OTU with higher relative abundances in the plant-associated sample than those in the bulk soil were considered, the apparent richness of the plant-associated microbial communities was significantly reduced. Clustering analysis identified OTU with distributions among the samples that strongly suggested a functional relationship with the plant. Classification of the reads observed in each sample the taxonomic level of bacterial Order revealed major differences between bulk soil and plant-associated communities. The distributions of a small number of OTU between samples suggest that these organisms had privileged relationships with the plant.