Selective progressive response of soil microbial community to wild oat roots

ISME J. 2009 Feb;3(2):168-78. doi: 10.1038/ismej.2008.103. Epub 2008 Nov 13.


Roots moving through soil induce physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. The use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies compositional changes reported earlier, including increases in chitinase- and protease-specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change compared with bulk soil in relative abundance for 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA terminal restriction fragment length polymorphism analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared with bulk soil, but then increased in older root zones. Quantitative PCR revealed rhizosphere abundance of beta-Proteobacteria and Actinobacteria at about 10(8) copies of 16S rRNA genes per g soil, with Nitrospira having about 10(5) copies per g soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Avena / microbiology*
  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Biodiversity*
  • Colony Count, Microbial
  • Microarray Analysis
  • Oligonucleotide Array Sequence Analysis
  • Plant Roots / microbiology*
  • Polymerase Chain Reaction / methods
  • RNA, Bacterial / genetics
  • RNA, Ribosomal, 16S / genetics
  • Soil Microbiology*


  • RNA, Bacterial
  • RNA, Ribosomal, 16S