Original Article

Subject Category: Microbial population and community ecology

The ISME Journal (2009) 3, 168–178; doi:10.1038/ismej.2008.103; published online 13 November 2008

Selective progressive response of soil microbial community to wild oat roots

Kristen M DeAngelis1,2, Eoin L Brodie1, Todd Z DeSantis1, Gary L Andersen1, Steven E Lindow2 and Mary K Firestone1,3

  1. 1Ecology Department, Lawrence Berkeley National Lab, Berkeley, CA, USA
  2. 2Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
  3. 3Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA

Correspondence: MK Firestone, Department of Ecosystem Science, Policy and Management, University of California, 137 Mulford Hall, Berkeley, CA 94720, USA. E-mail: mkfstone@nature.berkeley.edu

Received 1 June 2008; Revised 29 September 2008; Accepted 8 October 2008; Published online 13 November 2008.



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 β-Proteobacteria and Actinobacteria at about 108 copies of 16S rRNA genes per g soil, with Nitrospira having about 105 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.


rhizosphere soil, 16S rRNA, microarray, PhyloChip, T-RFLP, bacterial and archaeal populations