Diversity and heritability of the maize rhizosphere microbiome under field conditions

Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6548-53. doi: 10.1073/pnas.1302837110. Epub 2013 Apr 1.


The rhizosphere is a critical interface supporting the exchange of resources between plants and their associated soil environment. Rhizosphere microbial diversity is influenced by the physical and chemical properties of the rhizosphere, some of which are determined by the genetics of the host plant. However, within a plant species, the impact of genetic variation on the composition of the microbiota is poorly understood. Here, we characterized the rhizosphere bacterial diversity of 27 modern maize inbreds possessing exceptional genetic diversity grown under field conditions. Randomized and replicated plots of the inbreds were planted in five field environments in three states, each with unique soils and management conditions. Using pyrosequencing of bacterial 16S rRNA genes, we observed substantial variation in bacterial richness, diversity, and relative abundances of taxa between bulk soil and the maize rhizosphere, as well as between fields. The rhizospheres from maize inbreds exhibited both a small but significant proportion of heritable variation in total bacterial diversity across fields, and substantially more heritable variation between replicates of the inbreds within each field. The results of this study should facilitate expanded studies to identify robust heritable plant-microbe interactions at the level of individual polymorphisms by genome wide association, so that plant-microbiome interactions can ultimately be incorporated into plant breeding.

Publication types

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

MeSH terms

  • Bacteria / genetics*
  • Base Sequence
  • Cluster Analysis
  • DNA Primers / genetics
  • Genetic Variation*
  • Illinois
  • Metagenome / genetics*
  • Missouri
  • Molecular Sequence Data
  • New York
  • Phylogeny
  • Phylogeography
  • RNA, Ribosomal, 16S / genetics
  • Rhizosphere*
  • Sequence Analysis, DNA
  • Soil / analysis
  • Soil Microbiology*
  • Zea mays / microbiology*


  • DNA Primers
  • RNA, Ribosomal, 16S
  • Soil