Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions

PLoS One. 2013;8(2):e55731. doi: 10.1371/journal.pone.0055731. Epub 2013 Feb 1.


Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of in vitro grown Arabidopsis plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the in vitro root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p<0.05) between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development. In summary, our results suggest that the root exudation process of phytochemicals follows a developmental pattern that is genetically programmed.

Publication types

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

MeSH terms

  • Arabidopsis / chemistry*
  • Arabidopsis / growth & development
  • Base Sequence
  • Carbohydrates / analysis
  • Gas Chromatography-Mass Spectrometry
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental / genetics
  • Gene Expression Regulation, Developmental / physiology*
  • Gene Expression Regulation, Plant / genetics
  • Gene Expression Regulation, Plant / physiology*
  • Metagenome / genetics
  • Molecular Sequence Data
  • Plant Exudates / analysis*
  • Plant Roots / chemistry*
  • Principal Component Analysis
  • Reverse Transcriptase Polymerase Chain Reaction
  • Rhizosphere
  • Sequence Analysis, DNA
  • Sugar Acids / analysis


  • Carbohydrates
  • Plant Exudates
  • Sugar Acids

Grant support

Work was supported by a grant from the National Science Foundation to J.M.V. (MCB-0950857). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.