Arabidopsis thaliana as Model for Studies on the Bacterial Root Microbiota

Klaus Schlaeppi, Emiel Ver Loren van Themaat, Davide Bulgarelli, Paul Schulze-Lefert

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Citations (Scopus)


Bacterial communities distinct from those in unplanted soil colonize plant-associated microhabitats in the proximity of (rhizosphere), on the surface (rhizoplane), and the interior of roots. These communities of the reference plant Arabidopsis thaliana have recently been studied using high resolution pyrosequencing of the bacterial 16S rRNA gene, thereby revealing the taxonomic structure of its root microbiota (Bulgarelli et al., 2012; Lundberg et al., 2012). Arabidopsis roots mainly host soil-derived Proteobacteria, Actinobacteria, and Bacteroidetes. Most of the Proteobacteria inside roots also colonize soil-incubated wood indicating that this endophytic subcommunity is not host-specific and might be saprobes. The composition of the endophytic community is largely defined by the soil type and to a limited extent by the Arabidopsis genotype. These replicated experiments under controlled environmental conditions included four soil types on two continents, the utilization of different PCR-primer combinations, but similar sample preparation and computational protocols. Together this provides a foundation for future functional and molecular studies to infer general principles underlying the formation of the Arabidopsis root microbiota.

Original languageEnglish
Title of host publicationMolecular Microbial Ecology of the Rhizosphere
PublisherJohn Wiley & Sons Inc.
Number of pages14
ISBN (Print)9781118296172
Publication statusPublished - 3 May 2013


  • Actinobacteria
  • Arabidopsis thaliana
  • Community analysis
  • Pyrosequencing
  • Root-associated bacteria

ASJC Scopus subject areas

  • General Agricultural and Biological Sciences
  • General Environmental Science


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