Structure and functions of the bacterial microbiota of plants

Davide Bulgarelli, Klaus Schlaeppi, Stijn Spaepen, Emiel Ver Loren Van Themaat, Paul Schulze-Lefert

Research output: Contribution to journalReview articlepeer-review

2037 Citations (Scopus)


Plants host distinct bacterial communities on and inside various plant organs, of which those associated with roots and the leaf surface are best characterized. The phylogenetic composition of these communities is defined by relatively few bacterial phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. A synthesis of available data suggests a two-step selection process by which the bacterial microbiota of roots is differentiated from the surrounding soil biome. Rhizodeposition appears to fuel an initial substrate-driven community shift in the rhizosphere, which converges with host genotype-dependent fine-tuning of microbiota profiles in the selection of root endophyte assemblages. Substrate-driven selection also underlies the establishment of phyllosphere communities but takes place solely at the immediate leaf surface. Both the leaf and root microbiota contain bacteria that provide indirect pathogen protection, but root microbiota members appear to serve additional host functions through the acquisition of nutrients from soil for plant growth. Thus, the plant microbiota emerges as a fundamental trait that includes mutualism enabled through diverse biochemical mechanisms, as revealed by studies on plant growth-promoting and plant health-promoting bacteria. ©

Original languageEnglish
Pages (from-to)807-838
Number of pages32
JournalAnnual Review of Plant Biology
Publication statusPublished - 1 Apr 2013


  • Endophyte
  • Phyllosphere
  • Plant growth-promoting rhizobacteria
  • Plant innate immunity
  • Rhizodeposition
  • Rhizosphere

ASJC Scopus subject areas

  • General Medicine
  • Physiology
  • Molecular Biology
  • Plant Science
  • Cell Biology


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