The Plant Microbiota: Systems-Level Insights and Perspectives

Annu Rev Genet. 2016 Nov 23;50:211-234. doi: 10.1146/annurev-genet-120215-034952. Epub 2016 Sep 14.


Plants do not grow as axenic organisms in nature, but host a diverse community of microorganisms, termed the plant microbiota. There is an increasing awareness that the plant microbiota plays a role in plant growth and can provide protection from invading pathogens. Apart from intense research on crop plants, Arabidopsis is emerging as a valuable model system to investigate the drivers shaping stable bacterial communities on leaves and roots and as a tool to decipher the intricate relationship among the host and its colonizing microorganisms. Gnotobiotic experimental systems help establish causal relationships between plant and microbiota genotypes and phenotypes and test hypotheses on biotic and abiotic perturbations in a systematic way. We highlight major recent findings in plant microbiota research using comparative community profiling and omics analyses, and discuss these approaches in light of community establishment and beneficial traits like nutrient acquisition and plant health.

Keywords: Arabidopsis; bacterial community; commensal; gnotobiotic; microbiome; plant protection.

Publication types

  • Review

MeSH terms

  • Adaptation, Biological
  • Arabidopsis / microbiology
  • Ecosystem
  • Microbial Consortia
  • Microbiota*
  • Phylogeny
  • Plant Roots / microbiology
  • Plants / microbiology*