Elucidating Bacterial Gene Functions in the Plant Microbiome

Asaf Levy, Jonathan M. Conway, Jeffery L. Dangl, Tanja Woyke

Research output: Contribution to journalReview articlepeer-review

110 Scopus citations


There is a growing appreciation for the important roles microorganisms play in association with plants. Microorganisms are drawn to distinct plant surfaces by the nutrient-rich microenvironment, and in turn some of these colonizing microbes provide mutualistic benefits to their host. The development of plant probiotics to increase crop yield and provide plant resistance against biotic and abiotic stresses, while minimizing chemical inputs, would benefit from a deeper mechanistic understanding of plant-microbe interaction. Technological advances in molecular biology and high-throughput -omics provide stepping stones to the elucidation of critical microbiome gene functions that aid in improving plant performance. Here, we review -omics-based approaches that are propelling forward the current understanding of plant-associated bacterial gene functions, and describe how these technologies have helped unravel key bacterial genes and pathways that mediate pathogenic, beneficial, and commensal host interactions. Plants host large bacterial communities of importance to plant health and development. High-throughput -omics approaches have promoted elucidation of bacterial genes and pathways active at the plant-bacteria interface. We describe these methods and present functions performed by plant-associated bacterial genes that have been characterized by employing -omics methods.

Original languageEnglish (US)
Pages (from-to)475-485
Number of pages11
JournalCell Host and Microbe
Issue number4
StatePublished - Oct 10 2018
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Virology
  • Parasitology
  • Microbiology


  • gene function
  • genomics
  • metabolomics
  • omics
  • phytopathogens
  • plant growth-promoting bacteria
  • plant microbiome
  • plant-associated bacteria
  • proteomics
  • transcriptomics


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