Elucidating Bacterial Gene Functions in the Plant Microbiome

Asaf Levy; Jonathan M Conway; Jeffery L Dangl; Tanja Woyke

doi:10.1016/j.chom.2018.09.005

Elucidating Bacterial Gene Functions in the Plant Microbiome

Cell Host Microbe. 2018 Oct 10;24(4):475-485. doi: 10.1016/j.chom.2018.09.005.

Authors

Asaf Levy¹, Jonathan M Conway², Jeffery L Dangl³, Tanja Woyke⁴

Affiliations

¹ DOE Joint Genome Institute, Walnut Creek, CA, USA. Electronic address: alevy@mail.huji.ac.il.
² Department of Biology, University of North Carolina, Chapel Hill, NC, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
³ Department of Biology, University of North Carolina, Chapel Hill, NC, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
⁴ DOE Joint Genome Institute, Walnut Creek, CA, USA; School of Natural Sciences, University of California, Merced, Merced, CA, USA.

PMID: 30308154
DOI: 10.1016/j.chom.2018.09.005

Abstract

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.

Keywords: gene function; genomics; metabolomics; omics; phytopathogens; plant growth-promoting bacteria; plant microbiome; plant-associated bacteria; proteomics; transcriptomics.

Publication types

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

MeSH terms

Genes, Bacterial / genetics*
Genomics
Host Microbial Interactions / genetics*
Metabolomics
Microbiota / genetics*
Plants / microbiology*
Proteomics
Symbiosis
Transcriptome
Whole Genome Sequencing