Genomic features of bacterial adaptation to plants

Asaf Levy, Isai Salas Gonzalez, Maximilian Mittelviefhaus, Scott Clingenpeel, Sur Herrera Paredes, Jiamin Miao, Kunru Wang, Giulia Devescovi, Kyra Stillman, Freddy Monteiro, Bryan Rangel Alvarez, Derek S. Lundberg, Tse Yuan Lu, Sarah Lebeis, Zhao Jin, Meredith McDonald, Andrew P. Klein, Meghan E. Feltcher, Tijana Glavina Rio, Sarah R. GrantSharon L. Doty, Ruth E. Ley, Bingyu Zhao, Vittorio Venturi, Dale A. Pelletier, Julia A. Vorholt, Susannah G. Tringe*, Tanja Woyke, Jeffery L. Dangl

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

334 Scopus citations

Abstract

Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe-microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.

Original languageAmerican English
Pages (from-to)138-150
Number of pages13
JournalNature Genetics
Volume50
Issue number1
DOIs
StatePublished - 1 Jan 2018
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2017 The Author(s).

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