Genomic Features of Bacterial Adaptation to Plants
ARTICLES https://doi.org/10.1038/s41588-017-0012-9 Genomic features of bacterial adaptation to plants Asaf Levy 1, Isai Salas Gonzalez2,3, Maximilian Mittelviefhaus4, Scott Clingenpeel 1, Sur Herrera Paredes 2,3,15, Jiamin Miao5,16, Kunru Wang5, Giulia Devescovi6, Kyra Stillman1, Freddy Monteiro2,3, Bryan Rangel Alvarez1, Derek S. Lundberg2,3, Tse-Yuan Lu7, Sarah Lebeis8, Zhao Jin9, Meredith McDonald2,3, Andrew P. Klein2,3, Meghan E. Feltcher2,3,17, Tijana Glavina Rio1, Sarah R. Grant 2, Sharon L. Doty 10, Ruth E. Ley 11, Bingyu Zhao5, Vittorio Venturi6, Dale A. Pelletier7, Julia A. Vorholt4, Susannah G. Tringe 1,12*, Tanja Woyke 1,12* and Jeffery L. Dangl 2,3,13,14* 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 com- pared 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 pro- tein 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 sustain- able agriculture through microbiome engineering.
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