Genomic Features of Bacterial Adaptation to Plants

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¹Microbial Program, US DOE Joint Genome Institute, USA
²Department of Biology, Univeristy of North Carolina at Chapel Hill, USA
³Institute of Microbiology, ETH, Switzerland
⁴Department of Horticulture, VirginiaTech, USA
⁵School of Environmental and Forest Sciences, University of Washington, WA, USA
⁶NA, International Centre for Genetic Engineering and Biotechnology, Italy
⁷Biosciences Division, Oak Ridge National Laboratory, USA
⁸Department of Microbiology, University of Tennessee, USA
⁹NA, Max Planck Institute for Developmental Biology, Germany

Plants intimately associate with diverse bacteria. Plant-associated (PA) bacteria have ostensibly evolved genes enabling adaptation to the plant environment. 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 3837 bacterial genomes to identify thousands of PA gene clusters. Genomes of PA bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant associated genomes. We experimentally validated candidates from two sets of PA genes, one involved in plant colonization, the other serving in microbe-microbe competition between PA bacteria. We also identified 64 PA protein domains that potentially mimic plant domains; some are shared with PA fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides leads for efficient and sustainable agriculture through microbiome engineering.