Abstract
Plants intimately associate with an array of 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 performed a large-scale comparative genomics analysis encompassing 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 likely involved in plant colonization, the other serving in microbe-microbe competition predicted to occur on the plant. We also identified 64 PA protein domains that potentially mimic plant domains; some of these are also shared with PA fungi and oomycetes. This work significantly expands the genome-based understanding of plant-microbe interactions and provides leads for efficient and sustainable agriculture through microbiome engineering.
