Journal
NATURE GENETICS
Volume 50, Issue 1, Pages 138-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/s41588-017-0012-9
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Funding
- Office of Science of the US Department of Energy [DE-AC02-05CH11231]
- NSF INSPIRE grant [IOS-1343020]
- DOE-USDA Feedstock Award [DE-SC001043]
- Office of Science (BER), US Department of Energy [DE-SC0014395]
- NIH [T32 GM067553-06, T32 GM07092-34]
- HHMI
- Gordon and Betty Moore Foundation [GBMF3030]
- NIH Dr. Ruth L. Kirschstein NRSA Fellowship [F32-GM112345]
- Genomic Science Program, US Department of Energy, Office of Science, Biological and Environmental Research as part of the Oak Ridge National Laboratory Plant Microbe Interfaces Scientific Focus Area
- Plant Feedstock Genomics Award [DE-SC001043]
- US Department of Energy [DE-AC05-00OR22725]
- SystemsX.ch grant (Micro2X)
- European Research Council (ERC) advanced grant (PhyMo)
- Direct For Biological Sciences [1343020] Funding Source: National Science Foundation
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [T32GM067553, T32GM007092, F32GM112345] Funding Source: NIH RePORTER
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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.
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