Genomic features of bacterial adaptation to plants.
- Levy A DOE Joint Genome Institute, Walnut Creek, CA, USA.
- Salas Gonzalez I Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
- Mittelviefhaus M Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
- Clingenpeel S DOE Joint Genome Institute, Walnut Creek, CA, USA.
- Herrera Paredes S Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
- Miao J Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.
- Wang K Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.
- Devescovi G International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
- Stillman K DOE Joint Genome Institute, Walnut Creek, CA, USA.
- Monteiro F Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
- Rangel Alvarez B DOE Joint Genome Institute, Walnut Creek, CA, USA.
- Lundberg DS Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
- Lu TY Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- Lebeis S Department of Microbiology, University of Tennessee, Knoxville, TN, USA.
- Jin Z Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
- McDonald M Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
- Klein AP Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
- Feltcher ME Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
- Rio TG DOE Joint Genome Institute, Walnut Creek, CA, USA.
- Grant SR Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
- Doty SL School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA.
- Ley RE Max Planck Institute for Developmental Biology, Tübingen, Germany.
- Zhao B Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.
- Venturi V International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
- Pelletier DA Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- Vorholt JA Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
- Tringe SG DOE Joint Genome Institute, Walnut Creek, CA, USA. sgtringe@lbl.gov.
- Woyke T DOE Joint Genome Institute, Walnut Creek, CA, USA. twoyke@lbl.gov.
- Dangl JL Department of Biology, University of North Carolina, Chapel Hill, NC, USA. dangl@email.unc.edu.
- 2017-12-20
Published in:
- Nature genetics. - 2017
Adaptation, Physiological
Bacteria
Genome, Bacterial
Genomics
Host-Pathogen Interactions
Plant Roots
Plants
Symbiosis
English
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.
- Language
-
- English
- Open access status
- green
- Identifiers
-
- DOI 10.1038/s41588-017-0012-9
- PMID 29255260
- Persistent URL
- https://sonar.ch/global/documents/54997
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