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This content will become publicly available on December 18, 2018

Title: Genomic features of bacterial adaptation to plants

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. In this study, 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. In conclusion, this work expands the genome-based understanding of plant–microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.
Authors:
ORCiD logo [1] ;  [2] ;  [3] ; ORCiD logo [1] ; ORCiD logo [4] ;  [5] ;  [6] ;  [7] ;  [1] ;  [2] ;  [1] ;  [2] ;  [8] ;  [9] ;  [10] ;  [2] ;  [2] ;  [11] ;  [1] ; ORCiD logo [12] more »; ORCiD logo [13] ; ORCiD logo [14] ;  [6] ;  [7] ; ORCiD logo [8] ;  [3] ; ORCiD logo [15] ; ORCiD logo [15] ; ORCiD logo [16] « less
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Univ. of North Carolina, Chapel Hill, NC (United States). Department of Biology; Howard Hughes Medical Institute, Chevy Chase, MD (United States)
  3. Institute of Microbiology, ETH Zurich (Switzerland)
  4. Univ. of North Carolina, Chapel Hill, NC (United States). Department of Biology; Howard Hughes Medical Institute, Chevy Chase, MD (United States); Stanford Univ., CA (United States). Department of Biology
  5. Virginia Tech, Blacksburg, VA (United States). Department of Horticulture; Gansu Agricultural University (China). The Grassland College
  6. Virginia Tech, Blacksburg, VA (United States). Department of Horticulture
  7. International Centre for Genetic Engineering and Biotechnology, Trieste (Italy)
  8. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  9. Univ. of Tennessee, Knoxville, TN (United States). Department of Microbiology
  10. Cornell Univ., Ithaca, NY (United States). Department of Molecular Biology and Genetics
  11. Univ. of North Carolina, Chapel Hill, NC (United States). Department of Biology; Howard Hughes Medical Institute, Chevy Chase, MD (United States); BD Technologies and Innovation, Research Triangle Park, NC (United States)
  12. Univ. of North Carolina, Chapel Hill, NC (United States). Department of Biology
  13. Univ. of Washington, Seattle, WA (United States). School of Environmental and Forest Sciences
  14. Max Planck Institute for Developmental Biology, Tubingen (Germany)
  15. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); University of California, Merced, CA (United States)
  16. Univ. of North Carolina, Chapel Hill, NC (United States). Department of Biology, The Carolina Center for Genome Sciences and Department of Microbiology and Immunology; Howard Hughes Medical Institute, Chevy Chase, MD (United States)
Publication Date:
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231; SC001043; SC0014395
Type:
Accepted Manuscript
Journal Name:
Nature Genetics
Additional Journal Information:
Journal Volume: 50; Journal Issue: 1; Journal ID: ISSN 1061-4036
Publisher:
Nature Publishing Group
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1415202