Genomic features of bacterial adaptation to plants

Levy, Asaf; Salas Gonzalez, Isai; Mittelviefhaus, Maximilian; Clingenpeel, Scott; Herrera Paredes, Sur; Miao, Jiamin; Wang, Kunru; Devescovi, Giulia; Stillman, Kyra; Monteiro, Freddy; Rangel Alvarez, Bryan; Lundberg, Derek S.; Lu, Tse-Yuan; Lebeis, Sarah; Jin, Zhao; McDonald, Meredith; Klein, Andrew P.; Feltcher, Meghan E.; Rio, Tijana Glavina; Grant, Sarah R.; Doty, Sharon L.; Ley, Ruth E.; Zhao, Bingyu; Venturi, Vittorio; Pelletier, Dale A.; Vorholt, Julia A.; Tringe, Susannah G.; Woyke, Tanja; Dangl, Jeffery L.

doi:10.1038/s41588-017-0012-9

Genomic features of bacterial adaptation to plants

Journal Article · Mon Dec 18 00:00:00 EST 2017 · Nature Genetics

DOI:https://doi.org/10.1038/s41588-017-0012-9· OSTI ID:1415202

^[1]; Salas Gonzalez, Isai ^[2]; Mittelviefhaus, Maximilian ^[3]; ^[1]; ^[4]; Miao, Jiamin ^[5]; Wang, Kunru ^[6]; Devescovi, Giulia ^[7]; Stillman, Kyra ^[1]; Monteiro, Freddy ^[2]; Rangel Alvarez, Bryan ^[1]; Lundberg, Derek S. ^[2]; Lu, Tse-Yuan ^[8]; Lebeis, Sarah ^[9]; Jin, Zhao ^[10]; McDonald, Meredith ^[2]; Klein, Andrew P. ^[2]; Feltcher, Meghan E. ^[11]; Rio, Tijana Glavina ^[1]; ^[12] more »

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of North Carolina, Chapel Hill, NC (United States). Department of Biology; Howard Hughes Medical Institute, Chevy Chase, MD (United States)
Institute of Microbiology, ETH Zurich (Switzerland)
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
Virginia Tech, Blacksburg, VA (United States). Department of Horticulture; Gansu Agricultural University (China). The Grassland College
Virginia Tech, Blacksburg, VA (United States). Department of Horticulture
International Centre for Genetic Engineering and Biotechnology, Trieste (Italy)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
Univ. of Tennessee, Knoxville, TN (United States). Department of Microbiology
Cornell Univ., Ithaca, NY (United States). Department of Molecular Biology and Genetics
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)
Univ. of North Carolina, Chapel Hill, NC (United States). Department of Biology
Univ. of Washington, Seattle, WA (United States). School of Environmental and Forest Sciences
Max Planck Institute for Developmental Biology, Tubingen (Germany)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); University of California, Merced, CA (United States)
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)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23), Biological Systems Science Division (SC-23.2 )

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725; SC0010423; SC0014395

OSTI ID:: 1415202

Alternate ID(s):: OSTI ID: 1529504
OSTI ID: 1571092

Journal Information:: Nature Genetics, Journal Name: Nature Genetics Journal Issue: 1 Vol. 50; ISSN 1061-4036

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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