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Title: Genome-wide identification of bacterial plant colonization genes

Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system. Among the genes we identified were some with obvious colonization-related roles in motility and carbon metabolism, as well as 44 other genes that had no or vague functional predictions. Independent validation assays of individual genes confirmed colonization functions for 20 of 22 (91%) cases tested. To further characterize genes identified by our screen, we compared the functional contributions of P. simiae genes to growth in 90 distinct in vitro conditions by RB-TnSeq, highlighting specific metabolic functions associated with root colonization genes. Here, our analysis of bacterial genes by sequence-driven saturation mutagenesis revealed a genome-wide map of the genetic determinants of plant root colonization and offers a starting point for targeted improvement of the colonization capabilities of plant-beneficial microbes.
Authors:
ORCiD logo [1] ;  [2] ;  [1] ;  [3] ;  [2] ;  [1] ;  [1] ;  [4] ;  [2] ;  [5] ;  [1] ;  [3] ;  [2] ;  [6]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Univ. of North Carolina, Chapel Hill, NC (United States). Howard Hughes Medical Inst., Dept. of Biology, Dept. of Microbiology and Immunology
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Merced, CA (United States). School of Natural Sciences
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; Univ. of California, Merced, CA (United States). School of Natural Sciences
Publication Date:
Grant/Contract Number:
AC02-05CH11231; F32-GM112345-02; SC0014395; IOS-1343020; GBMF3030
Type:
Accepted Manuscript
Journal Name:
PLoS biology (Online)
Additional Journal Information:
Journal Name: PLoS biology (Online); Journal Volume: 15; Journal Issue: 9; Journal ID: ISSN 1545-7885
Publisher:
Public Library of Science
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Institutes of Health (NIH); National Science Foundation (NSF); Gordon and Betty Moore Foundation (GBMF)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES
OSTI Identifier:
1416925

Cole, Benjamin J., Feltcher, Meghan E., Waters, Robert J., Wetmore, Kelly M., Mucyn, Tatiana S., Ryan, Elizabeth M., Wang, Gaoyan, Ul-Hasan, Sabah, McDonald, Meredith, Yoshikuni, Yasuo, Malmstrom, Rex R., Deutschbauer, Adam M., Dangl, Jeffery L., and Visel, Axel. Genome-wide identification of bacterial plant colonization genes. United States: N. p., Web. doi:10.1371/journal.pbio.2002860.
Cole, Benjamin J., Feltcher, Meghan E., Waters, Robert J., Wetmore, Kelly M., Mucyn, Tatiana S., Ryan, Elizabeth M., Wang, Gaoyan, Ul-Hasan, Sabah, McDonald, Meredith, Yoshikuni, Yasuo, Malmstrom, Rex R., Deutschbauer, Adam M., Dangl, Jeffery L., & Visel, Axel. Genome-wide identification of bacterial plant colonization genes. United States. doi:10.1371/journal.pbio.2002860.
Cole, Benjamin J., Feltcher, Meghan E., Waters, Robert J., Wetmore, Kelly M., Mucyn, Tatiana S., Ryan, Elizabeth M., Wang, Gaoyan, Ul-Hasan, Sabah, McDonald, Meredith, Yoshikuni, Yasuo, Malmstrom, Rex R., Deutschbauer, Adam M., Dangl, Jeffery L., and Visel, Axel. 2017. "Genome-wide identification of bacterial plant colonization genes". United States. doi:10.1371/journal.pbio.2002860. https://www.osti.gov/servlets/purl/1416925.
@article{osti_1416925,
title = {Genome-wide identification of bacterial plant colonization genes},
author = {Cole, Benjamin J. and Feltcher, Meghan E. and Waters, Robert J. and Wetmore, Kelly M. and Mucyn, Tatiana S. and Ryan, Elizabeth M. and Wang, Gaoyan and Ul-Hasan, Sabah and McDonald, Meredith and Yoshikuni, Yasuo and Malmstrom, Rex R. and Deutschbauer, Adam M. and Dangl, Jeffery L. and Visel, Axel},
abstractNote = {Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system. Among the genes we identified were some with obvious colonization-related roles in motility and carbon metabolism, as well as 44 other genes that had no or vague functional predictions. Independent validation assays of individual genes confirmed colonization functions for 20 of 22 (91%) cases tested. To further characterize genes identified by our screen, we compared the functional contributions of P. simiae genes to growth in 90 distinct in vitro conditions by RB-TnSeq, highlighting specific metabolic functions associated with root colonization genes. Here, our analysis of bacterial genes by sequence-driven saturation mutagenesis revealed a genome-wide map of the genetic determinants of plant root colonization and offers a starting point for targeted improvement of the colonization capabilities of plant-beneficial microbes.},
doi = {10.1371/journal.pbio.2002860},
journal = {PLoS biology (Online)},
number = 9,
volume = 15,
place = {United States},
year = {2017},
month = {9}
}

Works referenced in this record:

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons
journal, May 2015
  • Wetmore, Kelly M.; Price, Morgan N.; Waters, Robert J.
  • mBio, Vol. 6, Issue 3, Article No. e00306-15
  • DOI: 10.1128/mBio.00306-15