Genome-wide identification of bacterial plant colonization genes

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

doi:10.1371/journal.pbio.2002860

Title: Genome-wide identification of bacterial plant colonization genes

Journal Article · Fri Sep 22 00:00:00 EDT 2017 · PLoS Biology (Online)

DOI:https://doi.org/10.1371/journal.pbio.2002860· OSTI ID:1416925

^[1]; Feltcher, Meghan E. ^[2]; Waters, Robert J. ^[1]; Wetmore, Kelly M. ^[3]; Mucyn, Tatiana S. ^[2]; Ryan, Elizabeth M. ^[1]; Wang, Gaoyan ^[1]; Ul-Hasan, Sabah ^[4]; McDonald, Meredith ^[2]; Yoshikuni, Yasuo ^[5]; Malmstrom, Rex R. ^[1]; Deutschbauer, Adam M. ^[3]; Dangl, Jeffery L. ^[2]; Visel, Axel ^[6]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of North Carolina, Chapel Hill, NC (United States). Howard Hughes Medical Inst., Dept. of Biology, Dept. of Microbiology and Immunology
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Merced, CA (United States). School of Natural Sciences
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
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

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF); Gordon and Betty Moore Foundation (GBMF)

Grant/Contract Number:: AC02-05CH11231; F32-GM112345-02; SC0014395; IOS-1343020; GBMF3030

OSTI ID:: 1416925

Journal Information:: PLoS Biology (Online), Vol. 15, Issue 9; ISSN 1545-7885

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 102 works

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