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Title: Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

Abstract

The bacterial microbiota of plants is diverse, with ~1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work we investigate how 19 sequenced Pseudomonas fluorescens strains representing a single OTU isolated from Populus deltoides rhizosphere and endosphere differ using phenotypic analysis, comparative genomics, and metabolic models. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for bacterial-plant interactions are enriched in endosphere isolate genomes and growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased towards endosphere isolates. Endosphere isolates have more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways important for bacterial-plant interactions but show metabolic bias towards chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria that are enriched in event he most closely related isolates.

Authors:
 [1];  [2];  [1];  [1];  [3];  [3];  [1];  [1];  [1];  [1];  [1];  [1];  [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Northwest Missouri State Univ., Maryville, MS (United States)
  3. Univ. of California, Davis, CA (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1234335
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Timm, Collin M., Campbell, Alicia G., Utturkar, Sagar M., Jun, Se Ran, Parales, Rebecca E., Tan, Mesa, Robeson, Michael S., Lu, Tse-Yuan S., Jawdy, Sara, Schadt, Christopher Warren, Doktycz, Mitchel John, Weston, David, and Pelletier, Dale A. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. United States: N. p., 2015. Web. https://doi.org/10.3389/fmicb.2015.01118.
Timm, Collin M., Campbell, Alicia G., Utturkar, Sagar M., Jun, Se Ran, Parales, Rebecca E., Tan, Mesa, Robeson, Michael S., Lu, Tse-Yuan S., Jawdy, Sara, Schadt, Christopher Warren, Doktycz, Mitchel John, Weston, David, & Pelletier, Dale A. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. United States. https://doi.org/10.3389/fmicb.2015.01118
Timm, Collin M., Campbell, Alicia G., Utturkar, Sagar M., Jun, Se Ran, Parales, Rebecca E., Tan, Mesa, Robeson, Michael S., Lu, Tse-Yuan S., Jawdy, Sara, Schadt, Christopher Warren, Doktycz, Mitchel John, Weston, David, and Pelletier, Dale A. Wed . "Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment". United States. https://doi.org/10.3389/fmicb.2015.01118. https://www.osti.gov/servlets/purl/1234335.
@article{osti_1234335,
title = {Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment},
author = {Timm, Collin M. and Campbell, Alicia G. and Utturkar, Sagar M. and Jun, Se Ran and Parales, Rebecca E. and Tan, Mesa and Robeson, Michael S. and Lu, Tse-Yuan S. and Jawdy, Sara and Schadt, Christopher Warren and Doktycz, Mitchel John and Weston, David and Pelletier, Dale A.},
abstractNote = {The bacterial microbiota of plants is diverse, with ~1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work we investigate how 19 sequenced Pseudomonas fluorescens strains representing a single OTU isolated from Populus deltoides rhizosphere and endosphere differ using phenotypic analysis, comparative genomics, and metabolic models. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for bacterial-plant interactions are enriched in endosphere isolate genomes and growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased towards endosphere isolates. Endosphere isolates have more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways important for bacterial-plant interactions but show metabolic bias towards chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria that are enriched in event he most closely related isolates.},
doi = {10.3389/fmicb.2015.01118},
journal = {Frontiers in Microbiology},
number = ,
volume = 6,
place = {United States},
year = {2015},
month = {10}
}

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