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

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.

doi:10.3389/fmicb.2015.01118

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

Journal Article · Wed Oct 14 00:00:00 EDT 2015 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2015.01118· OSTI ID:1234335

Timm, Collin M. ^[1]; Campbell, Alicia G. ^[2]; Utturkar, Sagar M. ^[1]; Jun, Se Ran ^[1]; Parales, Rebecca E. ^[3]; Tan, Mesa ^[3]; Robeson, Michael S. ^[1]; Lu, Tse-Yuan S. ^[1]; Jawdy, Sara ^[1]; Schadt, Christopher Warren ^[1]; Doktycz, Mitchel John ^[1]; Weston, David ^[1]; Pelletier, Dale A. ^[1]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Northwest Missouri State Univ., Maryville, MS (United States)
Univ. of California, Davis, CA (United States)

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.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1234335

Journal Information:: Frontiers in Microbiology, Vol. 6; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 40 works

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Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation Noirot-Gros, Marie-Francoise; Shinde, Shalaka; Larsen, Peter E. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00853	journal	May 2018
Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis BenIsrael, Michael; Wanner, Philipp; Aravena, Ramon Figshare https://doi.org/10.6084/m9.figshare.7593968	text	January 2019
Giving back to the community: microbial mechanisms of plant-soil interactions Herrera Paredes, Sur; Lebeis, Sarah L. Functional Ecology, Vol. 30, Issue 7 https://doi.org/10.1111/1365-2435.12684	journal	June 2016
Quantifying the Spatiotemporal Dynamics of Plant Root Colonization by Beneficial Bacteria in a Microfluidic Habitat Aufrecht, Jayde A.; Timm, Collin M.; Bible, Amber Advanced Biosystems, Vol. 2, Issue 6 https://doi.org/10.1002/adbi.201800048	journal	April 2018
Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates Yi, Yanglei; de Jong, Anne; Frenzel, Elrike Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01487	journal	August 2017
Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis BenIsrael, Michael; Wanner, Philipp; Aravena, Ramon Taylor & Francis https://doi.org/10.6084/m9.figshare.7593968.v1	text	January 2019
Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population Lopes, Lucas Dantas; Pereira e. Silva, Michele de C.; Weisberg, Alexandra J. Environmental Microbiology, Vol. 20, Issue 12 https://doi.org/10.1111/1462-2920.14363	journal	September 2018
Isolated Bacillus subtilis strain 330-2 and its antagonistic genes identified by the removing PCR Ahmad, Zahoor; Wu, Jia; Chen, Lulu Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-01940-9	journal	May 2017
Host genotype and age shape the leaf and root microbiomes of a wild perennial plant S., Lundberg, Derek; L., Dangl, Jeffery; G., Del Rio, Tijana The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/18y1-ek17	text	January 2016

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