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 used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly 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 representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
authors.forename: Collin M
authors.initials: CM
authors.lastname: Timm
authors.affiliation: Department of Natural Sciences, Northwest Missouri State University Maryville, MO, USA.
authors.forename: Alisha G
authors.initials: AG
authors.lastname: Campbell
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA.
authors.forename: Sagar M
authors.initials: SM
authors.lastname: Utturkar
authors.affiliation: Joint Institute for Computational Sciences, University of Tennessee, Knoxville Knoxville, TN, USA.
authors.forename: Se-Ran
authors.initials: SR
authors.lastname: Jun
authors.affiliation: Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA.
authors.forename: Rebecca E
authors.initials: RE
authors.lastname: Parales
authors.affiliation: Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA.
authors.forename: Watumesa A
authors.initials: WA
authors.lastname: Tan
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Fish, Wildlife and Conservation Biology, Colorado State University Fort Collins, CO, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Robeson
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
authors.forename: Tse-Yuan S
authors.initials: TY
authors.lastname: Lu
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Jawdy
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Brown
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
authors.forename: David W
authors.initials: DW
authors.lastname: Ussery
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Department of Microbiology, University of Tennessee, Knoxville Knoxville, TN, USA.
authors.forename: Christopher W
authors.initials: CW
authors.lastname: Schadt
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Tuskan
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
authors.forename: Mitchel J
authors.initials: MJ
authors.lastname: Doktycz
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Weston
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
authors.forename: Dale A
authors.initials: DA
authors.lastname: Pelletier
keywords: Populus; endosphere; metabolic modeling; metabolism; microbiome; rhizosphere