Predicting ecological roles in the rhizosphere using metabolome and transportome modeling
Abstract
The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. New algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad’s ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter of plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism’s transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbialmore »
- Authors:
-
- Argonne National Lab., Argonne, IL (United States). Biosciences Div.; Univ. of Chicago, Chicago, IL (United States). Dept. of Bioengineering.
- Argonne National Lab., Argonne, IL (United States). Biosciences Div.
- Univ. of Chicago, Chicago, IL (United States). Dept. of Bioengineering
- Univ. of Massachusetts, Worcester, MA (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1221792
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 9; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; ecological niches; enzyme metabolism; plant genomics; metabolomics; enzymes; rhizosphere; secondary metabolism; genome analysis
Citation Formats
Larsen, Peter E., Collart, Frank R., Dai, Yang, and Blanchard, Jeffrey L. Predicting ecological roles in the rhizosphere using metabolome and transportome modeling. United States: N. p., 2015.
Web. doi:10.1371/journal.pone.0132837.
Larsen, Peter E., Collart, Frank R., Dai, Yang, & Blanchard, Jeffrey L. Predicting ecological roles in the rhizosphere using metabolome and transportome modeling. United States. https://doi.org/10.1371/journal.pone.0132837
Larsen, Peter E., Collart, Frank R., Dai, Yang, and Blanchard, Jeffrey L. Wed .
"Predicting ecological roles in the rhizosphere using metabolome and transportome modeling". United States. https://doi.org/10.1371/journal.pone.0132837. https://www.osti.gov/servlets/purl/1221792.
@article{osti_1221792,
title = {Predicting ecological roles in the rhizosphere using metabolome and transportome modeling},
author = {Larsen, Peter E. and Collart, Frank R. and Dai, Yang and Blanchard, Jeffrey L.},
abstractNote = {The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. New algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad’s ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter of plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism’s transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.},
doi = {10.1371/journal.pone.0132837},
journal = {PLoS ONE},
number = 9,
volume = 10,
place = {United States},
year = {Wed Sep 02 00:00:00 EDT 2015},
month = {Wed Sep 02 00:00:00 EDT 2015}
}
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Development of a poly(ether urethane) system for the controlled release of two novel anti-biofilm agents based on gallium or zinc and its efficacy to prevent bacterial biofilm formation
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Plant pathogenesis-related (PR) proteins: A focus on PR peptides
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The Cpx system of Escherichia coli, a strategic signaling pathway for confronting adverse conditions and for settling biofilm communities?
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Temporal and spatial distributions of ammonia-oxidizing archaea and bacteria and their ratio as an indicator of oligotrophic conditions in natural wetlands
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Satellite remote sensing data can be used to model marine microbial metabolite turnover
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Biological control of soil-borne pathogens by fluorescent pseudomonads
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journal, July 2008
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- Proceedings of the National Academy of Sciences, Vol. 105, Issue 28
Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2
journal, June 2010
- Drigo, B.; Pijl, A. S.; Duyts, H.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 24
Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals
journal, December 2012
- Hu, X.; Zhao, J.; DeGrado, W. F.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 2
On the production of glycogen by Pseudomonas fluorescens during biofilm development: an in situ study by attenuated total reflection-infrared with chemometrics
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Causes and consequences of plant-associated biofilms: Causes and consequences of plant-associated biofilms
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- FEMS Microbiology Ecology, Vol. 64, Issue 2
Bacterial endophytes: recent developments and applications
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Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida
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- FEMS Microbiology Reviews, Vol. 35, Issue 2
Periplasmic glucans of Pseudomonas syringae pv. syringae.
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Pseudomonas aeruginosa PA1006, Which Plays a Role in Molybdenum Homeostasis, Is Required for Nitrate Utilization, Biofilm Formation, and Virulence
journal, February 2013
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Regulatory and Metabolic Networks for the Adaptation of Pseudomonas aeruginosa Biofilms to Urinary Tract-Like Conditions
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Type VI Secretion: Not Just for Pathogenesis Anymore
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- The University of North Carolina at Chapel Hill University Libraries
Mapping the niche space of soil microorganisms using taxonomy and traits
journal, August 2012
- Lennon, Jay T.; Aanderud, Zachary T.; Lehmkuhl, B. K.
- Ecology, Vol. 93, Issue 8
The Dual Function of Sugar Carriers: Transport and Sugar Sensing
journal, April 1999
- Lalonde, Sylvie; Boles, Eckhard; Hellmann, Hanjo
- The Plant Cell, Vol. 11, Issue 4
The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments
journal, March 2014
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Analysis of plant microbe interactions in the era of next generation sequencing technologies
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Flavonoids and Strigolactones in Root Exudates as Signals in Symbiotic and Pathogenic Plant-Fungus Interactions
journal, July 2007
- Steinkellner, Siegrid; Lendzemo, Venasius; Langer, Ingrid
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