Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling

Larsen, Peter E.; Collart, Frank R.; Dai, Yang; Blanchard, Jeffrey L.

doi:10.1371/journal.pone.0132837

Title: Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling

Journal Article · Wed Sep 02 00:00:00 EDT 2015 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0132837· OSTI ID:1391831

Larsen, Peter E.; Collart, Frank R.; Dai, Yang; Blanchard, Jeffrey L.

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. However, 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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science - Office of Biological and Environmental Research

DOE Contract Number:: AC02-06CH11357

OSTI ID:: 1391831

Journal Information:: PLoS ONE, Vol. 10, Issue 9; ISSN 1932-6203

Publisher:: Public Library of Science

Country of Publication:: United States

Language:: English

References (75)

Catecholamines are active compounds in plants Kulma, Anna; Szopa, Jan Plant Science, Vol. 172, Issue 3 https://doi.org/10.1016/j.plantsci.2006.10.013	journal	March 2007
Multiple roles of siderophores in free-living nitrogen-fixing bacteria Kraepiel, A. M. L.; Bellenger, J. P.; Wichard, T. BioMetals, Vol. 22, Issue 4 https://doi.org/10.1007/s10534-009-9222-7	journal	March 2009
Activation of calcium- and calmodulin-dependent protein kinase (CCaMK), the central regulator of plant root endosymbiosis Singh, Sylvia; Parniske, Martin Current Opinion in Plant Biology, Vol. 15, Issue 4 https://doi.org/10.1016/j.pbi.2012.04.002	journal	August 2012
Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals Hu, X.; Zhao, J.; DeGrado, W. F. Proceedings of the National Academy of Sciences, Vol. 110, Issue 2 https://doi.org/10.1073/pnas.1215033110	journal	December 2012
Polyamines: Natural and engineered abiotic and biotic stress tolerance in plants Hussain, Syed Sarfraz; Ali, Muhammad; Ahmad, Maqbool Biotechnology Advances, Vol. 29, Issue 3 https://doi.org/10.1016/j.biotechadv.2011.01.003	journal	May 2011
Predicting Prokaryotic Ecological Niches Using Genome Sequence Analysis Suen, Garret; Goldman, Barry S.; Welch, Roy D. PLoS ONE, Vol. 2, Issue 8 https://doi.org/10.1371/journal.pone.0000743	journal	August 2007
Temporal and spatial distributions of ammonia-oxidizing archaea and bacteria and their ratio as an indicator of oligotrophic conditions in natural wetlands Sims, Atreyee; Horton, John; Gajaraj, Shashikanth Water Research, Vol. 46, Issue 13 https://doi.org/10.1016/j.watres.2012.05.007	journal	September 2012
Mycorrhizas improve nitrogen nutrition of Trifolium repens after 8 yr of selection under elevated atmospheric CO2 partial pressure Gamper, Hannes; Hartwig, Ueli A.; Leuchtmann, Adrian New Phytologist, Vol. 167, Issue 2 https://doi.org/10.1111/j.1469-8137.2005.01440.x	journal	April 2005
The mycorrhiza helper bacteria revisited Frey-Klett, P.; Garbaye, J.; Tarkka, M. New Phytologist, Vol. 176, Issue 1 https://doi.org/10.1111/j.1469-8137.2007.02191.x	journal	October 2007
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 Ma, Hongyan; Darmawan, Erica T.; Zhang, Min Journal of Controlled Release, Vol. 172, Issue 3 https://doi.org/10.1016/j.jconrel.2013.10.005	journal	December 2013
Flavonoids and Strigolactones in Root Exudates as Signals in Symbiotic and Pathogenic Plant-Fungus Interactions Steinkellner, Siegrid; Lendzemo, Venasius; Langer, Ingrid Molecules, Vol. 12, Issue 7 https://doi.org/10.3390/12071290	journal	July 2007
Type VI Secretion: Not Just for Pathogenesis Anymore Jani, Andrea J.; Cotter, Peggy A. Cell Host & Microbe, Vol. 8, Issue 1 https://doi.org/10.1016/j.chom.2010.06.012	journal	July 2010
Ammonia-oxidizing archaea involved in nitrogen removal You, Jia; Das, Atreyee; Dolan, Elizabeth M. Water Research, Vol. 43, Issue 7 https://doi.org/10.1016/j.watres.2009.01.016	journal	April 2009
Iron uptake and metabolism in pseudomonads Cornelis, Pierre Applied Microbiology and Biotechnology, Vol. 86, Issue 6 https://doi.org/10.1007/s00253-010-2550-2	journal	March 2010
Differential and chaotic calcium signatures in the symbiosis signaling pathway of legumes Kosuta, S.; Hazledine, S.; Sun, J. Proceedings of the National Academy of Sciences, Vol. 105, Issue 28 https://doi.org/10.1073/pnas.0803499105	journal	July 2008
An Oxyferrous Heme/Protein-based Radical Intermediate Is Catalytically Competent in the Catalase Reaction of Mycobacterium tuberculosis Catalase-Peroxidase (KatG) Suarez, Javier; Ranguelova, Kalina; Jarzecki, Andrzej A. Journal of Biological Chemistry, Vol. 284, Issue 11 https://doi.org/10.1074/jbc.M808106200	journal	January 2009
KEGG for integration and interpretation of large-scale molecular data sets Kanehisa, M.; Goto, S.; Sato, Y. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr988	journal	November 2011
Bacterial endophytes: recent developments and applications Ryan, Robert P.; Germaine, Kieran; Franks, Ashley FEMS Microbiology Letters, Vol. 278, Issue 1 https://doi.org/10.1111/j.1574-6968.2007.00918.x	journal	January 2008
From perception to attenuation: auxin signalling and responses Peer, Wendy Ann Current Opinion in Plant Biology, Vol. 16, Issue 5 https://doi.org/10.1016/j.pbi.2013.08.003	journal	October 2013
Periplasmic glucans of Pseudomonas syringae pv. syringae. Talaga, P.; Fournet, B.; Bohin, J. P. Journal of Bacteriology, Vol. 176, Issue 21 https://doi.org/10.1128/jb.176.21.6538-6544.1994	journal	November 1994
Gallium(III), cobalt(III) and copper(II) protoporphyrin IX exhibit antimicrobial activity against Porphyromonas gingivalis by reducing planktonic and biofilm growth and invasion of host epithelial cells Olczak, Teresa; Maszczak-Seneczko, Dorota; Smalley, John W. Archives of Microbiology, Vol. 194, Issue 8 https://doi.org/10.1007/s00203-012-0804-3	journal	March 2012
Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEED Devoid, Scott; Overbeek, Ross; DeJongh, Matthew Methods in Molecular Biology https://doi.org/10.1007/978-1-62703-299-5_2	book	January 2013
Mapping the niche space of soil microorganisms using taxonomy and traits Lennon, Jay T.; Aanderud, Zachary T.; Lehmkuhl, B. K. Ecology, Vol. 93, Issue 8 https://doi.org/10.1890/11-1745.1	journal	August 2012
Methylglyoxal: (active agent of manuka honey) in vitro activity against bacterial biofilms Kilty, Shaun J.; Duval, Melanie; Chan, Francis T. International Forum of Allergy & Rhinology, Vol. 1, Issue 5 https://doi.org/10.1002/alr.20073	journal	May 2011
Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2 Drigo, B.; Pijl, A. S.; Duyts, H. Proceedings of the National Academy of Sciences, Vol. 107, Issue 24 https://doi.org/10.1073/pnas.0912421107	journal	June 2010
Plant pathogenesis-related (PR) proteins: A focus on PR peptides Sels, Jan; Mathys, Janick; De Coninck, Barbara M. A. Plant Physiology and Biochemistry, Vol. 46, Issue 11 https://doi.org/10.1016/j.plaphy.2008.06.011	journal	November 2008
Satellite remote sensing data can be used to model marine microbial metabolite turnover Larsen, Peter E.; Scott, Nicole; Post, Anton F. The ISME Journal, Vol. 9, Issue 1 https://doi.org/10.1038/ismej.2014.107	journal	July 2014
KEGG: Kyoto Encyclopedia of Genes and Genomes Ogata, H.; Goto, S.; Sato, K. Nucleic Acids Research, Vol. 27, Issue 1 https://doi.org/10.1093/nar/27.1.29	journal	January 1999
Causes and consequences of plant-associated biofilms: Causes and consequences of plant-associated biofilms Rudrappa, Thimmaraju; Biedrzycki, Meredith L.; Bais, Harsh P. FEMS Microbiology Ecology, Vol. 64, Issue 2 https://doi.org/10.1111/j.1574-6941.2008.00465.x	journal	May 2008
The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments Scott, Nicole M.; Hess, Matthias; Bouskill, Nick J. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00108	journal	March 2014
Top 10 plant pathogenic bacteria in molecular plant pathology: Top 10 plant pathogenic bacteria Mansfield, John; Genin, Stephane; Magori, Shimpei Molecular Plant Pathology, Vol. 13, Issue 6 https://doi.org/10.1111/j.1364-3703.2012.00804.x	journal	June 2012
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates Kunin, Victor; Engelbrektson, Anna; Ochman, Howard Environmental Microbiology, Vol. 12, Issue 1 https://doi.org/10.1111/j.1462-2920.2009.02051.x	journal	January 2010
The role of flavonoids in the establishment of plant roots endosymbioses with arbuscular mycorrhiza fungi, rhizobia and Frankia bacteria Abdel-Lateif, Khalid; Bogusz, Didier; Hocher, Valérie Plant Signaling & Behavior, Vol. 7, Issue 6 https://doi.org/10.4161/psb.20039	journal	June 2012
Biological control of soil-borne pathogens by fluorescent pseudomonads Haas, Dieter; Défago, Geneviève Nature Reviews Microbiology, Vol. 3, Issue 4 https://doi.org/10.1038/nrmicro1129	journal	March 2005
Going back to the roots: the microbial ecology of the rhizosphere Philippot, Laurent; Raaijmakers, Jos M.; Lemanceau, Philippe Nature Reviews Microbiology, Vol. 11, Issue 11 https://doi.org/10.1038/nrmicro3109	journal	September 2013
Inter-specific Interactions Between Carbon-limited Soil Bacteria Affect Behavior and Gene Expression Garbeva, Paolina; de Boer, Wietse Microbial Ecology, Vol. 58, Issue 1 https://doi.org/10.1007/s00248-009-9502-3	journal	March 2009
Isolation of Streptococcus pneumoniae Biofilm Mutants and Their Characterization during Nasopharyngeal Colonization Munoz-Elias, E. J.; Marcano, J.; Camilli, A. Infection and Immunity, Vol. 76, Issue 11 https://doi.org/10.1128/IAI.00425-08	journal	September 2008
Regulatory and Metabolic Networks for the Adaptation of Pseudomonas aeruginosa Biofilms to Urinary Tract-Like Conditions Tielen, Petra; Rosin, Nathalie; Meyer, Ann-Kathrin PLoS ONE, Vol. 8, Issue 8 https://doi.org/10.1371/journal.pone.0071845	journal	August 2013
The ENZYME database in 2000 Bairoch, A. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.304	journal	January 2000
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000 Buell, C. R.; Joardar, V.; Lindeberg, M. Proceedings of the National Academy of Sciences, Vol. 100, Issue 18 https://doi.org/10.1073/pnas.1731982100	journal	August 2003
Emerging science of the human microbiome Jones, Mitchell L.; Ganopolsky, Jorge G.; Martoni, Christopher J. Gut Microbes, Vol. 5, Issue 4 https://doi.org/10.4161/gmic.29810	journal	July 2014
Pathways of Glucose Regulation of Monosaccharide Transport in Grape Cells Conde, Carlos; Agasse, Alice; Glissant, David Plant Physiology, Vol. 141, Issue 4 https://doi.org/10.1104/pp.106.080804	journal	June 2006
Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond Rajendhran, J.; Gunasekaran, P. Microbiological Research, Vol. 166, Issue 2 https://doi.org/10.1016/j.micres.2010.02.003	journal	February 2011
The Cpx system of Escherichia coli, a strategic signaling pathway for confronting adverse conditions and for settling biofilm communities? Dorel, Corinne; Lejeune, Philippe; Rodrigue, Agnès Research in Microbiology, Vol. 157, Issue 4 https://doi.org/10.1016/j.resmic.2005.12.003	journal	May 2006
Evidence for the involvement of the anthranilate degradation pathway in Pseudomonas aeruginosa biofilm formation Costaglioli, Patricia; Barthe, Christophe; Claverol, Stephane MicrobiologyOpen, Vol. 1, Issue 3 https://doi.org/10.1002/mbo3.33	journal	September 2012
Microbial degradation of lignin: how a bulky recalcitrant polymer is efficiently recycled in nature and how we can take advantage of this Ruiz-Dueñas, Francisco J.; Martínez, Ángel T. Microbial Biotechnology, Vol. 2, Issue 2 https://doi.org/10.1111/j.1751-7915.2008.00078.x	journal	March 2009
Pathogenesis, parasitism and mutualism in the trophic space of microbe–plant interactions Newton, Adrian C.; Fitt, Bruce D. L.; Atkins, Simon D. Trends in Microbiology, Vol. 18, Issue 8 https://doi.org/10.1016/j.tim.2010.06.002	journal	August 2010
Metagenomics - a guide from sampling to data analysis Thomas, Torsten; Gilbert, Jack; Meyer, Folker Microbial Informatics and Experimentation, Vol. 2, Issue 1 https://doi.org/10.1186/2042-5783-2-3	journal	February 2012
Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida Wu, Xiao; Monchy, Sébastien; Taghavi, Safiyh FEMS Microbiology Reviews, Vol. 35, Issue 2 https://doi.org/10.1111/j.1574-6976.2010.00249.x	journal	March 2011
The type VI secretion toolkit Cascales, Eric EMBO reports, Vol. 9, Issue 8 https://doi.org/10.1038/embor.2008.131	journal	July 2008
The Dual Function of Sugar Carriers: Transport and Sugar Sensing Lalonde, Sylvie; Boles, Eckhard; Hellmann, Hanjo The Plant Cell, Vol. 11, Issue 4 https://doi.org/10.1105/tpc.11.4.707	journal	April 1999
Osmotic adaptation by gram-negative bacteria: possible role for periplasmic oligosaccharides Miller, K.; Kennedy, E.; Reinhold, V. Science, Vol. 231, Issue 4733 https://doi.org/10.1126/science.3941890	journal	January 1986
Pseudomonas aeruginosa PA1006, Which Plays a Role in Molybdenum Homeostasis, Is Required for Nitrate Utilization, Biofilm Formation, and Virulence Filiatrault, Melanie J.; Tombline, Gregory; Wagner, Victoria E. PLoS ONE, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pone.0055594	journal	February 2013
Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere: Plant species, soil type and rhizosphere communities Berg, Gabriele; Smalla, Kornelia FEMS Microbiology Ecology, Vol. 68, Issue 1 https://doi.org/10.1111/j.1574-6941.2009.00654.x	journal	April 2009
Changes in Diversity and Functional Gene Abundances of Microbial Communities Involved in Nitrogen Fixation, Nitrification, and Denitrification in a Tidal Wetland versus Paddy Soils Cultivated for Different Time Periods Bannert, Andrea; Kleineidam, Kristina; Wissing, Livia Applied and Environmental Microbiology, Vol. 77, Issue 17 https://doi.org/10.1128/AEM.01751-10	journal	July 2011
On the production of glycogen by Pseudomonas fluorescens during biofilm development: an in situ study by attenuated total reflection-infrared with chemometrics Quilès, Fabienne; Humbert, François Biofouling, Vol. 30, Issue 6 https://doi.org/10.1080/08927014.2014.915956	journal	April 2014
Pseudomonas genomes: diverse and adaptable Silby, Mark W.; Winstanley, Craig; Godfrey, Scott A. C. FEMS Microbiology Reviews, Vol. 35, Issue 4 https://doi.org/10.1111/j.1574-6976.2011.00269.x	journal	July 2011
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary Mao, X.; Cai, T.; Olyarchuk, J. G. Bioinformatics, Vol. 21, Issue 19 https://doi.org/10.1093/bioinformatics/bti430	journal	April 2005
Nutritional Influences on Biofilm Development Bowden, G. H. W.; Li, Y. H. Advances in Dental Research, Vol. 11, Issue 1 https://doi.org/10.1177/08959374970110012101	journal	April 1997
Anti-biofilm Effects of Honey Against Wound Pathogens Proteus mirabilis and Enterobacter cloacae : HONEY KILLS WOUND BIOFILM Majtan, Juraj; Bohova, Jana; Horniackova, Miroslava Phytotherapy Research, Vol. 28, Issue 1 https://doi.org/10.1002/ptr.4957	journal	March 2013
Flavonoids as plant signals to rhizosphere microbes Phillips, D. A.; Tsai, S. M. Mycorrhiza, Vol. 1, Issue 2 https://doi.org/10.1007/BF00206136	journal	March 1992
Genomics of secondary metabolite production by Pseudomonas spp. Gross, Harald; Loper, Joyce E. Natural Product Reports, Vol. 26, Issue 11 https://doi.org/10.1039/b817075b	journal	January 2009
The metabolic versatility of pseudomonads Clarke, Patricia H. Antonie van Leeuwenhoek, Vol. 48, Issue 2 https://doi.org/10.1007/BF00405197	journal	January 1982
The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms Mendes, Rodrigo; Garbeva, Paolina; Raaijmakers, Jos M. FEMS Microbiology Reviews, Vol. 37, Issue 5 https://doi.org/10.1111/1574-6976.12028	journal	September 2013
16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls Janda, J. M.; Abbott, S. L. Journal of Clinical Microbiology, Vol. 45, Issue 9 https://doi.org/10.1128/JCM.01228-07	journal	July 2007
Molecular mechanisms of lytic enzymes involved in the biocontrol activity of Trichoderma harzianum Haran, S.; Schickler, H.; Chet, I. Microbiology, Vol. 142, Issue 9 https://doi.org/10.1099/00221287-142-9-2321	journal	September 1996
Deadly syringes: type VI secretion system activities in pathogenicity and interbacterial competition Kapitein, Nicole; Mogk, Axel Current Opinion in Microbiology, Vol. 16, Issue 1 https://doi.org/10.1016/j.mib.2012.11.009	journal	February 2013
Very long chain fatty acid and lipid signaling in the response of plants to pathogens Raffaele, Sylvain; Leger, Amandine; Roby, Dominique Plant Signaling & Behavior, Vol. 4, Issue 2 https://doi.org/10.4161/psb.4.2.7580	journal	February 2009
Fluxomics - connecting ‘omics analysis and phenotypes: Fluxomics - a systems biology tool Winter, Gal; Krömer, Jens O. Environmental Microbiology, Vol. 15, Issue 7 https://doi.org/10.1111/1462-2920.12064	journal	January 2013
Taxonomy of Phytopathogenic Pseudomonads1 Sands, D. C.; Schroth, M. N.; Hildebrand, D. C. Journal of Bacteriology, Vol. 101, Issue 1 https://doi.org/10.1128/JB.101.1.9-23.1970	journal	January 1970
Using metabolomic and transportomic modeling and machine learning to identify putative novel therapeutic targets for antibiotic resistant Pseudomonad infections Larsen, Peter E.; Collart, Frank R. 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society https://doi.org/10.1109/embc.2014.6943592	conference	August 2014
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset Larsen, Peter E.; Collart, Frank R.; Field, Dawn Microbial Informatics and Experimentation, Vol. 1, Issue 1 https://doi.org/10.1186/2042-5783-1-4	journal	June 2011
Type VI Secretion: Not Just for Pathogenesis Anymore A., Cotter, Peggy; J., Jani, Andrea The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/bcp2-ma26	text	January 2010
The Dual Function of Sugar Carriers: Transport and Sugar Sensing Lalonde, Sylvie; Boles, Eckhard; Hellmann, Hanjo The Plant Cell, Vol. 11, Issue 4 https://doi.org/10.2307/3870894	journal	April 1999
Analysis of plant microbe interactions in the era of next generation sequencing technologies Knief, Claudia Frontiers in Plant Science, Vol. 5 https://doi.org/10.3389/fpls.2014.00216	journal	May 2014

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