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:
-
- 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)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (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. doi: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 = {Wed Oct 14 00:00:00 EDT 2015},
month = {Wed Oct 14 00:00:00 EDT 2015}
}
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Works referenced in this record:
Bacterial volatiles promote growth in Arabidopsis
journal, April 2003
- Ryu, C. -M.; Farag, M. A.; Hu, C. -H.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 8
Extreme genome reduction in symbiotic bacteria
journal, November 2011
- McCutcheon, John P.; Moran, Nancy A.
- Nature Reviews Microbiology, Vol. 10, Issue 1
Genomics of Secondary Metabolism in Populus : Interactions with Biotic and Abiotic Environments
journal, October 2009
- Chen, Feng; Liu, Chang-Jun; Tschaplinski, Timothy J.
- Critical Reviews in Plant Sciences, Vol. 28, Issue 5
Is l-arabinose important for the endophytic lifestyle of Pseudomonas spp.?
journal, September 2012
- Malfanova, Natalia; Kamilova, Faina; Validov, Shamil
- Archives of Microbiology, Vol. 195, Issue 1
Iron acquisition and its control in pseudomonas aeruginosa many roads lead to rome
journal, January 2003
- Poole, Keith
- Frontiers in Bioscience, Vol. 8, Issue 4
Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency
journal, December 2010
- Carvalhais, Lilia C.; Dennis, Paul G.; Fedoseyenko, Dmitri
- Journal of Plant Nutrition and Soil Science, Vol. 174, Issue 1
Defining the core Arabidopsis thaliana root microbiome
journal, August 2012
- Lundberg, Derek S.; Lebeis, Sarah L.; Paredes, Sur Herrera
- Nature, Vol. 488, Issue 7409
Aerobic degradation of aromatic compounds
journal, June 2013
- Díaz, Eduardo; Jiménez, José Ignacio; Nogales, Juan
- Current Opinion in Biotechnology, Vol. 24, Issue 3
Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture
journal, April 2011
- Pérez-García, Alejandro; Romero, Diego; de Vicente, Antonio
- Current Opinion in Biotechnology, Vol. 22, Issue 2
Modeling Phosphorus Uptake by a Growing and Exuding Root System
journal, January 2012
- Schnepf, A.; Leitner, D.; Klepsch, S.
- Vadose Zone Journal, Vol. 11, Issue 3
The Aerobic Pseudomonads a Taxonomic Study
journal, May 1966
- Stanier, R. Y.; Palleroni, N. J.; Doudoroff, M.
- Journal of General Microbiology, Vol. 43, Issue 2
Plant growth promoting activities of phosphate-solubilizing Enterobacter asburiae as influenced by fungicides
journal, January 2010
- Ahemad, Munees; Khan, Mohammad Saghir
- EurAsian Journal of Biosciences
Exudation of organic anions by roots of cabbage, carrot, and potato as influenced by environmental factors and plant age
journal, October 2004
- Dechassa, Nigussie; Schenk, Manfred K.
- Journal of Plant Nutrition and Soil Science, Vol. 167, Issue 5
What lies beneath: belowground defense strategies in plants
journal, February 2015
- De Coninck, Barbara; Timmermans, Pieter; Vos, Christine
- Trends in Plant Science, Vol. 20, Issue 2
Pseudomonas fluorescens Induces Strain-Dependent and Strain-Independent Host Plant Responses in Defense Networks, Primary Metabolism, Photosynthesis, and Fitness
journal, June 2012
- Weston, David J.; Pelletier, Dale A.; Morrell-Falvey, Jennifer L.
- Molecular Plant-Microbe Interactions, Vol. 25, Issue 6
Soil properties are key determinants for the development of exudate gradients in a rhizosphere simulation model
journal, February 2010
- Raynaud, Xavier
- Soil Biology and Biochemistry, Vol. 42, Issue 2
Metabolic Activity and Phosphate-Dissolving Capability of Bacterial Isolates from Wheat Roots, Rhizosphere, and Non-Rhizosphere soil
journal, February 1959
- Katznelson, H.; Bose, B.
- Canadian Journal of Microbiology, Vol. 5, Issue 1
Bacteria and fungi controlling plant growth by manipulating auxin: Balance between development and defense
journal, January 2015
- Ludwig-Müller, Jutta
- Journal of Plant Physiology, Vol. 172
Short-term physiological and developmental responses to nitrogen availability in hybrid poplar
journal, April 2005
- Cooke, Janice E. K.; Martin, Timothy A.; Davis, John M.
- New Phytologist, Vol. 167, Issue 1
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
journal, November 2013
- Monk, J. M.; Charusanti, P.; Aziz, R. K.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 50
Plant hormone cross-talk: the pivot of root growth
journal, January 2015
- Pacifici, Elena; Polverari, Laura; Sabatini, Sabrina
- Journal of Experimental Botany, Vol. 66, Issue 4
The Bacterial Oxidation of Tryptophan: A Study in Comparative Biochemistry
journal, September 1951
- Stanier, R. Y.; Hayaishi, O.
- Science, Vol. 114, Issue 2961
Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization
journal, May 2010
- Compant, Stéphane; Clément, Christophe; Sessitsch, Angela
- Soil Biology and Biochemistry, Vol. 42, Issue 5
PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa: PhyloChip analysis of potato rhizosphere bacteria
journal, January 2011
- Weinert, Nicole; Piceno, Yvette; Ding, Guo-Chun
- FEMS Microbiology Ecology, Vol. 75, Issue 3
Populus deltoides females are more selective in nitrogen assimilation than males under different nitrogen forms supply
journal, September 2014
- Li, Junyu; Dong, Tingfa; Guo, Qingxue
- Trees, Vol. 29, Issue 1
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
journal, January 2009
- Silby, Mark W.; Cerdeño-Tárraga, Ana M.; Vernikos, Georgios S.
- Genome Biology, Vol. 10, Issue 5
Phosphate solubilization by Rhizobium strains
journal, March 2009
- Sridevi, M.; Mallaiah, K. V.
- Indian Journal of Microbiology, Vol. 49, Issue 1
Selective progressive response of soil microbial community to wild oat roots
journal, November 2008
- DeAngelis, Kristen M.; Brodie, Eoin L.; DeSantis, Todd Z.
- The ISME Journal, Vol. 3, Issue 2
Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1 : PGPR properties
journal, December 2012
- Roca, Amalia; Pizarro-Tobías, Paloma; Udaondo, Zulema
- Environmental Microbiology, Vol. 15, Issue 3
Organic acid production in vitro and plant growth promotion in maize under controlled environment by phosphate-solubilizing fluorescent Pseudomonas
journal, January 2009
- Vyas, Pratibha; Gulati, Arvind
- BMC Microbiology, Vol. 9, Issue 1
Linking Plant Nutritional Status to Plant-Microbe Interactions
journal, July 2013
- Carvalhais, Lilia C.; Dennis, Paul G.; Fan, Ben
- PLoS ONE, Vol. 8, Issue 7
Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees
journal, December 2008
- Taghavi, S.; Garafola, C.; Monchy, S.
- Applied and Environmental Microbiology, Vol. 75, Issue 3
Functional analyses of genes involved in the metabolism of ferulic acid in Pseudomonas putida KT2440
journal, March 2003
- Plaggenborg, R.; Overhage, J.; Steinbüchel, A.
- Applied Microbiology and Biotechnology, Vol. 61, Issue 5-6
Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440
journal, December 2002
- Jimenez, Jose Ignacio; Minambres, Baltasar; Garcia, Jose Luis
- Environmental Microbiology, Vol. 4, Issue 12, p. 824-841
Modelling root–soil interactions using three–dimensional models of root growth, architecture and function
journal, June 2013
- Dunbabin, Vanessa M.; Postma, Johannes A.; Schnepf, Andrea
- Plant and Soil, Vol. 372, Issue 1-2
Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions.
journal, January 1996
- Kaiser, J. P.; Feng, Y.; Bollag, J. M.
- Microbiological reviews, Vol. 60, Issue 3
The role of root Exudates in Rhizosphere Interactions with Plants and Other Organisms
journal, June 2006
- Bais, Harsh P.; Weir, Tiffany L.; Perry, Laura G.
- Annual Review of Plant Biology, Vol. 57, Issue 1
Discovery of a bacterial gene cluster for catabolism of the plant hormone indole 3-acetic acid: Genes in Pseudomonas putida 1290 for the degradation of IAA
journal, August 2008
- Leveau, Johan H. J.; Gerards, Saskia
- FEMS Microbiology Ecology, Vol. 65, Issue 2
Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions
journal, July 2012
- Loper, Joyce E.; Hassan, Karl A.; Mavrodi, Dmitri V.
- PLoS Genetics, Vol. 8, Issue 7
Use of chrome azurol S reagents to evaluate siderophore production by rhizosphere bacteria
journal, September 1991
- Alexander, D. B.; Zuberer, D. A.
- Biology and Fertility of Soils, Vol. 12, Issue 1
Interactions between proteolytic and non-proteolytic Pseudomonas fluorescens affect protein degradation in a model community
journal, April 2000
- Worm, Jakob; Jensen, Linda E.; Hansen, Thomas S.
- FEMS Microbiology Ecology, Vol. 32, Issue 2
Bacterial degradation of pyridine, indole, quinoline, and their derivatives under different redox conditions
journal, March 1998
- Fetzner, S.
- Applied Microbiology and Biotechnology, Vol. 49, Issue 3
The Effect of Phylogenetically Different Bacteria on the Fitness of Pseudomonas fluorescens in Sand Microcosms
journal, March 2015
- Tyc, Olaf; Wolf, Alexandra B.; Garbeva, Paolina
- PLOS ONE, Vol. 10, Issue 3
Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase
journal, October 2005
- Glick, Bernard R.
- FEMS Microbiology Letters, Vol. 251, Issue 1
Physiology and Molecular Biology of Phenylpropanoid Metabolism
journal, June 1989
- Hahlbrock, K.; Scheel, D.
- Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 40, Issue 1
Regulation of ferulic catabolic genes in Pseudomonas fluorescens BF13: involvement of a MarR family regulator
journal, June 2008
- Calisti, C.; Ficca, A. G.; Barghini, P.
- Applied Microbiology and Biotechnology, Vol. 80, Issue 3
Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440
journal, December 2002
- Jimenez, Jose Ignacio; Minambres, Baltasar; Garcia, Jose Luis
- Environmental Microbiology, Vol. 4, Issue 12, p. 824-841
Phenol biosynthesis in higher plants. Gallic acid
journal, July 1969
- Dewick, P. M.; Haslam, E.
- Biochemical Journal, Vol. 113, Issue 3
The role of auxin in shaping shoot architecture
journal, May 2013
- Gallavotti, Andrea
- Journal of Experimental Botany, Vol. 64, Issue 9
Molecular characterization of genes of Pseudomonas sp. strain HR199 involved in bioconversion of vanillin to protocatechuate.
journal, April 1997
- Priefert, H.; Rabenhorst, J.; Steinbüchel, A.
- Journal of Bacteriology, Vol. 179, Issue 8
Linking Plant Nutritional Status to Plant-Microbe Interactions
journal, July 2013
- Carvalhais, Lilia C.; Dennis, Paul G.; Fan, Ben
- PLoS ONE, Vol. 8, Issue 7
p-Cumate catabolic pathway in Pseudomonas putida Fl: cloning and characterization of DNA carrying the cmt operon.
journal, March 1996
- Eaton, R. W.
- Journal of Bacteriology, Vol. 178, Issue 5
Recent advances and emerging trends in plant hormone signalling
journal, June 2009
- Santner, Aaron; Estelle, Mark
- Nature, Vol. 459, Issue 7250
Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions
journal, July 2012
- Loper, Joyce E.; Hassan, Karl A.; Mavrodi, Dmitri V.
- PLoS Genetics, Vol. 8, Issue 7
PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa: PhyloChip analysis of potato rhizosphere bacteria
journal, January 2011
- Weinert, Nicole; Piceno, Yvette; Ding, Guo-Chun
- FEMS Microbiology Ecology, Vol. 75, Issue 3
Phosphate solubilization by organic anion excretion from rice growing in aerobic soil: rates of excretion and decomposition, effects on rhizosphere pH and effects on phosphate solubility and uptake
journal, May 1999
- Kirk, G. J. D.; Santos, E. E.; Santos, M. B.
- New Phytologist, Vol. 142, Issue 2
p-Cymene pathway in Pseudomonas putida: ring cleavage of 2,3-dihydroxy-p-cumate and subsequent reactions.
journal, January 1977
- DeFrank, J. J.; Ribbons, D. W.
- Journal of Bacteriology, Vol. 129, Issue 3
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences
journal, June 2014
- Utturkar, Sagar M.; Klingeman, Dawn M.; Land, Miriam L.
- Bioinformatics, Vol. 30, Issue 19
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
journal, February 2012
- Ronquist, Fredrik; Teslenko, Maxim; van der Mark, Paul
- Systematic Biology, Vol. 61, Issue 3
Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico
journal, October 2011
- Vetsigian, Kalin; Jajoo, Rishi; Kishony, Roy
- PLoS Biology, Vol. 9, Issue 10
Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture
journal, April 2011
- Pérez-García, Alejandro; Romero, Diego; de Vicente, Antonio
- Current Opinion in Biotechnology, Vol. 22, Issue 2
Markers and signals associated with nitrogen assimilation in higher plants
journal, January 2003
- Foyer, C. H.; Parry, M.; Noctor, G.
- Journal of Experimental Botany, Vol. 54, Issue 382
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
journal, November 2013
- Monk, J. M.; Charusanti, P.; Aziz, R. K.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 50
Short-term physiological and developmental responses to nitrogen availability in hybrid poplar
journal, April 2005
- Cooke, Janice E. K.; Martin, Timothy A.; Davis, John M.
- New Phytologist, Vol. 167, Issue 1
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
journal, January 2009
- Silby, Mark W.; Cerdeño-Tárraga, Ana M.; Vernikos, Georgios S.
- Genome Biology, Vol. 10, Issue 5
Cloning, Sequence, and Expression of Kynureninase fromPseudomonas fluorescens
journal, August 1997
- Koushik, Srinagesh V.; Sundararaju, Bakthavatsalam; McGraw, Royal A.
- Archives of Biochemistry and Biophysics, Vol. 344, Issue 2
Exudation of organic anions by roots of cabbage, carrot, and potato as influenced by environmental factors and plant age
journal, October 2004
- Dechassa, Nigussie; Schenk, Manfred K.
- Journal of Plant Nutrition and Soil Science, Vol. 167, Issue 5
Phosphate solubilization of Paenibacillus polymyxa and Paenibacillus macerans from mycorrhizal and non-mycorrhizal cucumber plants
journal, June 2012
- Yanli Wang,
- African Journal of Microbiology Research, Vol. 6, Issue 21
Root traits and microbial community interactions in relation to phosphorus availability and acquisition, with particular reference to Brassica
journal, January 2014
- Hunter, Paul J.; Teakle, Grahams R.; Bending, Gary D.
- Frontiers in Plant Science, Vol. 5
Structure and Functions of the Bacterial Microbiota of Plants
journal, April 2013
- Bulgarelli, Davide; Schlaeppi, Klaus; Spaepen, Stijn
- Annual Review of Plant Biology, Vol. 64, Issue 1
Solubilization of zinc phosphate by a strain of Pseudomonas fluorescens isolated from a forest soil
journal, November 1998
- Di Simine, C. D.; Sayer, J. A.; Gadd, G. M.
- Biology and Fertility of Soils, Vol. 28, Issue 1
Bacterial volatiles promote growth in Arabidopsis
journal, April 2003
- Ryu, C. -M.; Farag, M. A.; Hu, C. -H.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 8
Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants
journal, March 2013
- Oldroyd, Giles E. D.
- Nature Reviews Microbiology, Vol. 11, Issue 4
Organic acid production in vitro and plant growth promotion in maize under controlled environment by phosphate-solubilizing fluorescent Pseudomonas
journal, January 2009
- Vyas, Pratibha; Gulati, Arvind
- BMC Microbiology, Vol. 9, Issue 1
Plant growth promoting activities of phosphate-solubilizing Enterobacter asburiae as influenced by fungicides
journal, January 2010
- Ahemad, Munees; Khan, Mohammad Saghir
- EurAsian Journal of Biosciences
Functional analyses of genes involved in the metabolism of ferulic acid in Pseudomonas putida KT2440
journal, March 2003
- Plaggenborg, R.; Overhage, J.; Steinbüchel, A.
- Applied Microbiology and Biotechnology, Vol. 61, Issue 5-6
Relative involvement of nitrate and nitrite reduction in the competitiveness of Pseudomonas fluorescens in the rhizosphere of maize under non-limiting nitrate conditions
journal, February 2002
- Ghiglione, Jean-François; Richaume, Agnès; Philippot, Laurent
- FEMS Microbiology Ecology, Vol. 39, Issue 2
Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency
journal, December 2010
- Carvalhais, Lilia C.; Dennis, Paul G.; Fedoseyenko, Dmitri
- Journal of Plant Nutrition and Soil Science, Vol. 174, Issue 1
Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization
journal, May 2010
- Compant, Stéphane; Clément, Christophe; Sessitsch, Angela
- Soil Biology and Biochemistry, Vol. 42, Issue 5
Degradation of 2,3-Dihydroxybenzoate by a Novel meta-Cleavage Pathway
journal, May 2012
- Marin, M.; Plumeier, I.; Pieper, D. H.
- Journal of Bacteriology, Vol. 194, Issue 15
Selective progressive response of soil microbial community to wild oat roots
journal, November 2008
- DeAngelis, Kristen M.; Brodie, Eoin L.; DeSantis, Todd Z.
- The ISME Journal, Vol. 3, Issue 2
Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1 : PGPR properties
journal, December 2012
- Roca, Amalia; Pizarro-Tobías, Paloma; Udaondo, Zulema
- Environmental Microbiology, Vol. 15, Issue 3
Extreme genome reduction in symbiotic bacteria
journal, November 2011
- McCutcheon, John P.; Moran, Nancy A.
- Nature Reviews Microbiology, Vol. 10, Issue 1
Inside the root microbiome: Bacterial root endophytes and plant growth promotion
journal, September 2013
- Gaiero, Jonathan R.; McCall, Crystal A.; Thompson, Karen A.
- American Journal of Botany, Vol. 100, Issue 9
Root traits and microbial community interactions in relation to phosphorus availability and acquisition, with particular reference to Brassica
journal, January 2014
- Hunter, Paul J.; Teakle, Grahams R.; Bending, Gary D.
- Frontiers in Plant Science, Vol. 5
Populus deltoides females are more selective in nitrogen assimilation than males under different nitrogen forms supply
journal, September 2014
- Li, Junyu; Dong, Tingfa; Guo, Qingxue
- Trees, Vol. 29, Issue 1
Ralstonia solanacearum Uses Inorganic Nitrogen Metabolism for Virulence, ATP Production, and Detoxification in the Oxygen-Limited Host Xylem Environment
journal, March 2015
- Dalsing, Beth L.; Truchon, Alicia N.; Gonzalez-Orta, Enid T.
- mBio, Vol. 6, Issue 2
Phosphate solubilization by Rhizobium strains
journal, March 2009
- Sridevi, M.; Mallaiah, K. V.
- Indian Journal of Microbiology, Vol. 49, Issue 1
Metabolic Activity and Phosphate-Dissolving Capability of Bacterial Isolates from Wheat Roots, Rhizosphere, and Non-Rhizosphere soil
journal, February 1959
- Katznelson, H.; Bose, B.
- Canadian Journal of Microbiology, Vol. 5, Issue 1
Indole-3-acetic acid in microbial and microorganism-plant signaling
journal, July 2007
- Spaepen, Stijn; Vanderleyden, Jos; Remans, Roseline
- FEMS Microbiology Reviews, Vol. 31, Issue 4
The Aerobic Pseudomonads a Taxonomic Study
journal, May 1966
- Stanier, R. Y.; Palleroni, N. J.; Doudoroff, M.
- Journal of General Microbiology, Vol. 43, Issue 2
Plant hormone cross-talk: the pivot of root growth
journal, January 2015
- Pacifici, Elena; Polverari, Laura; Sabatini, Sabrina
- Journal of Experimental Botany, Vol. 66, Issue 4
Structure and Functions of the Bacterial Microbiota of Plants
journal, April 2013
- Bulgarelli, Davide; Schlaeppi, Klaus; Spaepen, Stijn
- Annual Review of Plant Biology, Vol. 64, Issue 1
Phenol biosynthesis in higher plants. Gallic acid
journal, July 1969
- Dewick, P. M.; Haslam, E.
- Biochemical Journal, Vol. 113, Issue 3
Gluconic acid production and phosphate solubilization by the plant growth-promoting bacterium Azospirillum spp.
journal, October 2004
- Rodriguez, Hilda; Gonzalez, Tania; Goire, Isabel
- Naturwissenschaften, Vol. 91, Issue 11
Genotypic variation in aluminum resistance, cellular aluminum fractions, callose and pectin formation and organic acid accumulation in roots of Populus hybrids
journal, September 2011
- Smith, Ernest; Naik, Dhiraj; Cumming, Jonathan R.
- Environmental and Experimental Botany, Vol. 72, Issue 2
Defining the core Arabidopsis thaliana root microbiome
journal, August 2012
- Lundberg, Derek S.; Lebeis, Sarah L.; Paredes, Sur Herrera
- Nature, Vol. 488, Issue 7409
Effects of Bacterial ACC Deaminase on Brassica napus Gene Expression
journal, May 2012
- Stearns, Jennifer C.; Woody, Owen Z.; McConkey, Brendan J.
- Molecular Plant-Microbe Interactions, Vol. 25, Issue 5
A More Sensitive Plate Assay for Detection of Protease Production by
Pseudomonas aeruginosa
journal, April 1979
- Sokol, Pamela A.; Ohman, Dennis E.; Iglewski, Barbara H.
- Journal of Clinical Microbiology, Vol. 9, Issue 4
Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil
journal, April 2010
- Uroz, Stéphane; Buée, Marc; Murat, Claude
- Environmental Microbiology Reports, Vol. 2, Issue 2
Is l-arabinose important for the endophytic lifestyle of Pseudomonas spp.?
journal, September 2012
- Malfanova, Natalia; Kamilova, Faina; Validov, Shamil
- Archives of Microbiology, Vol. 195, Issue 1
Physiology and Molecular Biology of Phenylpropanoid Metabolism
journal, June 1989
- Hahlbrock, K.; Scheel, D.
- Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 40, Issue 1
The β-Ketoadipate Pathway And The Biology Of Self-Identity
journal, October 1996
- Harwood, Caroline S.; Parales, Rebecca E.
- Annual Review of Microbiology, Vol. 50, Issue 1, p. 553-590
Modeling Phosphorus Uptake by a Growing and Exuding Root System
journal, January 2012
- Schnepf, A.; Leitner, D.; Klepsch, S.
- Vadose Zone Journal, Vol. 11, Issue 3
What lies beneath: belowground defense strategies in plants
journal, February 2015
- De Coninck, Barbara; Timmermans, Pieter; Vos, Christine
- Trends in Plant Science, Vol. 20, Issue 2
Plant-driven selection of microbes
journal, November 2008
- Hartmann, Anton; Schmid, Michael; Tuinen, Diederik van
- Plant and Soil, Vol. 321, Issue 1-2
Biological nitrogen fixation and phosphate solubilization by bacteria isolated from tropical soils
journal, March 2012
- Marciano Marra, Leandro; Fonsêca Sousa Soares, Cláudio Roberto; de Oliveira, Silvia Maria
- Plant and Soil, Vol. 357, Issue 1-2
Transcriptional Responses to Sucrose Mimic the Plant-Associated Life Style of the Plant Growth Promoting Endophyte Enterobacter sp. 638
journal, January 2015
- Taghavi, Safiyh; Wu, Xiao; Ouyang, Liming
- PLOS ONE, Vol. 10, Issue 1
A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees
journal, October 2013
- Shakya, Migun; Gottel, Neil; Castro, Hector
- PLoS ONE, Vol. 8, Issue 10
Traits of fluorescent Pseudomonas spp. involved in suppression of plant root pathogens
journal, December 1992
- O'Sullivan, D. J.; O'Gara, F.
- Microbiological Reviews, Vol. 56, Issue 4
Phosphate solubilization by organic anion excretion from rice growing in aerobic soil: rates of excretion and decomposition, effects on rhizosphere pH and effects on phosphate solubility and uptake
journal, May 1999
- Kirk, G. J. D.; Santos, E. E.; Santos, M. B.
- New Phytologist, Vol. 142, Issue 2
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences
journal, June 2014
- Utturkar, Sagar M.; Klingeman, Dawn M.; Land, Miriam L.
- Bioinformatics, Vol. 30, Issue 19
The role of root Exudates in Rhizosphere Interactions with Plants and Other Organisms
journal, June 2006
- Bais, Harsh P.; Weir, Tiffany L.; Perry, Laura G.
- Annual Review of Plant Biology, Vol. 57, Issue 1
Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase
journal, October 2005
- Glick, Bernard R.
- FEMS Microbiology Letters, Vol. 251, Issue 1
Interactions between proteolytic and non-proteolytic Pseudomonas fluorescens affect protein degradation in a model community
journal, April 2000
- Worm, Jakob; Jensen, Linda E.; Hansen, Thomas S.
- FEMS Microbiology Ecology, Vol. 32, Issue 2
Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions
journal, September 1996
- Kaiser, J. P.; Feng, Y.; Bollag, J. M.
- Microbiological Reviews, Vol. 60, Issue 3
The Effect of Phylogenetically Different Bacteria on the Fitness of Pseudomonas fluorescens in Sand Microcosms
journal, March 2015
- Tyc, Olaf; Wolf, Alexandra B.; Garbeva, Paolina
- PLOS ONE, Vol. 10, Issue 3
Brassica Seed Meal Soil Amendments Transform the Rhizosphere Microbiome and Improve Apple Production Through Resistance to Pathogen Reinfestation
journal, April 2015
- Mazzola, Mark; Hewavitharana, Shashika S.; Strauss, Sarah L.
- Phytopathology, Vol. 105, Issue 4
Discovery of a bacterial gene cluster for catabolism of the plant hormone indole 3-acetic acid: Genes in Pseudomonas putida 1290 for the degradation of IAA
journal, August 2008
- Leveau, Johan H. J.; Gerards, Saskia
- FEMS Microbiology Ecology, Vol. 65, Issue 2
A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees
journal, October 2013
- Shakya, Migun; Gottel, Neil; Castro, Hector
- PLoS ONE, Vol. 8, Issue 10
Aerobic tryptophan degradation pathway in bacteria: novel kynurenine formamidase
journal, October 2003
- Kurnasov, Oleg; Jablonski, Lynn; Polanuyer, Boris
- FEMS Microbiology Letters, Vol. 227, Issue 2
Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida: Aerobic gallic acid degradation
journal, November 2010
- Nogales, Juan; Canales, Ángeles; Jiménez-Barbero, Jesús
- Molecular Microbiology, Vol. 79, Issue 2
Cloning, Sequence, and Expression of Kynureninase fromPseudomonas fluorescens
journal, August 1997
- Koushik, Srinagesh V.; Sundararaju, Bakthavatsalam; McGraw, Royal A.
- Archives of Biochemistry and Biophysics, Vol. 344, Issue 2
Modelling root–soil interactions using three–dimensional models of root growth, architecture and function
journal, June 2013
- Dunbabin, Vanessa M.; Postma, Johannes A.; Schnepf, Andrea
- Plant and Soil, Vol. 372, Issue 1-2
Bacterial degradation of pyridine, indole, quinoline, and their derivatives under different redox conditions
journal, March 1998
- Fetzner, S.
- Applied Microbiology and Biotechnology, Vol. 49, Issue 3
Gluconic acid production and phosphate solubilization by the plant growth-promoting bacterium Azospirillum spp.
journal, October 2004
- Rodriguez, Hilda; Gonzalez, Tania; Goire, Isabel
- Naturwissenschaften, Vol. 91, Issue 11
Traits of fluorescent Pseudomonas spp. involved in suppression of plant root pathogens.
journal, January 1992
- O'Sullivan, D. J.; O'Gara, F.
- Microbiological Reviews, Vol. 56, Issue 4
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
journal, February 2012
- Ronquist, Fredrik; Teslenko, Maxim; van der Mark, Paul
- Systematic Biology, Vol. 61, Issue 3
Soil properties are key determinants for the development of exudate gradients in a rhizosphere simulation model
journal, February 2010
- Raynaud, Xavier
- Soil Biology and Biochemistry, Vol. 42, Issue 2
Markers and signals associated with nitrogen assimilation in higher plants
journal, January 2003
- Foyer, C. H.; Parry, M.; Noctor, G.
- Journal of Experimental Botany, Vol. 54, Issue 382
Biochemical and Genetic Analyses of Ferulic Acid Catabolism in Pseudomonas sp. Strain HR199
journal, November 1999
- Overhage, Jörg; Priefert, Horst; Steinbüchel, Alexander
- Applied and Environmental Microbiology, Vol. 65, Issue 11
The role of auxin in shaping shoot architecture
journal, May 2013
- Gallavotti, Andrea
- Journal of Experimental Botany, Vol. 64, Issue 9
Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico
journal, October 2011
- Vetsigian, Kalin; Jajoo, Rishi; Kishony, Roy
- PLoS Biology, Vol. 9, Issue 10
Regulation of ferulic catabolic genes in Pseudomonas fluorescens BF13: involvement of a MarR family regulator
journal, June 2008
- Calisti, C.; Ficca, A. G.; Barghini, P.
- Applied Microbiology and Biotechnology, Vol. 80, Issue 3
Bacteria and fungi controlling plant growth by manipulating auxin: Balance between development and defense
journal, January 2015
- Ludwig-Müller, Jutta
- Journal of Plant Physiology, Vol. 172
Relative involvement of nitrate and nitrite reduction in the competitiveness of Pseudomonas fluorescens in the rhizosphere of maize under non-limiting nitrate conditions
journal, February 2002
- Ghiglione, Jean-François; Richaume, Agnès; Philippot, Laurent
- FEMS Microbiology Ecology, Vol. 39, Issue 2
Genomics of Secondary Metabolism in Populus : Interactions with Biotic and Abiotic Environments
journal, October 2009
- Chen, Feng; Liu, Chang-Jun; Tschaplinski, Timothy J.
- Critical Reviews in Plant Sciences, Vol. 28, Issue 5
Inside the root microbiome: Bacterial root endophytes and plant growth promotion
journal, September 2013
- Gaiero, Jonathan R.; McCall, Crystal A.; Thompson, Karen A.
- American Journal of Botany, Vol. 100, Issue 9
Genotypic variation in aluminum resistance, cellular aluminum fractions, callose and pectin formation and organic acid accumulation in roots of Populus hybrids
journal, September 2011
- Smith, Ernest; Naik, Dhiraj; Cumming, Jonathan R.
- Environmental and Experimental Botany, Vol. 72, Issue 2
Recent advances and emerging trends in plant hormone signalling
journal, June 2009
- Santner, Aaron; Estelle, Mark
- Nature, Vol. 459, Issue 7250
The Bacterial Oxidation of Tryptophan: A Study in Comparative Biochemistry
journal, September 1951
- Stanier, R. Y.; Hayaishi, O.
- Science, Vol. 114, Issue 2961
Molecular characterization of genes of Pseudomonas sp. strain HR199 involved in bioconversion of vanillin to protocatechuate.
journal, April 1997
- Priefert, H.; Rabenhorst, J.; Steinbüchel, A.
- Journal of Bacteriology, Vol. 179, Issue 8
p-Cumate catabolic pathway in Pseudomonas putida Fl: cloning and characterization of DNA carrying the cmt operon.
journal, March 1996
- Eaton, R. W.
- Journal of Bacteriology, Vol. 178, Issue 5
Two Distinct Pathways Supply Anthranilate as a Precursor of the Pseudomonas Quinolone Signal
journal, March 2007
- Farrow, J. M.; Pesci, E. C.
- Journal of Bacteriology, Vol. 189, Issue 9
A critical examination of the specificity of the salkowski reagent for indolic compounds produced by phytopathogenic bacteria.
journal, January 1995
- Glickmann, E.; Dessaux, Y.
- Applied and environmental microbiology, Vol. 61, Issue 2
A More Sensitive Plate Assay for Detection of Protease Production by
Pseudomonas aeruginosa
journal, April 1979
- Sokol, Pamela A.; Ohman, Dennis E.; Iglewski, Barbara H.
- Journal of Clinical Microbiology, Vol. 9, Issue 4
Works referencing / citing this record:
Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System
journal, April 2016
- Timm, Collin M.; Pelletier, Dale A.; Jawdy, Sara S.
- Frontiers in Plant Science, Vol. 7
Emergence of plant and rhizospheric microbiota as stable interactomes
journal, July 2016
- Bandyopadhyay, Prasun; Bhuyan, Soubhagya Kumar; Yadava, Pramod Kumar
- Protoplasma, Vol. 254, Issue 2
Host genotype and age shape the leaf and root microbiomes of a wild perennial plant
journal, July 2016
- Wagner, Maggie R.; Lundberg, Derek S.; del Rio, Tijana G.
- Nature Communications, Vol. 7, Issue 1
Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System
journal, April 2016
- Timm, Collin M.; Pelletier, Dale A.; Jawdy, Sara S.
- Frontiers in Plant Science, Vol. 7
Root Associated Bacillus sp. Improves Growth, Yield and Zinc Translocation for Basmati Rice (Oryza sativa) Varieties
journal, November 2015
- Shakeel, Muhammad; Rais, Afroz; Hassan, Muhammad Nadeem
- Frontiers in Microbiology, Vol. 6
Relatively rare root endophytic bacteria drive plant resource allocation patterns and tissue nutrient concentration in unpredictable ways
journal, October 2019
- Henning, Jeremiah A.; Weston, David J.; Pelletier, Dale A.
- American Journal of Botany, Vol. 106, Issue 11
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions
journal, September 2017
- Jacoby, Richard; Peukert, Manuela; Succurro, Antonella
- Frontiers in Plant Science, Vol. 8
Root Associated Bacillus sp. Improves Growth, Yield and Zinc Translocation for Basmati Rice (Oryza sativa) Varieties
journal, November 2015
- Shakeel, Muhammad; Rais, Afroz; Hassan, Muhammad Nadeem
- Frontiers in Microbiology, Vol. 6
Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes
journal, June 2018
- Metz, Zachary P.; Ding, Tong; Baumler, David J.
- PLOS ONE, Vol. 13, Issue 6
Root bacterial endophytes alter plant phenotype, but not physiology
journal, January 2016
- Henning, Jeremiah A.; Weston, David J.; Pelletier, Dale A.
- PeerJ, Vol. 4
Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis
journal, January 2019
- BenIsrael, Michael; Wanner, Philipp; Aravena, Ramon
- International Journal of Phytoremediation, Vol. 21, Issue 1
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions
journal, September 2017
- Jacoby, Richard; Peukert, Manuela; Succurro, Antonella
- Frontiers in Plant Science, Vol. 8
Root bacterial endophytes alter plant phenotype, but not physiology
journal, January 2016
- Henning, Jeremiah A.; Weston, David J.; Pelletier, Dale A.
- PeerJ, Vol. 4
Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation
journal, May 2018
- Noirot-Gros, Marie-Francoise; Shinde, Shalaka; Larsen, Peter E.
- Frontiers in Microbiology, Vol. 9
Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis
text, January 2019
- BenIsrael, Michael; Wanner, Philipp; Aravena, Ramon
- Figshare
Giving back to the community: microbial mechanisms of plant-soil interactions
journal, June 2016
- Herrera Paredes, Sur; Lebeis, Sarah L.
- Functional Ecology, Vol. 30, Issue 7
Quantifying the Spatiotemporal Dynamics of Plant Root Colonization by Beneficial Bacteria in a Microfluidic Habitat
journal, April 2018
- Aufrecht, Jayde A.; Timm, Collin M.; Bible, Amber
- Advanced Biosystems, Vol. 2, Issue 6
Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates
journal, August 2017
- Yi, Yanglei; de Jong, Anne; Frenzel, Elrike
- Frontiers in Microbiology, Vol. 8
Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis
text, January 2019
- BenIsrael, Michael; Wanner, Philipp; Aravena, Ramon
- Taylor & Francis
Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population
journal, September 2018
- Lopes, Lucas Dantas; Pereira e. Silva, Michele de C.; Weisberg, Alexandra J.
- Environmental Microbiology, Vol. 20, Issue 12
Isolated Bacillus subtilis strain 330-2 and its antagonistic genes identified by the removing PCR
journal, May 2017
- Ahmad, Zahoor; Wu, Jia; Chen, Lulu
- Scientific Reports, Vol. 7, Issue 1
Isolated Bacillus subtilis strain 330-2 and its antagonistic genes identified by the removing PCR
journal, May 2017
- Ahmad, Zahoor; Wu, Jia; Chen, Lulu
- Scientific Reports, Vol. 7, Issue 1
Host genotype and age shape the leaf and root microbiomes of a wild perennial plant
text, January 2016
- S., Lundberg, Derek; L., Dangl, Jeffery; G., Del Rio, Tijana
- The University of North Carolina at Chapel Hill University Libraries