Skip to content
naulon
Get started

No retraction, correction or concern found when last checked on Oct 18, 2026.

The rhizosphere revisited: root microbiomics

Peter A. H. M. Bakker, Roeland L. Berendsen, Rogier F. Doornbos and 2 more

Frontiers in Plant Science · 2013

doi:10.3389/fpls.2013.00165

Abstract

The rhizosphere was defined over 100 years ago as the zone around the root where microorganisms and processes important for plant growth and health are located. Recent studies show that the diversity of microorganisms associated with the root system is enormous. This rhizosphere microbiome extends the functional repertoire of the plant beyond imagination. The rhizosphere microbiome of Arabidopsis thaliana is currently being studied for the obvious reason that it allows the use of the extensive toolbox that comes with this model plant. Deciphering plant traits that drive selection and activities of the microbiome is now a major challenge in which Arabidopsis will undoubtedly be a major research object. Here we review recent microbiome studies and discuss future research directions and applicability of the generated knowledge.

Full text

From PubMed Central, U.S. National Library of Medicine, as current on Oct 18, 2026. Paragraph numbers are ours, so an answer can point at one.

INTRODUCTION

Ever since Lorenz Hiltner, more than a century ago, defined the rhizosphere as the soil compartment influenced by plant roots, this hotspot for microbial interactions and activities has received ample attention from scientists in different disciplines. Also the above ground plant surface, the so-called phyllosphere, harbors microbial communities that have more recently been studied in detail. The microbial activity in the rhizosphere is essential for plant functioning as it assists the plant in nutrient uptake and offers protection against pathogen attack. Microbiological studies in the soil environment are hampered by the fact that the largest proportion of soil bacteria as yet cannot be cultured. However, developments in metagenomics provide a more complete picture of the rhizosphere microbiome. Thus the microbial players in the rhizosphere are on their way to be exposed and, perhaps more importantly, transcriptomic studies of the microbiome have been initiated to reveal microbial activities in complex environments. Unraveling processes that drive selection and activities of the rhizosphere microbiome will open up new avenues to manipulate crop health and yield. In this paper, we review and discuss recent developments in rhizosphere microbiome studies.

THE RHIZOSPHERE EFFECT

Compared to non-rooted bulk soil, the soil compartment directly around the plant root contains much larger populations of microorganisms. The increased microbial numbers and activities in the rhizosphere are due to the release of large amounts of organic carbon by the plant roots. In their extensive review, describe loss of root cap and border cells, insoluble mucilage, soluble root exudates, volatile organic carbon, flow of carbon to root associated symbionts, and death and lysis of root cells as the major processes of rhizodeposition. Soil microorganisms are chemotactically attracted to the plant root exudates, after which they proliferate in this carbon rich environment. Carbon limitation could be demonstrated in bulk soil but not in the rhizosphere using Pseudomonas fluorescens strains carrying carbon-limitation reporter systems. Given the fact that plant root exudates differ between plant species, differences in rhizosphere microbiomes of different plant species are to be expected. Indeed plant-specific microbial communities could be isolated from roots in studies comparing, for example, wheat, ryegrass, bentgrass, and clover, or wheat and canola. Also within a specific bacterial group like fluorescent Pseudomonas spp., plant species-specific rhizosphere populations could be isolated. More recent studies, in which the rhizosphere microbiomes were characterized based on direct extraction of total community DNA, also provide strong evidence for plant species-specific microbiomes. The roots of wheat, maize, rape, and barrel clover were shown to carry different bacterial communities as a consequence of assimilation of root exudates. Bacterial community structures in field grown potato rhizospheres were affected by the growth stage of the plant. Also at the genotype level within a plant species, specificity of the rhizosphere microbiome has been described. used A. thaliana and showed that the rhizosphere of this model plant mediates a significant change in the bacterial community relative to the bulk soil. To illustrate the rhizosphere effect we compared rhizosphere bacterial communities of tobacco and A. thaliana grown on a potting and a clay soil. In Figure 1A total bacterial counts on 1/10 strength tryptic soy agar (TSA) and counts of fluorescent pseudomonads on Kings medium B agar (KB) in bulk soil and in the rhizospheres of A. thaliana Col-0 and tobacco are presented. The rhizosphere effect is exemplified by the observation that numbers in the rhizosphere are about 10- to 100-fold higher compared to the numbers in bulk soil for both plant species. In Figures 1B, C, Pseudomonas-specific denaturing gradient gel electrophoresis (DGGE) profiles are shown and compared in a redundancy analysis. For both tobacco and A. thaliana, rhizosphere Pseudomonas communities are different from those in the bulk soil, and the communities differ between the plant species. In two recent papers the A. thaliana root microbiome has been described in detail using pyrosequencing of 16S rRNA gene amplicons. Whereas differences between bacterial communities in bulk soil and the rhizosphere were observed in these studies, their focus was on the endophytic compartment. Inside the root, the microbiome clearly differed from the bulk soil and was enriched in Actinobacteria and Proteobacteria.

RECRUITMENT OF THE RHIZOSPHERE MICROBIOME

The rhizosphere bacterial community is recruited from the main reservoir of microorganisms present in soil. Thus the soil is an important factor in shaping the rhizosphere microbiome. As described in the previous section, plant genotype is also a driving force for the selection of specific elements from the bulk soil microbial community. Furthermore, when under attack, plants seem to actively select specific elements of their bacterial rhizosphere microflora. This is most clearly observed in so-called disease suppressive soils, in which disease will not develop despite the presence of a virulent pathogen and a susceptible plant. Disease suppressiveness is due to microbial activity and usually needs an outbreak of disease to develop. A well-studied example is take-all decline (TAD), which develops in continuous wheat cultures after a severe outbreak of the take-all disease caused by Gaeumannomyces graminis var. tritici. Heat treatment abolishes suppressiveness and the suppressiveness of TAD soil is transferable to a disease conducive soil by mixing small quantities of decline soil through conducive soil. Under continuous wheat cropping, a specific group of fluorescent pseudomonads that produce 2,4-diacetylphloroglucinol (DAPG) is enriched in the rhizosphere and these bacteria appear to be responsible for TAD. Additional bacterial taxa that may be involved in TAD have more recently been identified using 16S rRNA-based techniques. The specific selection of plant protecting bacteria in the rhizosphere under pathogen attack is supported by a recent study of. They observed that under irrigation the wheat rhizosphere recruits DAPG producing pseudomonads, whereas under dry conditions phenazine producing pseudomonads are recruited. Under irrigated conditions G. graminis var. tritici is the major soil borne pathogen of wheat, whereas under dry conditions Rhizoctonia solani is the main problem. Strikingly G. graminis var. tritici is more sensitive to DAPG, whereas R. solani is more sensitive to phenazines. Thus, under conditions that favor a specific pathogen, antagonists that are most effective against this pathogen are selected by the plant. Also for other disease suppressive soils specific elements of the microbiome have been identified that are associated with suppressiveness. In a Fusarium wilt suppressive soil the production of redox-active phenazines by fluorescent pseudomonads and competition for carbon by non-pathogenic Fusarium oxysporum have a synergistic effect that may establish suppressiveness. In a soil suppressive to potato common scab a microbial consortium that is associated with suppressiveness was identified. For a soil suppressive to black root rot of tobacco, caused by Thielaviopsis basicola, several bacterial taxa, including Pseudomonas, Azospirillum, Gluconacetobacter, Burkholderia, Comamonas, and Sphingomonadaceae, were shown to be more prevalent in the suppressive than in the conducive soil. To identify bacteria involved in soil suppressiveness against R. solani, used PhyloChip analysis, which allows simultaneous detection of ~60,000 bacterial and archaeal operational taxonomic units (OTUs). Over 33,000 OTUs were detected in the rhizospheres of sugar beet grown in R. solani suppressive and conducive soil. Taxa that were more abundant in suppressive soil and in a mixture of conducive soil with 10% suppressive soil than in conducive soil, but also more abundant in suppressive soil amended with R. solani than in suppressive soil without the pathogen, were identified. Seventeen taxa belonging to the β-proteobacteria, γ-proteobacteria, and the firmicutes were closely associated with disease suppressiveness. In all disease suppressive soils mentioned here, consortia of antagonistic microorganisms seem to be recruited by the rhizosphere under pathogen attack.

Not only attack by soil borne pathogens results in the recruitment of beneficial microbes in the rhizosphere. Foliar feeding of aphids on pepper plants reduced disease development caused by the bacterial pathogen Xanthomonas axonopodis pv. vesicatoria. Aphid infestation resulted in increased population densities of the plant beneficial Bacillus subtilis, whereas it reduced rhizosphere populations of plant pathogenic Ralstonia solanacearum. Similar results were found for whitefly infestation of pepper plants, leading to increased resistance to pathogens and to changes in the rhizosphere microbiome. In the aphid and whitefly systems it would be interesting to investigate possible recruitment of rhizobacteria that produce insecticidal toxins, a feature of certain rhizosphere pseudomonads that was recently reported A. thaliana plants exposed to methyl jasmonate showed a shift in their bacterial rhizosphere microbiome, including taxa that are associated with disease suppression, based on 16S rRNA gene amplicon pyrosequencing. However, in a study by, leaf application of jasmonic acid did not significantly affect the rhizosphere bacterial community of A. thaliana, based on DGGE analysis of 16S rRNA gene amplicons. showed that A. thaliana plants infected by the bacterial leaf pathogen P. syringae pv. tomato, secrete elevated levels of malic acid in the rhizosphere. Malic acid stimulates binding to roots and biofilm formation on roots by Bacillus subtilis strain FB17, a beneficial microbe that can induce systemic resistance against diseases. Thus the plant benefits from protection against disease by the bacteria and in turn provides the bacteria with a more favorable environment. The recruitment of FB17 was recently shown to be mediated by root responses triggered by pathogen-derived microbe-associated molecular patterns in the leaves. Early suppression of defense genes by FB17 was postulated to facilitate colonization of this Bacillus subtilis strain on A. thaliana roots. Induced systemic resistance by P. putida KT2440 in A. thaliana is related to as yet unknown compounds in the root exudate that are modulated by the bacterium. Thus not only pathogenic and symbiotic microorganisms seem to modulate host immunity to their own benefit, but also plant beneficial microorganisms seem to use this strategy.

Drought stress is also a shaping factor for the rhizosphere microbiome. Drought-sensitive pepper plants that were grown under desert farming selected for a root microbiome that was enriched for bacteria that can increase photosynthesis and plant biomass production under drought stress. Soil nitrogen availability influenced rhizosphere microbial communities of Medicago truncatula only in the presence of the plant, and it was suggested that the adaptive strategy of the plant to environmental constraints is a major factor in shaping the rhizosphere microbiome.

Root exudates play an important role in shaping the rhizosphere microbiome. In the rhizosphere of maize, exudation of the benzoxazinone DIMBOA (2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one) resulted in increased population densities of a P. putida strain with plant beneficial characteristics. In A. thaliana, active exudation of phytochemicals mediated by ABC (ATP-binding cassette) transporters was demonstrated. In the absence of the plant, blends of collected A. thaliana root exudates modulated the soil microbiome. Phenolic compounds in the root exudates were suggested to act as specific substrates and signals for soil bacteria. Plant age affects rhizosphere bacterial communities of A. thaliana, suggested to be due to changes in root exudation. In an elegant study by, combining metatranscriptomics and metabolomics, a strong correlation was observed between compounds released from the roots at different stages of plant development and the expression of microbial genes involved in metabolism of specific compounds.

Overall, evidence is accumulating that plants shape their rhizosphere microbiome to their own benefit, making sophisticated use of the functional repertoire of the microbiome.

ACTIVATION OF MICROBIOME FUNCTIONS

Next to recruitment of specific soil microbes into the rhizosphere microbiome, plant roots also influence specific functions of the microbiome. Quorum sensing, regulation of microbial gene expression in response to cell density, is an important mechanism to regulate microbial activities. Such activities include antibiotic production, biofilm formation, conjugation, motility, symbiosis, and virulence. This regulatory mechanism is not only important within a bacterial population but also between bacterial populations. Interkingdom communication based on quorum sensing signaling molecules, N-acyl homoserine lactone (AHL) signals, has also been reported. Proteome analysis revealed that M. truncatula responds significantly to AHLs from both symbiotic and pathogenic bacteria. AHL signal molecules produced by Serratia liquefaciens and P. putida in the rhizosphere of tomato, protected the tomato plants against the fungal leaf pathogen Alternaria alternata, through the induction of systemic resistance. Similarly, growth and disease resistance of A. thaliana are modulated by AHLs. Interkingdom communication can also involve effects of eukaryotes on bacterial gene expression. Plants can effectively interfere with quorum sensing in bacteria by producing so called AHL mimics. Thus there seems to be a plant-mediated fine tuning of bacterial gene expression in the rhizosphere. Microarray-based transcriptomic profiling of specific bacteria in response to root exudates of axenically grown plants has been used to identify genes in Pseudomonas and Bacillus amyloliquefaciens that are involved in plant microbe interactions. Using a similar approach, effects of phosphate availability on transcriptional responses of Pseudomonas in the rhizosphere of Lolium perenne was investigated. All these studies show that there is a significant impact of root exudates on bacterial gene expression. The studies by and focused on effects of host cultivar on the production of DAPG by fluorescent pseudomonads. The production of this antifungal metabolite, that plays a central role in TAD, depends on the genotypes of both the plant and the bacterial strain involved in the interaction. Effects of pathogen infection on gene expression and functional diversity has been the focus of several studies. Infection of wheat roots by G. graminis var. tritici changed gene expression of P. fluorescens Pf29Arp. Strain Pf29Arp was suggested to show an adaptive response to the so called pathorhizosphere of necrotic roots. In the rhizosphere of strawberry, infection with Verticillium dahliae increased hydrogen cyanide (HCN) biosynthesis gene expression in Pseudomonas sp. LBUM300. HCN production by beneficial rhizobacteria has been suggested as a mechanism of biological control, and thus this study suggests that upon root pathogen attack such biocontrol activity is stimulated. Even stronger evidence that suggests up-regulation of antifungal activity upon pathogen attack comes from an elegant study by. They demonstrated in a split root system that infection of barley roots with Pythium ultimum on one side of the system, enhanced phlA gene expression, required for DAPG production, in P. fluorescens CHA0 that colonized the other side of the root system. Root exudation of fumaric acid, p-coumaric acid and vanillic acid was increased in Pythium infected plants and these phenolic acids increase phlA gene expression in a dose-dependent manner. Thus plants seem to respond to pathogen infection by systemic signaling leading to enhanced biocontrol activity in the microbiome.

PERSPECTIVE

Exciting new insights in interkingdom signaling in the rhizosphere and the resulting effects on plant performance have emerged during the last decade. A. thaliana has been the model system of choice in several recent studies because a large number of accessions and well characterized mutants are readily available, and transcriptomic and metabolomic analyses are standard procedure for this plant species. Revealing the composition of the microbiome and unraveling the metatranscriptome will certainly help to shed light on the very dark rhizosphere environment. However, the rhizosphere is a dynamic environment in which the microbiome will rapidly evolve in space and time. Obviously, to date many rhizosphere metagenomic studies have focused on a single or a few time points and most studies do not take spatial dynamics into account. Metabolic profiling of living microbial colonies facilitates studying spatiotemporal dynamics of metabolite production in microbial communities. The nanospray desorption electrospray ionization (nano-DESI) mass spectrometry technology used in these studies allows for direct sampling from plant surfaces and is thus a promising development for rhizosphere studies. Given the rapid technological developments, the editors of the classic book “Plant roots: the hidden half”, may want to look for a new title for the next edition.

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

References 91

  1. 1.

    Amann R. I. Ludwig W. Schleifer K. H. (1995 ). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59 143–169

    Not in our library10.1128/mr.59.1.143-169.1995

  2. 2.

    Badri D. V. Chaparro J. M. Manter D. K. Martinoia E. Vivanco J. M. (2012 ). Influence of ATP-binding cassette transporters in root exudation of phytoalexins, signals, and in disease resistance. Front. Plant Sci. 3:149

    Not in our library10.3389/fpls.2012.00149

  3. 3.

    Badri D. V. Chaparro J. H. Zhang R. Shen Q. Vivanco J. M. (2013 ). Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J. Biol. Chem. 288 4502–4512

    Not in our library10.1074/jbc.m112.433300

  4. 4.

    Bais H. P. Weir T. L. Perry L. G. Gilroy S. Vivanco J. M. (2006 ). The role of root exudates in rhizosphere interactions with plants and other organisms. Annu. Rev. Plant Biol. 57 233–266

    Not in our library10.1146/annurev.arplant.57.032905.105159

  5. 5.

    Barret M. Frey-Klett P. Guillerm-Erckelboudt A. V. Boutin M. Guernec G. Sarniguet A. (2009 ). Effect of wheat roots infected with the pathogenic fungus Gaeumannomyces graminis var. tritici on gene expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp. Mol. Plant Microbe Interact. 22 1611–1623

    Not in our library10.1094/mpmi-22-12-1611

  6. 6.

    Berendsen R. L. Pieterse C. M. J Bakker P. A. H. M. (2012 ). The rhizosphere microbiome and plant health. Trends Plant Sci. 17 478–486

    Not in our library10.1016/j.tplants.2012.04.001

  7. 7.

    Berg G. Smalla K. (2009 ). Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol. Ecol. 68 1–13

    Not in our library10.1111/j.1574-6941.2009.00654.x

  8. 8.

    Bulgarelli D. Rott M. Schlaeppi K. Ver Loren van Themaat E. Ahmadinejad N. Assenza F. (2012 ). Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488 91–95

    Not in our library10.1038/nature11336

  9. 9.
    Activation of the Jasmonic Acid Plant Defence Pathway Alters the Composition of Rhizosphere Bacterial Communities · 2013
    No notice
  10. 10.
    Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions · 2013
    Corrected
  11. 11.

    DeCoste N. J. Gadkar V. J. Filion M. (2010 ). Verticillium dahliae alters Pseudomonas spp. populations and HCN gene expression in the rhizosphere of strawberry. Can. J. Microbiol. 56 906–915.

    Not in our library10.1139/w10-080

  12. 12.

    De Ridder-Duine A. S. Kowalchuk G. A. Klein Gunnewiek P. J. A. Smant W. Van Veen J. A De Boer W. (2005 ). Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition. Soil Biol. Biochem. 37 349–357

    Not in our library10.1016/j.soilbio.2004.08.005

  13. 13.

    Doornbos R. F. Geraats B. P. J. Kuramae E. E. Van Loon L. C Bakker P. A. H. M. (2011 ). Effects of jasmonic acid, ethylene, and salicylic acid signaling on the rhizosphere bacterial community of Arabidopsis thaliana. Mol. Plant Microbe Interact. 24 395–407

    Not in our library10.1094/mpmi-05-10-0115

  14. 14.

    Doornbos R. F. Van Loon L. C Bakker P. A. H. M. (2012 ). Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. Agron. Sustain. Dev. 32 227–243

    Not in our library10.1007/s13593-011-0028-y

  15. 15.

    Eshel A. Beeckman T. (2013 ). Plant Roots: The Hidden Half. 4th Edn Boca Raton, FL: CRC Press

    Not in our library

  16. 16.

    Fan B. Cravalhais L. C. Becker A. Fedoseyenko D. Von Wiren N. Borriss R. (2012 ). Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates. BMC Microbiol. 12:116

    Not in our library10.1186/1471-2180-12-116

  17. 17.

    Foster R. C. Rovira A. D. Cock T. W. (1983 ). Ultrastructure of the Root–Soil Interface. St. Paul, MN: The American Phytopathological Society

    Not in our library

  18. 18.

    Gao M. Teplitski M. Robinson J. B. Bauer D. W. (2003 ). Production of substances by Medicago truncatula that affect bacterial quorum sensing. Mol. Plant Microbe Interact. 16 827–834

    Not in our library10.1094/mpmi.2003.16.9.827

  19. 19.

    Garbeva P. V. Van Elsas J. D Van Veen J. A. (2008 ). Rhizosphere microbial community and its response to plant species and soil history. Plant Soil 302 19–32

    Not in our library10.1007/s11104-007-9432-0

  20. 20.

    Germida J. J. Siciliano S. D. De Freitas J. R. Seib A. M. (1998 ). Diversity of root-associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.). FEMS Microbiol. Ecol. 26 43–50

    Not in our library10.1111/j.1574-6941.1998.tb01560.x

  21. 21.

    Glandorf D. C. M. Peters L. G. L. Van der Sluis I. Bakker P. A. H. M. Schippers B. (1993 ). Crop specificity of rhizosphere pseudomonads and the involvement of root agglutinins. Soil Biol. Biochem. 25 981–989

    Not in our library10.1016/0038-0717(93)90144-z

  22. 22.

    Gosalbes M. J. Abellan J. J. Durban A. Perez-Cobas A. E. Latorre A. Moya A. (2012 ). Metagenomics of human microbiome: beyond 16s rDNA. Clin. Microbiol. Infect. Dis. 18 47–49

    Not in our library10.1111/j.1469-0691.2012.03865.x

  23. 23.

    Grayston S. J. Wang S. Campbell C. D. Edwards A. C. (1998 ). Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol. Biochem. 30 369–378

    Not in our library10.1016/s0038-0717(97)00124-7

  24. 24.

    Haichar F. Z. Marol C. Berge O. Rangel-Castro J. I. Prosser J. I. Balesdent J. (2008 ). Plant host habitat and root exudates shape soil bacterial community structure. ISME J. 2 1221–1230

    Not in our library10.1038/ismej.2008.80

  25. 25.

    Hartmann A. Rothballer M. Schmid M. (2008 ). Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant Soil 312 7–14

    Not in our library10.1007/s11104-007-9514-z

  26. 26.

    Hartmann A. Schmid M. Van Tuinen D. Berg G. (2009 ). Plant-driven selection of microbes. Plant Soil 321 235–257

    Not in our library10.1007/s11104-008-9814-y

  27. 27.

    Hiltner L. (1904 ). Uber neuere Erfahrungen und Probleme auf dem Gebiete der Bodenbakteriologie unter besonderden berucksichtigung und Brache. Arb. Dtsch. Landwirtsch. Gesellschaft 98 59–78

    Not in our library

  28. 28.

    Hirsch P. R. Mauchline T. H. (2012 ). Who’s who in the plant root microbiome? Nat. Biotechnol. 30 961–962

    Not in our library10.1038/nbt.2387

  29. 29.

    Hosni T. Moretti C. Devescovi G. Suarez-Moreno Z. R. Fatmi M. B. Guarnaccia C. (2011 ). Sharing of quorum-sensing signals and role of interspecies communities in a bacterial plant disease. ISME J. 5 1857–1870.

    Not in our library10.1038/ismej.2011.65

  30. 30.

    Inceoglu O. Van Overbeek L. S. Salles J. F Van Elsas J. D. (2013 ). The normal operating range of bacterial communities in soil used for potato cropping. Appl. Environ. Microbiol. 79 1160–1170

    Not in our library10.1128/aem.02811-12

  31. 31.

    Jansson J. K. Neufeld J. D. Moran M. A. Gilbert J. A. (2012 ). Omics for understanding microbial functional dynamics. Environ. Microbiol. 14 1–3

    Not in our library10.1111/j.1462-2920.2011.02518.x

  32. 32.

    Jones D. L. Nguyen C. Finlay R. D. (2009 ). Carbon flow in the rhizosphere: carbon trading at the soil–root interface. Plant Soil 321 5–33

    Not in our library10.1007/s11104-009-9925-0

  33. 33.

    Jousset A. Rochat L. Lanoue A. Bonkowski M. Keel C. Scheu S. (2011 ). Plants respond to pathogen infection by enhancing the antifungal gene expression of root-associated bacteria. Mol. Plant Microbe Interact. 24 352–358

    Not in our library10.1094/mpmi-09-10-0208

  34. 34.

    Kent A. D. Triplett E. W. (2002 ). Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu. Rev. Microbiol. 56 211–236

    Not in our library10.1146/annurev.micro.56.012302.161120

  35. 35.

    Kirk J. L. Klironomos J. N. Lee H. Trevors J. T. (2005 ). The effects of perennial ryegrass and alfalfa on microbial abundance and diversity in petroleum contaminated soil. Environ. Pollut. 133 455–465

    Not in our library10.1016/j.envpol.2004.06.002

  36. 36.

    Koch B. Worm J. Jensen L. E. Hojberg O. Nybroe O. (2001 ). Carbon limitation induces σ-dependent gene expression in Pseudomonas fluorescens in soil. Appl. Environ. Microbiol. 67 3363–3370

    Not in our library10.1128/aem.67.8.3363-3370.2001

  37. 37.

    Kwak Y. S. Bonsall R. F. Okubara P. A. Paulitz T. C. Thomashow L. S. Weller D. M. (2012 ). Factors impacting the activity of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens against take-all of wheat. Soil Biol. Biochem. 54 48–56

    Not in our library10.1016/j.soilbio.2012.05.012

  38. 38.

    Kyselkova M. Kopecky J. Frapolli M. Defago G. Sagova-Mareckova M. Grundmann G. L. (2009 ). Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. ISME J. 3 1127–1138

    Not in our library10.1038/ismej.2009.61

  39. 39.

    Lakshmanan V. Kitto S. L. Caplan J. L. Hsueh Y. H. Kearns D. B. Wu Y. S. (2012 ). Microbe-associated molecular patterns-triggered root responses mediate beneficial rhizobacterial recruitment in Arabidopsis. Plant Physiol. 160 1642–1661

    Not in our library10.1104/pp.112.200386

  40. 40.

    Lee B. Lee S. Ryu M. R. (2012 ). Foliar aphid feeding recruits rhizosphere bacteria and primes plant immunity against pathogenic and non-pathogenic bacteria in pepper. Ann. Bot. 110 281–290

    Not in our library10.1093/aob/mcs055

  41. 41.

    Lemanceau P. Corberand T. Gardan L. Latour X. Laguerre G. Boeufgras J.-M. (1995 ). Effect of two plant species, flax (Linum usitatissimum L.) and tomato (Lycopersicon esculentum Mill.), on the diversity of soilborne populations of fluorescent pseudomonads. Appl. Environ. Microbiol. 61 1004–1012

    Not in our library10.1128/aem.61.3.1004-1012.1995

  42. 42.

    Leveau J. H. J. (2007 ). The magic and menace of metagenomics: prospects for the study of plant growth-promoting rhizobacteria. Eur. J. Plant Pathol. 119 279–300

    Not in our library10.1007/s10658-007-9186-9

  43. 43.

    Liu F. Bian Z. Jia Z. Zhao Q. Song S. (2012 ). The GCR1 and GPA1 participate in promotion of Arabidopsis primary root elongation induced by N-acyl-homoserine lactones, the bacterial quorum-sensing signals. Mol. Plant Microbe Interact. 25 677–683

    Not in our library10.1094/mpmi-10-11-0274

  44. 44.

    Lugtenberg B. Kamilova F. (2009 ). Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63 541–556

    Not in our library10.1146/annurev.micro.62.081307.162918

  45. 45.

    Lundberg D. S. Lebeis S. L. Herrera Paredes S. Yourstone S. Gehring J. Malfatti S. (2012 ). Defining the core Arabidopsis thaliana root microbiome. Nature 488 86–90

    Not in our library10.1038/nature11237

  46. 46.
    A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming · 2012
    No notice
  47. 47.

    Mark G. L. Dow J. M. Kiely P. D. Higgings H. Haynes J. Baysse C. (2005 ). Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe–plant interactions. Proc. Natl. Acad. Sci. U.S.A. 102 17454–17459

    Not in our library10.1073/pnas.0506407102

  48. 48.

    Mathesius U. Mulders S. Gao M. Teplitski M. Caetano-Anolles G. Rolfe B. G. (2003 ). Extensive and specific responses of a eukaryote to bacterial quorum-sensing signals. Proc. Natl. Acad. Sc. U.S.A. 100 1444–1449

    Not in our library10.1073/pnas.262672599

  49. 49.

    Matilla M. A. Ramos J. L. Bakker P. A. H. M. Doornbos R. F. Vivanco J. M. Badri D. V. (2010 ). Pseudomonas putida KT2440 causes induced systemic resistance and changes in Arabidopsis root exudation. Environ. Microbiol. Rep. 2 381–388

    Not in our library10.1111/j.1758-2229.2009.00091.x

  50. 50.

    Mavrodi O. V. Mavrodi D. V. Parejko J. A. Thomashow L. S. Weller D. M. (2012 ). Irrigation differentially impacts populations of indigenous antibiotic-producing Pseudomonas spp. in the rhizosphere of wheat. Appl. Environ. Microbiol. 78 3214–3220

    Not in our library10.1128/aem.07968-11

  51. 51.

    Mazurier S. Corberand T. Lemanceau P. Raaijmakers J. M. (2009 ). Phenazine antibiotics produced by fluorescent pseudomonads contribute to natural soil suppressiveness to Fusarium wilt. ISME J. 3 977–991

    Not in our library10.1038/ismej.2009.33

  52. 52.

    Mazzola M. (2002 ). Mechanisms of natural soil suppressiveness to soilborne diseases. Antonie Van Leeuwenhoek 81 557–564

    Not in our library10.1023/a:1020557523557

  53. 53.

    Mendes R. Kruijt M. De Bruijn I. Dekkers E. Van der Voort M. Schneider J. H. M. (2011 ). Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332 1097–1100

    Not in our library10.1126/science.1203980

  54. 54.

    Micallef S. A. Channer S. Shiaris M. P. Colon-Carmona A. (2009a ). Plant age and genotype impact the progression of bacterial community succession in the Arabidopsis rhizosphere. Plant Signal. Behav. 4 777–780

    Not in our library10.4161/psb.4.8.9229

  55. 55.

    Micallef S. A. Shiaris M. P. Colon-Carmona A. (2009b ). Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J. Exp. Bot. 60 1729–1742

    Not in our library10.1093/jxb/erp053

  56. 56.

    Miethling R. Wieland G. Backhaus H. Tebbe C. C. (2000 ). Variation in microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33. Microb. Ecol. 40 43–56

    Not in our library10.1007/s002480000021

  57. 57.

    Miller M. B. Bassler B. L. (2001 ). Quorum sensing in bacteria. Annu. Rev. Microbiol. 55 165–199

    Not in our library10.1146/annurev.micro.55.1.165

  58. 58.

    Moree W. J. Phelan V. V. Wu C.-H. Bandeira N. Cornett D. S. Duggan B. M. (2012 ). Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 109 13811–13816

    Not in our library10.1073/pnas.1206855109

  59. 59.
    Benzoxazinoids in Root Exudates of Maize Attract Pseudomonas putida to the Rhizosphere · 2012
    No notice
  60. 60.

    Normander B. Prosser J. I. (2000 ). Bacterial origin and community composition in the barley phytosphere as a function of habitat and presowing conditions. Appl. Environ. Microbiol. 66 4372–4377

    Not in our library10.1128/aem.66.10.4372-4377.2000

  61. 61.

    Okubara P. A. Bonsall R. F. (2008 ). Accumulation of Pseudomonas-derived 2,4-diacetylphloroglucinol on wheat seedling roots is influenced by host cultivar. Biol. Control 46 322–331

    Not in our library10.1016/j.biocontrol.2008.03.013

  62. 62.

    Pechy-Tarr M. Borel N. Kupferschmied P. Turner V. Binggeli O. Radovanovic D. (2013 ). Control and host-dependent activation of insect toxin expression in a root-associated biocontrol pseudomonad. Environ. Microbiol. 15 736–750

    Not in our library10.1111/1462-2920.12050

  63. 63.

    Pierson L. S. III Pierson E. A. (2007 ). Roles of diffusible signals in communication among plant-associated bacteria. Phytopathology 97 227–232

    Not in our library10.1094/phyto-97-2-0227

  64. 64.

    Raaijmakers J. M. Weller D. M. (1998 ). Natural plant protection by 2,4-diacetylphloroglucinol-producing Pseudomonas spp. in take-all decline soils. Mol. Plant Microbe Interact. 11 144–152

    Not in our library10.1094/mpmi.1998.11.2.144

  65. 65.

    Rosenzweig N. Tiedje J. M. Quensen J. F. III Meng Q. Hao J. J. (2012 ). Microbial communities associated with potato common scab-suppressive soil determined by pyrosequencing analyses. Plant Dis. 96 718–725

    Not in our library10.1094/pdis-07-11-0571

  66. 66.

    Rovira A. D. (1969 ). Plant root exudates. Bot. Rev. 35 17–34

    Not in our library10.1007/bf02859887

  67. 67.

    Rudrappa T. Czymmek K. J. Paré P. W. Bais H. P. (2008 ). Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiol. 148 1547–1556

    Not in our library10.1104/pp.108.127613

  68. 68.

    Ruffner B. Pechy-Tarr M. Ryffel F. Hoegger P. Obrist C. Rindlisbacher A. (2013 ). Oral insecticidal activity of plant-associated pseudomonads. Eviron. Microbiol. 15 751–763

    Not in our library10.1111/j.1462-2920.2012.02884.x

  69. 69.

    Sanguin H. Sarniguet A. Gazengel K. Moenne-Loccoz Y. Grundmann G. L. (2009 ). Rhizosphere bacterial communities associated with disease suppressiveness stages of take-all decline in wheat monoculture. New Phytol. 184 694–707

    Not in our library10.1111/j.1469-8137.2009.03010.x

  70. 70.

    Schenk S. T. Stein E. Kogel K. H. Schikora A. (2012 ). Arabidopsis growth and defense are modulated by bacterial quorum sensing molecules. Plant Signal. Behav. 7 178–181

    Not in our library10.4161/psb.18789

  71. 71.

    Schikora A. Schenk S. T. Stein E. Molitor A. Zuccaro A. Kogel K. H. (2011 ). N-acyl-homoserine lactone confers resistance toward biotrophic and hemibiotrophic pathogens via altered activation of AtMPK6. Plant Physiol. 157 1407–1418

    Not in our library10.1104/pp.111.180604

  72. 72.

    Schreiner K. Hagn A. Kyselkova M. Moenne-Loccoz Y. Welzl G. Munch J. C. (2010 ). Comparison of barley succession and take-all disease as environmental factors shaping the rhizobacterial community during take-all decline. Appl. Environ. Microbiol. 76 4703–4712

    Not in our library10.1128/aem.00481-10

  73. 73.

    Schuhegger R. Ihring A. Gantner S. Bahnweg G. Knappe C. Vogg G. (2006 ). Induction of systemic resistance in tomato by N-acyl-L-homoserine lactone-producing rhizosphere bacteria. Plant Cell Environ. 29 909–918

    Not in our library10.1111/j.1365-3040.2005.01471.x

  74. 74.

    Schwachtje J. Karojet S. Thormalen I. Bernholz C. Kunz S. Brouwer S. (2011 ). A naturally associated rhizobacterium of Arabidopsis thaliana induces a starvation-like transcriptional response while promoting growth. PLoS ONE 6:e29382

    Not in our library10.1371/journal.pone.0029382

  75. 75.

    Smalla K. Wieland G. Buchner A. Zock A. Parzy J. Kaiser S. (2001 ). Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl. Environ. Microbiol. 67 4742–4751

    Not in our library10.1128/aem.67.10.4742-4751.2001

  76. 76.

    Sorensen J. Hauberg Nicolaisen M. Ron E. Simonet P. (2009 ). Molecular tools in rhizosphere microbiology – from single-cell to whole-community analysis. Plant Soil 321 483–512

    Not in our library10.1007/s11104-009-9946-8

  77. 77.

    Teplitski M. Robinson J. B. Bauer W. D. (2000 ). Plants secrete substances that mimic bacterial N-acyl homoserine lactone signal activities and affect population density-dependent behaviors in associated bacteria. Mol. Plant Microbe Interact. 13 637–648

    Not in our library10.1094/mpmi.2000.13.6.637

  78. 78.

    Traxler M. F. Kolter R. (2012 ). A massively spectacular view of the chemical lives of microbes. Proc. Natl. Acad. Sci. U.S.A. 109 10128–10129

    Not in our library10.1073/pnas.1207725109

  79. 79.
    Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome · 2008
    No notice
  80. 80.

    Van de Mortel J. E. De Vos R. C. H. Dekkers E. Pineda A. Guillod L. Bouwmeester K. (2012 ). Metabolic and transcriptomic changes induced in Arabidopsis by the rhizobacterium Pseudomonas fluorescens SS101. Plant Physiol. 160 2173–2188

    Not in our library10.1104/pp.112.207324

  81. 81.

    Van Overbeek L. S. Van Elsas J. D van Veen J. A. (1997 ). Pseudomonas fluorescens Tn5-B20 mutant RA92 responds to carbon limitation in soil. FEMS Microbiol. Ecol. 24 57–71

    Not in our library10.1016/s0168-6496(97)00045-7

  82. 82.

    Von Rad U. Klein I. Dobrev P. I. Kottova J. Zazimalova E. Fekete A. (2008 ). Response of Arabidopsis thaliana to N-hexanoyl-DL-homoserine-lactone, a bacterial quorum sensing molecule produced in the rhizosphere. Planta 229 73–85

    Not in our library10.1007/s00425-008-0811-4

  83. 83.

    Vorholt J. A. (2012 ). Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10 828–840

    Not in our library10.1038/nrmicro2910

  84. 84.

    Walker T. S. Bais H. P. Grotewold E. Vivanco J. M. (2003 ). Root exudation and rhizosphere biology. Plant Physiol. 132 44–51

    Not in our library10.1104/pp.102.019661

  85. 85.

    Watrous J. Roach P. Alexandrov T. Heath B. S. Yang J. Y. Kersten R. D. (2012 ). Mass spectral molecular networking of living microbial colonies. Proc. Natl. Acad. Sci. U.S.A. 109 E1743–E1752

    Not in our library10.1073/pnas.1203689109

  86. 86.

    Weinert N. Piceno Y. Ding G. C. Meincke R. Heuer H. Berg G. (2011 ). PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol. Ecol. 75 497–506

    Not in our library10.1111/j.1574-6941.2010.01025.x

  87. 87.

    Weller D. M. Raaijmakers J. M. McSpadden Gardener B. B. Thomashow L. S. (2002 ). Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu. Rev. Phytopathol. 40 309–348

    Not in our library10.1146/annurev.phyto.40.030402.110010

  88. 88.

    Yang J. W. Yi H. S. Kim H. Lee B. Lee S. Ghim S. Y. (2011 ). Whitefly infestation of pepper plants elicits defence responses against bacterial pathogens in leaves and roots and changes the below-ground microflora. J. Ecol. 99 46–56

    Not in our library10.1111/j.1365-2745.2010.01756.x

  89. 89.

    Zamioudis C Pieterse C. M. J. (2012 ). Modulation of host immunity by beneficial microbes. Mol. Plant Microbe Interact. 25 139–150

    Not in our library10.1094/mpmi-06-11-0179

  90. 90.
    Soil nitrogen availability and plant genotype modify the nutrition strategies of M. truncatula and the associated rhizosphere microbial communities. · 2012
    Not checked
  91. 91.

    Zysko A. Sanguin H. Hayes A. Wardleworth L. Zeef L. A. H. Sim A. (2012 ). Transcriptional response of Pseudomonas aeruginosa to a phosphate-deficient Lolium perenne rhizosphere. Plant Soil 359 25–44

    Not in our library10.1007/s11104-011-1060-z

Cited by papers we hold 10

Reads

Read by people on this page

None yet.

Checked or read by AI through naulon

None yet.

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.

Are you an author?

Is this your paper?

Claim it to add your note and be paid when agents cite it. Free.