Rhizosphere and Root Colonization by Bacterial Inoculants and Their Monitoring Methods: A Critical Area in PGPR Research

  • Farah AhmadEmail author
  • Fohad Mabood Husain
  • Iqbal Ahmad


Roots serve a multitude of functions in plants including anchorage, acquisition of nutrients and water, and production of exudates with growth regulatory properties. The root–soil interface, or rhizosphere, is the site of greatest biological and chemical activity within the soil matrix. Plant growth-promoting rhizobacteria (PGPR) are known to influence plant health by controlling plant pathogens or via direct enhancement of plant development in the laboratory and in greenhouse experiments. Unfortunately, however, results in the field have been less consistent. The colonization of roots by inoculated bacteria is an important step in the interaction between beneficial bacteria and the host plant. However, colonization is a complex phenomenon influenced by many biotic and abiotic parameters, some of which are only now apparent. Monitoring fate and metabolic activity of microbial inoculants as well as their impact on rhizosphere and soil microbial communities are needed to guarantee safe and reliable application, independent of whether they are genetically modified or not. The first and most crucial prerequisite for effective use of PGPRs is that strain identity and activity are continuously confirmed. A combination of both classical and molecular techniques must be perfected for more effective monitoring of inoculants strain (both genetically modified and unmodified) after release into the soil. Recent developments in techniques for studying rhizobacterial communities and detection and tracking systems of inoculated bacteria are important in future application and assessment of effectiveness and consistent performance of microbial inoculants in crop production and protection.


Rhizosphere colonization Rhizobacteria Monitoring methods Molecular techniques GFP PCR Marker gene Microscopy 



We are thankful to Dr. S. Hayat for his suggestions and Prof. John Pichtel (Ball State University, USA) for critical reading and improvement of this manuscript.


  1. Abbasi, P. A., Miller, S. A., Menlia, T., Hoitnk, H. A, O., And KIm, J. M. 1999. Precise detection and tracing of Trichoderma hamatum 382 in compost-amended potting mixes by using molecular markers. Appl. Environ. Microbiol. 65: 5421–5426.Google Scholar
  2. Ahmad, F. 2006. Diversity of potential bioprospection of certain plant growth promoting rhizobacteria. Ph.D. thesis, Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India.Google Scholar
  3. Ahmad, F., Ahmad, I., Aqil, F., Wani, A. A., and Sousche, Y. S. 2006. Plant growth promoting potential of free living diazotrophs and other rhizobacteria isolated from northern Indian soil. Biotechnol. J. 1: 1112–1123.CrossRefGoogle Scholar
  4. Ahmad, F., Ahmad, I., and Khan, M. S. 2008. Screening of free living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol. Res. 168: 173–181.CrossRefGoogle Scholar
  5. Alexander, M. 1985. Introduction to Soil Micobiology. 2nd Edition. John Wiley and Sons, Inc.: New York, USA.Google Scholar
  6. Alvarado M. C., Zsigmond, L. M., Kovács, I., Cséplö, Á., Koncz C., and Szabados, L. M. 2004. Gene trapping with firefly luciferase in arabidopsis. Tagging of stress responsive genes. Plant Physiol. 134: 18–27.CrossRefGoogle Scholar
  7. Amann, R. I., Ludwig, W., and Schleifer, K. H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143–169.Google Scholar
  8. Andersen, J. B., Sternberg, C., Poulsen, L. K., Bjorn, S. P., Givskov, M., and Molin, S. 1999. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 64: 2240–2246.Google Scholar
  9. Atkins, S. D., Clark, J. M., Pande, S., Hirsch, P. R., and Kerry, B. R. 2005. the use of real-time PCR and species-specific primers for the identificatrion and monitoring of Paecilomyces lilacinus. FEMS Microbiol. Ecol. 51: 257–264.CrossRefGoogle Scholar
  10. Atkins, S. D., Clark, J. M., and Kerry, B. R. 2003. Detection and quatification of Plectosphaerella cucumernia a potential biocontrol agent of potato cyst nematodes, by using conventional PCR, real-time PCR, selective media and baiting. Appl. Microbiol. Ecol. 69: 4788–4793.CrossRefGoogle Scholar
  11. Assmus, B., Hutzler, P., Kirchhof, G., Amann, R., Lawrence, J. R., and Hartmann, A. 1995. In situ localization of Azospirillum brasilense in the rhizosphere of wheat with fluorescently labeled rRNA targeted oligonucleotide probes and scanning confocal laser microscopy. Appl. Environ. Microbiol. 16: 1013–1019.Google Scholar
  12. Bacilio-Jime´nez, M., Aguilar-Flores, S., Ventura-Zapata, E., Pe´rez-Campos E., Bouquelet, S., and Zenteno, E. 2003. Chemical characterization of root exudates from rice (Oryza sativa) and their effects on the chemotactic response of endophytic bacteria. Plant Soil 249: 271–277.CrossRefGoogle Scholar
  13. Bais, H. P., Fall, R., and Vivanco, J. M. 2004a. Biocontrol of Bacillus subtilis against infection of Arabidopsis roots by Pseudomonas syringae is facilitated by biofilm formation and surfactin production. Plant Physiol. 134: 307–319.CrossRefGoogle Scholar
  14. Bais, H. P., Park, S. W., Weir, T. L., Callaway, R. M., and Vivanco, J. M. 2004b. How plants communicate using the underground information superhighway. Trends Plant Sci. 9: 26–32.CrossRefGoogle Scholar
  15. Bais, H. P., Weir, T. L., Perry, L. G., Gilroy, S., and Vivanco, J. M. 2006. The role of root exudates in rhizosphere interactions with plants and other organisms. Annu. Rev. Plant Biol. 57: 233–266.CrossRefGoogle Scholar
  16. Baudoin, E., Benizri, E., and Guckert, A. 2002. Impact of growth stage on the bacterial community structure along maize roots, as determined by metabolic and genetic fingerprinting. Appl. Soil Ecol. 19: 135–145.CrossRefGoogle Scholar
  17. Benizri, E., Baudoin, E., and Guckert, A. 2001. Root colonization by inoculated plant growth promoting rhizobacteria. Biocontrol Sci. Technol. 11: 557–574.CrossRefGoogle Scholar
  18. Berg, G., Roskot, N., Steidle, A., Eberl, L., Zock, A., and Smalla, K. 2002. Plant dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different Verticillium host plants. Appl. Environ. Microbiol. 68: 3328–3338.CrossRefGoogle Scholar
  19. Berger, S., Bell, E., Sadka, A., and Mullet, J. E. 1995. Arabidopsis thaliana Atvsp is homologous to soyabean VspA and VspB, genes encoding vegetative storage protein acid phosphate and is regulated similarly by methyl josmonate, wounding sugars, light and phosphate. Plant Mol. Biol. 27: 933–942.CrossRefGoogle Scholar
  20. Bloemberg, G. V. 2007. Microscopic analysis of plant–bacterium interactions using auto fluorescent proteins. Eur. J. Plant Pathol. 119: 301–309.CrossRefGoogle Scholar
  21. Bloemberg, G. V., and Camacho, M. 2006. Microbial interactions with plants: a hidden world? In Microbial Root Endophytes. Soil Biology, Eds. B. Schultz, C. Boyle, and T. Sieber, pp. 321–336. Springer Verlag: Berlin, Heidelberg.CrossRefGoogle Scholar
  22. Bloemberg, G. V., and Lugtenberg, B. J. J. 2004. Biofilm formation on plants, their relevance and phenotypic aspects. In Microbial Biofilms, Eds. M. Ghannoum, and G. O’Toole, pp. 141–159. ASM Press: Washington, DC.Google Scholar
  23. Bloemberg, G. V., Wijfjes, A. H. M., Lamers, G. E. M., Stuurman, N., and Lugtenberg, B. J. J. 2000. Simultaneous imaging of Pseudomonas fluorescens WCS365 populations expressing three different autofluorescent proteins in the rhizosphere: new perspectives for studying microbial communities. Mol. Plant Microbe Interact. 13: 1170–1176.CrossRefGoogle Scholar
  24. Bolemberg, G. V., and Lutenberg, B. J. J. 2001. Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr. Opin. Plant Biol. 4: 343.CrossRefGoogle Scholar
  25. Bolton, H. F., Fredrickson, J. K., and Elliot, L. F. 1993. Microbial ecology of the rhizosphere. In Soil Microbial Ecology, Ed. F. B. J. Melting, pp. 27–63. Marcel Dekker: New York.Google Scholar
  26. Bonnaterra, A., Camps, J., and Montesinos, E. 2005. Osmotically induced trehalose and glycine betaine accumulation improves tolerance to dessication, survival and efficacy of the post harvest biocontrol agent Pantoea agglomerans EPS125. FEMS Microbiol. Lett. 250: 1–8.CrossRefGoogle Scholar
  27. Bowen, G. D., and Rovira, A. D. 1999. The rhizosphere and its management to improve plant growth. Adv. Agron. 66: 1–102.CrossRefGoogle Scholar
  28. Broggini, G. A. L., Duffy, B., Hollinger, E., Scharer, H. J., Gessler, C., and Patocchi, A. 2005. Detection of fire blight biocontrol agent Bacillus subtilis BD170 in a Swiss apple orchard. Eur. J. Plant Pathol. 111: 93–100.CrossRefGoogle Scholar
  29. Buhariwalla, H. K., Srilakshmi, P., Kannan, S., Kanchi, R. S., Chandra S., Satyaprasad K., Waliyar, F., Thakur, R. P., and Crouch, J. H. 2005. AFLP analysis of Trichoderma spp. from India compared with sequence and morphological-based diagnostics. J. Phytopathol. 153: 389–400.CrossRefGoogle Scholar
  30. Cabrefiga, J. 2004. Fire blight(Erwinia amylovora) of rosaceous plants pathogen virulence and selection and characterization of biological control agents. Ph. D. thesis, Universitat de Girona.Google Scholar
  31. Cebolla, A., Ruiz-Berraquero, F., and Palomares, A. J. 1991. Expression and quantification of firefly luciferase under control of Rhizobium meliloti symbiotic promoters. J. Biolumin. Chemilumin. 6: 177–184.CrossRefGoogle Scholar
  32. Cebolla, A., Ruiz-Berraquero, F., and Palomares A. J. 1993. Stable tagging of Rhizobium meliloti with the firefly luciferase gene for environmental monitoring. Appl. Environ. Microbiol. 59: 2511–2519.Google Scholar
  33. Chabot, R., Antoun, H., Kloepper, J. W., and Beauchamp, C. J. 1996. Root colonization of maize and lettuce by bioluminescent Rhizobium leguminosarum biovar phaseoli. Appl. Environ. Microbiol. 62: 2767–2772.Google Scholar
  34. Chalfie, M., and Kain, S. R. 2005. Green fluorescent protein: properties, applications and protocols. In Methods of Biochemical Analysis, Eds. M. Chalfie, and S. R. Kain. Wiley: New York.Google Scholar
  35. Chalfie, M., Tu, Y., Euskirchen, G., Ward, W. W., and Prasher, D. C. 1994. Green fluorescent protein as a marker for gene expression. Science 263: 802–805.CrossRefGoogle Scholar
  36. Chapon, A., Boutin, M., Rime, D., Delalande, L., Guillerm, A. Y., and Sarniguet, A. 2003. Direct and specific assessment of colonization of wheat rhizoplane by Pseudomonas fluorescens Pf29A. Eur. J. Plant Pathol. 109: 61–70.CrossRefGoogle Scholar
  37. Chapon, A., Guillerm, A. Y., Delalande, L., Lebreton, L., and Sarniguet, A. 2002. Dominant colonization of wheat roots by Pseudomonas fluorescens Pf29A and selection of the indigenous microflora in the presence of take-all fungus. Eur. J. Plant Pathol. 108: 449–459.CrossRefGoogle Scholar
  38. Chauhan, P. S., and Nautiyal, C. S. 2010. The purB gene controls rhizosphere colonization by Pantoea agglomerans. Lett. Appl. Microbiol. 50: 205–210.CrossRefGoogle Scholar
  39. Choi, H. Y., Ryder, M. H., Gillings, M. R., Stokes, H. W., Ophele-Keller, K. M., and Veal, D. A. 2003. Survival of lacZY-marked strain of Pseudomonas corrugata following field release. FEMS Microbiol. Ecol. 43: 367-374.CrossRefGoogle Scholar
  40. Ciccillo, F., Fiore, A., Bevivino, A., Dalmastri, C., Tabacchioni, S., and Chiarini, L. 2002. Effects of two different application methods of Burkholderia ambifaria MCI 7 on plant growth and rhizospheric bacterial diversity. Environ. Microbiol. 4: 238–245.CrossRefGoogle Scholar
  41. Compant, S., Duffy, B., Nowak, J., and Clément, C. 2005. Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl. Environ. Microbiol. 71: 4951–4959.CrossRefGoogle Scholar
  42. Cook, R. J. 2002. Advances in plant health management in the twentieth century. Annu. Rev. Phytopathol. 38: 95–116.CrossRefGoogle Scholar
  43. Cross, N. C. P. 1995. Quantitative PCR techniques and application. Br. J. Haematol. 89: 693–697.CrossRefGoogle Scholar
  44. Dakora, F. D., and Philipps, D. A. 2002. Root exudates as mediators of mineral acquisition in low nutrient environments. Plant Soil 245: 35–47.CrossRefGoogle Scholar
  45. Dandie, C. E., Larrainzar, E., Mark, G. L., O’Gara, F., and Morrisey, J. P. 2005. Establishment of DsRed.T3_S4T as an improved autofluorescent marker for microbial ecology applications. Environ. Microbiol. 7: 1818–1825.CrossRefGoogle Scholar
  46. Darwent, M. J., Paterson, E., James, A., McDonald, S., and Tomos, A. D. 2003. Biosensor reporting of root exudation from Hordeum vulgare in relation to shoot nitrate concentration. J. Exp. Bot. 54: 325–334.CrossRefGoogle Scholar
  47. De Curtis, F., Caputo, L., Castoria, R., Lima, G., Stea, G., and De Cicco, V. 2004. Use of fluorescent amplified fragment length polymorphism (fAFLP) to identify specific molecular markers for the biocontrol agent Aureobasidium pullulans strain LS30. Postharvest Biol. Technol. 34: 179–186.CrossRefGoogle Scholar
  48. De Weert, S., and Bloemberg, G. V. 2006. Rhizosphere competence and the role of root colonization in biocontrol. In Plant-Associated Bacteria, Ed. S. S. Gnanamanickam, pp. 317–333. Springer: The Netherlands.CrossRefGoogle Scholar
  49. De Weger, L. A., van der Vlugt, C. I. M., Wijfjes, A. H. M., Bakker, P. A. H. M., Schippers, B., and Lugtenberg. B. J. J. 1987. Flagella of a plant-growth stimulating Pseudomonas fluorescens strain are required for colonization of potato roots. J. Bacteriol. 169: 2769–2773.Google Scholar
  50. De Weger, L. A., Bakker, P. A. H. M., Schippers, B., van Loosdrecht, M. C. M., and Lugtenberg, B. J. J. 1989. Pseudomonas spp. with mutational changes in the O-antigenic side chain of their lipopolysaccharides are affected in their ability to colonize potato roots. In Signal Molecules in Plant–Microbe Interactions, Ed. B. J. J. Lugtenberg, pp. 197–202. Springer-Verlag: Berlin, Germany.Google Scholar
  51. De Weger, L. A., Van Der Bij, A. J., Dekkers, L. C., Simons, M., Wijffelman, C. A., and Lugtenberg, B. J. J. 1995. Colonization of the rhizosphere of crop plants by plant-beneficial pseudomonads. FEMS Microbiol. Ecol. 17: 221–228.Google Scholar
  52. De Wet, J. R., Wood, K., Helinski, D., and DeLuca, M. 1985. Cloning of firefly luciferase cDNA and the expression of active luciferase in Escherichia coli. Proc. Natl. Acad. Sci. USA 82: 7870–7873.CrossRefGoogle Scholar
  53. Degenhardt, J., Gershenzon, J., Baldwin, I. T., and Kessler, A. 2003. Attracting friends to feast on foes: engineering terpene emission to make crop plants more attractive to herbivore enemies. Curr. Opin. Biotechnol. 14: 169–176.CrossRefGoogle Scholar
  54. Dekkers, L. C., van der Bij, A. J., Mulders, I. H. M., Phoelich, C. C., Wentwoord, R. A. R., Glandorf, D. C. M., Wijffelman, C. A., and Lugtenberg, B. J. J. 1998a. Role of the O-antigen of lipopolysaccheride, and possible roles of growth rate and of NADH: ubiquinone oxidoreductase (nuo) tomato root-tip colonization by Pseudomonas fluorescens WCS365. Mol. Plant Microbe Interact. 11: 763–771.CrossRefGoogle Scholar
  55. Dekkers, L. C., Phoelich, C. C., van der Fits, L., and Lugtenberg, B. J. J. 1998b. A site specific recombinase is required for competitive root colonization by Pseudomonas fluorescens WCS365. Proc. Natl. Acad. Sci. USA 95: 7051–7056.CrossRefGoogle Scholar
  56. Dekkers, L. C., Mulders, I. H., Phoelich, C. C., Chin-A-Woeng, T. F., Wijifies, A. H., and Lugtenberg, B. J. J. 2000. The sss colonization gene of tomato-Fusarium oxysporium f. sp. radicisly copersici biocontrol strain Pseudomonas flourescence WCS365 can improve root colonization of the wild type Pseudomonas spp. bacteria. Mol. Plant Microbe Interact. 13: 1177–1183.CrossRefGoogle Scholar
  57. Dennis, P. G., Miller A. J., and Hirsch P. R. 2010. Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol. Ecol. 72: 313–327.CrossRefGoogle Scholar
  58. Di Cello, F., Beffivino, A., Chiarini, L., Fani, R., Paffetti, D., Tabacchioni, S., and Dalmastri, C. 1997. Biodiversity of a Burkholderia cepacia population isolated from the maize rhizosphere at different plant growth stages. Appl. Environ. Microbiol. 63: 4485–4493.Google Scholar
  59. Drahos, D. J., Hemming, B. C., and McPherson, S. 1986. Tracking recombinant organisms in the environment: β-galactosidase as a selectable marker for fluorescent pseudomonads. Biotechnology 4: 439–444.CrossRefGoogle Scholar
  60. Duffy, B. K. 2001. Competition. In Encyclopedia of Plant Pathology, Eds. O. C. Maloy, and T. D. Murray, pp. 243–244. John Wiley & Sons, Inc.: New York, USA.Google Scholar
  61. Duijff, B. J., Gianinazzi-Pearson, V., and Lemanceau, P. 1997. Involvement of the outer membrane lipopolysaccharides in the endophytic colonization of tomato roots by biocontrol Pseudomonas fluorescens strain WCS417r. New Phytol. 135: 325–334.CrossRefGoogle Scholar
  62. Dunn, A. K., Klimowicz, A. K., and Handelsman, J. 2003. Use of a promoter trap to identify Bacillus cereus genes regulated by tomato seed exudate and a rhizosphere resident, Pseudomonas aureofaciens. Appl. Environ. Microbiol 69: 1197–1205.CrossRefGoogle Scholar
  63. Ellenberg, J., Lippincott, S. J., and Presley, J. F. 1999. Dual colour imaging with GFP variants. Trends Cell Biol. 9: 52–56.CrossRefGoogle Scholar
  64. Errampalli, D., Leung, K., Cassidy, M. B., Kostrzynska, M., Blears, M., Lee, H., and Treffors, J. T. 1999. Applications of the green fluorescent protein as a molecular marker in environmental microorganisms. J. Microbiol. Methods 35: 187–199.CrossRefGoogle Scholar
  65. Fray, R. G., Throup, J. P., Daykin, M., Wallace A., Williams, P., Stewart, G. S. A. B., and Grierson, D. 1999. Plants genetically modified to produce N-acylhomoserive lactones communicate with bacteria. Nat. Biotechnol. 17: 1017–1020.CrossRefGoogle Scholar
  66. Gage, D. J., Bobo, T., and Long, S. R. 1996. Use of green fluorescent protein to visualize the early events of symbiosis between Rhizobium meliloti and alfalfa (Medicago sativa). J. Bacteriol. 178: 7159–7166.Google Scholar
  67. Garbeva, P., Voesenek, K., and Van Elas J. D. 2004. Quantitative detection and diversity of the pyrrolnitrin biosynthetic locus in soil under different treatments. Soil Biol. Biochem. 36: 1453–1463.CrossRefGoogle Scholar
  68. Garland, J. L. 1996. Patterns of potential C source utilization by rhizosphere communities. Soil Biol. Biochem. 28: 223–230.CrossRefGoogle Scholar
  69. Germida, J. J., Siciliano, S. D., de Freitas, J. R., and Seib, A. M. 1998. Diversity of root associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum). FEMS Microbiol. Ecol. 26: 43–50.CrossRefGoogle Scholar
  70. Grayston, S. J., Wang, S., Campbell, C. D., and Edwards, A. C. 1998. Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol. Biochem. 30: 369–378.CrossRefGoogle Scholar
  71. Greer-Phillips, S. E., Stephens, B. B., and Alexandre, G. 2004. An energy taxis transducer promotes root colonization by Azospirillum brasilense. J. Bacteriol. 186: 6595–6604.CrossRefGoogle Scholar
  72. Heim, R., Prasher, D. C., and Tsien, R. Y. 1994. Wavelength mutations and post translational autoxidation of green fluorescent protein. Proc. Natl. Acad. Sci. USA 91: 12501–12504.CrossRefGoogle Scholar
  73. Herbert, R. A. 1990. Methods for enumerating microorganisms and determining biomass in natural environments. Methods Microbiol. 129: 207–212.Google Scholar
  74. Hiltner, L. 1904. Uber neure Erfahrungen und probleme auf dem gebeit der bodenbackteriologie and unter besonderer berucksichtigung der rundungung und brache. Arb. Deut. Landwirtsch Ges. 98: 59–78.Google Scholar
  75. Hinsa, S. M., Espinosa-Urgel, M., Ramos, J. L., O’Toole, G. A. 2003. Transition from reversible to irreversible attachment during biofilm formation by Pseudomonas fluorescens WCS365 requires an ABC transporter and a large secreted protein. Mol. Microbiol. 49: 905–918.CrossRefGoogle Scholar
  76. Holben, W. E., Jansson, J. K., Cheim, B. K., and Tiedje, J. M. 1988. DNA probe methods for the detection of specific microorganisms in the soil community. Appl. Environ. Microbiol. 54: 703–711.Google Scholar
  77. Imran, M. 2009. Interaction of heavy metals with indigenous isolates of free living rhizospheric fungi and their plant growth promoting potential. Ph.D. thesis, Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India.Google Scholar
  78. Jefferson, R. A. 1989. The GUS reporter gene system. Nature 342: 835–837.CrossRefGoogle Scholar
  79. Kennedy, A. C. 1999. The rhizosphere and spermophere. In: Principles and Applications of Soil Microbiology, Eds. D. M. Sylvia, J. J. Furhrmann, P. G. Hartel, D. A. Zuberer, pp. 402–403. Prentice Hall, Inc.: New Jersey, USA.Google Scholar
  80. Klein, I., von Rad, U., and Durner, J. 2009. Homoserine lactones: do plants really listen to bacterial talk? Plant Signal. Behav. 4: 50–51.CrossRefGoogle Scholar
  81. Kloepper, J. W. 1994. Plant growth-promoting rhizobacteria (other systems). In: Azospirillum/Plant Associations, Ed. Y. Okon, pp. 111–118. CRC Press: Boca Raton, FL, USA.Google Scholar
  82. Kloepper, J. W., and Schroth, M. N. 1978. Plant growth-promoting rhizobacteria on radishes. In Station de pathologie vegetale et phyto-bacteriologie, Proceedings of the 4th International Conference on Plant Pathogenic Bacteria, vol. II, pp. 879–882. Gilbert-Clarey, Tours, France.Google Scholar
  83. Kloepper, J. W., Leong, J., Teintze, M., and Schroth, M. N. 1980. Enhanced plant growth by siderophores produced by plant growth by promoting rhizobacteria. Nature 286: 885–886.CrossRefGoogle Scholar
  84. Kloepper, J. W., Zablotowick, R. M., Tipping, E. M., and Lifshitz, R. 1991. Plant growth promotion mediated by bacterial rhizosphere colonizers. In The Rhizosphere and Plant Growth, Eds. D. L. Keister, and P. B. Cregan. Kluwer Academic Press: Dordrecht, The Netherlands.Google Scholar
  85. Kloepper, J. W., Rodriguez-Kabana, R., Zehnder, G. W., Murphy, J., Sikora, E., and Fernandez, C. 1999. Plant root–bacterial interactions in biological control of soilborne diseases and potential extension to systemic and foliar diseases. Aust. J. Plant Pathol. 28: 27–33.CrossRefGoogle Scholar
  86. Koo, J., Kim, Y., Kim, J., Yeom, M., Lee, I. C., and Nam, H. G. 2007. A GUS/luciferase fusion reporter for plant gene trapping and for assay of promoter activity with luciferin dependent control of the reporter protein stability. Plant Cell Physiol. 48: 1121–1131.CrossRefGoogle Scholar
  87. Kozaczuk, M. M., and Skorupska, A. 2001. Production of B-group vitamins by plant growth-promoting Pseudomonas fluorescens strain 267 and the importance of vitamins in the colonization and nodulation of red clover. Biol. Fertil. Soil 33: 146–151.CrossRefGoogle Scholar
  88. Kragelund, L., and Nybroe, O. 1996. Competition between Pseudomonas fluorescens Ag1 and Alcaligenes eutrophus JMP134 (pJP4) during colonization of barley roots. FEMS Microbiol. Ecol. 20: 41–51.CrossRefGoogle Scholar
  89. Laguerre, G., Rigottier-Gois, L., and Lemanceau, P. 1994. Fluorescent Pseudomonas species categorized by using polymerase chain reaction (PCR)/restriction fragment analysis of 16S rDNA. Mol. Ecol. 3: 479–487.CrossRefGoogle Scholar
  90. Lampinen, J., Koivisto, L., Wahlsten, M., Mantsila, P., and Karp, M. 1992. Expression of luciferase genes from different origins in Bacillus subtilis. Mol. Gen. Genet. 232: 498–504.CrossRefGoogle Scholar
  91. Landa, B. B., Mavrodi, O. V., Raaijmakers, J. M., Gardener, B. B. M., Thomashow, L. S., and Weller, D. M. 2002. Differential ability of genotypes of 2,4-diacetylploroglucinol producing Pseudomonas fluorescens strains to colonize the roots of pea plants. Appl. Eniron. Microbiol. 68: 3226–3237.CrossRefGoogle Scholar
  92. Larrainzar, E., O’Gara, F., and Morrisey, J. P. 2005. Applications of autofluorescent proteins for in situ studies in microbial ecology. Annu. Rev. Microbiol. 59: 257–277.CrossRefGoogle Scholar
  93. Leeman, M., Den Ouden, F. M., Van Pelt, J. A., Dirkx, F. P. M., Steijl, H., Bakker, P. A. H. M., and Schippers, B. 1996. Iron availability affects induction of systemic resistance to Fusarium wilt of radish by Pseudomonas fluorescens. Phytopathology 86: 149–155.CrossRefGoogle Scholar
  94. Lima, G., De Curtis, F., Castoria, R., and De Cicco, V. 2003. Integrated control of apple postharvest pathogens and survival of biocontrol yeasts in semi-commercial conditions. Eur. J. Plant Pathol. 109: 341–349.CrossRefGoogle Scholar
  95. Lin, M., Smalla, K., Heuer, H., and van Elsas, J. D. 2000. Effect of an Alcaligenes faecalis inoculant on bacterial communities of flooded soil microcosms planted with rice seedlings. Appl. Soil Ecol. 15: 211–225.CrossRefGoogle Scholar
  96. Lindow, S. E., and Suslow, T. V. 2003. Temporal dynamics of the biocontrol agent Pseudomonas fluorescens strain A506 in flowers in inoculated pear trees. Phytopathology 93: 727–737.CrossRefGoogle Scholar
  97. Lottmann, J., Heuer, H., de Vries, J., Mahn, A., Düring, K., Wackernagel, W., Smalla, K., and Berg, G. 2000. Establishment of introduced antagonistic bacteria in the rhizosphere of transgenic potatoes and their effect on the bacterial community. FEMS Microb. Ecol. 33: 41–49.CrossRefGoogle Scholar
  98. Lowder, M., Unge, A., Maraha, N., Jansson, J. K., Swigget, J., and Oliver, J. D. 2000. Effect of starvation and the viable-but-nonculturable state on green fluoresecent protein (GFP) flourescence in GFP-tagged Pseudomonas fluorescens A506. Appl. Environ. Microbiol. 66: 3160–3165.CrossRefGoogle Scholar
  99. Lubeck, P. S., Hansen, M., and Sorensen, J. 2000. Simultaneous detection of the establishment of seed-inoculated Pseudomonas fluorescens strain DR54 and native soil bacteria on sugar beet root surfaces using flourescence antibody and in situ hybridization techniques. FEMS Microbiol. Ecol. 33: 11–19.Google Scholar
  100. Lugtenberg, B. J. J., Dekkers, L., and Bloemberg, G. V. 2001. Molecular determinants of rhizosphere colonization by Pseudomonas. Annu. Rev. Phytopathol. 39: 461–490.CrossRefGoogle Scholar
  101. Lutenberg, B. J. J., and Dekkers, L. C. 1999. What makes Pseudomonas bacteria rhizosphere competent? Environ. Microbiol. 1: 9–13.CrossRefGoogle Scholar
  102. Lutenberg, B. J. J., Van der Bij, A., Bloemberg, G., Chin-A-Woeng, T., Dekkers, L., Kravchenko, L., Mulders, I., Phoelich, C., Simons M., Spaink H., Tikhonovich, I., de Weger L., and Wiffelman, C. 1996. Molecular basis of rhizosphere colonization by Pseudomonas bacteria. In Biology of Plant Microbe Interactions, Eds. G. Stacey, B. Mullin, and P. M. Gresshoff, pp. 433–440. ISPMB: Minnesota, USA.Google Scholar
  103. Lynch, J. M. 1990. The Rhizosphere. Ecological and Applied Microbiology. John Wiley and Sons Ltd: West Sussex, UK.Google Scholar
  104. Madigan, M. T., and Martinko, J. M. 2006. Brock Biology of Microorganism. Pearson Prentice Hall, Pearson Education, Inc.: New Jersey, USA.Google Scholar
  105. Mahaffee, W. F., Bauske, E. M., van Vuurde, J. W. L., van der Wolf, J. M., van den Brink, M., and Kloepper J. W. 1997. Comparative analysis of antibiotic resistance, immunofluorescent colony staining, and a transgenic marker (bioluminescence) for monitoring the environmental fate of a rhizobacterium. Appl. Environ. Microbiol. 63: 1617–1622.Google Scholar
  106. Martínez-Granero, F., Capdevila, S., Sánchez-Contreras, M., Martín M., and Rivilla, R. 2005. Two site-specific recombinases are implicated in phenotypic variation and competitive rhizosphere colonization in Pseudomonas fluorescens. Microbiology 151: 975–983.CrossRefGoogle Scholar
  107. Matthysse, A. G., and McMahan, S. 1998. Root colonization by Agrobacterium tumefaciens is reduced in cel, attB, attD, and attR mutant. Appl. Environ. Microbiol. 64: 2341–2345.Google Scholar
  108. Matus, A. 1999. GFP in motion CD-ROM – introduction: GFP illuminates everything. Trends Cell Biol. 9: 43.CrossRefGoogle Scholar
  109. Matz, M. M. V., Fradkov, A. F., Labas, Y. A., Savitsky, A. P., Zaraisky, A. G., Markelov, M. L., and Lukyanov, S. A. 1999. Fluorescent proteins from non-bioluminescent Anthozoa species. Nat. Biotechnol. 17: 969–973.CrossRefGoogle Scholar
  110. Mavrodi, O. V., Mavrodi, D. V., Weller, D. M., and Thomashow L. S. 2006. Role of ptsP, orfT, and sss recombinase genes in root colonization by Pseudomonas fluorescens Q8r1–96. Appl. Environ. Microbiol. 72: 7111–7122.CrossRefGoogle Scholar
  111. Mauchline, T. H., Kerry, B. R., and Hirsch, P. R. 2002. Quantification in soil and rhizosphere of nematophagous fungus Verticillium chamydosporium by competitive PCR and Comparison with selective plating. Appl. Environ. Microbiol. 68: 1846-1853.CrossRefGoogle Scholar
  112. Meighen, E. A. 1993. Bacterial bioluminescence: organization, regulation, and application of the lux genes. FASEB J. 7: 1016–1022.Google Scholar
  113. Miller, C. D., Kim, Y. C., and Anderson, A. J. 2001. Competitiveness in root colonization by Pseudomonas putida requires the rpoS gene. Can. J. Microbiol. 47: 41–48.CrossRefGoogle Scholar
  114. Montesinos, E., and Bonaterra, A. 1996. Dose response models in biological control of plant pathogen: an empirical verification. Phytopathol. 86: 464–472.CrossRefGoogle Scholar
  115. Morris, C. E., Bardin, M., Berge, O., Frey-Klett, P., Fromin, N., Girardin, H., Guinebretiere, M. H., Lebaron, P., Thiery, J. M., and Troussellier, M. 2002. Microbial biodiversity: approaches to experimental design and hypothesis testing in primary scientific literature from 1975 and 1999. Microbiol. Mol. Biol. Rev. 66: 592–616.CrossRefGoogle Scholar
  116. Nautiyal, C. S. 2000. Plant beneficial rhizosphere competent bacteria. Proc. Natl Acad. Sci. India 70: 11.Google Scholar
  117. Normander, B., Hendriksen, N. B., and Nybroe, O. 1999. Green fluorescent protein-marked Pseudomonas flourescences: localization, viability and activity in the natural barley rhizosphere. Appl. Environ. Microbiol. 65: 4646–4651.Google Scholar
  118. Nuclo, R. L., Johnson, K. B., Stockwell, V. O., and Sugar, D. 1998. Secondary colonization of pear blossoms by two bacterial antagonists of the fire blight pathogen. Plant Dis. 82: 661–668.CrossRefGoogle Scholar
  119. Ozaktan, H., and Bora, T. 2004. Biological controlo of fire blight in pear orchards with a formulation of Pantoea agglomerans strain Eh24. Braz. J. Microbiol. 35: 224–229.CrossRefGoogle Scholar
  120. Pallai, R. 2005. Effect of plant growth-promoting rhizobacteria on canola (Brassica napus. l) and lentil (Lens culinaris. medik) plants. Ph.D. thesis, University of Saskatchewan, Saskatoon.Google Scholar
  121. Palomares, A. J., Cebolla, A., Caviedes, M. A., Sanchez, B., Rodriguez, D., Munoz, J. A., Coronado, C., and Ruiz-Berraquero, F. 1991. Firefly luciferase expression on nitrogen fixation with non-legumes. In Nitrogen Fixation, Eds. M. Posinelli, R. Marterassi, and M. Vicenzini, pp. 275–281. Kluwer Academic Publishers: Dordrecht, The Netherlands.Google Scholar
  122. Parke, J. L. 1991. Root colonization by indigenous and introduced microorganisms. In The Rhizosphere and Plant Growth, Eds. D. L. Keister, and P. B. Gregan, pp. 33–42. Kluwer Academic Publishers: Dordrecht, The Netherlands.Google Scholar
  123. Parsek, M. R., Fuqua, C. 2004. Biofilms: emerging themes and challenges in studies of surface-associated microbial life. J. Bacteriol. 186: 4427–4440.CrossRefGoogle Scholar
  124. Paulitz, T. C. 2000. Population dynamics of biocontrol agents and pathogen in soil and rhizosphere. Eur. J. Plant Pathol. 106: 401–413.CrossRefGoogle Scholar
  125. Persello-Cartieaux, F., Nussaume, L., and Robaglia, C. 2003. Tales from the underground: molecular plant–rhizobacteria interactions. Plant Cell Environ. 26: 189–199.CrossRefGoogle Scholar
  126. Pickup, R. W. 1991. Development of molecular methods for the detection of specific bacteria in the environment. J. Gen. Microbiol. 137: 1009–1019.Google Scholar
  127. Pierson, E. A., Wood, D. W., Cannon, J. A., Blachere, F. M., and Pierson III, L. S. 1998. Interpopulation signaling via N-acyl-homoserine lactones among bacteria in the wheat rhizosphere. Mol. Plant Microbe Interact. 11: 1078–1084.CrossRefGoogle Scholar
  128. Pillay, V. K., and Nowak, J. 1997. Inoculum density, temperature and genotype effects on in vitro growth promotion and epiphytic and enophytic colonization of tomato (Lypersicon esculeuntum L.) seedlings inoculated with a pseudomonad bacterium. Can. J. Microbiol. 43: 354–361.CrossRefGoogle Scholar
  129. Raaijmakers, J. M., and Weller, D. M. 2001. Exploiting genotypic diversity of 2,4-diacetylphloroglucinol-producing Pseudomonas spp: characterization of superior root-colonizing P. fluorescens strain Q8r1–96. Appl. Environ. Microbiol. 67: 2545–2554.CrossRefGoogle Scholar
  130. Rainey, P. B. 1999. Adaption of Pseudomonas fluorescens to the plant rhizosphere. Environ. Microbiol. 1: 243–257.CrossRefGoogle Scholar
  131. Ramey, B. E., Koutsoudis, M., von Bodman, S. B., and Fuqua, C. 2004. Biofilm formation in plant–microbe associations. Curr. Opin. Microbiol. 7: 602–609.CrossRefGoogle Scholar
  132. Raupach, G. S., and Kloepper J. W. 1998. Mixtures of plant growth-promoting rhizobacteria enhance biological control of multiple cucumber pathogens. Phytopathology 88: 1158–1164.CrossRefGoogle Scholar
  133. Rediers, H., Rainey, P. B., Vanderleyden, J., and De Mot, R. 2005. Unraveling the secret lives of bacteria: use of in vivo expression technology and differential flourescence induction promoter traps as tools for exploring niche specific gene expression. Microbiol. Mol. Biol. Rev. 69: 217–261.CrossRefGoogle Scholar
  134. Rezzonico, F., Moenne-Loccoz, Y., and Defago, G. 2003. Effect of stress on the ability of a phlA-based quantitative competitive PCR assay to monitor biocontrol strain Pseudomonas fluorescens CHA0. Appl. Environ. Microbiol. 69: 686–690.CrossRefGoogle Scholar
  135. Roberts, D. P., Dery, P. D., Yucel, I., Buyer, J. S., Holtman, M. A., and Kobayashi, D. Y. 1999. Role of pfkA and general carbohydrate catabolism in seed colonization by Enterobacter cloacae. Appl. Environ. Microbiol. 65: 2513–2519.Google Scholar
  136. Rochat, L., Péchy-Tarr, M., Baehler, E., Maurhofer, M., and Keel C. 2010. Combination of fluorescent reporters for simultaneous monitoring of root colonization and antifungal gene expression by a biocontrol pseudomonad on cereals with flow cytometry. Mol. Plant Microbe Interact. 23: 949–961.CrossRefGoogle Scholar
  137. Rondon, M. R., Goodman, R. M., and Handelsman, J. 1999. The earth’s bounty: assessing and accessing soil microbial diversity. Trends Biotechnol. 17: 403–409.CrossRefGoogle Scholar
  138. Rothballer, M., Schmid, M., and Hartmann, A. 2003. In situ localization and PGPR effect of Azospirillum brasilense strains colonizing roots of different wheat varieties. Symbiosis 34: 261–279.Google Scholar
  139. Rovira, A. D. 1965. Interactions between plant roots and soil microorganisms. Annu. Rev. Microbiol. 19: 241–266.CrossRefGoogle Scholar
  140. Rubio, M. B., Hermosa, M. R., Keck, E., and Monte, E. 2005. Specific PCR assays for the detection and quantification of DNA from the biocontrol strain Trichoderma harzianum 2413 in soil. Microb. Ecol. 49: 1646–1650.CrossRefGoogle Scholar
  141. Rudrappa, T., Biedrzycki, M. L., and Bais, H. P. 2008. Causes and consequences of plant associated biofilms. FEMS Microbiol. Ecol. 64: 153–166.CrossRefGoogle Scholar
  142. Ruppel, S., Ru¨hlmann, J., and Merbach, W. 2006. Quantification and localization of bacteria in plant tissues using quantitative real-time PCR and online emission fingerprinting. Plant Soil 286: 21–35.CrossRefGoogle Scholar
  143. Russek, E., and Colwell, R. R. 1983. Computation of the most probable number. Appl. Environ. Microb. Ecol. 49: 25–33.Google Scholar
  144. Sa´nchez-Contreras, M., Martı´n, M., Villacieros, M., O’Gara, F., Bonilla, I., and Rivilla, R. 2002. Phenotypic selection and phase variation occur during alfalfa root colonization by Pseudomonas fluorescens F113. Appl. Environ. Microbiol. 184: 1587–1596.Google Scholar
  145. Schena, L., Nigro, F., Ippolito, A., and Gallitelli, D. 2004. Real-time quatitative PCR: a new technology to detect and study phytopathogenic and antagonistic fungi. Eur. J. Plant Pathol. 110: 893–908.CrossRefGoogle Scholar
  146. Schroth, M. N., and Hancock, J. G. 1982. Disease-suppressive soil and root-colonizing bacteria. Science 216: 1376–1381.CrossRefGoogle Scholar
  147. Scott, R. A., Weil, J., Le, P. T., Williams, P., Fray, R., von Bodman, S., and Savka, M. A. 2006. Long- and short-chain plant produced bacterial N-acylhomoserine lactones become components of the phyllosphere, rhizosphere and soil. Mol. Plant Microbe Interact. 19: 227–239.CrossRefGoogle Scholar
  148. Shaner, N. C., Campbell, R. E., Steinbach, P. A., Giepmans, B. N. G., Palmer, A. E., and Tsien, R. Y. 2004. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22: 1567–1572.CrossRefGoogle Scholar
  149. Sharma, A., Sahgal, M., and Johri, B. N. 2003. Microbial communication in the rhizosphere: operation of quorum sensing. Curr. Sci. 85: 1164–1172.Google Scholar
  150. Siddiqui, Z. A. 2004. Effects of plant growth promoting bacteria and composed organic fertilizers on the reproduction of Meloidogyne incognita and tomato growth. Bioresour. Technol. 95: 223–227.CrossRefGoogle Scholar
  151. Siddiqui, Z. A. 2006. PGPR: prospective biocontrol agents of plant pathogens. In PGPR: Biocontrol and Biofertilization, Ed. Z. A. Siddiqui, pp. 111–142. Springer: The Netherlands.CrossRefGoogle Scholar
  152. Simons, M., van der Bij, A. J., de Weger, L. A., Wijffelman, C. A., and Lugtenberg, B. J. 1996. Gnotobiotic system for studying rhizosphere colonization by plant growth promoting Pseudomonas bacteria. Mol. Plant Microbe Interact. 9: 600–607.CrossRefGoogle Scholar
  153. Simons, M., Permentier, H. P., De Weger, L. A., Wijffelman, C. A., and Lugtenberg, B. J. J. 1997. Amino acid synthesis is necessary for tomato root colonization by Pseudomonas flourescences strain WCS365. Mol. Plant Microbe Interact. 10: 102–106.CrossRefGoogle Scholar
  154. Smalla, K., Wieland, G., Buchner, A., Zock, A., Parzy, J., Kaiser, S., Roskot, N., Heuer, H., and Berg, G. 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.CrossRefGoogle Scholar
  155. Somers, E., and Vanderleyden, J. 2004. Rhizosphere bacterial signaling: a love parade beneath our feet. Crit. Rev. Microbiol. 30: 205–240.CrossRefGoogle Scholar
  156. Sørensen, J., and Nybroe, O. 2006. Reporter genes in bacterial inoculants can monitor life conditions and functions in soil. In Nucleic Acids and Proteins in Soil, Eds. P. Nannipieri, and S. Kornelia, pp. 375–395. Springer-verlag: Berlin, Heidelberg, Germany.CrossRefGoogle Scholar
  157. Sørensen, J., Jensen, L. E., and Nybroe, O. 2001. Soil and rhizosphere as habitats for Pseudomonas inoculants: new knowledge on distribution, activity and physiological state derived from micro-scale and single-cell studies. Plant Soil 232: 97–108.CrossRefGoogle Scholar
  158. Sorensen, M., Lippuner, C., Kaiser, T., Misslitz, A., Aebischer, T., and Bumann, D. 2003. Rapidly maturing red fluorescent protein variants with strongly enhanced brightness in bacteria. FEBS Lett. 552: 110–114.CrossRefGoogle Scholar
  159. Sørensen, J., Nicolaisen, M. H., Ron, E., and Simonet, P. 2009. Molecular tools in rhizosphere microbiology—from single-cell to whole-community analysis. Plant Soil 321: 483–512CrossRefGoogle Scholar
  160. Southward, C. M., and Surette, M. G. 2002. The dynamic microbe: green fluorescent protein brings bacteria to light. Mol. Microbiol. 45: 1191.CrossRefGoogle Scholar
  161. Steddom, K., Menge, J. A., Crowley, D., and Borneman, J. 2002. Effect of repetititve applications of the biocontrol bacterium Pseudomonas putida 06909-rif/nal on citrus soil microbial communities. Phytopathology 92: 857–862.CrossRefGoogle Scholar
  162. Steenhoudt, O., and Vanderleyden, J. 2000. Azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: genetic, biochemical and ecological aspects. FEMS Microbiol. Rev. 24: 487–506.CrossRefGoogle Scholar
  163. Steffan, R. J., and Atlas, R. M. 1988. DNA amplification to enhance the detection of genetically engineered bacteria in environmental samples. Appl. Environ. Microbiol. 54: 2185–2191.Google Scholar
  164. Strom, M. S., and Lory, S. 1993. Structure–function and biogenesis of the type IV pili. Annu. Rev. Microbiol. 30: 565–596.CrossRefGoogle Scholar
  165. Stuurman, N., Pacios Bras, C., Schlaman, C. H. R. M., Wijfjes, A. H. M., Bloemberg, G. V., and Spaink, H. P. 2000. The use of GFP color variants expressed on stable broad-host range vectors to visualize rhizobia interacting with plants. Mol. Plant Microbe Interact. 13: 1063–1069.CrossRefGoogle Scholar
  166. Sundin, P. 1990. Plant root exudates in interaction between plant and soil microorganisms. Ph. D. thesis, Lund University, SwedenGoogle Scholar
  167. Sylvia, D. M., Fuhrman, J. J., Hartel, P. G., and Zuberer, D. A. 1999. Principles and Applications of Soil Microbiology, pp. 35–38. Prentice Hall: New Jersey, USA.Google Scholar
  168. Tans-Kersten, J., Huang, H., and Allen, C. 2001. Ralstonia solanacearum needs motility for invasive virulence on tomato. J. Bacteriol. 183: 3597–3605.CrossRefGoogle Scholar
  169. Timmusk, S., Grantcharova, N., Gerhart E., and Wagner H. 2005. Paenibacillus polymyxa invades plant roots and forms biofilms. Appl. Environ. Microbiol. 71: 7292–7300CrossRefGoogle Scholar
  170. Tombolini, R., Van Der Gaag, D. J., Gerhardson, B., and Jansson, J. K. 1999. Colonization pattern of the biocontrol strain Pseudomonas chlororaphis MA 342 on barley seeds vizualized by using green fluorescent protein. Appl. Environ. Microbiol. 65: 3674–3680.Google Scholar
  171. Troxler, J., Zala, M., Natsch, A., Moënne-Loccoz, Y., and Défago, G. 1997. Autecology of the biocontrol strain Pseudomonas fluorescens CHA0 in the rhizosphere and inside roots at later stages of plant development. FEMS Microbiol. Ecol. 23: 119–130.CrossRefGoogle Scholar
  172. Tsien, R. Y. 1998. The green fluorescent protein. Annu. Rev. Biochem. 67: 509–544.CrossRefGoogle Scholar
  173. Tsuchiya, K., Homma, Y., Komoto, Y., and Susui, T. 1995. Practical detection of Pseudomonas cepacia from rhizosphere antagonistic to plant pathogens with a combination of selective media and ELISA. Ann. Phytopathol. Soc. Japan 61: 318–324.Google Scholar
  174. Tunlid, A., and White, D. 1992. Biochemical analysis of biomass, community structure, nutritional status, and metabolic activity of microbial communities in soil. In: Soil Biochemistry, vol. 7, Eds. G. Stotzky, and J. M. Bollag, pp. 229–262. Marcel Dekker Inc.: New York, USA.Google Scholar
  175. Unge, A., Tombolini, R., Molbak, L., and Jansson, J. K. 1999. Simultaneous monitoring of cell number and metabolic activity of specific bacterial populations with dual gfp-luxAB marker system. Appl. Environ. Microbiol. 65: 813–821.Google Scholar
  176. Urbanczyk, H., Ast, J. C., Kaeding, A. J., Oliver, J. D., and Dunlap P. V. 2008. Phylogenetic analysis of the incidence of lux gene horizontal transfer in vibrionaceae. J. Bacteriol. 190: 3494–3504.CrossRefGoogle Scholar
  177. Uren, N. C. 2000. Types, amounts, and possible functions of compunds released into the rhizosphere by soil-grown plants. In The Rhizosphere: Biochemistry and Organic Substances at the Soil–Plant Interface, Eds. R. Pinton, Z. Varanini, and P. Nannipieri, pp. 19–40. Marcel Dekker Inc.: New York, USA.Google Scholar
  178. Utermark, J., and Karlovsky, P. 2006. Quantification of green fluorescent protein flourescence using real-time PCR thermal cycler. Biotechniques 41: 150–154.CrossRefGoogle Scholar
  179. Van der Broek, D., Chin-A-Woeng, T. F. C., Eijkemans, K., Mulders, I. H. M., Bloemberg, G. V., and Lugtenberg, B. J. J. 2003. Biocontrol traits of Pseudomonas spp. are regulated by phase variation. Mol. Plant Microbe Interact. 16: 1003–1012.CrossRefGoogle Scholar
  180. Van Elsas J. D., Trevors, J. T., and Starodub, M. E. 1998. Bacterial conjugation between pseudomonads in the rhizosphere of wheat. FEMS Microbiol. Lett. 53: 299–306.CrossRefGoogle Scholar
  181. Van vurude, J. W. L., and Van-DerWolf, J. M. 1995. Immunoflourescence colonoy staining (IFC). In Molecular Microbial Ecology, Eds. A. D. L. Manual Akkermans, J. D. Van Elsas, and F. J. De Bruin. Kluwer Academics: Dordrecht, The Netherlands.Google Scholar
  182. vande Broek, A., and Venderleyden, J. 1995. The role of bacterial motility, chemotaxis, and attachment in bacterial–plant interactions. Mol. Plant Microbe Interact. 8: 80–810.CrossRefGoogle Scholar
  183. Walker, T. S., Bais, H. P., Grotewold, E., and Vivanco, J. M. 2003. Root exudation and rhizosphere biology. Plant Physiol. 132: 44–51.CrossRefGoogle Scholar
  184. Walker, T. S., Bais, H. P., Deziel, E., Schweitzer, H. P., Rahme, L. G., Fall, R., and Vivanco, J. M. 2004. Pseudomonas aeruginosa–plant root interactions. Pathogenicity, biofilm formations, and root exudation. Plant Physiol. 134: 3210–3331.CrossRefGoogle Scholar
  185. Webb, J. S., Givskov, M., and Kjelleberg, S. 2003. Bacterial biofilms: prokaryotic adventures in multicellularity. Curr. Opin. Microbiol. 6: 578–585.CrossRefGoogle Scholar
  186. Wei, H. L., and Zhang L. Q. 2006. Quorum-sensing system influences root colonization and biological control ability in Pseudomonas fluorescens 2P24. Anton van Leeuwenhoek 89: 267–280.CrossRefGoogle Scholar
  187. Weller, D. M. 1983. Colonization of wheat roots by a flourescent pseudomonads suppressive to take-all. Phytopathology 73: 1548–1553.CrossRefGoogle Scholar
  188. Williams, P. 2007. Quorum sensing, communication and cross-kingdom signalling in the bacterial world. Microbiology 153: 3923–3938.CrossRefGoogle Scholar
  189. Wilson, K. J., Sessitsch, A., and Akkermans, A. 1994. Molecular markers as tools to study the ecology of microorganisms. In Beyond the Biomass, Eds. K. Ritz, J. Dighton, and K. E Giller, pp. 149–156. British Society of Soil Science: London.Google Scholar
  190. Wilson, K. J., Sessitsch, A., Corbo, J. C. Giller, K. E., Akkermans, A. D. L., and Jefferson, R. A. 1995. β-glucuronidase (GUS) transposons for ecological and genetic studies of rhizobia and other gram negative bacteria. Microbiology 141: 1691–1705.CrossRefGoogle Scholar
  191. Wood, K., Amy Lam, Y., Seliger, H. H., and McElroy, W. 1989. Complementary DNA coding click beetle luciferases can elicit bioluminescence of different colors. Science 244: 700–702.CrossRefGoogle Scholar
  192. Yang, T. T., Sina, P., Green, G., Kitts, P. A., Chen, Y. T., Lybarger, L., Chervenak, R., Patterson, G. H., Piston, D. W., and Kain, S. R. 1998. Improved flourescence and dual color detection with enhanced blue and green variants of the green fluorescent protein. J. Biol. Chem. 273: 8212–8216.CrossRefGoogle Scholar
  193. Zhang, L., Liu, X., Zhu, S., and Chen, S. 2006. Detection of nematophagous fungus Hirustella rhossiliensis in soil by real-time PCR and parasitism bioassay. Bio. Control. 36: 316–323.CrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.Department of MicrobiologySardar Bhagwan Singh Post Graduate Institute of Biomedical Sciences and ResearchDehradunIndia

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