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Rhizosphere: A Home for Human Pathogens

  • Richa Sharma
  • V. S. Bisaria
  • Shilpi SharmaEmail author
Chapter

Abstract

Rhizosphere is the zone where the microbe-mediated processes are influenced by root exudates. Owing to its high nutrient content due to root exudates, and ability to provide a safe home, it acts as a natural reservoir to not only beneficial bacteria but also to those which can be potential threat for humans, and hence acts as a ‘microbial hot spot’. There has been an increase in incidences of human infections by opportunistic human pathogens residing in the rhizosphere. Many bacterial species are known to have dual interactions with both plants and humans. These bacterial species share similar colonization mechanisms for the rhizosphere and human organs. Other phenomena of common occurrence in rhizosphere are the higher rate of horizontal gene transfer, enhanced competition, and presence of various antibiotics resulting in greater level of natural resistances. The present chapter highlights the prevalence and concern of human pathogens residing in the rhizosphere.

Keywords

Rhizosphere Opportunistic human pathogens Horizontal gene transfer Microbial hot spot 

Notes

Acknowledgements

The study was supported by grant received from the Department of Biotechnology, Government of India (BT/PR5499/AGR/21/355/2012). RS wishes to acknowledge the fellowship received from CSIR, Government of India.

References

  1. Barret M, Morrissey JP, O’Gara F (2011) Functional genomics analysis of plant growth-promoting rhizobacterial traits involved in rhizosphere competence. Biol Fertil Soils 47:729–743CrossRefGoogle Scholar
  2. Berg G (2009) Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. J Appl Microbiol Biotechnol 84:8–11CrossRefGoogle Scholar
  3. Berg G, Knaape C, Ballin G, Seidel D (1994) Biological control of Verticillium dahliae KLEB by naturally occurring rhizosphere bacteria. Arch Phytopathol Dis Protect 29:249–262CrossRefGoogle Scholar
  4. Berg G, Marten P, Ballin G (1996) Stenotrophomonas maltophilia in the rhizosphere of oilseed rape – occurrence, characterization and interaction with phytopathogenic fungi. Microbiol Res 151:19–27CrossRefGoogle Scholar
  5. Berg G, Roskot N, Smalla K (1999) Genotypic and phenotypic relationship in clinical and environmental isolates of Stenotrophomonas maltophilia. J Clin Microbiol 37:3594–3600PubMedPubMedCentralGoogle Scholar
  6. Berg G, Roskot N, Steidle A, Eberl L, Zock A, Smalla K (2002) Plant-dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different Verticillium host plants. Appl Environ Microbiol 68:3328–3338CrossRefPubMedPubMedCentralGoogle Scholar
  7. Berg G, Eberl L, Hartmann A (2005) The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ Microbiol 71:4203–4213CrossRefGoogle Scholar
  8. Berg G, Zachow C, Cardinale M, Műller H (2010) Ecology and human pathogenicity of plant-associated bacteria. In: Ehlers RU (ed) Regulation of biological control agents. Springer, Berlin, pp 175–189Google Scholar
  9. Bernier SP, Silo-Suh L, Woods DE, Ohman DE, Sokol PA (2003) Comparative analysis of plant and animal models for characterization of Burkholderia cepacia virulence. Infect Immun 71:5306–5313CrossRefPubMedPubMedCentralGoogle Scholar
  10. Binks PR, Nicklin S, Bruce NC (1995) Degradation of RDX by Stenotrophomonas maltophilia PB1. Appl Environ Microbiol 61:1813–1322Google Scholar
  11. Bonkowski M, Villenave C, Griffiths B (2009) Rhizosphere fauna: the functional anö structural diversity of intimate interactions of soil fauna with plant roots. Plant Soil 321:213–233CrossRefGoogle Scholar
  12. Bulgarelli D et al (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95CrossRefPubMedPubMedCentralGoogle Scholar
  13. Cao H, Baldini RL, Rahme LG (2001) Common mechanisms for pathogens of plants and animals. Annu Rev Phytopathol 39:259–284CrossRefPubMedPubMedCentralGoogle Scholar
  14. Chelius MK, Triplett EW (2000) Immunolocalization of dinitrogenase reductase produced by Klebsiella pneumoniae in association with Zea mays L. Appl Environ Microbiol 66:783–787CrossRefPubMedPubMedCentralGoogle Scholar
  15. Cheuk W, Woo PCY, Yuen KY, Yu PH, Chan JKC (2000) Intestinal inflammatory pseudotumour with regional lymph node involvement: identification of a new bacterium as the etiological agent. J Pathol 192:289–292CrossRefPubMedPubMedCentralGoogle Scholar
  16. Coenye T, Vandamme P (2003) Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ Microbiol 5:719–729CrossRefGoogle Scholar
  17. Cook RJ, Tomashow LS, Weller DM, Fujimoto D, Mazzola M, Bangera G, Kim DS (1995) Molecular mechanisms of defense by rhizobacteria against root disease. Proc Natl Acad Sci U S A 92:4197–4201CrossRefPubMedPubMedCentralGoogle Scholar
  18. Cooley MB, Miller WG, Mandrell RE (2003) Colonization of Arabidopsis thaliana with Salmonella enterica and enterohemorrhagic Escherichia coli O157:H7 and competition by Enterobacter asburiae. Appl Environ Microbiol 69:4915–4926CrossRefPubMedPubMedCentralGoogle Scholar
  19. Coutinho TH, Venter SN (2009) Pathogen profile. Pantoea ananatis: an unconventional plant pathogen. Mol Plant Pathol 10:325–335CrossRefPubMedPubMedCentralGoogle Scholar
  20. Critzer FJ, Doyle MP (2010) Microbial ecology of foodborne pathogens associated with produce. Curr Opin Biotechnol 21:125–130CrossRefPubMedPubMedCentralGoogle Scholar
  21. Cruz AT, Andreea C, Allen CH (2007) Pantonea agglomerans, a plant pathogen causing human disease. J Clin Microbiol 45:1989–1992CrossRefPubMedPubMedCentralGoogle Scholar
  22. Dalmastri C, Chiarini L, Cantale C, Bevivino A, Tabacchioni S (1999) Soil type and maize cultivar affect the genetic diversity of maize root-associated Burkholderia cepacia populations. Microb Ecol 38:273–284CrossRefPubMedPubMedCentralGoogle Scholar
  23. De Souza JT, De Boer M, De Waard P, Van Beek TA, Raaijmakers JM (2003) Biochemical, genetic, and zoosporicidal properties of cyclic lipopeptide surfactants produced by Pseudomonas fluorescens. Appl Environ Microbiol 69:7161–7172CrossRefPubMedPubMedCentralGoogle Scholar
  24. Delmotte N et al (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. P Natl Acad Sci USA 106:16428–16433CrossRefGoogle Scholar
  25. Dennis PG, Miller AJ, Hirsch PR (2010) Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol Ecol 72:313–327CrossRefPubMedPubMedCentralGoogle Scholar
  26. Denton M, Kerr KG (1998) Microbiological and clinical aspects of infections associated with Stenotrophomonas maltophilia. Clin Microbiol Rev 11:7–80CrossRefGoogle Scholar
  27. Dörr J, Hurek T, Reinhold-Hurek B (1998) Type IV pili are involved in plant–microbe and fungus–microbe interactions. Mol Microbiol 30:7–17CrossRefPubMedPubMedCentralGoogle Scholar
  28. Dowe MJ, Jackson ED, Mori JG, Bell CR (1997) Listeria monocytogenes survival in soil and incidence in agricultural soils. J Food Prot 60:1201–1207CrossRefPubMedPubMedCentralGoogle Scholar
  29. Eberl L, Vandamme P (2016) Members of the genus Burkholderia: good and bad guys. F1000 Res 5: 1–10Google Scholar
  30. Eckburg PB, Relman DA (2007) The role of microbes in Crohn’s disease. Clin Infect Dis 44:256–262CrossRefGoogle Scholar
  31. Fravel DR (1988) Role of antibiosis in the biocontrol of plant diseases. Annu Rev Phytopathol 26:75–91CrossRefGoogle Scholar
  32. Germida JJ, Siciliano SD (2001) Taxonomic diversity of bacteria associated with the roots of modern, recent and ancient wheat cultivars. Biol Fertil Soils 33:410–415CrossRefGoogle Scholar
  33. Goris J, Boon N, Lebbe L, Verstraete W, De Vos P (2003) Diversity of activated sludge bacteria receiving the 3-chloroaniline degradative plasmid pC1gfp. FEMS Microbiol Ecol 46:221–230CrossRefPubMedPubMedCentralGoogle Scholar
  34. Govan JRW, Hughes JE, Vandamme P (1996) Burkholderia cepacia: medical, taxonomic and ecological issues. J Med Microbiol 45:395–407CrossRefPubMedPubMedCentralGoogle Scholar
  35. Govan JRW, Balendreau J, Vandamme P (2000) Burkholderia cepacia – friend and foe. ASM News 66:124–125Google Scholar
  36. Graner G, Persson P, Meijer J, Alstrøm S (2003) A study on microbial diversity in different cultivars of Brassica napus in relation to its wilt pathogen, Verticillium longisporum. FEMS Microbiol Lett 29:269–276CrossRefGoogle Scholar
  37. Gupta CP, Sharma A, Dubey RC, Maheshwari DK (2001) Effect of metal ions on growth of Pseudomonas aeruginosa and siderophore and protein production. Indian J Exp Biol 39:1318–1321PubMedPubMedCentralGoogle Scholar
  38. Gyaneshwar P, James EK, Mathan N, Reddy PM, Reinhold-Hurek B, Ladha JK (2001) Endophytic colonization of rice by a diazotrophic strain of Serratia marcescens. J Bacteriol 183:2634–2645CrossRefPubMedPubMedCentralGoogle Scholar
  39. Hacker J, Hentschel U, Dobrindt U (2003) Prokaryotic chromosomes and diseases. Science 301:790–793CrossRefGoogle Scholar
  40. Hadley WM et al (1987) Five month oral (diet) toxicity/infectivity study of Bacillus thuringiensis insecticides in sheep. Fundam Appl Toxicol 8:236–242CrossRefGoogle Scholar
  41. Hartmann A, Gantner S, Schuhegger R, Steidle A, Dürr C, Schmid M et al (2004) N-acyl homoserine lactones of rhizosphere bacteria trigger systemic resistance in tomato plants. In: Lugtenberg B, Tikhonovich I, Provorov N (eds) Biology of molecular plant–microbe interactions, vol 4. MPMI, St Paul, MN, pp 554–556Google Scholar
  42. Hartmann A, Schmid M, van Tuinen D, Berg G (2009) Plant-driven selection of microbes. Plant Soil 321:235–257CrossRefGoogle Scholar
  43. Hauben L, Vauterin L, Moore ERB, Hoste M, Swings J (1999) Genomic diversity of the genus Stenotrophomonas. Int J Syst Bacteriol 49:1749–1760CrossRefGoogle Scholar
  44. Hebbar KP, Martel MH, Heulin T (1998) Suppression of pre- and postemergence damping-off in corn by Burkholderia cepacia. Europ J Plant Pathol 104:29–36CrossRefGoogle Scholar
  45. Hinsinger P, Marschner P (2006) Rhizosphere – perspectives and challenges – a tribute to Lorenz Hiltner. Plant Soil 283:vii–viiiCrossRefGoogle Scholar
  46. Hinsinger P, Bengough AG, Vetterlein D, Young IM (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant Soil 321:117–152CrossRefGoogle Scholar
  47. Holden N, Pritchard L, Toth I (2009) Colonization outwith the colon: plants as an alternative environmental reservoir for human pathogenic enterobacteria. FEMS Microbiol Rev 33:689–703CrossRefGoogle Scholar
  48. Holmes A, Govan J, Goldstein R (1998) Agricultural use of Burkholderia (Pseudomonas) cepacia: a threat to human health? Emerg Infect Dis 4:221–227CrossRefPubMedPubMedCentralGoogle Scholar
  49. Ikemoto S, Suzuki K, Kaneko T, Komagata K (1980) Characterization of strains of Pseudomonas maltophilia which do not require methionine. Int J Syst Bacteriol 30:437–447CrossRefGoogle Scholar
  50. Jelveh N, Cunha BA (1999) Ochrobactrum anthropic bacteremia. Heart Lung 28:145–146CrossRefGoogle Scholar
  51. Jensen GB, Hansen MB, Eilenberg J, Maillon J (2003) The hidden lifestyle of Bacillus cereus and relatives. Environ Microbiol 5:631–640CrossRefGoogle Scholar
  52. Jones DL, Nguyen C, Finlay RD (2009) Carbon flow in the rhizosphere: carbon trading at the soil-root interface. Plant Soil 321:5–33CrossRefGoogle Scholar
  53. Juhas M, vander Meer JR, Gaillard M, Harding RM, Hood DW, Crook DW (2009) Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 33:376–393CrossRefGoogle Scholar
  54. Kaestli M et al (2012) Out of the ground: aerial and exotic habitats of the melioidosis bacterium Burkholderia pseudomallei in grasses in Australia. Environ Microbiol 14:2058–2070CrossRefGoogle Scholar
  55. Kang YW, Carlson R, Tharpe W, Schell MA (1998) Characterization of genes involved in biosynthesis of a novel antibiotic from Burkholderia cepacia BC11 and their role in biological control of Rhizoctonia solani. Appl Environ Microbiol 64:3939–3947PubMedPubMedCentralGoogle Scholar
  56. Klerks MM, Franz E, van Gent-Pelzer M, Zijlstra C, van Bruggen AHC (2007) Differential interaction of Salmonella enterica serovars with lettuce cultivars and plant–microbe factors influencing the colonization efficiency. ISME J 1:620–631CrossRefGoogle Scholar
  57. Knief C et al (2011) Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6:1378–1390CrossRefPubMedPubMedCentralGoogle Scholar
  58. Knudsen GR, Walter MV, Porteous LA, Prince VJ, Amstrong JL, Seidler RJ (1988) Predictive model of conjugated plasmid transfer in the rhizosphere and phyllosphere. Appl Environ Microbiol 54:343–347PubMedPubMedCentralGoogle Scholar
  59. Kobayashi DY, Gugliemoni M, Clarke BB (1995) Isolation of chitinolytic bacteria Xanthomonas maltophilia and Serratia marcescens as biological control agents for summer patch disease of turf grass. Soil Biol Biochem 27:1479–1487CrossRefGoogle Scholar
  60. Krechel A, Faupel A, Hallmann J, Ulrich A, Berg G (2002) Potato-associated bacteria and their antagonistic potential towards plant pathogenic fungi and the plant parasitic nematode Meloidogyne incognita (Kofoid and White) Chitwood. Can J Microbiol 48:772–786CrossRefGoogle Scholar
  61. Kumar A, Munder A, Aravind R, Eapen SJ, Tűmmler B, Raaijmakers JM (2013) Friend or foe: genetic and functional characterization of plant endophytic Pseudomonas aeruginosa. Environ Microbiol 15:764–779CrossRefGoogle Scholar
  62. Lambert B, Frederik L, Van Rooyen L, Gossele F, Papon Y, Swings J (1987) Rhizobacteria of maize and their antifungal activities. Appl Environ Microbiol 53:1866–1871PubMedPubMedCentralGoogle Scholar
  63. Lee EY, Jun YS, Cho KS, Ryu HW (2002) Degradation characteristics of toluene, benzene, ethylbenzene, and xylene by Stenotrophomonas maltophilia T3-c. J Air Waste Manag Assoc 52:400–406CrossRefGoogle Scholar
  64. Lottmann J, Berg G (2001) Phenotypic and genotypic characterization of antagonistic bacteria associated with roots of transgenic and non-transgenic potato plants. Microbiol Res 156:75–82CrossRefGoogle Scholar
  65. Lottmann J, Heuer H, Smalla K, Berg G (1999) Influence of transgenic T4-lysozyme-producing plants on beneficial plant-associated bacteria. FEMS Microb Ecol 29:365–377CrossRefGoogle Scholar
  66. Lugtenberg BJJ, Dekkers LC (1999) What makes Pseudomonas bacteria rhizosphere competent? Environ Microbiol 1:9–13CrossRefPubMedPubMedCentralGoogle Scholar
  67. Lundberg DS et al (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90CrossRefPubMedPubMedCentralGoogle Scholar
  68. Lynch JM (1990) Introduction: some consequences of microbial rhizosphere competence for plant and soil. In: Lynch JM (ed) The Rhizosphere. Wiley, Chichester, pp 1–10Google Scholar
  69. Mark GL et al (2005) Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe–plant interactions. P Natl Acad Sci USA 102:17454–17459CrossRefGoogle Scholar
  70. Meeting FB (1992) Soil microbial ecology: applications in agricultural and environmental management. Marcel Dekker, New YorkGoogle Scholar
  71. Mehnaz S, Mirza MS, Haurat J, Bally R, Normand P, Bano A, Malik KA (2001) Isolation and 16S rRNA sequence analysis of the beneficial bacteria from the rhizosphere of rice. Can J Microbiol 47:110–117CrossRefGoogle Scholar
  72. Mendes A, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663CrossRefGoogle Scholar
  73. Miller KJ, Wood JM (1996) Osmoadaption by rhizosphere bacteria. Ann Rev Microbiol 50:101–136CrossRefGoogle Scholar
  74. Moller LV, Arends JP, Harmsen HJ, Talens A, Terpstra P, Slooff MJ (1999) Ochrobactrum intermedium infection after liver transplantation. J Clin Microbiol 37:241–244PubMedPubMedCentralGoogle Scholar
  75. Morales A, Garland JL, Lim DV (1996) Survival of potentially pathogenic human-associated bacteria in the rhizosphere of hydroponically grown wheat. FEMS Microb Ecol 20:155–162CrossRefGoogle Scholar
  76. Nakayama T, Homma Y, Hashidoko Y, Mitzutani J, Tahara S (1999) Possible role of xanthobaccins produced by Stenotrophomonas sp. strain SB-K88 in suppression of sugar beet damping-off disease. Appl Environ Microbiol 65:4334–4339PubMedPubMedCentralGoogle Scholar
  77. Neumann G, Römheld V (2001) The release of root exudates as affected by the plant’s physiological status. In: Pinton R, Varanini Z, Nannipieri P (eds) The rhizosphere. Marcel Dekker, New York, NY, pp 41–93Google Scholar
  78. Nithya A, Babu S (2017) Prevalence of plant beneficial and human pathogenic bacteria isolated from salad vegetables in India. BMC Microbiol 17:1–16CrossRefGoogle Scholar
  79. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:206–214CrossRefGoogle Scholar
  80. Parke JL, Gurian-Sherman D (2001) Diversity of the Burkholderia cepacia complex and implications for risk assessment of biological control strains. Annu Rev Phytopathol 39:225–258CrossRefPubMedPubMedCentralGoogle Scholar
  81. Pierret A, Doussan C, Capowiez Y, Bastardie F, Pagès L (2007) Root functional architecture: a framework for modeling the interplay between roots and soil. Vadose Zone J 6:269–281CrossRefGoogle Scholar
  82. Raaijmakers JM, Vlami M, de Souza JT (2002) Antibiotic production by bacterial biocontrol agents. Antonie Leeuwenhoek 81:537–547CrossRefGoogle Scholar
  83. Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361CrossRefGoogle Scholar
  84. Rahme LG, Stevens EJ, Wolfort SF, Shoa J, Tompkins RG, Ausubel FM (1995) Common virulence factors for bacterial pathogenicity in plants and animals. Science 268:1899–1902CrossRefGoogle Scholar
  85. Reiter B, Pfeifer U, Schwab H, Sessitsch A (2002) Response of endophytic bacterial communities in potato plants to infection with Erwinia carotovora subsp. atroseptica. Appl Environ Microbiol 68:2261–2268CrossRefPubMedPubMedCentralGoogle Scholar
  86. Riesenfeld CS, Goodman RM, Handelsman J (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 6:981–989CrossRefGoogle Scholar
  87. Saunders JR, Allison H, James CE, McCarthy AJ, Sharp R (2001) Phage-mediated transfer of virulence genes. J Chem Technol Biotechnol 76:662–666CrossRefGoogle Scholar
  88. Schwieger F, Tebbe CC (2000) Effect of field inoculation with Sinorhizobium meliloti L33 on the composition of bacterial communities in rhizospheres of a target plant (Medicago sativa) and a non-target plant (Chenopodium album)–linking of 16S rRNA gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria. Appl Environ Microbiol 66:3556–3565CrossRefPubMedPubMedCentralGoogle Scholar
  89. Sessitsch A, Reiter B, Berg G (2004) Endophytic bacterial communities of field-grown potato plants and their plant growth-promoting abilities. Can J Microbiol 50:239–249CrossRefPubMedPubMedCentralGoogle Scholar
  90. Sharma R, Paliwal JS, Chopra P, Dogra D, Pooniya V, Bisaria VS, Swarnalakshmi K, Sharma S (2017) Survival, efficacy and risk assessment of bacterial inoculants in Cajanus cajan. Agric Ecosyst Environ 240:244–252CrossRefGoogle Scholar
  91. Sørensen J (1997) The rhizosphere as a habitat for soil microorganisms. In: Van Elsas JD, Trevors JT, EMH W (eds) Modern soil microbiology. Marcel Dekker, New York, NY, pp 21–45Google Scholar
  92. Steinkamp G, Wiedemann B, Rietschel E, Krahl A, Giehlen J, Barmeier H, Ratjen F (2005) Prospective evaluation of emerging bacteria in cystis fibrosis. J Cyst Fibros 4:41–48CrossRefPubMedPubMedCentralGoogle Scholar
  93. Strawn LK et al (2013) Landscape and meteorological factors affecting prevalence of three food-borne pathogens in fruit and vegetable farms. Appl Environ Microbiol 79:588–600CrossRefPubMedPubMedCentralGoogle Scholar
  94. Suckstorff I, Berg G (2003) Evidence for dose-dependent effects on plant growth by Stenotrophomonas strains from different origins. J Appl Microbiol 95:656–663CrossRefPubMedPubMedCentralGoogle Scholar
  95. Tabacchioni S, Bevivino A, Dalmastri C, Chiarini L (2002) Burkholderia cepacia complex in the rhizosphere: a minireview. Ann Microbiol 52:103–117Google Scholar
  96. Tan MW, Rahme LG, Sternberg JA, Tompkins RG, Ausubel FM (1999) Pseudomonas aeruginosa killing of Caenorhabditis elegans used to identify P. aeruginosa virulence factors. Proc Natl Acad Sci U S A 96:2408–2413CrossRefPubMedPubMedCentralGoogle Scholar
  97. Teplitski M, Barak JD, Schneider KR (2009) Human enteric pathogens in produce: un-answered ecological questions with direct implications for food safety. Curr Opin Biotechnol 20:166–171CrossRefPubMedPubMedCentralGoogle Scholar
  98. Thomashow LS, Bonsall RF, Weller DM (1997) Antibiotic production by soil and rhizosphere microbes in situ. In: Hurst CJ, Knudson GR, MJ MI, Setzenbach LD, Walter MV (eds) Manual of environmental microbiology. American Society for Microbiology Press, Washington, DC, pp 493–499Google Scholar
  99. Toth IK, Pritchard L, Birch PR (2006) Comparative genomics reveals what makes an enterobacterial plant pathogen. Annu Rev Phytopathol 44:305–336CrossRefPubMedPubMedCentralGoogle Scholar
  100. Tripathi AK, Verma SC, Ron EZ (2002) Molecular characterization of a salt-tolerant bacterial community in the rice rhizosphere. Res Microbiol 153:579–584CrossRefPubMedPubMedCentralGoogle Scholar
  101. Troxler J, Azelvandre P, Zala M, Defago G, Haas D (1997) Conjugative transfer of chromosomal genes between fluorescents pseudomonads in the rhizosphere of wheat. Appl Environ Microbiol 63:213–219PubMedPubMedCentralGoogle Scholar
  102. Turnbaugh PJ et al (2009) A core gut microbiome in obese and lean twins. Nature 457:480–484CrossRefGoogle Scholar
  103. Tyler HL, Triplett EW (2008) Plants as a habitat for beneficial and/or human pathogenic bacteria. Annu Rev Phytopathol 46:53–73CrossRefPubMedPubMedCentralGoogle Scholar
  104. Ursell LK, Metcalf JL, Parfrey LW, Knight R (2012) Defining the human microbiome. Nutr Rev 70:S38–S44CrossRefPubMedPubMedCentralGoogle Scholar
  105. van Baarlen P, van Belkum A, Summerbell RC, Crous PW, Thomma B (2007) Molecular mechanisms of pathogenicity: how do pathogenic microorganisms develop cross-kingdom host jumps? FEMS Microbiol Rev 31:239–277CrossRefPubMedPubMedCentralGoogle Scholar
  106. van Loon LC, Bakker PA, Pieterse CM (1998) Systemic resistance induced by rhizosphere bacteria. Annu Rev Phytopathol 36:453–483CrossRefGoogle Scholar
  107. Wang HB et al (2011) Characterization of metaproteomics in crop rhizospheric soil. J Proteome Res 10:932–940CrossRefGoogle Scholar
  108. Wei B, Huang T, Dalwadi H, Sutton CL, Bruckner D, Braun J (2002) Pseudomonas fluorescens encodes the Crohn’s disease-associated I2 sequenceand T-cell superantigen. Infect Immun 70:6567–6575CrossRefPubMedPubMedCentralGoogle Scholar
  109. Whipps J (2001) Microbial interactions and biocontrol in the rhizosphere. J Exp Bot 52:487–511CrossRefGoogle Scholar
  110. Wu L, Wang H, Zhang Z, Lin R, Lin W (2011) Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil. PLoS One 6:e20611CrossRefPubMedPubMedCentralGoogle Scholar
  111. Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H, Hashimoto Y, Ezaki T, Arakawa M (1992) Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 36:1251–1275CrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.Department of Biochemical Engineering and BiotechnologyIndian Institute of Technology DelhiHauz KhasIndia

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