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Horizontal Gene Transfer Between Bacteria Under Natural Conditions

  • Elisabeth GrohmannEmail author
Chapter

Abstract

Conjugative plasmid transfer is the most important mechanism for bacteria to deliver and acquire genetic information to cope with rapidly changing environmental conditions. An update of knowledge of conjugative plasmid transfer in aquatic and terrestrial habitats, including environments of particular concern such as agricultural areas and contaminated soils and sediments, is presented. Environmental factors affecting horizontal gene transfer in nature are discussed. Recent advances in the design of in situ monitoring tools to assess conjugative plasmid transfer in nature and laboratory model systems to simulate environmental conditions are critically reviewed. The impacts of horizontal gene transfer on biodegradation as well as recent approaches to model conjugative plasmid transfer in complex microbial communities are presented.

Keywords

Antibiotic resistance Heavy-metal resistance Aquatic systems Bioremediation Conjugative plasmid transfer Soil 

Notes

Acknowledgements

I sincerely thank Miquel Salgot for critical reading of the manuscript. I regret that not all valuable contributions of colleagues in the field of ecology of HGT are included due to space limitations.

References

  1. Agersø, Y., Wulff, G., Vaclavik, E., Halling-Sørensen, B., and Jensen, L. B. 2006. Effect of tetracycline residues in pig manure slurry on tetracycline-resistant bacteria and resistance gene tet(M) in soil microcosms. Environ. Int. 32:876–882.Google Scholar
  2. Ansari, M. I. 2009. Effect of industrial wastewater on soil microbiological characteristics and genotoxicity assessment of agricultural soils. PhD thesis, Aligarh Muslim University, Aligarh, India.Google Scholar
  3. Ansari, M. I., Grohmann, E., and Malik, A. 2008. Conjugative plasmids in multi-resistant bacterial isolates from Indian soil. J. Appl. Microbiol. 104:1774–1781.Google Scholar
  4. Arnold, D. L., Pitman, A., and Jackson, R. W. 2003. Pathogenicity and other genomic islands in plant pathogenic bacteria. Mol. Plant Pathol. 4:407–420.Google Scholar
  5. Ashelford, K. E., Fry, J. C., and Learner, M. A. 1995. Plasmid transfer between strains of Pseudomonas putida, and their survival, within a pilot scale percolating-filter sewage treatment system. FEMS Microbiol. Ecol. 18:15–26.Google Scholar
  6. Ashelford, K. E., Fry, J. C., Day, M. J., Hill, K. E., Learner, M. A., Marchesi, J. R., Perkins, C. D., and Weightman, A. J. 1997. Using microcosms to study gene transfer in aquatic habitats. FEMS Microbiol. Ecol. 23:81–94.Google Scholar
  7. Aspray, T. J., Hansen, S. K., and Burns, R. G. 2005. A soil-based microbial biofilm exposed to 2,4-D: bacterial community development and establishment of conjugative plasmid pJP4. FEMS Microbiol. Ecol. 54:317–327.Google Scholar
  8. Babic, A., Lindner, A. B., Vulic, M., Stewart, E. J., and Radman, M. 2008. Direct visualization of horizontal gene transfer. Science. 319:1533–1536.Google Scholar
  9. Baker-Austin, C., Wright, M. S., Stepanauskas, R., and McArthur, J. V. 2006. Co-selection of antibiotic and metal resistance. Trends Microbiol. 14:176–182. Review.Google Scholar
  10. Bale, M. J., Fry, J. C., and Day, M. J. 1987. Plasmid transfer between strains of Pseudomonas aeruginosa on membrane filters attached to river stones. J. Gen. Microbiol. 133:3099–3107.Google Scholar
  11. Bale, M. J., Fry, J. C., and Day, M. J. 1988a. Transfer and occurrence of large mercury resistance plasmids in river epilithon. Appl. Environ. Microbiol. 54:972–978.Google Scholar
  12. Bale, M. J., Day, M. J., and Fry, J. C. 1988b. Novel method for studying plasmid transfer in undisturbed river epilithon. Appl. Environ. Microbiol. 54:2756–2758.Google Scholar
  13. Barber, L. B., II, Thurman, E. M., and Runnells, D. D. 1992. Geochemical heterogeneity in a sand gravel aquifer: effect of sediment mineralogy and particle size on the sorption of chlorobenzenes. J. Contam. Hydrol. 9:35–54.Google Scholar
  14. Barkay, T., Kroer, N., Rasmussen, L. D., and Sorensen, S. J. 1995. Conjugative transfer at natural population densities in a microcosm simulating an estuarine environment. FEMS Microbiol. Ecol. 16:43–54.Google Scholar
  15. Barkay, T., Miller, S. M., and Summers, A. O. 2003. Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol. Rev. 27:355–384.Google Scholar
  16. Basta, T., Keck, A., Klein, J., and Stolz, A. 2004. Detection and characterization of conjugative degradative plasmids in xenobiotic-degrading Sphingomonas strains. J. Bacteriol. 186:3862–3872.Google Scholar
  17. Bathe, S., Mohan, T. V. K., Wuertz, S., and Hausner, M. 2004. Bioaugmentation of a sequencing batch biofilm reactor by horizontal gene transfer. Water Sci. Technol. 49:337–344.Google Scholar
  18. Bertini, I., Cavallaro, G., and Rosato, A. 2007. Evolution of mitochondrial-type cytochrome c domains and of the protein machinery for their assembly. J. Inorg. Biochem. 101:1798–1811.Google Scholar
  19. Binh, C. T., Heuer, H., Gomes, N. C., Kotzerke, A., Fulle, M., Wilke, B. M., Schloter, M., and Smalla, K. 2007. Short-term effects of amoxicillin on bacterial communities in manured soil. FEMS Microbiol. Ecol. 62:290–302.Google Scholar
  20. Binh, C. T., Heuer, H., Kaupenjohann, M., and Smalla, K. 2008. Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids. FEMS Microbiol. Ecol. 66:25–37.Google Scholar
  21. Björklöf, K., Suoniemi, A., Haahtela, K., and Romantschuk, M. 1995. High frequency of conjugation versus plasmid segregation of RP1 in epiphytic Pseudomonas syringae populations. Microbiology. 141:2719–2727.Google Scholar
  22. Breittmayer, V. A. and Gauthier, M. J. 1990. Influence of glycine betaine on the transfer of plasmid RP4 between Escherichia coli strains in marine sediments. Lett. Appl. Microbiol. 10:65–68.Google Scholar
  23. Büttner, D., Noël, L., Stuttmann, J., and Bonas U. 2007. Characterization of the nonconserved hpaBhrpF region in the hrp pathogenicity island from Xanthomonas campestris pv. vesicatoria. Mol. Plant Microbe Interact. 20:1063–1074.Google Scholar
  24. Christensen, B. B., Sternberg, C., and Molin S. 1996. Bacterial plasmid conjugation on semi-solid surfaces monitored with the green fluorescent protein (GFP) from Aequorea victoria as a marker. Gene 173:59–65.Google Scholar
  25. Christensen, B. B., Sternberg, C., Andersen, J. B., Eberl, L., Moller, S., Givskov, M., and Molin, S. 1998. Establishment of new genetic traits in a microbial biofilm community. Appl. Environ. Microbiol. 64:2247–2255.Google Scholar
  26. Clewlow, L. J., Cresswell, N., and Wellington, E. M. 1990. Mathematical model of plasmid transfer between strains of streptomycetes in soil microcosms. Appl. Environ. Microbiol. 56:3139–3145.Google Scholar
  27. Coombs, J. M., and Barkay, T. 2004. Molecular evidence for the evolution of metal homeostasis genes by lateral gene transfer in bacteria from the deep terrestrial subsurface. Appl. Environ. Microbiol. 70:1698–1707.Google Scholar
  28. Cozzarelli, I. M., and Weiss, J. V. 2007. Biochemistry of aquifer systems. ASM Press, Washington, DC.Google Scholar
  29. Crossman, L. C., Castillo-Ramírez, S., McAnnula, C., Lozano, L., Vernikos, G. S., Acosta, J. L., Ghazoui, Z. F., Hernández-González, I., Meakin, G., Walker, A. W., Hynes, M. F., Young, J. P., Downie, J. A., Romero, D., Johnston, A. W., Dávila, G., Parkhill, J., and González, V. A. 2008. Common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. PLoS One. 3(7):e2567. Erratum in: PLoS One. 2008 3(8).Google Scholar
  30. Daane, L. L., Molina, J. A., Berry, E. C., and Sadowsky, M. J. 1996. Influence of earthworm activity on gene transfer from Pseudomonas fluorescens to indigenous soil bacteria. Appl. Environ. Microbiol. 62:515–521.Google Scholar
  31. Dahlberg, C., Bergström, M., and Hermansson M. 1998. In situ detection of high levels of horizontal plasmid transfer in marine bacterial communities. Appl. Environ. Microbiol. 64:2670–2675.Google Scholar
  32. De Gelder, L., Vandecasteele, F. P., Brown, C. J., Forney, L. J., and Top, E. M. 2005. Plasmid donor affects host range of promiscuous IncP-1beta plasmid pB10 in an activated-sludge microbial community. Appl. Environ. Microbiol. 71:5309–5317.Google Scholar
  33. Denap, J. C., Thomas, J. R., Musk, D. J., and Hergenrother, P. J. 2004. Combating drug-resistant bacteria: small molecule mimics of plasmid incompatibility as antiplasmid compounds. J. Am. Chem. Soc. 126:15402–15404.Google Scholar
  34. Ding, H., and Hynes, M. F. 2009. Plasmid transfer systems in the rhizobia. Can. J. Microbiol. 55:917–927.Google Scholar
  35. Dobrindt, U., Hochhut, B., Hentschel U., and Hacker, J. 2004. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2:414–424.Google Scholar
  36. Dronen, A. K., Torsvik, V., Goksoyr, J., and Top, E. M. 1998. Effect of mercury addition on plasmid incidence and gene mobilising capacity in bulk soil. FEMS Microbiol. Ecol. 27:381–394.Google Scholar
  37. Gealt, M. A., Chai, M. D., Alpert, K. B., and Boyer, J. C. 1985. Transfer of plasmids pBR322 and pBR325 in wastewater from laboratory strains of Escherichia coli to bacteria indigenous to the waste disposal system. Appl. Environ. Microbiol. 49:836–841.Google Scholar
  38. Gillings, M. R., Holley, M. P., Stokes, H. W., and Holmes, A. J. 2005. Integrons in Xanthomonas: a source of species genome diversity. Proc. Nat. Acad. Sci. USA. 102:4419–4424.Google Scholar
  39. Gilmour, M. W., Thomson, N. R., Sanders, M., Parkhill, J., and Taylor, D. E. 2004. The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics. Plasmid 52:182–202.Google Scholar
  40. Goodman, A. E., Hild, E., Marshall, K. C., and Hermansson, M. 1993. Conjugative plasmid transfer between bacteria under simulated marine oligotrophic conditions. Appl. Environ. Microbiol. 59:1035–1040.Google Scholar
  41. Götz, A., and Smalla, K. 1996. Manure enhances plasmid mobilization and survival of Pseudomonas putida introduced into field soil. Appl. Environ. Microbiol. 63:1980–1986.Google Scholar
  42. Gray, N. F. 1992. Biology of wastewater treatment. Oxford University Press, Oxford, UK.Google Scholar
  43. Gregory, R., Saunders, J. R., and Saunders, V. A. 2008a. Rule-based modelling of conjugative plasmid transfer and incompatibility. BioSystems 91:201–215.Google Scholar
  44. Gregory, R., Saunders, V. A., and Saunders, J. R. 2008b. Rule-based computing system for microbial interactions and communications: evolution in virtual bacterial populations. BioSystems 91:216–230.Google Scholar
  45. Haagensen, J. A., Hansen, S. K., Johansen, T., and Molin, S. 2002. In situ detection of horizontal transfer of mobile genetic elements. FEMS Microbiol. Ecol. 42:261–268.Google Scholar
  46. Head, M. I., and Bailey, M. J. 2003. Environmental biotechnology methodological advances spawn new concepts in environmental biotechnology. Curr. Opin. Biotechnol. 14:245–247.Google Scholar
  47. Henschke, R. B., and Schmidt, F. R. J. 1990. Plasmid mobilization from genetically engineered bacteria to members of the indigenous soil microflora in situ. Curr. Microbiol. 20:105–110.Google Scholar
  48. Heuer, H., and Smalla, K. 2007. Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two months. Environ. Microbiol. 9:657–666.Google Scholar
  49. Heuer, H., Krögerrecklenfort, E., Egan, S., van Overbeck, L., Guillaume, G., Nikolakopoulou, T. L., Wellington, E. M. H., van Elsas, J. D., Collard, J. M., Karagouni, A. D., and Smalla, K. 2002. Gentamicin resistance genes in environmental bacteria: prevalence and transfer. FEMS Microbiol. Ecol. 42:289–302.Google Scholar
  50. Heuer, H., Abdo, Z., and Smalla, K. 2008. Patchy distribution of flexible genetic elements in bacterial populations mediates robustness to environmental uncertainty. FEMS Microbiol. Ecol. 65:361–371.Google Scholar
  51. Heuer, H., Kopmann, C., Binh, C. T., Top, E. M., and Smalla, K. 2009. Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content. Environ. Microbiol. 11:937–949.Google Scholar
  52. Heydorn, A., Nielsen, A. T., Hentzer, M., Parsek, M. R., Givskov, M., and Molin, S. 2000. Experimental reproducibility in flow-chamber biofilms. Microbiology. 146:2409–2415.Google Scholar
  53. Hill, K. E., Fry, J. C., and Weightman, A. J. 1994. Gene transfer in the aquatic environment: persistence and mobilization of the catabolic recombinant plasmid pD10 in the epilithon. Microbiology. 140:1555–1563.Google Scholar
  54. Hill, K. E., Marchesi, J. R., and Fry, J. C. 1996. Conjugation and mobilization in the epilithon. In: Akkermans, A. D. L., van Elsas, J. D., and de Bruijn, F. J. (eds). Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, Netherlands. pp. 5.2.2.1–5.2.2.28.Google Scholar
  55. Hoffmann, A., Thimm, T., Dröge, M., Moore, E. R., Munch, J. C., and Tebbe, C. C. 1998. Intergeneric transfer of conjugative and mobilizable plasmids harbored by Escherichia coli in the gut of the soil microarthropod Folsomia candida (Collembola). Appl. Environ. Microbiol. 64:2652–2659.Google Scholar
  56. Hoffmann A., Thimm T., and Tebbe C. C. 1999. Fate of plasmid-bearing, luciferase marker gene tagged bacteria after feeding to the soil microarthropod Onychiurus fimatus (Collembola). FEMS Microbiol. Ecol. 30:125–135.Google Scholar
  57. Inoue, D., Soda, S., Tsutsui, H., Yamazaki, Y., Murashige, K., Sei, K., Fujita, M., and Ike, M. 2009. Occurrence and persistence of indigenous transconjugants carrying conjugative plasmids in soil. J. Biosci. Bioeng. 108:231–234.Google Scholar
  58. Jackson, C. R., and Dugas, S. L. 2003. Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase. BMC Evol. Biol. 3:18.Google Scholar
  59. Jones, G. W., Baines, L., and Genthner, F. J. 1991. Heterotrophic bacteria of the freshwater neuston and their ability to act as plasmid recipients under nutrient deprived conditions. Microb. Ecol. 22:15–25.Google Scholar
  60. Kawasaki, H., Yahara, H., and Tonomura, K. 1981. Isolation and characterization of plasmid pUO1 mediating dehalogenation of haloacetate and mercury resistance in Moraxella sp. B. Agric. Biol. Chem. 45:1477–1481.Google Scholar
  61. Kay, E., Vogel, T. M., Bertolla, F., Nalin, R., and Simonet, P. 2002. In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria. Appl. Environ. Microbiol. 68:3345–3351.Google Scholar
  62. Kholodii, G., Gorlenko, Z., Mindlin, S., Hobman, J., and Nikiforov, V. 2002. Tn5041-like transposons: molecular diversity, evolutionary relationships and distribution of distinct variants in environmental bacteria. Microbiology. 148:3569–3582.Google Scholar
  63. Knudsen, G. R., Walter, M. V., Porteous, L. A., Prince. V. J., Armstrong, J. L., and Seidler R. J. 1988. Predictive model of conjugative plasmid transfer in the rhizosphere and phyllosphere. Appl. Environ. Microbiol. 54:343–347.Google Scholar
  64. Kobayashi, N., and Bailey, M. J. 1994. Plasmids isolated from the sugar beet phyllosphere show little or no homology to molecular probes currently available for plasmid typing. Microbiology. 140:289–296.Google Scholar
  65. Krasovsky, V. N., and Stotzky, G. 1987. Conjugation and genetic recombination in Escherichia coli in sterile and non-sterile soil. Soil Biol. Biochem. 19:631–638.Google Scholar
  66. Kroer, N., Barkay, T., Sörensen, S., and Weber, D. 1998. Effect of root exudates and bacterial metabolic activity on conjugative gene transfer in the rhizosphere of a marsh plant. FEMS Microbiol. Ecol. 25:375–384.Google Scholar
  67. Lebaron, P., Batailler, N., and Baleux, B. 1994. Mobilization of a recombinant nonconjugative plasmid at the interface between wastewater and the marine coastal environment. FEMS Microbiol. Ecol. 15:61–70.Google Scholar
  68. Levin, B. R., and Bergstrom, C. T. 2000. Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. Proc. Natl. Acad. Sci. USA. 97:6981–6985. Review.Google Scholar
  69. Levin, B. R., Stewart, F. M., and Rice, V. A. 1979. The kinetics of conjugative plasmid transmission: fit of a simple mass action model. Plasmid. 2:247–260.Google Scholar
  70. Li, F., Hou, B., and Hong, G. 2008. Symbiotic plasmid is required for NolR to fully repress nodulation genes in Rhizobium leguminosarum A34. Acta Biochim. Biophys. Sin. (Shanghai). 40:901–907.Google Scholar
  71. Liebert, C. A., Hall, R. M., and Summers, A. 1999. Transposon Tn21, flagship of the floating genome. Microbiol. Mol. Biol. Rev. 63:507–522.Google Scholar
  72. Lilley, A. K., and Bailey, M. J. 1997. Impact of plasmid pQBR103 acquisition and carriage on the phytosphere fitness of Pseudomonas fluorescens SBW25: burden and benefit. Appl. Environ. Microbiol. 63:1584–1587.Google Scholar
  73. Lilley, A. K., Fry, J. C., Day, M. J., and Bailey, M. J. 1994. In situ transfer of an exogenously isolated plasmid between indigenous donor and recipient Pseudomonas spp. in sugar beet rhizosphere. Microbiology. 140:27–33.Google Scholar
  74. Lilley, A. K., Bailey, M. J., Day, M. J., and Fry, J. C. 1996. Diversity of mercury resistance plasmids obtained by exogenous isolation from the bacteria of sugar beet in three successive years. FEMS Microbiol. Ecol. 20:211–227.Google Scholar
  75. Lilley, A. K., Bailey, M. J., Barr, M., Kilshaw, K., Timms-Wilson, T. M., Day, M. J., Norris, S. J., Jones, T. H., and Godfray, H. C. 2003. Population dynamics and gene transfer in genetically modified bacteria in a model microcosm. Mol. Ecol. 12:3097–3107.Google Scholar
  76. Lloyd, J. R., Ridley, J., Khizniak, T., Lyalikova, N. N., and Macaskie, L. E. 1999. Reduction of technetium by Desulfovibrio desulfuricans: biocatalyst characterization and use in a flowthrough bioreactor. Appl. Environ. Microbiol. 65:2691–2696.Google Scholar
  77. Lloyd, J. R., Sole, V. A., Van Praagh, C. V., and Lovley, D. R. 2000. Direct and Fe(II)-mediated reduction of technetium by Fe(III)-reducing bacteria. Appl. Environ. Microbiol. 66:3743–3749.Google Scholar
  78. Lock, M. A., Wallace, R. R., Costerton, J. W., Ventullo, R. M., and Charlton, S. E. 1984. River epilithon: toward a structural–functional model. Oikos 42:10–22.Google Scholar
  79. Lovley, D. R., Phillips, E. J. P., Gorby, Y. A., and Landa, E. R. 1991. Microbial reduction of uranium. Nature. 350:413–416.Google Scholar
  80. Lovley, D. R., Widman, P. K., Woodward, J. C., and Phillips, E. J. 1993. Reduction of uranium by cytochrome c3 of Desulfovibrio vulgaris. Appl. Environ. Microbiol. 59:3572–3576.Google Scholar
  81. Malik, A., Celik, E.-K., Bohn, C., Boeckelmann, U., Knobel, K., and Grohmann, E. 2008. Molecular detection of conjugative plasmids and antibiotic resistance genes in anthropogenic soils from Germany and India. FEMS Microbiol. Lett. 279:207–216.Google Scholar
  82. Mancini, P., Fertels, S., Nave, D., and Gealt, M. A. 1987. Mobilization of plasmid pHSV106 from Escherichia coli HB101 in a laboratory-scale waste treatment facility. Appl. Environ. Microbiol. 53:665–671.Google Scholar
  83. Marshall, M. J., Plymale, A. E., Kennedy, D. W., Shi, L., Wang, Z., Reed, S. B., Dohnalkova, A. C., Simonson, C. J., Liu, C., Saffarini, D. A., Romine, M. F., Zachara, J. M., Beliaev, A. S., and Fredrickson, J. K. 2008. Hydrogenase- and outer membrane c-type cytochrome-facilitated reduction of technetium(VII) by Shewanella oneidensis MR-1. Environ. Microbiol. 10:125–136.Google Scholar
  84. Martinez, R. J., Wang, Y., Raimondo, M. A., Coombs, J. M., Barkay, T., and Sobecky, P. A. 2006. Horizontal gene transfer of PIB-type ATPases among bacteria isolated from radionuclide- and metal-contaminated subsurface soils. Appl. Environ. Microbiol. 72:3111–3118.Google Scholar
  85. Massoudieh, A., Crain, C., Lambertini, E., Nelson, K. E., Barkouki, T., L’amoreaux, P., Loge, F. J., and Ginn, T. R. 2010. Kinetics of conjugative gene transfer on surfaces in granular porous media. J. Contam. Hydrol. 112:91–102.Google Scholar
  86. Mazel, D. 2006. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4:608–620.Google Scholar
  87. McClure, N. C., Weightman, A. J., and Fry, J. C. 1989. Survival of Pseudomonas putida UWC1 containing catabolic genes in a model activated-sludge unit. Appl. Environ. Microbiol. 55:2627–2634.Google Scholar
  88. Mendum, T. A., Clark, I. M., and Hirsch, P. R. 2001. Characterization of two novel Rhizobium leguminosarum bacteriophages from a field release site of genetically-modified rhizobia. Antonie Van Leeuwenhoek. 79:189–197.Google Scholar
  89. Mergeay, M., Monchy, S., Vallaeys, T., Auquier, V., Benotmane, A., Bertin, P., Taghavi, S., Dunn, J., van der Lelie, D., and Wattiez, R. 2003. Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes. FEMS Microbiol. Rev. 27:385–410. Review.Google Scholar
  90. Mindlin, S., Kholodii, G., Gorlenko, Z., Minakhina, S., Minakhin, L., Kalyaeva, E., Kopteva, A., Petrova, M., Yurieva, O., and Nikiforov, V. 2001. Mercury resistance transposons of gram-negative environmental bacteria and their classification. Res. Microbiol. 152:811–822.Google Scholar
  91. Miyazaki, R., Sato, Y., Ito, M., Ohtsubo, Y., Nagata, Y., and Tsuda M. 2006. Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation. Appl. Environ. Microbiol. 72:6923–6933.Google Scholar
  92. Molin, S., and Tolker-Nielsen, T. 2003. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr. Opin. Biotechnol. 14:255–261.Google Scholar
  93. Muela, A., Pocino, M., Arana, I., Justo, J. I., Iriberri, J., and Barcina, I. 1994. Effect of growth phase and parental cell survival in river water on plasmid transfer between Escherichia coli strains. Appl. Environ. Microbiol. 60:4273–4278.Google Scholar
  94. Nakatsukasa, H., Uchiumi, T., Kucho, K., Suzuki, A., Higashi, S., and Abe, M. 2008. Transposon mediation allows a symbiotic plasmid of Rhizobium leguminosarum bv. trifolii to become a symbiosis island in Agrobacterium and Rhizobium. J. Gen. Appl. Microbiol. 54:107–118.Google Scholar
  95. Nandasena, K. G., O’Hara, G. W., Tiwari, R. P., Sezmiş, E., and Howieson, J. G. 2007. In situ lateral transfer of symbiosis islands results in rapid evolution of diverse competitive strains of mesorhizobia suboptimal in symbiotic nitrogen fixation on the pasture legume Biserrula pelecinus L. Environ. Microbiol. 9:2496–2511.Google Scholar
  96. Neilson, J. W., Josephson, K. L., Pepper, I. L., Arnold, R. B., Di Giovanni, G. D., and Sinclair, N. A. 1994. Frequency of horizontal gene transfer of a large catabolic plasmid (pJP4) in soil. Appl. Environ. Microbiol. 60:4053–4058.Google Scholar
  97. Newby, D. T., Gentry, T. J., and Pepper, I. L. 2000. Comparison of 2,4-dichlorophenoxyacetic acid degradation and plasmid transfer in soil resulting from bioaugmentation with two different pJP4 donors. Appl. Environ. Microbiol. 66:3399–3407.Google Scholar
  98. Nucifora, G., Chu, L., Misra, T. K., and Silver, S. 1989. Cadmium resistance from Staphylococcus aureus plasmid pI258 cadA gene results from a cadmium-efflux ATPase. Proc. Natl. Acad. Sci. USA. 86:3544–3548.Google Scholar
  99. O’Morchoe, S. B., Ogunseitan, O., Sayler, G. S., and Miller, R. V. 1988. Conjugal transfer of R68.45 and FP5 between Pseudomonas aeruginosa strains in a freshwater environment. Appl. Environ. Microbiol. 54:1923–1929.Google Scholar
  100. O’Sullivan, D., Ross, R. P., Twomey, D. P., Fitzgerald, G. F., Hill, C., and Coffey, A. 2001. Naturally occurring lactococcal plasmid pAH90 links bacteriophage resistance and mobility functions to a food-grade selectable marker. Appl. Environ. Microbiol. 67:929–937.Google Scholar
  101. Ochman, H., Lawrence, J. G., and Grolsman, E. A. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature. 405:299–304.Google Scholar
  102. Ohlsen, K., Ternes, T., Werner, G., Wallner, U., Löffler, D., Ziebuhr, W., Witte, W., and Hacker, J. 2003. Impact of antibiotics on conjugational resistance gene transfer in Staphylococcus aureus in sewage. Environ. Microbiol. 5:711–716.Google Scholar
  103. Ono, A., Miyazaki, R., Sota, M., Ohtsubo, Y., Nagata, Y., and Tsuda M. 2007. Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl. Microbiol. Biotechnol. 74:501–510.Google Scholar
  104. Payne, R. B., Casalot, L., Rivere, T., Terry, J. H., Larsen, L., Giles, B. J., and Wall, J. D. 2004. Interaction between uranium and the cytochrome c3 of Desulfovibrio desulfuricans strain G20. Arch. Microbiol. 181:398–406.Google Scholar
  105. Pinedo, C. A., and Smets, B. F. 2005. Conjugal TOL transfer from Pseudomonas putida to Pseudomonas aeruginosa: effects of restriction proficiency, toxicant exposure, cell density ratios, and conjugation detection method on observed transfer efficiencies. Appl. Environ. Microbiol. 71:51–57.Google Scholar
  106. Popova, L. Y., Kargatova, T. V., Ganusova, E. E., Lobova, T. I., Boyandin, A. N., Mogilnaya, O. A., and Pechurkin, N. S. 2005. Population dynamics of transgenic strain Escherichia coli Z905/pPHL7 in freshwater and saline lake water microcosms with differing microbial community structures. Adv. Space Res. 35:1573–1578.Google Scholar
  107. Powell, B. J., Purdy, K. J., Thompson, I. P., and Bailey, M. J. 1993. Demonstration of tra + plasmid activity in bacteria indigenous to the phyllosphere of sugar beet; gene transfer to a recombinant pseudomonad. FEMS Microbiol. Ecol. 12:195–206.Google Scholar
  108. Pukall, R., Tschäpe, H., and Smalla, K. 1996. Monitoring the spread of broad host and narrow host-range plasmids in soil microcosms. FEMS Microbiol. Ecol. 20:53–66.Google Scholar
  109. Ramsay, J. P., Sullivan, J. T., Stuart, G. S., Lamont, I. L., and Ronson, C. W. 2006. Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS. Mol. Microbiol. 62:723–734.Google Scholar
  110. Rasmussen, L. D., and Sørensen, S. J. 1998. The effect of long term exposure to mercury on the bacterial community in marine sediment. Curr. Microbiol. 36:291–297.Google Scholar
  111. Richaume, A., Angle, J. S., and Sadowski, M. J. 1989. Influence of soil variables on in situ plasmid transfer from Escherichia coli to Rhizobium fredii. Appl. Environ. Microbiol. 55:1730–1734.Google Scholar
  112. Sandaa, R.-A. 1993. Transfer and maintenance of the plasmid RP4 in marine sediments. Microb. Releases. 2:115–119.Google Scholar
  113. Sandt, C. H., and Herson, D. S. 1991. Mobilization of the genetically engineered plasmid pHSV106 from Escherichia coli HB101 (pHSV106) to Enterobacter cloacae in drinking water. Appl. Environ. Microbiol. 57:194–200.Google Scholar
  114. Schneiker, S., Keller, M., Dröge, M., Lanka, E., Pühler, A., and Selbitschka W. 2001. The genetic organization and evolution of the broad host range mercury resistance plasmid pSB102 isolated from a microbial population residing in the rhizosphere of alfalfa. Nucleic Acids Res. 29:5169–5181.Google Scholar
  115. Schofield, P. R., Gibson, A. H., Dudman, W. F., and Watson, J. M. 1987. Evidence for genetic exchange and recombination of Rhizobium symbiotic plasmids in a soil population. Appl. Environ. Microbiol. 53:2942–2947.Google Scholar
  116. Sentchilo, V., Ravatn, R., Werlen, C., Zehnder, A. J., and van der Meer, J. R. 2003. Unusual integrase gene expression on the clc genomic island in Pseudomonas sp. strain B13. J. Bacteriol. 185:4530–4538.Google Scholar
  117. Shelobolina, E. S., Coppi, M. V., Korenevsky, A. A., DiDonato, L. N., Sullivan, S. A., Konishi, H., Xu, H., Leang, C., Butler, J. E., Kim, B. C., and Lovley, D. R 2007. Importance of c-type cytochromes for U(VI) reduction by Geobacter sulfurreducens. BMC Microbiol. 7:16.Google Scholar
  118. Shintani, M., Fukushima, N., Tezuka, M., Yamane, H., and Nojiri, H. 2008. Conjugative transfer of the IncP-7 carbazole degradative plasmid, pCAR1, in river water samples. Biotechnol. Lett. 30:117–122.Google Scholar
  119. Silver, S., Budd, K., Leahy, K. M., Shaw, W. V., Hammond, D., Novick, R. P., Willsky, G. R., Malamy, M. H., and Rosenberg, H. 1981. Inducible plasmid-determined resistance to arsenate, arsenite, and antimony (III) in Escherichia coli and Staphylococcus aureus. J. Bacteriol. 146:983–996.Google Scholar
  120. Slater, F. R., Bailey, M. J., Tett, A. J., and Turner, S. L. 2008. Progress towards understanding the fate of plasmids in bacterial communities. FEMS Microbiol. Lett. 66:3–13.Google Scholar
  121. Smalla, K., and Sobecky, P. A. 2002. The prevalence and diversity of mobile genetic elements in bacterial communities of different environmental habitats: insights gained from different methodological approaches. FEMS Microbiol. Ecol. 42:165–175.Google Scholar
  122. Smalla, K., Krogerrecklenfort, E., Heuer, H., Dejonghe, W., Top, E., Osborn, M., Niewint, J., Tebbe, C., Barr, M., Bailey, M., Greated, A., Thomas, C., Turner, S., Young, P., Nikolakopoulou, D., Karagouni, A., Wolters, A., van Elsas, J. D., Dronen, K., Sandaa, R., Borin, S., Prabhu, J., Grohmann, E., and Sobecky, P. 2000. PCR-based detection of mobile genetic elements in total ­community DNA. Microbiology. 146:1256–1257.Google Scholar
  123. Smalla, K., Haines, A. S., Jones, K., Krögerrecklenfort, E., Heuer, H., Schloter, M., and Thomas, C. M. 2006. Increased abundance of IncP-1beta plasmids and mercury resistance genes in mercury-polluted river sediments: first discovery of IncP-1beta plasmids with a complex mer transposon as the sole accessory element. Appl. Environ. Microbiol. 72:7253–7259.Google Scholar
  124. Smets, B. F., and Barkay, T. 2005. Horizontal gene transfer: Perspectives at a crossroads of scientific disciplines. Nat. Rev. Microbiol. 3:675–678.Google Scholar
  125. Smit, E., van Elsas, J. D., van Veen, J. A., and de Vos, W. M. 1991. Detection of plasmid transfer from Pseudomonas fluorescens to indigenous bacteria in soil by using bacteriophage phiR2f for donor counterselection. Appl. Environ. Microbiol. 57:3482–3488.Google Scholar
  126. Smit, E., Venne, D., and van Elsas J. D. 1993. Mobilization of a recombinant IncQ plasmid between bacteria on agar and in soil via cotransfer or retrotransfer. Appl. Environ. Microbiol. 59:2257–2263.Google Scholar
  127. Smit, E., Wolters, A., and van Elsas, J. D. 1998. Self-transmissible mercury resistance plasmids with gene-mobilizing capacity in soil bacterial populations: influence of wheat roots and mercury addition. Appl. Environ. Microbiol. 64:1210–1219.Google Scholar
  128. Sobecky, P. A., and Coombs, J. M. 2009. Horizontal gene transfer in metal and radionuclide contaminated soils. In: Gogarten M. B. (ed). Horizontal gene transfer: genomes in flux, vol. 532. Humana Press, New York. pp. 455–472.Google Scholar
  129. Sobecky, P. A., and Hazen, T. H. 2009. Horizontal gene transfer and mobile genetic elements in marine systems. Methods Mol. Biol. 532:435–453.Google Scholar
  130. Sørensen, S. J., and Jensen, L. E. 1998. Transfer of plasmid RP4 in the spermosphere and rhizosphere of barley seedling. Antonie Van Leeuwenhoek. 73:69–77.Google Scholar
  131. Sørensen, S. J., Sørensen, A. H., Hansen, L. H., Oregaard, G., and Veal D. 2003. Direct detection and quantification of horizontal gene transfer by using flow cytometry and gfp as a reporter gene. Curr. Microbiol. 47:129–133.Google Scholar
  132. Sørensen, S. J., Bailey, M., Hansen, L. H., Kroer, N., and Wuertz, S. 2005. Studying plasmid horizontal transfer in situ: a critical review. Nat. Rev. Microbiol. 3:700–710.Google Scholar
  133. Springael, D., and Top, E. M. 2004. Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies. Trends Microbiol. 12:53–58.Google Scholar
  134. Springael, D., Peys, K., Ryngaert, A., Van Roy, S., Hooyberghs, L., Ravatn, R., Heyndrickx, M., van der Meer, J. R., Vandecasteele, C., Mergeay, M., and Diels, L. 2002. Community shifts in a seeded 3-chlorobenzoate degrading membrane biofilm reactor: indications for involvement of in situ horizontal transfer of the clc-element from inoculum to contaminant bacteria. Environ. Microbiol. 4:70–80.Google Scholar
  135. Stolz, J. F., Basu, P., Santini, J. M., and Oremland, R. S. 2006. Arsenic and selenium in microbial metabolism. Annu. Rev. Microbiol. 60:107–130. Review.Google Scholar
  136. Sudarshana, P., and Knudsen, G. R. 2006. Quantification and modeling of plasmid mobilization on seeds and roots. Curr. Microbiol. 52:455–459.Google Scholar
  137. Summers, A., and Silver, S. 1972. Mercury resistance in a plasmid-bearing strain of Escherichia coli. J. Bacteriol. 112:1228–1236.Google Scholar
  138. Sundin, G. W. 2007. Genomic insights into the contribution of phytopathogenic bacterial plasmids to the evolutionary history of their hosts. Annu. Rev. Phytopathol. 45:129–151. Review.Google Scholar
  139. Szczepanowski, R., Krahn, I., Linke, B., Goesmann, A., Pühler, A., and Schlüter, A. 2004. Antibiotic multiresistance plasmid pRSB101 isolated from a wastewater treatment plant is related to plasmids residing in phytopathogenic bacteria and carries eight different resistance determinants including a multidrug transport system. Microbiology. 150:3613–3630.Google Scholar
  140. Thimm, R., Hoffmann, A., Fritz, I., and Tebbe, C.C. 2001. Contribution of the earthworm Lumbricus rubellus (Annelida, Oligochaeta) to the establishment of plasmids in soil bacterial communities. Microb. Ecol. 41:341–351.Google Scholar
  141. Toomey, N., Monaghan, A., Fanning, S., and Bolton, D. 2009. Transfer of antibiotic resistance marker genes between lactic acid bacteria in model rumen and plant environments. Appl. Environ. Microbiol. 75:3146–3152.Google Scholar
  142. Top, E. M., Holben, W. E., and Forney, L. J. 1995. Characterization of diverse 2,4-dichlorophenoxyacetic acid-degradative plasmids isolated from soil by complementation. Appl. Environ. Microbiol. 61:1691–1698.Google Scholar
  143. Top, E. M., Maltseva, O. V., and Forney, L. J. 1996. Capture of a catabolic plasmid that encodes only 2,4-dichlorophenoxyacetic acid:alpha-ketoglutaric acid dioxygenase (TfdA) by genetic complementation. Appl. Environ. Microbiol. 62:2470–2476.Google Scholar
  144. Toussaint, A., Merlin, C., Monchy, S., Benotmane, M. A., Leplae, R., Mergeay, M., and Springael, D. 2003. The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. Appl. Environ. Microbiol. 69:4837–4845.Google Scholar
  145. van der Meer, J. R., and Sentchilo, V. 2003. Genomic islands and evolution of catabolic pathways in bacteria. Curr. Opin. Biotechnol. 14:248–354.Google Scholar
  146. van der Meer, J. R., Werlen, C., Nishino, S. F., and Spain, J. C. 1998. Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater. Appl. Environ. Microbiol. 64:4185–4193.Google Scholar
  147. van Elsas, J. D., and Bailey, M. J. 2002. The ecology of transfer of mobile genetic elements. FEMS Microbiol. Ecol. 42:187–197. MiniReview.Google Scholar
  148. van Elsas, J. D., Trevors, J. T., and Starodub, M.-E. 1988a. Bacterial conjugation between pseudomonads in the rhizosphere of wheat. FEMS Microbiol. Ecol. 53:299–306.Google Scholar
  149. van Elsas, J. D., Trevors, J. T., and Starodub, M.-E. 1988b. Plasmid transfer in soil and rhizosphere. In: Klingmuller, W. (ed). Risk assessment for deliberate releases. Springer, Heidelberg. pp. 89–99.Google Scholar
  150. van Elsas, J. D., Gardener, B. B., Wolters, A. C., and Smit, E. 1998. Isolation, characterization, and transfer of cryptic gene-mobilizing plasmids in the wheat rhizosphere. Appl. Environ. Microbiol. 64:880–889.Google Scholar
  151. van Elsas, J. D., Fry, J., Hirsch, P., and Molin, S. 2000. Ecology of plasmid transfer and spread. In: Thomas, C. M. (ed). The horizontal gene pool. Bacterial plasmids and gene spread. Harwood Academic Publishers, Amsterdam. pp. 175–206.Google Scholar
  152. van Overbeck, L. S., Wellington, E. M. H., Egan, S., Smalla, K., Heuer, H., Collard, J. M., Guillaume, G., Karagouni, A. D., Nikolakopoulou, T. L., and van Elsas, J. D. 2002. Prevalence of streptomycin resistance genes in bacterial populations in European habitats. FEMS Microbiol. Ecol. 42:277–288.Google Scholar
  153. Venkata Mohan, S., Falkentoft, C., Venkata Nancharaiah, Y., Sturm, B. S., Wattiau, P., Wilderer, P. A., Wuertz, S., and Hausner, M. 2009. Bioaugmentation of microbial communities in laboratory and pilot scale sequencing batch biofilm reactors using the TOL plasmid. Bioresour. Technol. 100:1746–1753.Google Scholar
  154. Vivian, A., Murillo, J., and Jackson, R. W. 2001. The roles of plasmids in phytopathogenic bacteria: mobile arsenals? Microbiology. 147:763–780.Google Scholar
  155. Wright, M. S., Peltier, G. L., Stepanauskas, R., and McArthur, J. V. 2006. Bacterial tolerances to metals and antibiotics in metal-contaminated and reference streams. FEMS Microbiol. Ecol. 58:293–302.Google Scholar
  156. Wuertz, S. 2002. In: Bitton, G. (ed). Encyclopedia of environmental microbiology. Wiley, New York. pp. 1408–1420.Google Scholar
  157. Wuertz, S., Okabe, S., and Hausner, M. 2004. Microbial communities and their interactions in biofilm systems: an overview. Water Sci. Technol. 49:327–336.Google Scholar
  158. Wyndham, R. C., Cashore, A. E., Nakatsu, C. H., and Peel, M. C. 1994. Catabolic transposons. Biodegradation 5:323–342. Review.Google Scholar
  159. Zhao, Y., Ma, Z., and Sundin, G. W. 2005. Comparative genomic analysis of the pPT23A plasmid family of Pseudomonas syringae. J. Bacteriol. 187:2113–2126.Google Scholar

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© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of Infectious DiseasesUniversity Hospital FreiburgFreiburgGermany

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