Free Access
Issue
Environ. Biosafety Res.
Volume 6, Number 1-2, January-June 2007
Thematic Issue on Horizontal Gene Transfer
Page(s) 15 - 35
DOI https://doi.org/10.1051/ebr:2007037
Published online 26 October 2007
  • Ahrenholtz I, Lorenz MG, Wackernagel W (1994) The extracellular nuclease of Serratia marcescens: studies on the activity in vitro and effect on transforming DNA in a groundwater aquifer microcosm. Arch. Microbiol. 161: 176–183 [PubMed]
  • Altieri MA, Gurr GM, Wratten SD (2004) Genetic engineering and ecological engineering: A clash of paradigms or scope for synergy? In Gurr GM, Wratten SD, Altieri MA, eds, Ecological engineering for pest management: Advances in habitat manipulation for arthropods, Collingwood, Australia: CSIRO Publishing, pp 13–31
  • Ando T, Xu Q, Torres M, Kusugami K, Israel DA, Blaser MJ (2000) Restriction-modification system differences in Helicobacter pylori are a barrier to interstrain plasmid transfer. Mol. Microbiol. 37: 1052–65 [CrossRef] [PubMed]
  • Angle JS (1994) Release of Transgenic Plants - Biodiversity and Population-Level Considerations. Mol. Ecol. 3: 45–50 [CrossRef]
  • Aragao FJL, Sarokin L, Vianna GR, Rech EL (2000) Selection of transgenic meristematic cells utilizing a herbicidal molecule results in the recovery of fertile transgenic soybean [Glycine max (L.) Merril] plants at a high frequency. Theoret. Appl. Genet. 101: 1–6 [CrossRef]
  • Avery OT, MacLeod CM, McCarthy M (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types. I. Induction of transformation by a deoxyribonucleic acid fraction isolated from Pneumococcus type III. J. Exp. Med. 79: 137
  • Barry G, Kishore G, Padgette S, Talor M, Kolacz K, Weldon M, Re D, Eichholtz D, Fincher K, Hallas L (1992) Inhibitors of amino acid biosynthesis: strategies for imparting glyphosate tolerance to plants. In Singh BK, Flores HE, Shannon JC, eds, Biosynthesis and Molecular Regulation of Amino Acids in Plants, American Society of Plant Physiology, pp 139–145
  • Baur B, Hanselmann K, Schlimme W, Jenni B (1996) Genetic transformation in freshwater: Escherichia coli is able to develop natural competence. Appl. Environ. Microbiol. 62: 3673–3678 [PubMed]
  • Becker R, Ulrich A, Hedtke C, Hornermeier B (2001) Einfluss des Anbaus von transgenem herbizidresistentem Raps auf das Agrarökosystem. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 44: 159–167 [CrossRef]
  • Belzile FJ (2002) Transgenic, transplastomic and other genetically modified plants: a Canadian perspective. Biochimie 84: 1111–1118 [CrossRef] [PubMed]
  • Berndt C, Meier P, Wackernagel W (2003) DNA restriction is a barrier to natural transformation in Pseudomonas stutzeri JM300. Microbiol. 149: 895–901 [CrossRef]
  • Bertolla F, Van Gijsegem F, Nesme X, Simonet P (1997) Conditions for natural transformation of Ralstonia solanacearum. Appl. Environ. Microbiol. 63: 4965–4968 [PubMed]
  • Bertolla F, Frostegard A, Brito B, Nesme X, Simonet P (1999) During infection of its host, the plant pathogen Ralstonia solanacearum naturally develops a state of competence and exchanges genetic material. Mol. Plant Microbe Interact. 12: 467–472 [CrossRef]
  • Bertolla F, Pepin R, Passelegue-Robe E, Paget E, Simkin A, Nesme X, Simonet P (2000) Plant genome complexity may be a factor limiting in situ the transfer of transgenic plant genes to the phytopathogen Ralstonia solanacearum. Appl. Environ. Microbiol. 66: 4161–4167 [CrossRef] [PubMed]
  • Bickle TA, Kruger DH (1993) Biology of DNA restriction. Microbiol. Rev. 57: 434–450 [PubMed]
  • Björklöf K, Suoniemi A, Haahtela K, Romantschuk M (1995) High frequency of conjugation versus plasmid segregation of RP1 in epiphytic Pseudomonas syringae populations. Microbiol. 141: 2719–2727 [CrossRef]
  • Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A (2001) The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 11: 731–753 [CrossRef] [PubMed]
  • Boyle JR, Lundkvist H, Smith CT (2001) Ecological considerations for potentially sustainable plantation forests. In Strauss SH, Bradshaw HD, eds, Proc. of the 1st Int. Symp. on Ecological and Societal Aspects of Transgenic Plantations, Stevenson, WA, 22–24 July 2001, College of Forestry, Oregon State University, Corvallis, pp 151–157
  • Bron S, Luxen E, Venema G (1980) Restriction and modification in Bacillus subtilis. Mol. Gen. Genet. 179: 103–110
  • Carrer H, Hockenberry TN, Svab Z, Maliga P (1993) Kanamycin resistance as a selectable marker for plastid transformation in tobacco. Mol. Gen. Genet. 241: 49–56 [CrossRef] [PubMed]
  • Castaldini M, Turrini A, Sbrana C, Benedetti A, Marchionni M, Mocali S, Fabiani A, Landi S, Santomassimo F, Pietrangeli B, Nuti MP, Miclaus N, Giovannetti M (2005) Impact of Bt corn on rhizospheric and soil eubacterial communities and on beneficial mycorrhizal symbiosis in experimental microcosms. Appl. Environ. Microbiol. 71: 6719–6729 [CrossRef] [PubMed]
  • Ceccherini MT, Castialdini M, Piovanelli C, Hastings RC, McCarthy AJ, Bazzicalupo M, Miclaus N (1998) Effects of swine manure on autotrophic ammonia-oxidizing bacteria in soil microcosms. Appl. Soil. Ecol. 7: 149–157 [CrossRef]
  • Ceccherini M, Pote J, Kay E, Van VT, Marechal J, Pietramellara G, Nannipieri P, Vogel TM, Simonet P (2003) Degradation and transformability of DNA from transgenic leaves. Appl. Environ. Microbiol. 69: 673–678 [CrossRef] [PubMed]
  • Cérémonie H, Buret F, Simonet P, Vogel TM (2004) Isolation of lightning-competent soil bacteria. Appl. Environ. Microbiol. 70: 6342–6346 [CrossRef] [PubMed]
  • Cérémonie H, Buret F, Simonet P, Vogel TM (2006) Natural electro-transformation of lightning competent Pseudomonas strain in artificial soil microcosms. Appl. Environ. Microbiol. 72: 2385–2389
  • Claverys J-P, Martin B (2003) Bacterial competence genes: signatures of active transformation, or only remnants? Trends Microbiol. 11: 161–165 [CrossRef] [PubMed]
  • Comai L, Facciotti D, Hiatt WR, Thompson G, Rose RE, Stalker DM (1985) Expression in plants of a mutant aroA gene from Salmonella typhimurium confers tolerance to glyphosate. Nature 317: 741–744 [CrossRef]
  • Comai L, Larson-Kelly N, Kiser J, Mau CJ, Pokalsky AR, Shewmaker CK, McBride K, Jones A, Stalker DM (1988) Chloroplast transport of a ribulose bisphosphate carboxylase small subunit-5-enolpyruvyl 3-phosphoshikimate synthase chimeric protein requires part of the mature small subunit in addition to the transit peptide. J. Biol. Chem. 263: 15104–15109
  • Crecchio C, Stotzky G (1998) Binding of DNA on humic acids: effect on transformation of Bacillus subtilis and resistance to DNase. Soil Biol. Biochem. 30: 1061–1067 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Daniell H, Muthukumar B, Lee SB (2001a) Marker free transgenic plants: engineering the chloroplast genome without the use of antibiotic selection. Curr. Genet. 39: 109–116 [CrossRef] [PubMed]
  • Daniell H, Wiebe PO, Millan AF (2001b) Antibiotic-free chloroplast genetic engineering - an environmentally friendly approach. Trends Plant Sci. 6: 237–239 [CrossRef] [PubMed]
  • Daniell H, Khan MS, Allison L (2002) Milestones in chloroplast genetic engineering: an environmentally friendly era in biotechnology. Trends Plant. Sci. 7: 84–91 [CrossRef] [PubMed]
  • Davies J (1994) Inactivation of antibiotics and the dissemination of resistance genes. Science 264: 375–382 [CrossRef] [PubMed]
  • De Leij F, Sutton E, Whipps J, Fenlon J, Lynch J (1995) Impact of field release of genetically modified Pseudomonas fluorescens on indigenous microbial populations of wheat. Appl. Environ. Microbiol. 61: 3443–3453 [PubMed]
  • de Lipthay JR, Barkay T, Sorensen SJ (2001) Enhanced degradation of phenoxyacetic acid in soil by horizontal transfer of the tfdA gene encoding a 2,4-dichlorophenoxyacetic acid dioxygenase. FEMS Microbiol. Ecol. 35: 75–84 [PubMed]
  • de Vries J, Wackernagel W (1998) Detection of nptII (kanamycin resistance) genes in genomes of transgenic plants by marker-rescue transformation. Mol. Gen. Genet. 257: 606–613 [CrossRef] [PubMed]
  • de Vries J, Wackernagel W (2002) Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination. Proc Natl. Acad. Sci. USA 99: 2094–2099 [CrossRef]
  • de Vries J, Wackernagel W (2004) Microbial horizontal gene transfer and the DNA release from transgenic crop plants. Plant Soil 266: 91–104
  • de Vries J, Meier P, Wackernagel W (2001) The natural transformation of the soil bacteria Pseudomonas stutzeri and Acinetobacter sp. by transgenic plant DNA strictly depends on homologous sequences in the recipient cells. FEMS Microbiol. Lett. 195: 211–215 [PubMed]
  • DeBlock M, Herrera-Estrella L, Van Montagu M, Schell J, Zambryski P (1984) Expression of foreign genes in regenerated plants and in their progeny. EMBO J. 3: 1681–1689 [PubMed]
  • DeBlock M, Schell J, Van Montagu M (1985) Chloroplast transformation by Agrobacterium tumefaciens. EMBO J. 4: 1367–1372 [PubMed]
  • DeBlock M, De Brower D, Tenning P (1989) Transformation of Brassica napus and Brassica oleracea using Agrobacterium tumefaciens and the expression of the bar and neo genes in the transgenic plants. Plant Physiol. 91: 694–701 [CrossRef] [PubMed]
  • Della Cioppa G, Christopher Bauer S, Taylor ML, Rochester DE, Klein BK, Shah DM, Fraley RT, Kishore GM (1987) Targeting a herbicide-resistant enzyme from Escherichia coli to chloroplasts of higher plants. Nat. Biotech. 5: 579–584 [CrossRef]
  • Demanèche S, Bertolla F, Buret F, Nalin R, Sailland A, Auriol P, Vogel TM, Simonet P (2001a) Laboratory-scale evidence for lightning-mediated gene transfer in soil. Appl. Environ. Microbiol. 67: 3440–3444 [CrossRef] [PubMed]
  • Demanèche S, Jocteur-Monrozier L, Quiquampoix H, Simonet P (2001b) Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA. Appl. Environ. Microbiol. 67: 293–299 [CrossRef] [PubMed]
  • Demanèche S, Kay E, Gourbière F, Simonet P (2001c) Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil. Appl. Environ. Microbiol. 67: 2617–2621 [CrossRef] [PubMed]
  • Di Giovanni GD, Watrud LS, Seidler RJ, Widmer F (1999) Comparison of parental and transgenic alfalfa rhizosphere bacterial communities using Biolog GN metabolic fingerprinting and enterobacterial repetitive intergenic consensus sequence-PCR (ERIC-PCR). Microb. Ecol. 37: 129–139 [CrossRef] [PubMed]
  • Donegan KK, Seidler RJ, Doyle JD, Porteous LA, Digiovanni G, Widmer F, Watrud LS (1999) A field study with genetically engineered alfalfa inoculated with recombinant Sinorhizobium meliloti: effects on the soil ecosystem. J. Appl. Ecol. 36: 920–936
  • Dubnau D (1999) DNA uptake in bacteria. Annu. Rev. Microbiol. 53: 217–244
  • Dunfield KE, Germida JJ (2001) Diversity of bacterial communities in the rhizosphere and root interior of field-grown genetically modified Brassica napus. FEMS Microbiol. Ecol. 38: 1–9 [CrossRef]
  • Dunfield KE, Germida JJ (2003) Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus). Appl. Environ. Microbiol. 69: 7310–7318 [CrossRef] [PubMed]
  • Dunfield KE, Germida JJ (2004) Impact of genetically modified crops on soil- and plant-associated microbial communities. J. Environ. Qual. 33: 806–815 [CrossRef] [PubMed]
  • Dunwell JM (1999) Transgenic Crops: The next generation, or an example of 2020 vision. Annals Botan. 84: 269–277 [CrossRef]
  • Dykhuizen DE (1998) Santa Rosalia revisited: Why are there so many species of bacteria? Antonie van Leeuwenhoek 73: 25–33
  • Eichholtz DA, Rogers SG, Horsch RB, Klee HJ, Hayford M, Hoffmann NL, Braford SB, Fink C, Flick J, O'Connell KM, Froley RT (1987) Expression of mouse dihydrofolate reductase gene confers methotrexate resistance in transgenic petunia plants. Somatic Cell. Mol. Genet. 13: 67–76
  • Fraley RT, Rogers SG, Horsch RB, Sanders PR, Flick JS, Adams SP, Bittner ML, Brand LA, Fink CL, Fry JS, Galluppi GR, Goldberg SB, Hoffmann NL, Woo SC (1983) Expression of bacterial genes in plant cells. Proc. Natl. Acad. Sci. USA 80: 4803–4807 [CrossRef]
  • Franchi M, Bramanti E, Morassi Bonzi L, Luigi Orioli P, Vettori C, Gallori E (1999) Clay-nucleic acid complexes: characteristics and implications for the preservation of genetic material in primeval habitats. Orig. Life Evol. Biosph. 29: 297–315 [CrossRef] [PubMed]
  • Freyssinet G, Pelissier B, Freyssinet M, Delon R (1996) Crops resistant to oxynils: from the laboratory to the market. Field Crops Res. 45: 125–133
  • Frostegard A, Courtois S, Ramisse V, Clerc S, Bernillon D, Le Gall F, Jeannin P, Nesme X, Simonet P (1999) Quantification of bias related to the extraction of DNA directly from soils. Appl. Environ. Microbiol. 65: 5409–5420 [PubMed]
  • Gallori E, Bazzicalupo M, Dal Canto L, Fani R, Nannipieri P, Vettori C, Stotzky G (1994) Transformation of Bacillus subtilis by DNA bound on clay in non-sterile soil. FEMS Microbiol. Ecol. 15: 119–126 [CrossRef]
  • Gebhard F, Smalla K (1998) Transformation of Acinetobacter sp. strain BD413 by transgenic sugar beet DNA. Appl. Environ. Microbiol. 64: 1550–1554 [PubMed]
  • Gebhard F, Smalla K (1999) Monitoring field releases of genetically modified sugar beets for persistence of transgenic plant DNA and horizontal gene transfer. FEMS Microbiol. Ecol. 28: 261–272 [CrossRef]
  • Goddijn OJ, van der Duyn Schouten PM, Schilperoort RA, Hoge JH (1993) A chimaeric tryptophan decarboxylase gene as a novel selectable marker in plant cells. Plant. Mol. Biol. 22: 907–912 [CrossRef] [PubMed]
  • Goldstein DA, Tinland B, Gilbertson LA, Staub JM, Bannon GA, Goodman RE, McCoy RL, Silvanovich A (2005) Human safety and genetically modified plants: a review of antibiotic resistance markers and future transformation selection technologies. J. Appl. Microbiol. 99: 7–23 [CrossRef] [PubMed]
  • Gossele V, Aarssen R, Cornelissen M (1994) A 6' gentamicin acetyltransferase gene allows effective selection of tobacco transformants using kanamycin as a substrate. Plant Mol. Biol. 26: 2009–2012
  • Gough KC, Hawes WS, Kilpatrick J, Whitelam GC (2001) Cyanobacterial GR6 glutamate-1-semialdehyde aminotransferase: A novel enzyme-based selectable marker for plant transformation. Plant Cell Rep. 20: 296–300 [CrossRef]
  • Graham JB, Istock CA (1978) Genetic exchange in Bacillus subtilis in soil. Mol. Genet. Genom. 166: 287–290
  • Graham JB, Istock CA (1979) Gene exchange and natural selection cause Bacillus subtilis to evolve in soil culture. Science 204: 637–639 [CrossRef] [PubMed]
  • Greaves MP, Wilson MJ (1970) The degradation of nucleic acids and montmorillonite-nucleic-acid complexes by soil microorganisms. Soil Biol. Biochem. 2: 257–268 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Greenpeace (2003) Monsanto out of our food. Greenpeace International Briefing for the World Social Forum, Porto Alegre, Brazil
  • Griffith F (1928) The significance of pneumococcal types. J. Hyg. 27: 113–159 [CrossRef] [PubMed]
  • Griffiths B, Caul S, Thompson JA, Birch N, Scrimgeour C, Cortet J, Foggo A, Hackett C, Henning Krogh P (2006) Soil microbial and faunal community responses to Bt maize and insecticide in two soils. J. Environ. Qual. 35: 734–741 [CrossRef] [PubMed]
  • Guerineau F, Brooks L, Meadows J, Lucy A, Robinson C, Mullineaux P (1990) Sulfonamide resistance gene for plant transformation. Plant Mol. Biol. 15: 127–136 [CrossRef] [PubMed]
  • Gulden R, Lerat HS, Hart MM, Powell JR, Trevors JT, Pauls PK, Klironomos JN, Swanton CJ (2005) Quantitation of transgenic plant DNA in Leachate water: real-time polymerase chain reaction analysis. J. Agric. Food Chem. 53: 5858–5865 [CrossRef] [PubMed]
  • Gyamfi S, Pfeifer U, Stierschneider M, Sessitsch A (2002) Effects of transgenic glufosinate-tolerant oilseed rape (Brassica napus) and the associated herbicide application on eubacterial and Pseudomonas communities in the rhizosphere. FEMS Microbiol. Ecol. 41: 181–190 [CrossRef] [PubMed]
  • Hails R, Kinderlerer J (2003) The GM public debate: context and communication strategies. Nat. Rev. Genet. 4: 819–825 [CrossRef] [PubMed]
  • Haldrup A, Petersen SG, Okkels FT (1998a) Positive selection: a plant selection principle based on xylose isomerase, an enzyme used in the food industry. Plant Cell Rep. 18: 76–81 [CrossRef]
  • Haldrup A, Petersen SG, Okkels FT (1998b) The xylose isomerase gene from Thermoanaerobacterium thermosulfurogenes allows effective selection of transgenic plant cells using D-xylose as the selection agent. Plant Mol. Biol. 37: 287–296 [CrossRef] [PubMed]
  • Hall L, Topinka K, Huffman J, Davis L, Good A (2000) Pollen flow between herbicide-resistant Brassica napus is the cause of multiple-resistant B. napus volunteers. Weed Sci. 48: 688–694 [CrossRef]
  • Hastings RC, Ceccherini MT, Miclaus N, Saunders JR, Bazzicalupo M, McCarthy AJ (1997) Direct molecular biological analysis of ammonia oxidising bacteria populations in cultivated soil plots treated with swine manure. FEMS Microbiol. Ecol. 23: 45–54 [CrossRef]
  • Hayford MB, Medford JI, Hoffman NL, Rogers SG, Klee HJ (1988) Development of a plant transformation selection system based on expression of genes encoding gentamycin acetyltransferases. Plant Physiol. 86: 1216–1222 [CrossRef] [PubMed]
  • Herrera-Estrella L, De Block M, Messens E, Hernalsteen J-P, Van Montagu M, Schell J (1983) Chimeric genes as dominant selectable markers in plant cells. EMBO J. 2: 987–995 [PubMed]
  • Heuer H, Kroppenstedt RM, Lottmann J, Berg G, Smalla K (2002) Effects of T4 lysozyme release from transgenic potato roots on bacterial rhizosphere communities are negligible relative to natural factors. Appl. Environ. Microbiol. 68: 1325–1335 [CrossRef] [PubMed]
  • Hille J, Verheggen F, Roelvink P, Franssen H, Kammen A, Zabel P (1986) Bleomycin resistance: a new dominant selectable marker for plant cell transformation. Plant. Mol. Biol. 7: 171–176 [CrossRef] [PubMed]
  • Hiltner L (1904) Über neue Erfahrungen und Probleme auf dem Gebiete der Bodenbakteriologie. Arbeiten der Deutschen Landwirtschaftsgesellschaft 98: 59–78
  • Horsch RB, Fry JE, Hoffmann NL, Eicholtz D, Rogers SG, Fraley RT (1985) A simple and general method for transferring genes into plants. Science 227: 1229–1231 [CrossRef] [PubMed]
  • Howe AR, Gasser CS, Brown SM, Padgette SR, Hart J, Parker GB, Fromm ME, Armstrong CL (2002) Glyphosate as a selective agent for the production of fertile transgenic maize (Zea mays) plants. Mol. Breed. 10: 153–164 [CrossRef]
  • Irdani T, Bogani P, Mengoni A, Mastromei G, Buiatti M (1998) Construction of a new vector conferring methotrexate resistance in Nicotiana tabacum plants. Plant Mol. Biol. 37: 1079–1084 [CrossRef] [PubMed]
  • James C (2006) Executive summary of global status of commercialized Biotech/GM Crops: 2006. ISAAA Briefs No. 35, ISAAA: Ithaca, NY
  • Jelenska J, Tietze E, Tempe J, Brevet J (2000) Streptothricin resistance as a novel selectable marker for transgenic plant cells. Plant Cell Rep. 19: 298–303 [CrossRef]
  • Joersbo M, Okkels FT (1996) A novel principle for selection of transgenic plant cells: positive selection. Plant Cell Rep. 16: 219–221 [CrossRef] [PubMed]
  • Joersbo M, Donaldson I, Kreiberg J, Peterson SG, Brunstedt J, Okkels FT (1998) Analysis of mannose selection used for transformation of sugar beet. Mol. Breed. 4: 111–117 [CrossRef]
  • Kaeberlein T, Lewis K, Epstein SS (2002) Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296: 1127–1129 [CrossRef] [PubMed]
  • Kay E, Bertolla F, Vogel TM, Simonet P (2002a) Opportunistic colonization of Ralstonia solanacearum-infected plants by Acinetobacter sp. and its natural competence development. Microbiol. Ecol. 43: 291–297 [CrossRef] [PubMed]
  • Kay E, Vogel TM, Bertolla F, Nalin R, Simonet P (2002b) In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria. Appl. Environ. Microbiol. 68: 3345–3351 [CrossRef] [PubMed]
  • Khan SM, Maliga P (1999) Fluorescent antibiotic resistance marker for tracking plastid transformation in higher plants. Nat. Biotechnol. 17: 910–915 [CrossRef]
  • Khanna M, Stotzky G (1992) Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of DNase on the transforming ability of bound DNA. Appl. Environ. Microbiol. 58: 1930–1939 [PubMed]
  • Kobayashi I (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucl. Acids Res. 29: 3742–3756 [CrossRef]
  • Koziel MG, Adams TL, Hazlet MA, Damm D, Miller J, Dahlbeck D, Jayne S, Staskawicz BJ (1984) A cauliflower mosaic virus promoter directs expression of kanamycin resistance in morphogenic transformed plant cells. J. Mol. Appl. Genet. 2: 549–562 [PubMed]
  • Krens FA, Molendijk L, Wullems GJ, Schilperoort RA (1982) In vitro transformation of plant protoplasts with Ti-plasmid DNA. Nature 296: 72–74
  • Kunze I, Ebneth M, Heim U, Geiger M, Sonnewald U, Herbers K (2001) 2-Deoxyglucose resistance: A novel selection marker for plant transformation. Mol. Breed. 7: 221–227 [CrossRef]
  • Lacks SA, Springhorn SS (1984) Transfer of recombinant plasmids containing the gene for DpnII DNA methylase into strains of Streptococcus pneumoniae that produce DpnI or DpnII restriction endonucleases. J. Bacteriol. 158: 905–909
  • Lederberg J, Tatum EL (1946) Gene recombination in Escherichia coli. Nature 158: 558 [CrossRef]
  • Li YH, Lau PC, Lee JH, Ellen RP, Cvitkovitch DG (2001) Natural genetic transformation of Streptococcus mutans growing in biofilms. J. Bacteriol. 183: 897–908 [CrossRef] [PubMed]
  • Li YH, Tang N, Aspiras MB, Lau PC, Lee JH, Ellen RP, Cvitkovitch DG (2002) A quorum-sensing signaling system essential for genetic competence in Streptococcus mutans is involved in biofilm formation. J. Bacteriol. 184: 2699–2708 [CrossRef] [PubMed]
  • Lorenz MG, Sikorski J (2000) The potential for intraspecific horizontal gene exchange by natural genetic transformation: sexual isolation among genomovars of Pseudomonas stutzeri. Microbiol. 146: 3081–3090
  • Lorenz MG, Wackernagel W (1991) High frequency of natural genetic transformation of Pseudomonas stutzeri in soil extract supplemented with a carbon/energy and phosphorus source. Appl. Environ. Microbiol. 57: 1246–1251 [PubMed]
  • Lorenz MG, Wackernagel W (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58: 563–602 [PubMed]
  • Lukow T, Dunfield PF, Liesack W (2000) Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiol. Ecol. 32: 241–247 [CrossRef] [PubMed]
  • Macneil DJ (1988) Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis. J. Bacteriol. 170: 5607–5612
  • Majewski J, Zawadzki P, Pickerill P, Cohan FM, Dowson CG (2000) Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J. Bacteriol. 182: 1016–1023 [CrossRef] [PubMed]
  • Maliga P, Svab Z, Harper EC, Jones JDG (1988) Improved expression of streptomycin resistance in plants due to a deletion in the streptomycin phosphotransferase coding sequence. Mol. Genet. Genom. 214: 456–459
  • Mansouri H, Petit A, Oger P, Dessaux Y (2002) Engineered rhizosphere: the trophic bias generated by opine-producing plants is independent of the opine type, the soil origin, and the plant species. Appl. Environ. Microbiol. 68: 2562–2566 [CrossRef] [PubMed]
  • Margulis L (1981) Symbiosis in Cell Evolution. WH Freeman and Company, New York
  • Marvier M (2001) Ecology of transgenic crops. Am. Sci. 89: 160–167
  • Marvier M, van Acker RC (2005) Can crop transgenes be kept on a leash? Front. Ecol. Environ. 3: 99–106 [CrossRef]
  • Matic I, Rayssiguier C, Radman M (1995) Interspecies gene exchange in bacteria: The role of SOS and mismatch repair systems in evolution of species. Cell 80: 507–515 [CrossRef] [PubMed]
  • McFadden GI (2001) Chloroplast origin and integration. Plant Physiol. 125: 50–53 [CrossRef] [PubMed]
  • Meier P, Wackernagel W (2003a) Mechanisms of homology-facilitated illegitimate recombination for foreign DNA acquisition in transformable Pseudomonas stutzeri. Mol. Microbiol. 48: 1107–1118
  • Meier P, Wackernagel W (2003b) Monitoring the spread of recombinant DNA from field plots with transgenic sugar beet plants by PCR and natural transformation of Pseudomonas stutzeri. Transgenic Res. 12: 293–304
  • Melzak KA, Sherwood CS, Turner RFB, Haynes CA (1996) Driving forces for DNA adsorption to silica in perchlorate solutions. J. Coll. Interface Sci. 181: 635–644 [CrossRef]
  • Mendum TA, Clark IM, Hirsch PR (2001) Characterization of two novel Rhizobium leguminosarum bacteriophages from a field release site of genetically-modified rhizobia. Antonie van Leeuwenhoek 79: 189–197 [CrossRef] [PubMed]
  • Miki B, McHugh S (2004) Selectable marker genes in transgenic plants: applications, alternatives and biosafety. J. Biotechnol. 107: 193–232 [CrossRef] [PubMed]
  • Molin S, 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
  • Motavalli PP, Kremer RJ, Fang M, Means NE (2004) Impact of genetically modified crops and their management on soil microbially mediated plant nutrient transformations. J. Environ. Qual. 33: 816–824 [CrossRef] [PubMed]
  • Nakamura Y, Itoh T, Matsuda H, Gobori T (2004) Biased function of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 36: 760–766 [CrossRef] [PubMed]
  • Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Europ. J. Soil Sci. 54: 655–670 [CrossRef]
  • Nielsen KM, Townsend JP (2004) Monitoring and modeling horizontal gene transfer. Nat. Biotechnol. 22: 1110–1114 [CrossRef] [PubMed]
  • Nielsen KM, van Elsas JD (2001) Stimulatory effects of compounds present in the rhizosphere on natural transformation of Acinetobacter sp. BD413 in soil. Soil Biol. Biochem. 33: 345–357 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Nielsen KM, van Weerelt MD, Berg TN, Bones AM, Hagler AN, van Elsas JD (1997) Natural transformation and availability of transforming DNA to Acinetobacter calcoaceticus in soil microcosms. Appl. Environ. Microbiol. 63: 1945–1952 [PubMed]
  • Nielsen KM, Bones AM, Smalla K, van Elsas JD (1998) Horizontal gene transfer from transgenic plants to terrestrial bacteria: a rare event? FEMS Microbiol. Rev. 22: 99–103
  • Nielsen KM, Smalla K, van Elsas JD (2000a) Natural transformation of Acinetobacter sp. strain BD413 with cell lysates of Acinetobacter sp., Pseudomonas fluorescens, and Burkholderia cepacia in soil microcosms. Appl. Environ. Microbiol. 66: 206–212 [CrossRef] [PubMed]
  • Nielsen KM, van Elsas JD, Smalla K (2000b) Transformation of Acinetobacter sp. strain BD413 (pFG4Formula nptII) with transgenic plant DNA in soil microcosms and effects of kanamycin on selection of transformants. Appl. Environ. Microbiol. 66: 1237–1242 [CrossRef] [PubMed]
  • Normander B, Christensen BB, Molin S, Kroer N (1998) Effect of bacterial distribution and activity on conjugal gene transfer on the phylloplane of the bush bean (Phaseolus vulgaris). Appl. Environ. Microbiol. 64: 1902–1909 [PubMed]
  • Oger P, Petit A, Dessaux Y (1997) Genetically engineered plants producing opines alter their biological environment. Nat. Biotechnol. 15: 369–372
  • Oger P, Mansouri H, Dessaux Y (2000) Effect of crop rotation and soil cover on alteration of the soil microflora generated by the culture of transgenic plants producing opines. Mol. Ecol. 9: 881–890 [CrossRef] [PubMed]
  • Ogram A, Sayler GS, Gustin D, Lewis RJ (1988) DNA Adsorption to soils and sediments. Environ. Sci. Technol. 22: 982–984 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Olszewski NE, Martin FB, Ausubel FM (1988) Specialized binary vector for plant transformation: expression of the Arabidopsis thaliana AHAS gene in Nicotiana tabacum. Nucleic Acids Res. 16: 10765–10781 [CrossRef] [PubMed]
  • Otero RDC, Hsieh P (1995) Homologous recombination proteins in prokaryotes and eukaryotes. Annual Rev. Genet. 29: 509–552 [CrossRef]
  • Ow DW (2002) Recombinase-directed plant transformation for the post-genomic era. Plant. Mol. Biol. 48: 183–200 [CrossRef] [PubMed]
  • Paget E, Simonet P (1994) On the track of natural transformation in soil. FEMS Microbiol. Ecol. 15: 109–117 [CrossRef]
  • Paget E, Jocteur Monrozier L, Simonet P (1992) Adsorption of DNA on clay minerals: protection against DNase I and influence on gene transfer. FEMS Microbiol. Lett. 97: 31–40
  • Paget E, Lebrun M, Freyssinet G, Simonet P (1998) The fate of recombinant plant DNA in soil. Europ. J. Soil Biol. 34: 81–88
  • Perez P, Tiraby G, Kallerhoff J, Perret J (1989) Phleomycin resistance as a dominant selectable marker for plant cell transformation. Plant Mol. Biol. 13: 365–373 [CrossRef] [PubMed]
  • Perl A, Galili S, Shaul O, Ben-Tzvi I, Galili G (1993) Bacterial dihydrodipicolinate synthase and desensitized aspartate kinase: Two novel selectable markers for plant transformation. Biotechnol. 11: 715–718
  • Pietramellara G, Dal Canto L, Vettori C, Gallori E, Nannipieri P (1997) Effects of air-drying and wetting cycles on the transforming ability of DNA bound on clay minerals. Soil Biol. Biochem. 29: 55–61 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Pietramellara G, Franchi M, Gallori E, Nannipieri P (2001) Effect of molecular characteristics of DNA on its adsorption and binding on homoionic montmorillonite and kaolinite. Biol. Fertil. Soils 33: 402–409 [CrossRef]
  • Poly F, Chenu C, Simonet P, Rouiller J, Jocteur Monrozier L (2000) Differences between linear chromosomal and supercoiled plasmid DNA in their mechanisms and extent of adsorption on clay minerals. Langmuir 16: 1233–1238 [CrossRef]
  • Poté J, Ceccherini M, Van VT, Rosselli W, Wildi W, Simonet P, Vogel TM (2003) Fate and transport of antibiotic resistance genes in saturated soil columns. Europ. J. Soil Biol. 39: 65–71 [CrossRef]
  • Prudhomme M, Libante V, Claverys J-P (2002) Homologous recombination at the border: Insertion-deletions and the trapping of foreign DNA in Streptococcus pneumoniae. Proc. Natl. Acad. Sci. USA 99: 2100–2105 [CrossRef]
  • Quist D (2004) Transgene ecology: An ecological perspective for GMO risk assessment. In Breckling B, Verhoeven R, eds, Risk Hazard Damage - Specification of criteria to assess environmental impact of genetically modified organisms. Bundesamt für Naturschutz. Naturschutz und Biologische Vielfalt, Bonn, pp 239–244
  • Ray JL, Nielsen KM (2005) Experimental methods for assaying natural transformation and inferring horizontal gene transfer. In Zimmer EA, Roalson EH, eds, Methods in Enzymology, Academic Press, pp 491–520
  • Rayssiguier C, Thaler DS, Radman M (1989) The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342: 396–401 [CrossRef] [PubMed]
  • Redaschi N, Bickle TA (1996) Posttranscriptional regulation of EcoP1I and EcoP15I restriction activity. J. Mol. Biol. 257: 790–803
  • Roberts MS, Cohan FM (1993) The effect of DNA sequence divergence on sexual isolation in Bacillus. Genetics 134: 401–408 [PubMed]
  • Romanowski G, Lorenz MG, Wackernagel W (1991) Adsorption of plasmid DNA to mineral surfaces and protection against DNase I. Appl. Environ. Microbiol. 57: 1057–1061 [PubMed]
  • Romanowski G, Lorenz MG, Wackernagel W (1993) Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils. Appl. Environ. Microbiol. 59: 3438–3446 [PubMed]
  • Saxena D, Stotzky G (2000) Insecticidal toxin from Bacillus thuringiensis is released from roots of transgenic Bt corn in vitro and in situ. FEMS Microbiol. Ecol. 33: 35–39 [CrossRef] [PubMed]
  • Saxena D, Flores S, Stotzky G (1999) Insecticidal toxin in root exudates from Bt corn. Nature 402: 480 [PubMed]
  • Schlüter K, Fütterer J, Potrykus I (1995) Horizontal gene transfer from a transgenic potato line to a bacterial pathogen (Erwinia chrysanthemi) occurs – if at all – at an extremely low frequency. Biotechnol. 13: 1094–1098 [CrossRef]
  • Schmalenberger A, Tebbe CC (2002) Bacterial community composition in the rhizosphere of a transgenic, herbicide-resistant maize (Zea mays) and comparison to its non-transgenic cultivar Bosphore. FEMS Microbiol. Ecol. 40: 29–37 [CrossRef] [PubMed]
  • Sengelov G, Kowalchuk GA, Sørensen SJ (2000) Influence of fungal-bacterial interactions on bacterial conjugation in the residuesphere. FEMS Microbiol. Ecol. 31: 39–45 [PubMed]
  • Siciliano SD, Germida JJ (1999) Taxonomic diversity of bacteria associated with the roots of field-grown transgenic Brassica napus cv. Quest, compared to the non-transgenic B. napus cv. Excel and B. rapa cv. Parkland. FEMS Microbiol. Ecol. 29: 263–272 [CrossRef]
  • Sikorski J, Graupner S, Lorenz M, Wackernagel W (1998) Natural genetic transformation of Pseudomonas stutzeri in a non-sterile soil. Microbiol. 144: 569–576 [CrossRef]
  • Smiles D (1988) Aspects of the physical environment of soil organisms. Biol. Fertil. Soils 6: 204–215
  • Smith HO, Danner DB, Deich RA (1981) Genetic transformation. Annu. Rev. Biochem. 50: 41–68 [CrossRef] [PubMed]
  • Smith H, Tomb J, Dougherty B, Fleischmann R, Venter J (1995) Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome. Science 269: 538–540 [CrossRef] [PubMed]
  • Spoering AL, Gilmore MS (2006) Quorum sensing and DNA release in bacterial biofilms. Curr. Opin. Microbiol. 9: 133–137 [CrossRef] [PubMed]
  • Stephens PM, O'Sullivan M, O'Gara F (1987) Effect of bacteriophage on colonization of sugar beet roots by fluorescent Pseudomonas spp. Appl. Environ. Microbiol. 53: 1164–1167 [PubMed]
  • Stuy JH (1976) Restriction enzymes do not play a significant role in Haemophilus homospecific or heterospecific transformation. J. Bacteriol. 128: 212–220
  • Svab Z, Maliga P (1993) High-frequency plastid transformation in tobacco by selection for a chimeric aadA gene. Proc. Natl. Acad. Sci. USA 90: 913–917 [CrossRef]
  • Svab Z, Harper EC, Jones JDG, Maliga P (1990) Aminoglycoside-3'-adenyltransferase confers resistance to spectinomycin and streptomycin in Nicotiana tabacum. Plant Mol. Biol. 14: 197–205 [CrossRef] [PubMed]
  • Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nature 3: 711–721
  • Trevors JT (1996) Nucleic acids in the environment. Curr. Opin. Biotechnol. 7: 331–336 [CrossRef] [PubMed]
  • Ursin VM (1996) Aldehyde dehydrogenase selectable markers for plant transformation. WO 96/12029
  • van Elsas JD, Bailey MJ (2002) The ecology of transfer of mobile genetic elements. FEMS Microbiol. Ecol. 42: 187–197 [PubMed]
  • van Elsas JD, Turner S, Bailey MJ (2003) Horizontal gene transfer in the phytosphere. New Phytol. 157: 525–537 [CrossRef]
  • Vettori C, Paffetti D, Pietramellara G, Stotzky G, Gallori E (1996) Amplification of bacterial DNA bound on clay minerals by the random amplified polymorphic DNA (RAPD) technique. FEMS Microbiol. Ecol. 20: 251–260 [CrossRef]
  • Waipara NW, Obanor FO, Walter M (2002) Impact of phylloplane management on microbial populations. New Zealand Pl. Prot. 55: 125–128
  • Waldron C, Murphy EB, Roberts JL, Gustafson GD, Armour SL, Malcolm SK (1985) Resistance to hygromycin B. Plant Mol. Biol. 5: 103–108 [CrossRef] [PubMed]
  • Watrud L, Lee E, Fairbrother A, Burdick C, Reichman J, Bollman M, Storm M, King G, Van de Water P (2004) Evidence for landscape-level, pollen-mediated gene flow from genetically modified creeping bentgrass with CP4 EPSPS as a marker. Proc. Natl. Acad. Sci. USA 101: 14533–14538
  • Weeks JT, Koshiyama KY, Maier-Greiner U, Schaeffner T, Anderson OD (2000) Wheat transformation using cyanamide as a new selective agent. Crop Sci. 40: 1749–1754 [CrossRef]
  • Widmer F, Seidler RJ, Donegan KK, Reed GL (1997) Quantification of transgenic plant marker gene persistence in the field. Mol. Ecol. 6: 1–7 [CrossRef]
  • Widmer F, Seidler RJ, Wartrud LS (1996) Sensitive detection of transgenic plant marker gene persistence in soil microcosms. Mol. Ecol. 5: 603–613
  • Wisniewski JP, Frangne N, Massonneau A, Dumas C (2002) Between myth and reality: genetically modified maize, an example of a sizeable scientific controversy. Biochimie 84: 1095–1103 [CrossRef] [PubMed]
  • Zahrt TC, Maloy S (1997) Barriers to recombination between closely related bacteria: MutS and RecBCD inhibit recombination between Salmonella typhimurium and Salmonella typhi. Proc. Natl. Acad. Sci. USA 94: 9786–9791
  • Zahrt TC, Buchmeier N, Maloy S (1999) Effect of mutS and recD mutations on Salmonella virulence. Infect. Immun. 67: 6168–6172 [PubMed]
  • Zhou H, Arrowsmith JW, Fromm ME, Hironaka CM, Taylor ML, Rodriguez D, Pajeau ME, Brown SM, Santino CG, Fry JE (1995) Glyphosate-tolerant CP4 and GOX genes as a selectable marker in wheat transformation. Plant Cell Rep. 15: 159–163 [PubMed]
  • Zinder N, Lederberg J (1952) Genetic exchange in Salmonella. J. Bacteriol. 64: 679–699