Free Access
Environ. Biosafety Res.
Volume 7, Number 1, January-March 2008
Page(s) 11 - 24
Published online 03 April 2008
  • Andersen JM, Pedersen WB (1983) Analysis of plant phenolics by High-Performance Liquid Chromatography. J. Chromatogr. 259: 131–139
  • Baudoin E, Benizri E, Guckert A (2002) Impact of growth stage on the bacterial community structure along maize roots as determined by metabolic and genetic fingerprinting. Appl. Soil Ecol. 19: 135–145 [CrossRef]
  • Brusetti L, Francia P, Bertolini C, Pagliuca A, Borin S, Sorlini C, Abruzzese A, Sacchi G, Viti C, Giovannetti L, Giuntini E, Bazzicalupo M, Daffonchio D (2004) Bacterial communities associated with the rhizosphere of transgenic Bt 176 maize (Zea mays) and its non transgenic counterpart. Plant Soil 266: 11–21 [CrossRef]
  • Brusetti L, Borin S, Mora D, Rizzi A, Raddadi N, Sorlini C, Daffonchio D (2006) Usefulness of length heterogeneity-PCR for monitoring lactic acid bacteria succession during maize ensiling. FEMS Microbiol. Ecol. 56: 154–164
  • Cardinale M, Brusetti L, Quatrini P, Borin S, Puglia AM, Rizzi A, Zanardini E, Sorlini C, Corselli C, Daffonchio D (2004) Comparison of different primer sets for the Automated Ribosomal Intergenic Spacer Analysis (ARISA) of complex bacterial communities. Appl. Environ. Microbiol. 70: 6147–6156 [CrossRef] [PubMed]
  • Chiarini L, Bevivino A, Dalmastri C, Nacamulli C, Tabacchioni S (1998) Influence of plant development, cultivar and soil type on microbial colonisation of maize roots. Appl. Soil Ecol. 8: 11–18 [CrossRef]
  • Courtois J, Courtois B, Guillaume J (1988) High-frequency transformation of Rhizobium meliloti. J. Bacteriol. 170: 5925–5927 [PubMed]
  • Daffonchio D, Cherif A, Brusetti L, Rizzi A, Mora D, Boudabous A, Borin S (2003) Nature of polymorphisms in 16S-23S rRNA gene intergenic transcribed spacer fingerprinting of Bacillus and related genera. Appl. Environ. Microbiol. 69: 5128–5137 [CrossRef] [PubMed]
  • Daniell H, Datta R, Varma S, Gray S, Lee SB (1998) Containment of herbicide resistance through genetic engineering of the chloroplast genome. Nature Biotechnol. 16: 345–348
  • De Vries J, Herzfeld T, Wackernagel W (2004) Transfer of plastid DNA from tobacco to the soil bacterium Acinetobacter sp. by natural transformation. Mol. Microbiol. 53: 323–334 [CrossRef] [PubMed]
  • Demanèche S, Kay E, Gourbiere F, Simonet P (2001) Natural transformation of Pseudomonas fluorescence and Agrobacterium tumefaciens in soil. Appl. Environ. Microbiol. 67: 2617–1621
  • 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
  • Donegan KK, Palm CJ, Fieland VJ, Porteous LA, Ganio LM, Schaller DL, Bucao LQ, Seidler RJ (1995) Changes in levels, species and DNA fingerprints of soil microorganisms associated with cotton expressing the Bacillus thuringiensis var. kurstaki endotoxin. Appl. Soil Ecol. 2: 111–124
  • 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]
  • Einspanier R, Klotz A, Kraft J, Aulrich K, Poser R, Schwägele F, Jahreis G, Flachowsky G (2001) The fate of forage plant DNA in farm animals: a collaborative case-study investigating cattle and chicken fed recombinant plant material. Eur. Food Res. Technol. 212: 129–134
  • Falchini L, Naumova N, Kuikman PJ, Bloem J, Nannipieri P (2002) CO2 evolution and denaturing gradient gel electrophoresis profiles of bacterial communities in soil following addition of low molecular weight substrates to simulate root exudation. Soil Biol. Biochem. 36: 775–782 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Fan T, Lane A, Pedler J, Crowley D, Higashi R (1997) Comprehensive analysis of organic ligands in whole root exudates using Nuclear Magnetic Resonance and Gas Chromatography Mass Spectrometry. Anal. Biochem. 251: 57–68 [CrossRef] [PubMed]
  • Figurski D, Helinski DR (1979) Replication of an origin containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. PNAS 76: 1648–1652 [CrossRef]
  • Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl. Environ. Microbiol. 65: 4630–4636 [PubMed]
  • Gallori E, Bazzicalupo M, Dal Canto L, 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]
  • Gancedo MC, Luth BS (1986) HPLC analysis of organic acids and sugars in tomato juice. J. Food Science. 51: 571–573 [CrossRef]
  • Gomes NCM, Heuer H, Schönfeld J, Costa R, Mendonça-Hagler L, Smalla K (2001) Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil studied by temperature gradient gel electrophoresis. Plant Soil 232: 167–180 [CrossRef]
  • Gries D, Brunn S, Crowley D, Parker D (1995) Phytosiderophore release in relation to micronutrient metal deficiencies in barley. Plant Soil 172: 299–308
  • Gyamfi S, Pfeifer U, Stierschneider M, Sessitsch A (2002) Effects of transgenic gluphosinate-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]
  • Hammer Ø, Harper DAT, Ryan PD (2001) PAST: Paleontological Statistics Software Package for Education and Data Analysis. Palaeontologia Electronica 4: 1–9
  • 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]
  • Hinsinger P, Gobran GR, Gregory PJ, Wenzel WW (2005) Rhizosphere geometry and heterogeneity arising from root-mediated physical and chemical processes. New Phytologist. 168: 293–303
  • Jackman LM, Sternhell S (1969) Applications of Nuclear Magnetic Resonance Spectroscopy in Organic Chemistry, 2nd edn. Pergamon Press, UK, pp 207–214
  • Kay E, Vogel TM, Bertolla F, Nalin R, Simonet P (2002) In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria. Appl. Environ. Microbiol. 68: 3345–3351 [CrossRef] [PubMed]
  • Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Ann. Rev. Microbiol. 56: 211–36
  • Khanna M, Stotzky G (1992) Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of DNase on the availability of bound DNA. Appl. Environ. Microbiol. 58: 1930–1939 [PubMed]
  • Kok RG, Young DM, Ornston LN (1999) Phenotypic expression of PCR-generated random mutations in a Pseudomonas putida gene after its introduction into an Acinetobacter chromosome by natural transformation. Appl. Environ. Microbiol. 65: 1675–1780 [PubMed]
  • Lynch JM, Whipps JM (1990) Substrate flow in the rhizosphere. Plant Soil 129: 1–10 [CrossRef]
  • Magurran AE (1988) Ecological diversity and its measurement. Cambridge University Press, UK
  • 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]
  • McBee GG, Manes NO (1983) Determination of sucrose, glucose and fructose in plant tissue by HPLC. J. Chrom. 264: 474–478
  • Milling A, Smalla K, Maidl FX, Schloter M, Munch JC (2004) Effects of transgenic potatoes with an altered starch composition on the diversity of soil and rhizosphere bacteria and fungi. Plant Soil 266: 23–39 [CrossRef]
  • Nielsen KM, Ray JL, Van Elsas JD (2004) Natural transformation in soil: microcosm studies. In Molecular Microbial Ecology Manual, 2nd edn, Kluwer Academic Publishers, The Netherlands, pp 1–12
  • Oger P, Petit A, Dessaux Y (1997) Genetically engineered plants producing opines alter their biological environment. Nature Biotech. 15: 369–372 [CrossRef]
  • 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]
  • Paget E, Monrozier LJ, Simonet P (1992) Adsorption of DNA on clay minerals: protection against DNase I and influence on gene transfer. FEMS Microbiol. Lett. 97: 31–40
  • Pal KK, Tilak KVBR, Saxena AK, Dey R, Singh CS (2001) Suppression of maize root diseases caused by Macrophomina phaseolina, Fusarium moniliforme and Fusarium graminearum by plant growth promoting rhizobacteria. Microbiol. Res. 156: 209–223 [CrossRef] [PubMed]
  • Persello-Cartieaux F, Nussaume L, Robaglia C (2003) Tales from the underground: molecular plant-rhizobacteria interactions. Plant Cell Environ. 26: 189–199
  • 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]
  • Savka MA, Farrand SK (1997) Modification of rhizobacterial populations by engineering bacterium utilisation of a novel plant produced resource. Nature Biotech. 15: 363-368
  • Sessitsch A, Kan F-Y, Pfeifer U (2003) Diversity and community structure of culturable Bacillus spp. populations in the rhizospheres of transgenic potatoes expressing the lytic peptide cecropin B. Appl. Soil Ecol. 22: 149–158 [CrossRef]
  • 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]
  • Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl. Environ. Microbiol. 67: 4742–4751 [CrossRef] [PubMed]
  • Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S, Wernars K (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl. Environ. Microbiol. 67: 2284-2291 [CrossRef] [PubMed]
  • Tepfer D, Garcia-Gonzaleset R, Mansouri H, Seruga M, Message B, Leach F, Curkovic Perica M (2003) Homology-dependent DNA transfer from plants to a soil bacterium under laboratory conditions: implications in evolutions and horizontal gene transfer. Trans. Res. 12: 425–437 [CrossRef]
  • Vaneechoutte M, Young DM, Ornston LN, De Baere T, Nemec A, Van Der Reijden T, Carr E, Tjernberg I, Dijkshoorn L (2006) Naturally transformable Acinetobacter sp. strain ADP1 belongs to the newly described species Acinetobacter baylyi. Appl. Environ. Microbiol. 72: 932–936 [CrossRef] [PubMed]
  • Widmer F, Seidler RJ, Donegan KK, Reed GL (1997) Quantification of transgenic marker gene persistence in the field. Mol. Ecol. 6: 1–7 [CrossRef]
  • Wiren N, von Romheld V, Shioiri T, Marschner H (1995) Competition between micro-organism and roots of barley and sorghum for iron accumulated in the root apoplasm. New Phytol. 130: 511–521 [CrossRef]