Free Access
Issue
Environ. Biosafety Res.
Volume 7, Number 1, January-March 2008
Page(s) 11 - 24
DOI https://doi.org/10.1051/ebr:2008002
Published online 03 April 2008
  • Andersen JM, Pedersen WB (1983) Analysis of plant phenolics by High-Performance Liquid Chromatography. J. Chromatogr. 259: 131–139 [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • 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 [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • Courtois J, Courtois B, Guillaume J (1988) High-frequency transformation of Rhizobium meliloti. J. Bacteriol. 170: 5925–5927 [PubMed] [Google Scholar]
  • 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] [Google Scholar]
  • 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 [Google Scholar]
  • 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] [Google Scholar]
  • 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 [Google Scholar]
  • 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 [Google Scholar]
  • 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 [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • 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 [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • Gancedo MC, Luth BS (1986) HPLC analysis of organic acids and sugars in tomato juice. J. Food Science. 51: 571–573 [CrossRef] [Google Scholar]
  • 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] [Google Scholar]
  • Gries D, Brunn S, Crowley D, Parker D (1995) Phytosiderophore release in relation to micronutrient metal deficiencies in barley. Plant Soil 172: 299–308 [Google Scholar]
  • 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] [Google Scholar]
  • Hammer Ø, Harper DAT, Ryan PD (2001) PAST: Paleontological Statistics Software Package for Education and Data Analysis. Palaeontologia Electronica 4: 1–9 [Google Scholar]
  • 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] [Google Scholar]
  • 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 [Google Scholar]
  • Jackman LM, Sternhell S (1969) Applications of Nuclear Magnetic Resonance Spectroscopy in Organic Chemistry, 2nd edn. Pergamon Press, UK, pp 207–214 [Google Scholar]
  • 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] [Google Scholar]
  • Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Ann. Rev. Microbiol. 56: 211–36 [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • Lynch JM, Whipps JM (1990) Substrate flow in the rhizosphere. Plant Soil 129: 1–10 [CrossRef] [Google Scholar]
  • Magurran AE (1988) Ecological diversity and its measurement. Cambridge University Press, UK [Google Scholar]
  • 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] [Google Scholar]
  • McBee GG, Manes NO (1983) Determination of sucrose, glucose and fructose in plant tissue by HPLC. J. Chrom. 264: 474–478 [Google Scholar]
  • 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] [Google Scholar]
  • 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 [Google Scholar]
  • Oger P, Petit A, Dessaux Y (1997) Genetically engineered plants producing opines alter their biological environment. Nature Biotech. 15: 369–372 [CrossRef] [Google Scholar]
  • 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] [Google Scholar]
  • 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 [Google Scholar]
  • 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] [Google Scholar]
  • Persello-Cartieaux F, Nussaume L, Robaglia C (2003) Tales from the underground: molecular plant-rhizobacteria interactions. Plant Cell Environ. 26: 189–199 [Google Scholar]
  • 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] [Google Scholar]
  • Savka MA, Farrand SK (1997) Modification of rhizobacterial populations by engineering bacterium utilisation of a novel plant produced resource. Nature Biotech. 15: 363-368 [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • 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] [Google Scholar]
  • Widmer F, Seidler RJ, Donegan KK, Reed GL (1997) Quantification of transgenic marker gene persistence in the field. Mol. Ecol. 6: 1–7 [CrossRef] [Google Scholar]
  • 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] [Google Scholar]