Free Access
Issue
Environ. Biosafety Res.
Volume 6, Number 1-2, January-June 2007
Thematic Issue on Horizontal Gene Transfer
Page(s) 113 - 119
DOI https://doi.org/10.1051/ebr:2007025
Published online 20 September 2007
  • Appuhn A, Joergensen RG (2006) Microbial colonisation of roots as a function of plant species. Soil Biol. Biochem. 38: 1040–1051 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interations with plants and other organisms. Ann. Rev. Plant Biol. 57: 233–266 [CrossRef]
  • Baumgarte S, Tebbe CC (2005) Field studies on the environmental fate of the Cry1Ab Bt toxin produced by transgenic maize (MON810) and its effect on bacterial communities in the maize rhizosphere. Mol. Ecol. 14: 2539–2551 [CrossRef] [PubMed]
  • Dohrmann AB, Tebbe CC (2004) Microbial community analysis by PCR-single-strand conformation polymorphism (PCR-SSCP). Molecular Microbial Ecology Manual, Dodrecht: Kluwer Academic Publisher, pp 809–838
  • Dohrmann AB, Tebbe CC (2005) Effect of elevated tropospheric ozone on the structure of bacterial communities inhabiting the rhizosphere of herbaceous plants native to Germany. Appl. Environ. Microbiol. 71: 7750–7758 [CrossRef] [PubMed]
  • Dohrmann AB, Tebbe CC (2006) Genetic profiling of bacterial communities from the rhizospheres of ozone damaged Malva sylvestris (Malvaceae). Eur. J. Soil Biol. 42: 191–199 [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]
  • Felske A, Engelen B, Nübel U, Backhaus H (1996) Direct ribosome isolation from soil to extract bacterial rRNA for community analysis. Appl. Environ. Microbiol. 62: 4162–4167 [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]
  • 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
  • Kanagawa T (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR). J. Biosci. Bioeng. 96: 317–323 [PubMed]
  • Kato S, Haruta S, Cui ZJ, Ishii M, Igarashi Y (2004) Effective cellulose degradation by a mixed-culture system composed of a cellulolytic Clostridium and aerobic non-cellulolytic bacteria. FEMS Microbiol. Ecol. 51: 133–142 [CrossRef] [PubMed]
  • 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: 211–236 [CrossRef]
  • Klappenbach JA, Dunbar JM, Schmidt TM (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66: 1328–1333 [CrossRef] [PubMed]
  • Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PGL, van Veen JA (2002) Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Van Leeuwenhoek Int. J. Gen. Mol. Microbiol. 81: 509–520 [CrossRef]
  • Lueders T, Manefield M, Friedrich MW (2004) Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ. Microbiol. 6: 73–78 [CrossRef] [PubMed]
  • Marschner P, Yang CH, Lieberei R, Crowley DE (2001) Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol. Biochem. 33: 1437–1445 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Mawdsley JL, Burns RG (1994) Factors affecting the survival of a Flavobacterium species in non-planted and rhizosphere soil. Soil Biol. Biochem. 26: 849–859 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Miethling R, Wieland G, Backhaus H, Tebbe CC (2000) Variation of microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33. Microbial Ecol. 40: 43–56
  • Miller HJ, Henken G, van Veen JA (1989) Variation in the composition of bacterial populations in the rhizosphere of maize, wheat, and grass cultivars. Can. J. Microbiol. 35: 656–660 [CrossRef]
  • 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]
  • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695–700 [PubMed]
  • Peterson SB, Dunn AK, Klimowicz AK, Handelsman J (2006) Peptidoglycan from Bacillus cereus mediates commensalism with rhizosphere bacteria from the Cytophaga-Flavobacterium group. Appl. Environ. Microbiol. 72: 5421–5427 [CrossRef] [PubMed]
  • Rasche F, Hodl V, Poll C, Kandeler E, Gerzabek MH, van Elsas JD, Sessitsch A (2006) Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities compared with the effects of soil, wild-type potatoes, vegetation stage and pathogen exposure. FEMS Microbiol. Ecol. 56: 219–235 [CrossRef] [PubMed]
  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press
  • 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]
  • Schmalenberger A, Tebbe CC (2003a) Bacterial diversity in maize rhizospheres: conclusions on the use of genetic profiles based on PCR-amplified partial small subunit rRNA genes in ecological studies. Molecul. Ecol. 12: 251–261 [CrossRef]
  • Schmalenberger A, Tebbe CC (2003b) Genetic profiling of noncultivated bacteria from the rhizospheres of sugar beet (Beta vulgaris) reveal field and annual variability but no effect of a transgenic herbicide resistance. Can. J. Microbiol. 49: 1–8 [CrossRef] [PubMed]
  • Schmalenberger A, Schwieger F, Tebbe CC (2001) Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl. Environ. Microbiol. 67: 3557–3563 [CrossRef] [PubMed]
  • Schwieger F, Tebbe CC (1998) A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl. Environ. Microbiol. 64: 4870–4876 [PubMed]
  • Schwieger F, Tebbe CC (2000) Effect of field inoculation with Sinorhizobium meliloti L33 on the composition of bacterial communities in rhizospheres of a target plant (Medicago sativa) and a non-target plant (Chenopodium album) – Linking of 16S rRNA gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria. Appl. Environ. Microbiol. 66: 3556–3565 [CrossRef] [PubMed]
  • Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62: 625–30 [PubMed]
  • Tebbe CC, Schmalenberger A, Peters S, Schwieger F (2001) Single-strand conformation polymorphism (SSCP) for microbial community analysis. In Rochelle PA, ed, Environmental Molecular Microbiology: Protocols and Applications, Wymondham NR180 Ja: Horizon Scientific P, pp 161–175