Open Access
Issue
Environ. Biosafety Res.
Volume 9, Number 1, January-March 2010
Page(s) 25 - 40
Section Regular articles
DOI https://doi.org/10.1051/ebr/2010007
Published online 11 November 2010
  • Andreote FD, Mendes R, Dini-Andreote F, Rossetto PB, Labate CA, Pizzirani-Kleiner AA, van Elsas JD, Azevedo JL, Araújo WL (2008) Transgenic tobacco revealing altered bacterial diversity in the rhizosphere during early plant development. Antonie Van Leeuwenhoek 93: 415–424 [CrossRef] [PubMed]
  • Andreote FD, Carneiro RT, Salles JF, Marcon J, Labate CA, Azevedo JL, Araújo WL (2009) Culture-independent assessment of Rhizobiales-related Alphaproteobacteria and the diversity of Methylobacterium in the rhizosphere and rhizoplane of transgenic eucalyptus. Microbial Ecol. 57: 82–93 [CrossRef]
  • Batista R, Saibo N, Lourenco T, Oliveira MM (2008) Microarray analyses reveal that plant mutagenesis may induce more transcriptome changes than transgene insertion. PNAS 105: 3640–3645 [CrossRef]
  • Bishop-Hurley S, Zabkiewicz RJ, Grace LJ, Gardner RC, Wagner A, Walter C (2001) Conifer genetic engineering: transgenic Pinus radiata (D. Don) and Picea abies (Karst) plants are resistant to the herbicide Buster. Plant Cell Reports 20: 235–243 [CrossRef]
  • Chow ML, Radomski CC, McDermott JM, Davies J, Axelrood PE (2002) Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microb. Ecol. 42: 347–357 [CrossRef]
  • Chu-Chou M, Grace LJ (1988) Mycorrhizal fungi of Radiata pine in different forests of the North and South Islands in New Zealand. Soil Biol. Biochem. 20: 883–886 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Costa R, Götz M, Mrotzek N, Lottmann J, Berg G, Smalla K (2005) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol. Ecol. 56: 236–249
  • Costa R, Gomes NCM, Krögerrecklenfort E, Opelt K, Berg G, Smalla K (2007) Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses. Environ. Microbiol. 9: 2260–2273 [CrossRef] [PubMed]
  • Dunfield KE, Germida JJ, (2001) Diversity of bacterial communities in the rhizosphere and root interior of field-grown genetically modified Brassica napus. FEMS Microb. Ecol. 82: 1–9
  • Dunfield KE, Germida JJ (2004) Impact of genetically modified crops on soil and plant associated microbial communities. Environ. Quality 33: 806–815 [CrossRef] [PubMed]
  • Filion M, Hamelin RC, Bernier L, St-Arnaud M (2004) Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in a nursery. Appl. Environ. Microbiol. 70: 3541–3551 [CrossRef] [PubMed]
  • Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Mol. Ecol. 2: 113–118 [CrossRef] [PubMed]
  • Glasbey CA, Vali L, Gustafsson JS (2005) A statistical model for unwarping of 1-D electrophoresis gels. Electrophoresis 26: 4237–4242 [CrossRef] [PubMed]
  • Gomes NCM, Heuer H, Schönfeld J, Costa R, Hagler-Mendonca 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]
  • Gower JC, (1985) Measures of similarity, dissimilarity and distance. In Kotz S, Johnson NL, Read CB, eds, Encyclopaedia of Statistical Sciences 5, Wiley, New York
  • Grace LJ, Charity JA, Gresham B, Kay N, Walter C (2005) Insect resistant transgenic Pinus radiata. Plant Cell Reports 24: 103–111 [CrossRef] [PubMed]
  • Graff A, Conrad R (2005) Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees. FEMS Microbiol. Ecol. 53: 401–415 [CrossRef] [PubMed]
  • Grayston SJ, Griffith GS, Mawdsley JL, Campbell CD, Bardgett RD (2001) Accounting for variability in soil microbial communities of temperate upland grassland ecosystems. Soil Biol. Biochem. 33: 533–551 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [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 Microb. Ecol. 41: 181–190 [CrossRef] [PubMed]
  • Hampp R, Ecke M, Schaeffer C, Wallenda T, Wingler A, Kottke I, Sundberg B (1996) Axenic mycorrhization of wild type and transgenic hybrid aspen expressing T-DNA indole acetic acid-biosynthetic genes. Trees - Structure and function 11: 59–64
  • Henderson AR, Walter C (2006) Genetic engineering in Conifer Plantation Forestry. Silvae Genetica 55: 253–262
  • Heuer H, Krsek M, Baker P, Smalla K, Wellington EM (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63: 3233–3241 [PubMed]
  • Heuer H, Wieland G, Schönfeld J, Schönwälder A, Gomes NCM, Smalla K (2001) Bacterial community profiling using DGGE or TGGE analysis. In Rouchelle P, ed, Environmental molecular microbiology: protocols and applications, Horizon Scientific Press, Wymondham, pp 177–190
  • 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]
  • Hotelling H (1947) Multivariate quality control. In Eisenhart C, Hastay MW, Wallis WA, eds, Techniques of Statistical Analysis, McGraw-Hill, New York
  • Izumi H, Cairney JW, Killham K, Moore E, Alexander IJ, Anderson IC (2008) Bacteria associated with ectomycorrhizas of slash pine (Pinus elliottii) in south-eastern Queensland, Australia. FEMS Microbiol. Letters 282: 196–204 [CrossRef]
  • Kaldorf M, Fladung M, Muhs HJ, Buscot F (2002) Mycorrhizal colonization of transgenic aspen in a field trial. Planta 214: 653–660 [CrossRef] [PubMed]
  • Kataoka R, Taniguchi T, Ooshima H, Futai K (2008) Comparison of the bacterial communities established on the mycorrhizae formed on Pinus thunbergii root tips by eight species of fungi. Plant Soil 304: 267–275 [CrossRef]
  • Lamarche J, Hamelin RC (2007) No evidence of an impact on the rhizosphere diazotroph community by the expression of Bacillus thuringiensis Cry1Ab toxin by Bt white spruce. Appl. Environ. Microbiol. 73: 6577–6583 [CrossRef] [PubMed]
  • Landeweert R, Leeflang P, Smit E, Kuyper T (2005) Diversity of an ectomycorrhizal fungal community studied by a root tip and total soil DNA approach. Mycorrhiza 15: 1–6 [CrossRef] [PubMed]
  • Lane DJ (1991) 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M, eds, Nucleic Acid Techniques in Bacterial Systematics, Hoboken, Wiley, New York, pp 115–175
  • LeBlanc PM, Hamelin RC, Filion M (2007) Alteration of soil rhizosphere communities following genetic transformation of white spruce. Appl. Environ. Microbiol. 73: 4128–4134 [CrossRef] [PubMed]
  • Lottmann J, Heuer H, Smalla K, Berg G (1999) Influence of transgenic T4-lysozyme producing potato plants on potentially beneficial plant-associated bacteria. FEMS Microbiol. Ecol. 29: 365–377 [CrossRef]
  • Lottmann J, Heuer H, De Vries J, Mahn A, Düring K, Wackernagel W, Smalla K, Berg G (2000) Establishment of introduced antagonistic bacteria in the rhizosphere of transgenic potatoes and their effect on the bacterial community. FEMS Microbiol. Ecol. 33: 41–49 [CrossRef] [PubMed]
  • Lukow T, Dunfield PF, Liesack W (2000) Use of 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]
  • Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73: 127–141 [CrossRef] [PubMed]
  • 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]
  • Nübel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann RI, Ludwig W, Backhaus H (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178: 5636–5643 [PubMed]
  • O’Callaghan M, Gerard EM, Bell NL, Waipara NW, Aalders LT, Baird DB, Conner AJ (2008) Microbial and nematode communities associated with potatoes genetically modified to express the antimicrobial peptide magainin and unmodified potato cultivars. Soil Biol. Biochem. 40: 1446–1459 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Oliver KL, Hamelin RC, Hintz WE (2008) Effects of transgenic hybrid aspen overexpressing polyphenol oxidase on rhizosphere diversity. Appl. Envion. Microbiol. 74: 5340–5348 [CrossRef]
  • Opelt K, Chobot V, Hadacek F, Schönmann S, Eberl L, Berg G (2007) Investigations of the structure and function of bacterial communities associated with Sphagnum mosses. Environ. Microbiol. 9: 2795–2809 [CrossRef] [PubMed]
  • Parke JL, Gurian-Sherman D (2001) Diversity of the Burkholderia cepacia complex and implications for risk assessment of biological control strains. Annu. Rev. Phytopathol. 39: 225–258 [CrossRef] [PubMed]
  • Payne RW, Harding SA, Murray DA, Soutar DM, Baird DB, Welham SJ, Kane AF, Gilmour AR, Thompson R, Webster R, Tunnicliffe, Wilson G (2007) The Guide to GenStat Release 10, Part 2: Statistics. VSN International, Hemel Hempstead
  • Plaingam N, Somrithipol S, Jones EBG (2003) Infundibulomyces: a new genus of coelomycetes from Thailand. Can. J. Bot. 81: 732–737 [CrossRef]
  • Priha O, Grayston SJ, Hiukka R, Pennanen T, Smolander A (2001) Microbial community structure and characteristics of the organic matter in soils under Pinus sylvestris, Picea abies and Betula pendula at two forest sites. Biol. Fertil. Soils 33: 17–24 [CrossRef]
  • Seppänen SK, Pasonen HL, Vauramo S, Vahala J, Toikka M, Kilpeläinen I, Setälä H, Teeri TH, Timonen S, Pappinen A (2007) Decomposition of the leaf litter and mycorrhiza forming ability of silver birch with a genetically modified lignin biosynthesis pathway. Appl. Soil Ecol. 36: 100–106 [CrossRef]
  • Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana, pp 3–24
  • 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]
  • Smith SE, Read DJ (1997) Mycorrhizal Symbiosis. Second edition, Academic Press, London
  • Timonen S, Hurek T (2006) Characterisation of bacterial populations associating with Pinus sylvestrisSuillus bovinus mycorrhizospheres. Can. J. Microbiol. 52: 769–778 [CrossRef] [PubMed]
  • Vainio EJ, Hantula J (2000) Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol. Res. 104: 927–936 [CrossRef]
  • Valenzuela S, Balocchi C, Rodriguez J (2006) Transgenic trees and forest biosafety. Electronic J. Biotechnol. 9: 335–339
  • Van Frankenhuyzen K, Beardmore T (2004) Current status and environmental impact of transgenic forest trees. Can. J. Forest Res. 34: 1163–1180 [CrossRef]
  • Wagner A, Ralph J, Akiyama T, Flint H, Phillips L, Torr K, Nanayakkara B, Te Kiri L (2007) Exploring lignification in conifers by silencing hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase in Pinus radiata. PNAS 104: 11856–11861
  • Walter C (2004) Genetic engineering in conifer forestry: Technical and social considerations. In Vitro Cell Dev. Biol. Plant 40: 434–441 [NASA ADS] [CrossRef] [EDP Sciences] [MathSciNet] [PubMed]
  • Walter C, Grace LJ (2000) Genetic engineering of conifers for plantation forestry: Pinus radiata transformation. In Jain SM, Minocha SC, eds, Molecular biology of woody plants, Kluwer, Dordrecht, pp 79–104
  • Walter C, Grace LJ, Wagner A, White DWR, Walden AR, Donaldson SS, Hinton H, Gardner RC, Smith DR (1998) Stable transformation and regeneration of transgenic plants of Pinus radiata D. Don. Plant Cell Reports 17: 460–468 [CrossRef]
  • Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697–703 [PubMed]
  • White TJ, Bruns TD, Lee S, Taylor J (1990) Analysis of phylogenetic relationships by amplification and direct sequencing of ribosomal RNA genes. In Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds, PCR Protocols: a Guide to Methods and Applications, Academic Press, New York, pp 315–322

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