SEARCH

SEARCH BY CITATION

References

  • Abdo Z, Schuette UME, Bent SJ, Williams CJ, Forney LJ, Joyce P. 2006. Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environmental Microbiology 8: 929938.
  • Bååth E. 2003. The use of neutral lipid fatty acids to indicate the physiological conditions of soil fungi. Microbial Ecology 45: 373383.
  • Bååth E, Anderson TH. 2003. Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biology & Biochemistry 35: 955963.
  • Boschker HTS. 2004. Linking microbial community structure and functioning: stable isotope (13C) labeling in combination with PLFA analysis. In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans AD, van Elsas JD, ed. Microbial ecology. Dordrecht, the Netherlands: Kluwer Academic Publishers, 16731688.
  • Boschker JT, Nold SC, Wellsbury P, Bos D, de Graaf W, Pel R, Parkes RJ, Cappenberg TE. 1998. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392: 801805.
  • Botha A. 2011. The importance and ecology of yeasts in soil. Soil Biology & Biochemistry 43: 18.
  • Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM. 2008. Root exudates regulate soil fungal community composition and diversity. Applied and Environmental Microbiology 74: 738744.
  • Buée M, De Boer W, Martin F, van Overbeek L, Jurkevitch E. 2009. The rhizosphere zoo: an overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors. Plant and Soil 321: 189212.
  • Butler JL, Williams MA, Bottomley PJ, Myrold DD. 2003. Microbial community dynamics associated with rhizosphere carbon flow. Applied and Environmental Microbiology 69: 67936800.
  • Carlile MJ, Watkinson SC, Gooday GW. 2001. The fungi. San Diego, CA, USA: Academic Press.
  • Cesaro P, van Tuinen D, Copetta A, Chatagnier O, Berta G, Gianinazzi S, Lingua G. 2008. Preferential colonization of Solanum tuberosum L. roots by the fungus Glomus intraradices in arable soil of a potato farming area. Applied and Environmental Microbiology 74: 57765783.
  • Cheeke TE, Pace BA, Rosenstiel TN, Cruzan MB. 2011. The influence of fertilizer level and spore density on arbuscular mycorrhizal colonization of transgenic Bt 11 maize (Zea mays) in experimental microcosms. FEMS Microbiology Ecology 75: 304312.
  • Christensen M. 1989. A view of fungal ecology. Mycologia 81: 119.
  • Culman S, Bukowski R, Gauch H, Cadillo-Quiroz H, Buckley D. 2009. T-REX: software for the processing and analysis of T-RFLP data. BMC Bioinformatics 10: 171.
  • De Graaff MA, Classen AT, Castro HF, Schadt CW. 2010. Labile soil carbon inputs mediate the soil microbial community composition and plant residue decomposition rates. New Phytologist 188: 10551064.
  • Denef K, Bubenheim H, Lenhart K, Vermeulen J, van Cleemput O, Boeckx P, Müller C. 2007. Community shifts and carbon translocation within metabolically-active rhizosphere microorganisms in grasslands under elevated CO2. Biogeosciences 4: 769779.
  • Dennis PG, Miller AJ, Hirsch PR. 2010. Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiology Ecology 72: 313327.
  • Drigo B, Pijl AS, Duyts H, Kielak A, Gamper HA, Houtekamer MJ, Boschker HTS, Bodelier PLE, Whiteley AS, van Veen JA et al. 2010. Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2. Proceedings of the National Academy of Sciences, USA 107: 1093810942.
  • Dunfield KE, Germida JJ. 2001. Diversity of bacterial communities in the rhizosphere and root interior of field-grown genetically modified Brassica napus. FEMS Microbiology Ecology 38: 19.
  • Fitzjohn RG, Dickie IA. 2007. TRAMPR: an R package for analysis and matching of terminal-restriction fragment length polymorphism (TRFLP) profiles. Molecular Ecology Notes 7: 583587.
  • Frostegård A, Tunlid A, Bååth E. 1993. Phospholipid fatty-acid composition, biomass, and activity of microbial communities from 2 soil types experimentally exposed to different heavy-metals. Applied and Environmental Microbiology 59: 36053617.
  • Frostegård Å, Tunlid A, Bååth E. 2011. Use and misuse of PLFA measurements in soils. Soil Biology & Biochemistry 43: 16211625.
  • Gardes M, Bruns TD. 1993. ITS primers with enhanced specificity for Basidiomycetes – Application to the identification of Mycorrhizae and rusts. Molecular Ecology 2: 113118.
  • Girlanda M, Bianciotto V, Cappellazzo GA, Casieri L, Bergero R, Martino E, Luppi AM, Perotto S. 2008. Interactions between engineered tomato plants expressing antifungal enzymes and nontarget fungi in the rhizosphere and phyllosphere. FEMS Microbiology Letters 288: 918.
  • Gollotte A, van Tuinen D, Atkinson D. 2004. Diversity of arbuscular mycorrhizal fungi colonising roots of the grass species Agrostis capillaris and Lolium perenne in a field experiment. Mycorrhiza 14: 111117.
  • Götz M, Nirenberg H, Krause S, Wolters H, Draeger S, Buchner A, Lottmann J, Berg G, Smalla K. 2006. Fungal endophytes in potato roots studied by traditional isolation and cultivation-independent DNA-based methods. FEMS Microbiology Ecology 58: 404413.
  • Griffiths BS, Heckmann LH, Caul S, Thompson J, Scrimgeour C, Krogh PH. 2007. Varietal effects of eight paired lines of transgenic Bt maize and near-isogenic non-Bt maize on soil microbial and nematode community structure. Plant Biotechnology Journal 5: 6068.
  • Griffiths RI, Whiteley AS, O’Donnell AG, Bailey MJ. 2000. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Applied and Environmental Microbiology 66: 54885491.
  • Gschwendtner S, Esperschütz J, Buegger F, Reichmann M, Müller M, Munch JC, Schloter M. 2011. Effects of genetically modified starch metabolism in potato plants on photosynthate fluxes into the rhizosphere and on microbial degraders of root exudates. FEMS Microbiology Ecology 76: 564575.
  • Hack H, Gal H, Klemke T, Klose R, Meier U, Strauss R, Witzenberger A. 2001. The BBCH scale for phenological growth stages of potato (Solanum tuberosum L.). In: Meier U, ed. Growth stages of mono- and dicotyledonous plants, BBCH Monograph. Berlin, Braunchweig, Germany: Federal Biological Research Centre for Agriculture and Forestry, 716.
  • Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4: 9.
  • Hannula SE, de Boer W, van Veen JA. 2010. In situ dynamics of soil fungal communities under different genotypes of potato, including a genetically modified cultivar. Soil Biology & Biochemistry 42: 22112223.
  • Harman GE, Howell CR, Viterbo A, Chet I, Lorito M. 2004. Trichoderma species–opportunistic, avirulent plant symbionts. Nature Reviews Microbiology 2: 4356.
  • Hart MM, Powell JR, Gulden RH, Dunfield KE, Pauls KP, Swanton CJ, Klironomos JN, Antunes PM, Koch AM, Trevors JT. 2009. Separating the effect of crop from herbicide on soil microbial communities in glyphosate-resistant corn. Pedobiologia 52: 253262.
  • Inceoglu O, Salles JF, van Overbeek L, van Elsas JD. 2010. Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields. Applied and Environmental Microbiology 76: 36753684.
  • Jones DL, Nguyen C, Finlay RD. 2009. Carbon flow in the rhizosphere: carbon trading at the soil–root interface. Plant and Soil 321: 533.
  • Kowalchuk GA, Bruinsma M, van Veen JA. 2003. Assessing responses of soil microorganisms to GM plants. Trends in Ecology & Evolution 18: 403410.
  • Kuzyakov Y, Domanski G. 2000. Carbon input by plants into the soil. Review. Journal of Plant Nutrition and Soil Science-Zeitschrift Fur Pflanzenernahrung Und Bodenkunde 163: 421431.
  • Larena I, Salazar O, Gonzalez V, Julian MC, Rubio V. 1999. Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes. Journal of Biotechnology 75: 187194.
  • Lu YH, Abraham WR, Conrad R. 2007. Spatial variation of active microbiota in the rice rhizosphere revealed by in situ stable isotope probing of phospholipid fatty acids. Environmental Microbiology 9: 474481.
  • Lu Y, Murase J, Watanabe A, Sugimoto A, Kimura M. 2004. Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil. FEMS Microbiology Ecology 48: 179186.
  • Lynch JM, Whipps JM. 1990. Substrate flow in the rhizosphere. Plant and Soil 129: 110.
  • Manefield M, Whiteley AS, Griffiths RI, Bailey MJ. 2002. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Applied and Environmental Microbiology 68: 53675373.
  • Mauclaire L, Pelz O, Thullner M, Abraham WR, Zeyer J. 2003. Assimilation of toluene carbon along a bacteria-protist food chain determined by 13C-enrichment of biomarker fatty acids. Journal of Microbiological Methods 55: 635649.
  • Mestre CM, Rosa CA, Safar SVB, Libkind D, Fontenla SB. 2011. Yeast communities associated with the bulk-soil, rhizosphere and ectomycorrhizosphere of a Nothofagus pumilio forest in Northwestern Patagonia, Argentina. FEMS Microbiology Ecology 78: 531541.
  • 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 and Soil 266: 2339.
  • O’Callaghan M, Gerard EM, Bell NL, Waipara NW, Aalders LT, David BB, Conner AJ. 2008. Microbial and nematode communities associated with potatoes genetically modified to express the antimicrobial peptide magainin and unmodified potato cultivars. Soil Biology & Biochemistry 40: 14461459.
  • Olsson PA, Bååth E, Jakobsen I, Sölderström B. 1995. The use of phospholipid and neutral lipid fatty-acids to estimate biomass of arbuscular mycorrhizal fungi in soil. Mycological Research 99: 623629.
  • Olsson PA, Johnson NC. 2005. Tracking carbon from the atmosphere to the rhizosphere. Ecology Letters 8: 12641270.
  • van Overbeek L, van Elsas JD. 2008. Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.). FEMS Microbiology Ecology 64: 283296.
  • Radajewski S, Ineson P, Parekh NR, Murrell JC. 2000. Stable-isotope probing as a tool in microbial ecology. Nature 403: 646649.
  • Rangel-Castro JI, Killham K, Ostle N, Nicol GW, Anderson IC, Scrimgeour CM, Ineson P, Meharg A, Prosser JI. 2005. Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms. Environmental Microbiology 7: 828838.
  • Rasche F, Lueders T, Schloter M, Schaefer S, Buegger F, Gattinger A, Hood-Nowotny RC, Sessitsch A. 2009. DNA-based stable isotope probing enables the identification of active bacterial endophytes in potatoes. New Phytologist 181: 802807.
  • Rinnan R, Bååth E. 2009. Differential utilization of carbon substrates by bacteria and fungi in tundra soil. Applied and Environmental Microbiology 75: 36113620.
  • Rossi L, Costantini ML, Brilli M. 2007. Does stable isotope analysis separate transgenic and traditional corn (Zea mays L.) detritus and their consumers? Applied Soil Ecology 35: 449453.
  • 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 Microbiology Ecology 29: 263272.
  • Timlin D, Rahman SML, Baker J, Reddy VR, Fleisher D, Quebedeaux B. 2006. Whole plant photosynthesis, development, and carbon partitioning in potato as a function of temperature. Agronomy Journal 98: 11951203.
  • Turrini A, Sbrana C, Nuti MP, Pietrangeli BM, Giovannetti M. 2004. Development of a model system to assess the impact of genetically modified corn and aubergine plants on arbuscular mycorrhizal fungi. Plant and Soil 266: 6975.
  • Van der Wal A, Van Veen JA, Smant W, Boschker HTS, Bloem J, Kardol P, Van der Putten WH, De Boer W. 2006. Fungal biomass development in a chronosequence of land abandonment. Soil Biology & Biochemistry 38: 5160.
  • Vandenkoornhuyse P, Mahe S, Ineson P, Staddon P, Ostle N, Cliquet JB, Francez AJ, Fitter AH, Young JPW. 2007. Active root-inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA. Proceedings of the National Academy of Sciences, USA 104: 1697016975.
  • de Vetten N, Wolters AM, Raemakers K, van der Meer I, ter Stege R, Heeres E, Heeres P, Visser R. 2003. A transformation method for obtaining marker-free plants of a cross-pollinating and vegetatively propagated crop. Nature Biotechnology 21: 439442.
  • Weinert N, Meincke R, Gottwald C, Heuer H, Gomes NCM, Schloter M, Berg G, Smalla K. 2009. Rhizosphere communities of genetically modified zeaxanthin-accumulating potato plants and their parent cultivar differ less than those of different potato cultivars. Applied and Environmental Microbiology 75: 38593865.
  • Weinert N, Meincke R, Gottwald C, Heuer H, Schloter M, Berg G, Smalla K. 2010. Bacterial diversity on the surface of potato tubers in soil and the influence of the plant genotype. FEMS Microbiology Ecology 74: 114123.
  • Werner RA, Brand WA. 2001. Referencing strategies and techniques in stable isotope ratio analysis. Rapid Communications in Mass Spectrometry 15: 501519.
  • Wu WX, Liu W, Lu HH, Chen YX, Devare M, Thies J. 2009. Use of 13C labeling to assess carbon partitioning in transgenic and nontransgenic (parental) rice and their rhizosphere soil microbial communities. FEMS Microbiology Ecology 67: 93102.