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Exploration of methods used to describe bacterial communities in silage of maize (Zea mays) cultivars

Published online by Cambridge University Press:  03 April 2008

Lorenzo Brusetti ,
Sara Borin ,
Aurora Rizzi ,
Diego Mora ,
Claudia Sorlini  and
Daniele Daffonchio
Lorenzo Brusetti
Affiliation:
Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DISTAM), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy
Sara Borin
Affiliation:
Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DISTAM), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy
Aurora Rizzi
Affiliation:
Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DISTAM), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy
Diego Mora
Affiliation:
Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DISTAM), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy
Claudia Sorlini
Affiliation:
Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DISTAM), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy
Daniele Daffonchio
Affiliation:
Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DISTAM), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy

Abstract

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Different techniques to assess bacterial community structure and diversity were evaluated in silages prepared with four different maize cultivars, three conventional and one transgenic (cv. Tundra, event Bt-176). Plants were cultivated in the greenhouse and harvested after 30 days of growth. Silage samples were collected at successive times during fermentation and analyzed for bacterial counts and by various DNA-based fingerprinting techniques. Bacterial counts were similar between cultivars for the total culturable bacteria, sporeforming, and mesophilic and thermophilic lactic acid bacteria (LAB). Further analysis of the species composition of 388 LAB strains by intergenic transcribed spacer (ITS) PCR followed by sequencing of 16S rRNA gene did not reveal differences between cultivars. In contrast, molecular fingerprinting methods targeting whole bacterial communities, such as automated ribosomal intergenic spacers analysis (ARISA) and 16S rRNA gene length heterogeneity-PCR (LH-PCR), indicated that different maize silage batches or cultivars hosted different bacterial communities. Thus, ARISA and LH-PCR fingerprinting techniques offer a fast and sensitive method to compare bacterial communities, and to detect differences in silage bacterial communities.

Keywords

silage fermentationtransgenic plantsmaizemethodsbacterial communities
Type
Research Article
Information
Environmental Biosafety Research , Volume 7 , Issue 1 , January 2008 , pp. 25 - 33
Copyright
© ISBR, EDP Sciences, 2008

References

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J. Mol. Biol. 215: 403–410
Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1994) Current protocols in molecular biology. John Wiley and Sons, eds, USA
Brookes G, Barfoot P (2006) GM Crops: The First Ten Years - Global Socio-Economic and Environmental Impacts. ISAAA Brief No. 36, ISAAA: Ithaca, NY
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 Bt176 maize Zea mays and its non transgenic counterpart. Plant Soil 266: 11–26 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 CrossRef
Cai, Y, Benno, Y, Ogawa, M, Ohmomo, S, Kumai, S, Nakase T (1998) Influence of Lactobacillus spp. from an inoculant and of Weissella and Leuconostoc spp. from forage crops on silage fermentation. Appl. Environ. Microbiol. 64: 2982–2987
Cai, Y, Kumai, S, Ogawa, M, Benno, Y, Nakase, T (1999) Characterization and identification of Pediococcus species isolated from forage crops and their application for silage preparation. Appl. Environ. Microbiol. 65: 2901–2906
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
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
Costa, R, Götz, M, Mrotzek, N, Lottmann, J, Berg, G, Smalla, K (2006) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol. Ecol. 56: 236–249 CrossRef
Daffonchio, D, Borin, S, Frova, G, Manichini, PL, Sorlini, C (1998) PCR fingerprinting of whole genomes, the spacers between the 16S and 23S rRNA genes and of intergenic tRNA gene regions reveals a different intraspecific genomic variability of Bacillus cereus and Bacillus licheniformis. Int. J. Syst. Bacteriol. 48: 107–116 CrossRef
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 CrossRef
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
Escher, N, Käch, B, Nentwig, W (2000) Decomposition of transgenic Bacillus thuringiensis maize by microorganisms and woodlice Porcellio scaber (Crustacea: Isopoda). Basic Appl. Ecol. 1: 161–169 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
Gomes, NCM, Heuer, H, Schönfeld, J, Costa, R, Medonça-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
Griffiths, BS, Caul, S, Thompson, J, Birch, ANE, Scrimgeour, C, Andersen, MN, Cortet, J, Messé, A, Sausse, C, Lacroix, B, Krogh, PH (2005) A comparison of soil microbial community structure, protozoa and nematodes in field plots of conventional and genetically modified maize expressing the Bacillus thuringiensis CryIAb toxin. Plant Soil 275: 135–146 CrossRef
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
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
Koziel, MG, Beland, GL, Bowman, C, Carozzi, NB, Crenshaw, R, Crossland, L, Dawson, J, Desai, N, Hill, M, Kadwell, S, Launis, K, Lewis, K, Maddox, D, McPherson, K, Meghji, MR, Merlin, E, Rhodes, R, Warren, GW, Wright, M, Evola, SV (1993) Field performance of elite transgenic maize plants expressing an insecticidal protein derived from Bacillus thuringiensis. Bio-Technol. 11: 194–200
Lin, C, Bolsen, KK, Brent, BE, Hart, RA, Dickerson, JT, Feyerherm, AM, Aimutis, WR (1991) Epiphytic microflora on alfalfa and whole-plant corn. J. Dairy Sci. 75: 2484–2493 CrossRef
Lin, C, Bolsen, KK, Brent, BE, Fung, DYC (1992) Epiphytic lactic acid bacteria succession during the pre-ensiling and ensiling periods of alfalfa and maize. J. Appl. Bacteriol. 73: 375–387 CrossRef
Nielsen, KM, Bones, AT, Smalla, K, van Elsas, JD (1998) Horizontal gene transfer from transgenic plants to terrestrial bacteria – a rare event? FEMS Microbiol. Rev. 22: 79–103 CrossRef
Ritchie, NJ, Schutter, ME, Dick, RP, Myrold, DD (2000) Use of Length Heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil. Appl. Environ. Microbiol. 66: 1668–1675 CrossRef
Rizzi, A, Agosti, F, Daffonchio, D, Sorlini, C (2001) Detection of genetically modified Bt-maize in cooked food products by PCR. Ital. J. Food Sci. 13: 265–274
Rizzi, A, Panebianco, L, Giaccu, D, Sorlini, C, Daffonchio, D (2003) Stability and recovery of maize DNA during food processing. Ital. J. Food Sci. 15: 499–510
Saxena, D, Stotzky, G (2001) Bt corn has a higher lignin content than non-Bt corn. Am. J. Bot. 88: 1704–1706 CrossRef
Saxena, D, Flores, S, Stotzky, G (1999) Insecticidal toxin in root exudates from Bt corn. Nature 402: 480
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
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
Suzuki, M, Rappé, MS, Giovannoni, SJ (1998) Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. 64: 4522–4529
Tukey, JW (1949) Comparing individual means in the analysis of variance. Biometrics 5: 99–114 CrossRef
Urzì, C, Brusetti, L, Salamone, P, Sorlini, C, Stackebrandt, E, Daffonchio, D (2001) Biodiversity of Geodermatophilaceae isolated from altered stones and monuments in the Mediterranean basin. Environ. Microbiol. 3: 471–479 CrossRef
Weinberg ZG, Muck RE (1996) New trends and opportunities in the development and use of inoculants for silage. FEMS Microbiol. Rev. 19: 53–68