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Evaluation of the denaturing gradient gel electrophoresis-apparatus as a parameter influencing soil microbial community fingerprinting

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Abstract

We compared two denaturing gradient gel electrophoresis (DGGE) systems—DCode (Biorad, Hercules, CA, USA) and PhorU (Ingeny, Leiden, NL), performing community level 16S and 18S rRNA gene fragment-PCR-DGGE with total DNA extracted from upland pasture soil used for outdoor cattle husbandry. The methodological evaluation of the DGGE apparatus as parameter influencing DGGE fingerprinting, based on cluster analysis of soil bacterial and fungal community fingerprints, was made in terms of the resulting information about microbial community structures and their response to different degrees of cattle impact. Although the comparative DGGE analysis with different DGGE systems provided similar clustering of microbial community structures in correlation with the degree of cattle impact, our results suggest the DGGE system to be a factor influencing DGGE analysis. To our knowledge this is the first attempt to investigate the hypothetical impact of the DGGE system due to different technical characteristics, recommending the use of one and the same DGGE apparatus throughout an experiment, if the monitoring of microbial community structures requires multiple gel-to-gel analysis.

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Acknowledgments

The study was realized within the scientific cooperation between the Consiglio Nazionale di Ricerca, Italy, and the Academy of Sciences of the Czech Republic. We are grateful to the Ente Cassa di Risparmio di Firenze, the Ministry of Education of the Czech Republic (LC06066) and the Grant Agency of the Academy of Sciences of the Czech Republic (IAA600660605) for financial support. The authors are grateful for useful advice and suggestions from Dr. F. Valori and the anonymous referees.

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Authors and Affiliations

  1. Dipartimento di Scienza del Suolo e Nutrizione della Pianta, Università degli Studi di Firenze, Piazzale delle Cascine 28, 50144, Florence, Italy

    J. Ascher, M. T. Ceccherini, F. Borgogni & G. Pietramellara

  2. Institute of Soil Biology, Biology Centre AS CR, v. v. i., and Faculty of Science, University of South Bohemia, Na Sádkách 7, 370 05, Ceske Budejovice, Czech Republic

    A. Chroňáková, J. Jirout, D. Elhottová & M. Šimek

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  1. J. Ascher
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  2. M. T. Ceccherini
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  3. A. Chroňáková
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  4. J. Jirout
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  5. F. Borgogni
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  6. D. Elhottová
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  7. M. Šimek
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  8. G. Pietramellara
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Correspondence to J. Ascher.

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Ascher, J., Ceccherini, M.T., Chroňáková, A. et al. Evaluation of the denaturing gradient gel electrophoresis-apparatus as a parameter influencing soil microbial community fingerprinting. World J Microbiol Biotechnol 26, 1721–1726 (2010). https://doi.org/10.1007/s11274-010-0349-z

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  • DOI: https://doi.org/10.1007/s11274-010-0349-z

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