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Influence of DNA isolation method on the investigation of archaeal diversity and abundance in biogas plants

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Abstract

Various methods are available for DNA isolation from environmental samples. Because the chemical and biological composition of samples such as soil, sludge, or plant material is different, the effectiveness of DNA isolation can vary depending on the method applied and thus, have a substantial effect on the results of downstream analysis of the microbial community. Although the process of biogas formation is being intensely investigated, a systematic evaluation of kits for DNA isolation from material of biogas plants is still lacking. Since no DNA isolation kit specifically tailored for DNA isolation from sludge of biogas plants is available, this study compares five commercially available kits regarding their influence on downstream analyses such denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR). The results show that not all kits are equally suited for the DNA isolation from samples of different biogas plants, but highly reproducible DGGE fingerprints as well as qPCR results across the tested samples from biogas reactors using different substrate compositions could be produced using selected kits.

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Acknowledgments

This study was supported by the Bundesministerium für Bildung und Forschung (BMBF) via the BioPara network (Grant 03SF0421C). We thank Bioreact GmbH (Troisdorf, Germany) and the Stadtentwässerung of Dresden, Germany for the provision of sludge samples and Tobias Kern (Technische Universität Dresden, Germany) for his assistance.

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Authors and Affiliations

  1. Sächsische Akademie der Wissenschaften zu Leipzig, Karl-Tauchnitz-Straße 1, 04107, Leipzig, Germany

    Juliane Theiss & Kerstin Röske

  2. Technische Universität Dresden, Professur für Mikrobielle Diversität, Zellescher Weg 20b, 01217, Dresden, Germany

    Michael Rother

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  1. Juliane Theiss
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  2. Michael Rother
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  3. Kerstin Röske
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Correspondence to Kerstin Röske.

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Communicated by Harald Huber.

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Theiss, J., Rother, M. & Röske, K. Influence of DNA isolation method on the investigation of archaeal diversity and abundance in biogas plants. Arch Microbiol 198, 619–628 (2016). https://doi.org/10.1007/s00203-016-1221-9

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  • DOI: https://doi.org/10.1007/s00203-016-1221-9

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