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Use of order-specific primers to investigate the methanogenic diversity in acetate enrichment system

  • Original Paper
  • Published:
Journal of Industrial Microbiology & Biotechnology

Abstract

The applicability of order-specific primers in minimizing the possible underestimation of microbial diversity was evaluated via denaturing gradient gel electrophoresis (DGGE) analysis of a lab-scale anaerobic digester. Initially, a population analysis with real-time quantitative PCR demonstrated the existence of three methanogenic orders—Methanobacteriales, Methanomicrobiales, and Methanosarcinales—throughout the reaction period. DGGE analyses with three pairs of order-specific primers yielded eight operational taxonomic units (OTUs), whereas DGGE analysis with two independent Archaea-specific primers identified only five. Moreover, the order-specific primers amplified at least one OTU affiliated with each order, whereas no members of Methanobacteriales or Methanomicrobiales were identified with Archaea-specific primers in most samples. These findings provide evidence that order-specific analysis can detect the diversity of methanogens in greater detail than conventional Archaea-specific analysis.

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Acknowledgments

This work was supported in part by the Korea Ministry of Education (MOE) through the BK-21 program and by the Korea Science and Engineering Foundation (KOSEF) through the Advanced Environmental Biotechnology Research Center (R11-2003-006) at POSTECH. This research was also supported by New and Renewable Energy R&D program (2006-N-BI02-P-09) under the Korea Ministry of Commerce, Industry, and Energy (MOCIE).

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Authors and Affiliations

  1. School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), San 31, Hyoja-dong, Nam-gu, Pohang, Gyungbuk, 790-784, South Korea

    Seung Gu Shin, Kwanghyun Hwang & Seokhwan Hwang

  2. Microbial Ecology Laboratory, Department of Microbiology and Environmental Change Institute (ECI), National University of Ireland, Galway, Ireland

    Changsoo Lee

  3. Division of Environmental and Geosystem Engineering, College of Engineering, Kangwon National University, Hyoja-2-dong, Chuncheon, Kangwon, 200-701, South Korea

    Johng-Hwa Ahn

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  1. Seung Gu Shin
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  2. Changsoo Lee
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  3. Kwanghyun Hwang
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  4. Johng-Hwa Ahn
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  5. Seokhwan Hwang
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Correspondence to Seokhwan Hwang.

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Shin, S.G., Lee, C., Hwang, K. et al. Use of order-specific primers to investigate the methanogenic diversity in acetate enrichment system. J Ind Microbiol Biotechnol 35, 1345–1352 (2008). https://doi.org/10.1007/s10295-008-0417-7

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  • DOI: https://doi.org/10.1007/s10295-008-0417-7

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