Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: Population dynamics and community structures

Authors

  • Youngseob Yu,

    1. School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, South Korea; telephone: +82 (0)54 279 2282; fax: +82 (0)54 279 8299
    Current affiliation:
    1. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139.
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  • Jaai Kim,

    1. School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, South Korea; telephone: +82 (0)54 279 2282; fax: +82 (0)54 279 8299
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  • Seokhwan Hwang

    Corresponding author
    1. School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, South Korea; telephone: +82 (0)54 279 2282; fax: +82 (0)54 279 8299
    • School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, South Korea; telephone: +82 (0)54 279 2282; fax: +82 (0)54 279 8299
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Abstract

The TaqMan quantitative PCR (QPCR) method was used to detect and quantify the 16S rRNA genes of aceticlastic methanogens at different taxonomic levels. Three different sets of primers coupled with a TaqMan probe for QPCR assays to detect the 16S rRNA genes of the order Methanosarcinales, as well as the families Methanosarcinaceae and Methanosaetaceae, were separately used. Using these primer and probe sets, the 16S rRNA genes of aceticlastic methanogens in samples from various anaerobic processes (i.e., nine pure cultures, batch experiment, and three different continuous processes including a full-scale digester), were monitored and quantified by QPCR assays. A batch experiment cultivating a mixture of aceticlastic methanogens, was conducted to monitor their population dynamics. Using this group-specific quantification method, the dynamics of a competition between two aceticlastic populations, as modulated by the acetate concentration, could well be described. The target 16S rRNA genes in environmental samples, collected from three different anaerobic processes treating sludge, cheese whey, and synthetic wastewaters, were additionally quantified. The quantified 16S rRNA gene concentrations for all samples successfully represented the community structures of the target methanogens, which were correlated accurately with the operational parameters of the anaerobic processes. It was also successful to demonstrate probe nesting of aceticlastic methanogens at the levels of order and family. © 2005 Wiley Periodicals, Inc.

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