Journal
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
Volume 35, Issue 11, Pages 1345-1352Publisher
OXFORD UNIV PRESS
DOI: 10.1007/s10295-008-0417-7
Keywords
Diversity of methanogens; Taxonomic level; Order-specific primers; Real-time quantitative PCR; Denaturing gradient gel electrophoresis
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Funding
- Korea Institute of Industrial Technology(KITECH) [2006-N-BI02-P-09] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)
- National Research Foundation of Korea [R11-2003-006-04005-0, 핵C6A1603] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)
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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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