Use of order-specific primers to investigate the methanogenic diversity in acetate enrichment system.
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.
Shin
Seung Gu
SG
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.
Lee
Changsoo
C
Hwang
Kwanghyun
K
Ahn
Johng-Hwa
JH
Hwang
Seokhwan
S
D000085:Acetates / Q000378:metabolism*; D044822:Biodiversity; D019149:Bioreactors / Q000382:microbiology; D017931:DNA Primers / Q000235:genetics; D019641:DNA, Archaeal / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D019605:Euryarchaeota / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D013045:Species Specificity
D000085:Acetates; D017931:DNA Primers; D019641:DNA, Archaeal