Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea

• Published in: Microbial biotechnology Vol. 4; no. 5; pp. 585 - 602
• Main Authors: Narihiro, Takashi, Sekiguchi, Yuji
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01-09-2011; John Wiley & Sons, Inc
• Subjects: Archaea; Archaea - classification; Archaea - genetics; Archaea - isolation & purification; Archaea - metabolism; Bacterial Typing Techniques - instrumentation; Bacterial Typing Techniques - methods; Carbon dioxide; Climate change; Cloning; Coenzyme M; Deoxyribonucleic acid; DNA; DNA chips; DNA microarrays; DNA Primers - genetics; DNA probes; DNA Probes - genetics; Ecosystems; Environmental Microbiology; Environmental monitoring; Fluorescence; Fluorescence in situ hybridization; Genes; Identification methods; Mass spectrometry; Methane - metabolism; Methanogenic archaea; Methanogenic bacteria; Microbiology; Minireviews; Molecular Probe Techniques - instrumentation; Molecular Sequence Data; Oligonucleotides; Phylogeny; Polymerase chain reaction; Primers; Probes; Reductase; Reductases; Researchers; rRNA 16S; Scientific imaging; Sediments
• ISSN: 1751-7915; 1751-7915
• DOI: 10.1111/j.1751-7915.2010.00239.x

Summary
For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α‐subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers.