Methyl-coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane-oxidizing Archaea

Methods Enzymol. 2005;397:428-42. doi: 10.1016/S0076-6879(05)97026-2.


In many anoxic environments, methanogenesis is the predominant terminal electron accepting process involved in the mineralization of organic matter, which is catalyzed by methanogenic Archaea. These organisms represent a unique but phylogenetically diverse guild of prokaryotes, which can be conveniently tracked in the environment by targeting the mcrA gene as a functional marker. This gene encodes the alpha subunit of the methyl-coenzyme M reductase (MCR), which catalyzes the last step in methanogenesis and is present in all methanogens. Cultivation-independent analysis of methanogenic communities involves the polymerase chain reaction (PCR) amplification of the mcrA gene from extracted community DNA, comparative analysis of mcrA clone libraries, or PCR-based fingerprinting analysis by terminal restriction fragment polymorphism analysis (T-RFLP). It has also been suggested that anaerobic methane-oxidizing Archaea possess MCR, which facilitates detection of this novel group of "reverse methanogens" as well using the mcrA gene as a functional marker.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / genetics*
  • Cloning, Molecular
  • DNA, Archaeal / isolation & purification
  • Ecosystem
  • Genes, Archaeal / genetics*
  • Methanobacteriaceae / genetics
  • Methanomicrobiales / genetics
  • Methanosarcina barkeri / genetics
  • Methanosarcinales / genetics
  • Oxidoreductases / genetics*
  • Phylogeny
  • Polymerase Chain Reaction
  • Polymorphism, Restriction Fragment Length
  • Soil Microbiology


  • DNA, Archaeal
  • Oxidoreductases
  • methyl coenzyme M reductase