title: A novel fingerprint method to assess the diversity of methanogens in microbial systems.
abstract: Understanding the ecology of methanogens in natural and engineered environments is a prerequisite to predicting or managing methane emissions. In this study, a novel high-throughput fingerprint method was developed for determining methanogen diversity and relative abundance within environmental samples. The method described here, designated amplicon length heterogeneity PCR of the mcrA gene (LH-mcrA), is based on the natural length variation in the mcrA gene. The mcrA gene encodes the alpha-subunit of the methyl-coenzyme M reductase, which is involved in the terminal step of methane production by methanogens. The methanogenic communities from stored swine and dairy manures were distinct from each other. To validate the method, methanogenic communities in a plug flow-type bioreactor (PFBR) treating swine manure were characterized using LH-mcrA method and correlated to mcrA gene clone libraries. The diversity and relative abundance of the methanogenic groups were assessed. Methanobrevibacter, Methanosarcinaceae, Methanoculleus, Methanogenium, Methanocorpusculum and one unidentified group were assigned to particular LH-mcrA amplicons. Particular phylotypes related to Methanoculleus were predominant in the last compartment of the PFBR where the bulk of methane was produced. LH-mcrA method was found to be a reliable, fast and cost-effective alternative for diversity assessment of methanogenic communities in microbial systems.
authors.affiliation: Dairy and Swine Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Gagnon
authors.forename: Maialen
authors.initials: M
authors.lastname: Barret
authors.forename: Edward
authors.initials: E
authors.lastname: Topp
authors.forename: Martin
authors.initials: M
authors.lastname: Kalmokoff
authors.forename: Daniel
authors.initials: D
authors.lastname: Massé
authors.forename: Lucie
authors.initials: L
authors.lastname: Masse
authors.forename: Guylaine
authors.initials: G
authors.lastname: Talbot
mesh_terms: D000818:Animals; D019149:Bioreactors; D002417:Cattle; D016172:DNA Fingerprinting / Q000379:methods*; D019641:DNA, Archaeal / Q000737:chemistry / Q000302:isolation & purification; D019605:Euryarchaeota / Q000145:classification* / Q000201:enzymology / Q000235:genetics; D015723:Gene Library; D008372:Manure / Q000382:microbiology; D010088:Oxidoreductases / Q000235:genetics*; D010802:Phylogeny; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013552:Swine
chemical_list: D019641:DNA, Archaeal; D008372:Manure; D010088:Oxidoreductases; C021572:methyl coenzyme M reductase