Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage

Environmental Microbiology
Tillmann LuedersM W Friedrich

Abstract

The diversity of methanogen-specific methyl-coenzyme M reductase alpha-subunit (mcrA/mrtA) genes in Italian rice field soil was analysed using a combination of molecular techniques and enrichment cultures. From 75 mcrA/mrtA clones retrieved from rice field soil, 52 were related to members of the Methanosarcinaceae, Methanosaetaceae and Methanobacteriaceae. However, 19 and four clones formed two novel clusters of deeply branching mcrA sequences, respectively, which could not be affiliated to known methanogens. A new methanogen-specific fingerprinting assay based on terminal restriction fragment length polymorphism (T-RFLP) analysis of fluorescently labelled polymerase chain reaction (PCR) products allowed us to distinguish all environmental mcrA/mrtA sequences via group-specific Sau96I restriction sites. Even genes for the isoenzyme methyl-coenzyme M reductase two (mrtA) of Methanobacteriaceae present in rice field soil were represented by a unique 470 bp terminal restriction fragment (T-RF). Both cloning and T-RFLP analysis indicated a significant representation of novel environmental mcrA sequences in rice field soil (238 bp T-RF). To identify these mcrA sequences, methanogenic enrichment cultures with rice field soil as inocu...Continue Reading

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Citations

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Mar 18, 2008·Applied and Environmental Microbiology·Jingjing PengYahai Lu
Apr 2, 2008·Applied and Environmental Microbiology·Lisa M GiegJoseph M Suflita
Apr 12, 2011·Applied and Environmental Microbiology·Sindy HungerHarold L Drake
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Sep 15, 2009·Applied and Environmental Microbiology·Thomas E Freitag, James I Prosser
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May 19, 2009·Applied and Environmental Microbiology·Lisa M Steinberg, John M Regan
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Sep 6, 2003·Applied and Environmental Microbiology·Steven J HallamEdward F DeLong
Oct 7, 2004·Applied and Environmental Microbiology·Tillmann LuedersMichael W Friedrich
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