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Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities

Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater s...

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Autores principales: Dziewit, Lukasz, Pyzik, Adam, Romaniuk, Krzysztof, Sobczak, Adam, Szczesny, Pawel, Lipinski, Leszek, Bartosik, Dariusz, Drewniak, Lukasz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493836/
https://www.ncbi.nlm.nih.gov/pubmed/26217325
http://dx.doi.org/10.3389/fmicb.2015.00694
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author Dziewit, Lukasz
Pyzik, Adam
Romaniuk, Krzysztof
Sobczak, Adam
Szczesny, Pawel
Lipinski, Leszek
Bartosik, Dariusz
Drewniak, Lukasz
author_facet Dziewit, Lukasz
Pyzik, Adam
Romaniuk, Krzysztof
Sobczak, Adam
Szczesny, Pawel
Lipinski, Leszek
Bartosik, Dariusz
Drewniak, Lukasz
author_sort Dziewit, Lukasz
collection PubMed
description Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater sediments, landfills, anaerobic digesters and the intestinal tracts of ruminants. Research is also hampered by the inability to cultivate methanogenic Archaea. Therefore, biodiversity studies have relied on the use of 16S rRNA and mcrA [encoding the α subunit of the methyl coenzyme M (methyl-CoM) reductase] genes as molecular markers for the detection and phylogenetic analysis of methanogens. Here, we describe four novel molecular markers that should prove useful in the detailed analysis of methanogenic consortia, with a special focus on methylotrophic methanogens. We have developed and validated sets of degenerate PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis: mcrB and mcrG (encoding β and γ subunits of the methyl-CoM reductase, involved in the conversion of methyl-CoM to methane), mtaB (encoding methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase, catalyzing the conversion of methanol to methyl-CoM) and mtbA (encoding methylated [methylamine-specific corrinoid protein]:coenzyme M methyltransferase, involved in the conversion of mono-, di- and trimethylamine into methyl-CoM). The sensitivity of these primers was verified by high-throughput sequencing of PCR products amplified from DNA isolated from microorganisms present in anaerobic digesters. The selectivity of the markers was analyzed using phylogenetic methods. Our results indicate that the selected markers and the PCR primer sets can be used as specific tools for in-depth diversity analyses of methanogenic consortia.
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spelling pubmed-44938362015-07-27 Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities Dziewit, Lukasz Pyzik, Adam Romaniuk, Krzysztof Sobczak, Adam Szczesny, Pawel Lipinski, Leszek Bartosik, Dariusz Drewniak, Lukasz Front Microbiol Microbiology Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater sediments, landfills, anaerobic digesters and the intestinal tracts of ruminants. Research is also hampered by the inability to cultivate methanogenic Archaea. Therefore, biodiversity studies have relied on the use of 16S rRNA and mcrA [encoding the α subunit of the methyl coenzyme M (methyl-CoM) reductase] genes as molecular markers for the detection and phylogenetic analysis of methanogens. Here, we describe four novel molecular markers that should prove useful in the detailed analysis of methanogenic consortia, with a special focus on methylotrophic methanogens. We have developed and validated sets of degenerate PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis: mcrB and mcrG (encoding β and γ subunits of the methyl-CoM reductase, involved in the conversion of methyl-CoM to methane), mtaB (encoding methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase, catalyzing the conversion of methanol to methyl-CoM) and mtbA (encoding methylated [methylamine-specific corrinoid protein]:coenzyme M methyltransferase, involved in the conversion of mono-, di- and trimethylamine into methyl-CoM). The sensitivity of these primers was verified by high-throughput sequencing of PCR products amplified from DNA isolated from microorganisms present in anaerobic digesters. The selectivity of the markers was analyzed using phylogenetic methods. Our results indicate that the selected markers and the PCR primer sets can be used as specific tools for in-depth diversity analyses of methanogenic consortia. Frontiers Media S.A. 2015-07-07 /pmc/articles/PMC4493836/ /pubmed/26217325 http://dx.doi.org/10.3389/fmicb.2015.00694 Text en Copyright © 2015 Dziewit, Pyzik, Romaniuk, Sobczak, Szczesny, Lipinski, Bartosik and Drewniak. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Dziewit, Lukasz
Pyzik, Adam
Romaniuk, Krzysztof
Sobczak, Adam
Szczesny, Pawel
Lipinski, Leszek
Bartosik, Dariusz
Drewniak, Lukasz
Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities
title Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities
title_full Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities
title_fullStr Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities
title_full_unstemmed Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities
title_short Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities
title_sort novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493836/
https://www.ncbi.nlm.nih.gov/pubmed/26217325
http://dx.doi.org/10.3389/fmicb.2015.00694
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