title: McrA primers for the detection and quantification of the anaerobic archaeal methanotroph 'Candidatus Methanoperedens nitroreducens'.
abstract: The nitrogen and methane cycles are important biogeochemical processes. Recently, 'Candidatus Methanoperedens nitroreducens,' archaea that catalyze nitrate-dependent anaerobic oxidation of methane (AOM), were enriched, and their genomes were analyzed. Diagnostic molecular tools for the sensitive detection of 'Candidatus M. nitroreducens' are not yet available. Here, we report the design of two novel mcrA primer combinations that specifically target the alpha sub-unit of the methyl-coenzyme M reductase (mcrA) gene of 'Candidatus M. nitroreducens'. The first primer pair produces a fragment of 186-bp that can be used to quantify 'Candidatus M. nitroreducens' cells, whereas the second primer pair yields an 1191-bp amplicon that is with sufficient length and well suited for more detailed phylogenetic analyses. Six different environmental samples were evaluated with the new qPCR primer pair, and the abundances were compared with those determined using primers for the 16S rRNA gene. The qPCR results indicated that the number of copies of the 'Candidatus M. nitroreducens' mcrA gene was highest in rice field soil, with 5.6 ± 0.8 × 106copies g-1wet weight, whereas Indonesian river sediment had only 4.6 ± 2.7 × 102copies g-1wet weight. In addition to freshwater environments, sequences were also detected in marine sediment of the North Sea, which contained approximately 2.5 ± 0.7 × 104copies g-1wet weight. Phylogenetic analysis revealed that the amplified 1191-bp mcrA gene sequences from the different environments all clustered together with available genome sequences of mcrA from known 'Candidatus M. nitroreducens' archaea. Taken together, these results demonstrate the validity and utility of the new primers for the quantitative and sensitive detection of the mcrA gene sequences of these important nitrate-dependent AOM archaea. Furthermore, the newly obtained mcrA sequences will contribute to greater phylogenetic resolution of 'Candidatus M. nitroreducens' sequences, which have been only poorly captured by general methanogenic mcrA primers.
authors.affiliation: Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands. avaksmaa@science.ru.nl.
authors.forename: Annika
authors.identifier: http://orcid.org/0000-0001-8794-8942
authors.initials: A
authors.lastname: Vaksmaa
authors.affiliation: Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.|Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.|Soehngen Institute of Anaerobic Microbiology, Nijmegen, The Netherlands.
authors.forename: Mike S M
authors.initials: MS
authors.lastname: Jetten
authors.affiliation: Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.
authors.forename: Katharina F
authors.initials: KF
authors.lastname: Ettwig
authors.affiliation: Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands. clueke@science.ru.nl.
authors.forename: Claudia
authors.initials: C
authors.lastname: Lüke
mesh_terms: D001105:Archaea / Q000201:enzymology* / Q000235:genetics; D008697:Methane / Q000378:metabolism; D010088:Oxidoreductases / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; C021572:methyl coenzyme M reductase; D008697:Methane
keywords: ANME; Anaerobic oxidation of methane; mcrA; ‘Candidatus Methanoperedens nitroreducens’