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The newly discovered  Candidatus  ‘Methanoperedens nitroreducens’ ( M .  nitroreducens ), mediating nitrate-dependent anaerobic oxidation of methane, is an important microorganism in linking carbon and nitrogen cycles. In order to explore the diversity of  M .  nitroreducens -like archaea in various environmental niches with advanced high-throughput sequencing, new primers based on alpha subunit of methyl-coenzyme M reductase gene were designed. The PCR results demonstrated that the new primers could effectively detect  M .  nitroreducens -like archaea from an enrichment culture dominated by  M .  nitroreducens  as well as samples collected from a natural freshwater lake and a full-scale wastewater treatment plant (WWTP). By high-throughput sequencing, more than 30,000  M .  nitroreducens -like sequences were obtained. Phylogenetic analysis of these sequences along with published sequences showed that  M .  nitroreducens -like archaea could be divided into three sub-branches (named as Group A, Group B and Group C in this study). Clear geographical difference was observed, with Group A and Group B dominating samples in Queensland (Australia) and in European ecosystems, respectively. Further quantitative PCR revealed that the  M .  nitroreducens -like archaea were more abundant in WWTP than the freshwater lake. The study provided a large number of sequences for  M .  nitroreducens -like archaeal communities, thus expanded our understanding on the ecological diversity of  M .  nitroreducens -like archaea.

Different clusters of Candidatus ‘Methanoperedens nitroreducens’-like archaea as revealed by high-throughput sequencing with new primers