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

Scientific Reports
Sai XuShihu Hu

Abstract

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...Continue Reading

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Citations

Oct 7, 2018·Applied and Environmental Microbiology·Simon Guerrero-CruzAnnika Vaksmaa

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Methods Mentioned

BETA
PCR
electrophoresis
Illumina sequencing

Software Mentioned

Primer
UCLUST
Miseq
Primer Premier
MEGA
- Blast
Clustal X
Mothur

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