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

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 environme...

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Autores principales: Xu, Sai, Cai, Chen, Guo, Jianhua, Lu, Wenjing, Yuan, Zhiguo, Hu, Shihu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5955947/
https://www.ncbi.nlm.nih.gov/pubmed/29769540
http://dx.doi.org/10.1038/s41598-018-24974-z
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author Xu, Sai
Cai, Chen
Guo, Jianhua
Lu, Wenjing
Yuan, Zhiguo
Hu, Shihu
author_facet Xu, Sai
Cai, Chen
Guo, Jianhua
Lu, Wenjing
Yuan, Zhiguo
Hu, Shihu
author_sort Xu, Sai
collection PubMed
description 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.
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spelling pubmed-59559472018-05-21 Different clusters of Candidatus ‘Methanoperedens nitroreducens’-like archaea as revealed by high-throughput sequencing with new primers Xu, Sai Cai, Chen Guo, Jianhua Lu, Wenjing Yuan, Zhiguo Hu, Shihu Sci Rep Article 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. Nature Publishing Group UK 2018-05-16 /pmc/articles/PMC5955947/ /pubmed/29769540 http://dx.doi.org/10.1038/s41598-018-24974-z Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Xu, Sai
Cai, Chen
Guo, Jianhua
Lu, Wenjing
Yuan, Zhiguo
Hu, Shihu
Different clusters of Candidatus ‘Methanoperedens nitroreducens’-like archaea as revealed by high-throughput sequencing with new primers
title Different clusters of Candidatus ‘Methanoperedens nitroreducens’-like archaea as revealed by high-throughput sequencing with new primers
title_full Different clusters of Candidatus ‘Methanoperedens nitroreducens’-like archaea as revealed by high-throughput sequencing with new primers
title_fullStr Different clusters of Candidatus ‘Methanoperedens nitroreducens’-like archaea as revealed by high-throughput sequencing with new primers
title_full_unstemmed Different clusters of Candidatus ‘Methanoperedens nitroreducens’-like archaea as revealed by high-throughput sequencing with new primers
title_short Different clusters of Candidatus ‘Methanoperedens nitroreducens’-like archaea as revealed by high-throughput sequencing with new primers
title_sort different clusters of candidatus ‘methanoperedens nitroreducens’-like archaea as revealed by high-throughput sequencing with new primers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5955947/
https://www.ncbi.nlm.nih.gov/pubmed/29769540
http://dx.doi.org/10.1038/s41598-018-24974-z
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