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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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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. |
format | Online Article Text |
id | pubmed-5955947 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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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