Evaluation and update of cutoff values for methanotrophic pmoA gene sequences
文献类型：期刊论文
| 作者 | Wen, Xi1,2; Yang, Sizhong1,3; Liebner, Susanne1 |
| 刊名 | ARCHIVES OF MICROBIOLOGY
 |
| 出版日期 | 2016-09-01 |
| 卷号 | 198期号:7页码:629-636 |
| 关键词 | pmoA gene Cutoff Methanotrophs Mothur GC content |
| ISSN号 | 0302-8933 |
| DOI | 10.1007/s00203-016-1222-8 |
| 通讯作者 | Yang, Sizhong(syang@gfz-potsdam.de) |
| 英文摘要 | The functional pmoA gene is frequently used to probe the diversity and phylogeny of methane-oxidizing bacteria (MOB) in various environments. Here, we compared the similarities between the pmoA gene and the corresponding 16S rRNA gene sequences of 77 described species covering gamma- and alphaproteobacterial methanotrophs (type I and type II MOB, respectively) as well as methanotrophs from the phylum Verrucomicrobia. We updated and established the weighted mean pmoA gene cutoff values on the nucleotide level at 86, 82, and 71 % corresponding to the 97, 95, and 90 % similarity of the 16S rRNA gene. Based on these cutoffs, the functional gene fragments can be entirely processed at the nucleotide level throughout software platforms such as Mothur or QIIME which provide a user-friendly and command-based alternative to amino acid-based pipelines. Type II methanotrophs are less divergent than type I both with regard to ribosomal and functional gene sequence similarity and GC content. We suggest that this agrees with the theory of different life strategies proposed for type I and type II MOB. |
| 收录类别 | SCI |
| WOS关键词 | GUANINE-CYTOSINE CONTENT ; METHANE OXIDATION ; RIBOSOMAL-RNA ; POPULATION-DYNAMICS ; PADDY SOIL ; COMMUNITIES ; BACTERIA ; MONOOXYGENASE ; TEMPERATURE ; EVOLUTION |
| WOS研究方向 | Microbiology |
| WOS类目 | Microbiology |
| 语种 | 英语 |
| WOS记录号 | WOS:000380668100005 |
| 出版者 | SPRINGER |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2557439 |
| 专题 | 寒区旱区环境与工程研究所 |
| 通讯作者 | Yang, Sizhong |
| 作者单位 | 1.GFZ German Res Ctr Geosci, Helmholtz Ctr Potsdam, Sect Geomicrobiol 5 3, D-14473 Potsdam, Germany 2.Northwest Univ Nationalities, Coll Elect Engn, Lanzhou 730030, Peoples R China 3.Chinese Acad Sci, Cold & Arid Reg Environm & Engn Res Inst, State Key Lab Frozen Soils Engn, Lanzhou 730000, Peoples R China |
| 推荐引用方式 GB/T 7714 | Wen, Xi,Yang, Sizhong,Liebner, Susanne. Evaluation and update of cutoff values for methanotrophic pmoA gene sequences[J]. ARCHIVES OF MICROBIOLOGY,2016,198(7):629-636. |
| APA | Wen, Xi,Yang, Sizhong,&Liebner, Susanne.(2016).Evaluation and update of cutoff values for methanotrophic pmoA gene sequences.ARCHIVES OF MICROBIOLOGY,198(7),629-636. |
| MLA | Wen, Xi,et al."Evaluation and update of cutoff values for methanotrophic pmoA gene sequences".ARCHIVES OF MICROBIOLOGY 198.7(2016):629-636. |
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来源：寒区旱区环境与工程研究所
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