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一种新开发的用于计算机模拟末端限制性片段长度多态性分析的ARB软件集成工具的应用揭示了森林土壤中一个新的pmoA簇的优势地位。

Application of a newly developed ARB software-integrated tool for in silico terminal restriction fragment length polymorphism analysis reveals the dominance of a novel pmoA cluster in a forest soil.

作者信息

Ricke Peter, Kolb Steffen, Braker Gesche

机构信息

Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany.

出版信息

Appl Environ Microbiol. 2005 Mar;71(3):1671-3. doi: 10.1128/AEM.71.3.1671-1673.2005.

DOI:10.1128/AEM.71.3.1671-1673.2005
PMID:15746378
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1065180/
Abstract

TRF-CUT, an ARB-implemented tool, was developed to predict in silico the terminal restriction fragments of aligned small-subunit rRNA gene or functional gene sequences. Application of this new tool to perform directed terminal restriction fragment length polymorphism analysis of pmoA products obtained from a forest soil revealed that novel cluster I methanotrophic bacteria were dominant.

摘要

TRF-CUT是一种由ARB实现的工具，旨在通过计算机模拟预测比对后的小亚基rRNA基因或功能基因序列的末端限制性片段。将这一新工具应用于对从森林土壤中获得的pmoA产物进行定向末端限制性片段长度多态性分析，结果显示新型I型甲烷营养菌占主导地位。

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本文引用的文献

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ARB: a software environment for sequence data.ARB：一种用于序列数据的软件环境。
Nucleic Acids Res. 2004 Feb 25;32(4):1363-71. doi: 10.1093/nar/gkh293. Print 2004.
2
Diazotrophic community structure and function in two successional stages of biological soil crusts from the Colorado Plateau and Chihuahuan Desert.来自科罗拉多高原和奇瓦瓦沙漠生物土壤结皮两个演替阶段的固氮群落结构与功能
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Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities.用于分析微生物群落末端限制性片段长度多态性图谱的基于网络的系统发育分配工具。
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Diversity and activity of methanotrophic bacteria in different upland soils.不同旱地土壤中甲烷氧化菌的多样性与活性
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5
Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure.假末端限制性片段的形成，一种影响微生物群落结构末端限制性片段长度多态性分析的与聚合酶链式反应相关的偏差。
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Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays.通过新型靶向pmoA的实时PCR检测法对土壤中甲烷氧化菌进行定量检测。
Appl Environ Microbiol. 2003 May;69(5):2423-9. doi: 10.1128/AEM.69.5.2423-2429.2003.
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Effect of soil ammonium concentration on N2O release and on the community structure of ammonia oxidizers and denitrifiers.土壤铵浓度对一氧化二氮释放以及氨氧化菌和反硝化菌群落结构的影响。
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Detection of methanotrophs with highly divergent pmoA genes from Arctic soils.从北极土壤中检测具有高度不同pmoA基因的甲烷氧化菌。
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