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首页> 外文期刊>Applied Microbiology and Biotechnology >Comparative analysis of two 16S rRNA gene-based PCR primer sets provides insight into the diversity distribution patterns of anammox bacteria in different environments
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Comparative analysis of two 16S rRNA gene-based PCR primer sets provides insight into the diversity distribution patterns of anammox bacteria in different environments

机译：两种基于16S rRNA基因的PCR引物集的比较分析提供了对不同环境中厌氧氨氧化细菌多样性分布模式的深入了解

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摘要

Due to the high divergence among 16S rRNA genes of anammox bacteria, different diversity pattern of the community could be resulted from using different primer set. In this study, the efficiencies and specificities of two commonly used sets, Amx368F/Amx820R and Brod541F/Amx820R, were evaluated by exploring the diversity characteristics of anammox bacteria in sediments from marine, estuary, and freshwater wetland. Statistical analysis indicated that the base mispairing rate between bases on 16S rRNA gene sequences retrieved by Amx368F/Amx820R and their corresponding ones on primer Brod541F was quite high, suggesting the different efficiency and specificity of Amx368F/Amx820R and Brod541F/Amx820R. Further experimental results demonstrated that multiple genera of anammox bacteria, including Ca. Scalindua, Ca. Brocadia, and Ca. Kuenenia, were able to be detected by Amx368F/Amx820R, but only Ca. Scalindua could be retrieved by Brod541F/Amx820R. Moreover, the phylogenetic clusters of Ca. Scalindua by Amx368F/Amx820R were different completely from those by Brod541F/Amx820R, presenting a significant complementary effect. By joint application of these two primer sets, the diversity distribution patterns of anammox bacteria in different environments were analyzed. Almost all retrieved sequences from marine sediments belonged to Ca. Scalindua. Sequences from freshwater wetland were affiliated to Ca. Brocadia and two new clusters, while high diversity of anammox bacteria was found in estuary, including Ca. Scalindua, Ca. Brocadia, and Ca. Kuenenia, corresponding to the river-sea intersection environmental feature. In total, these two prime sets have different characteristic for anammox bacteria detecting from environmental samples, and their combined application could achieve better diversity display of anammox community.
机译：由于厌氧细菌的16S rRNA基因之间存在高度差异，因此使用不同的引物集可能会导致群落的不同多样性模式。在这项研究中，通过探索海洋，河口和淡水湿地沉积物中的厌氧菌细菌的多样性特征，评估了两个常用集Amx368F / Amx820R和Brod541F / Amx820R的效率和特异性。统计分析表明，Amx368F / Amx820R检索到的16S rRNA基因序列的碱基与相应的引物Brod541F碱基之间的碱基错配率很高，表明Amx368F / Amx820R和Brod541F / Amx820R的效率和特异性不同。进一步的实验结果表明，包括钙在内的多种厌氧细菌。加利福尼亚斯卡林杜阿Brocadia和Ca。 Kuxennia，可以被Amx368F / Amx820R检测到，但只能被Ca检测到。 Scalindua可以通过Brod541F / Amx820R检索。此外，钙的系统发育簇。 Amx368F / Amx820R的Scalindua与Brod541F / Amx820R的Scalindua完全不同，具有明显的互补作用。通过这两个引物组的联合应用，分析了不同环境下厌氧氨氧化细菌的多样性分布模式。从海洋沉积物中获得的几乎所有序列都属于钙。斯卡林杜瓦。淡水湿地的序列属于钙。 Brocadia和两个新的簇，同时在包括Ca在内的河口发现了高多样性的厌氧细菌。加利福尼亚斯卡林杜阿Brocadia和Ca。 Kuenenia，对应于河海交叉口的环境特征。总体而言，这两个主要集合对于从环境样品中检测出的厌氧菌具有不同的特性，并且它们的组合应用可以实现更好的厌氧菌群落多样性展示。

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