Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems
Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems
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DOI：
10.1111/j.1574-6941.2011.01190.x
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发表时间：
2011-12-01
影响因子：
4.2
通讯作者：
Debroas, Didier
中科院分区：
文献类型：
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作者：
Roux, Simon;Enault, Francois;Debroas, Didier
PCR扩增rRNA基因是评估微生物多样性最常用的方法。然而，这种分子标记通常在细胞中存在多个拷贝，此外，还表现出基因组内的异质性。在这种情况下，管家基因可以用作生态学研究的分类标记。然而，与16S rRNA基因相比，这些蛋白质编码基因的效率尚未在环境数据上进行测试。为此，我们选择了5个引物集可用的蛋白质标记基因（rplB、pyrG、fusA、leuS和rpoB），并与水生生态系统中16S rRNA基因的PCR扩增结果或宏基因组数据进行了比较。对这些生态系统中发现的主要类群（如放线菌门、拟杆菌门、变形菌门和蓝藻门）的分析表明，蛋白质标记与宏基因组读取的16S rRNA基因结果吻合良好。然而，与PCR扩增的16S rRNA结果相比，使用这些标记可以检测微生物组合中的小群体，提供更多细节。此外，使用一组蛋白质标记可以推断出rRNA操纵子的平均拷贝数。这个平均估计值基本上低于测序基因组估计值。
PCR amplification of the rRNA gene is the most popular method for assessing microbial diversity. However, this molecular marker is often present in multiple copies in cells presenting, in addition, an intragenomic heterogeneity. In this context, housekeeping genes may be used as taxonomic markers for ecological studies. However, the efficiency of these protein-coding genes compared to 16S rRNA genes has not been tested on environmental data. For this purpose, five protein marker genes for which primer sets are available, were selected (rplB, pyrG, fusA, leuS and rpoB) and compared with 16S rRNA gene results from PCR amplification or metagenomic data from aquatic ecosystems. Analysis of the major groups found in these ecosystems, such as Actinobacteria, Bacteroides, Proteobacteria and Cyanobacteria, showed good agreement between the protein markers and the results given by 16S rRNA genes from metagenomic reads. However, with the markers it was possible to detect minor groups among the microbial assemblages, providing more details compared to 16S rRNA results from PCR amplification. In addition, the use of a set of protein markers made it possible to deduce a mean copy number of rRNA operons. This average estimate is essentially lower than the one estimated in sequenced genomes.