Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa.
Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa.
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DOI：
10.1186/s12864-017-3888-y
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发表时间：
2017-06-29
期刊：
影响因子：
4.4
通讯作者：
Tamames J
中科院分区：
文献类型：
--
作者：
Cobo-Simón M;Tamames J
尽管微生物在环境过程中发挥着重要作用，但到目前为止，培养微生物的比例很低（5%），限制了我们对其生态策略的了解。然而，高通量测序的发展已经产生了大量的基因组和宏基因组数据，而无需培养，可用于研究生态问题。本研究的目的是估计不同类群的功能能力，基因组大小和16 S拷贝数与它们的普遍性和环境偏好的关系。为了实现这一目标，我们收集了关于不同环境中每个原核生物属的存在的数据。然后，基因组特征，如基因组大小，16 S rRNA基因拷贝数，基因组的功能内容与它们的普遍性和不同的环境偏好相应的类群。结果表明，基因组特征和环境条件之间存在明显的相关性。普遍性和适应性与基因组大小有关，而16 S拷贝数与普遍性没有直接关系。我们观察到，这两个特征的不同组合描绘了不同的环境。此外，对函数类的分析显示了一些与特定环境相关的清晰签名。本文的在线版本（doi：10.1186/s12864-017-3888-y）包含补充材料，可供授权用户使用。
Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput sequencing has generated a huge amount of genomic and metagenomic data without the need of culturing that can be used to study ecological questions. This study aims to estimate the functional capabilities, genomic sizes and 16S copy number of different taxa in relation to their ubiquity and their environmental preferences. To achieve this goal, we compiled data regarding the presence of each prokaryotic genera in diverse environments. Then, genomic characteristics such as genome size, 16S rRNA gene copy number, and functional content of the genomes were related to their ubiquity and different environmental preferences of the corresponding taxa. The results showed clear correlations between genomic characteristics and environmental conditions. Ubiquity and adaptation were linked to genome size, while 16S copy number was not directly related to ubiquity. We observed that different combinations of these two characteristics delineate the different environments. Besides, the analysis of functional classes showed some clear signatures linked to particular environments. The online version of this article (doi:10.1186/s12864-017-3888-y) contains supplementary material, which is available to authorized users.