Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein.
Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein.
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DOI：
10.1038/ismej.2014.43
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发表时间：
2014-10
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--
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Gokushovirinae 亚科的小型单链 DNA (ssDNA) 噬菌体传统上被认为是感染专性寄生细菌（例如衣原体）的狭隘目标、生态位特异性病毒。宏基因组学的出现揭示了 gokushovirus 在全球环境样本中广泛存在。这项研究通过开发简并 PCR 检测来扩增极谷病毒主要衣壳蛋白 (MCP) 基因的一部分，从而扩展了对环境中极谷病毒多样性的认识。对 10 个环境样本（沉积物、污水、海水和淡水）中的 500 多个扩增子进行了测序，揭示了这一未被充分研究的噬菌体群体的普遍性和高度多样性。将多重比对生成的残基水平保守数据与预测的 3D 结构相结合，揭示了结构内部残基比表面呈现的蛋白质-蛋白质或病毒-宿主相互作用结构域更加高度保守的趋势。将这些数据集汇总到系统发育框架中，许多 gokushovirus MCP 分支包含来自多个环境的样本，尽管不同的分支在不同的样本中占主导地位。南极沉积物样本包含最多样化的 gokushovirus 群落，而来自佛罗里达州的淡水泉水则最不多样化。观察到的多样性是否是由环境因素或宿主结合相互作用驱动的仍然是一个悬而未决的问题。这种先前被忽视的 ssDNA 病毒群具有高度的环境多样性，因此需要进一步研究阐明其自然宿主并探索其生态作用。
The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein–protein or viral–host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles.
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