The characterization of RNA viruses in tropical seawater using targeted PCR and metagenomics.
The characterization of RNA viruses in tropical seawater using targeted PCR and metagenomics.
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DOI：
10.1128/mbio.01210-14
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发表时间：
2014-06-17
期刊：
影响因子：
6.4
通讯作者：
Steward GF
中科院分区：
文献类型：
--
作者：
Culley AI;Mueller JA;Belcaid M;Wood-Charlson EM;Poisson G;Steward GF
病毒对浮游生物的生态和进化有着深远的影响，但我们对水生病毒群落组成的了解仍然是初级的。对于那些有RNA基因组的病毒来说尤其如此。已发表的有限数据表明，RNA微浮游生物由具有正意义的单链（+ss）基因组的病毒主导，这些病毒具有与小核糖核酸目（小核糖核酸）中真核感染病毒的共同特征。在这项研究中，我们利用靶向PCR和宏基因组学研究了热带沿海海水样本中RNA病毒组合的多样性。从浮力密度梯度的部分中扩增RNA依赖RNA聚合酶（RdRp）基因表明，海洋小核糖核酸病毒的两个主要亚枝的分布在很大程度上与总病毒样RNA的分布一致，这一发现与它们的优势地位一致。对文库中RdRp序列的分析显示存在许多不同的种型，其中大多数与培养病毒仅有较远的亲缘关系。系统发育分析表明，在一个35升的样本中，存在数百种独特的小核糖核酸样种型，它们彼此之间的差异至少与目前已知物种之间的差异一样多。在宏基因组中组装这些序列，重建了六个基本完整的病毒基因组，这些基因组具有与硅藻科、迪西特罗科和马尔纳病毒科病毒相似的特征。热带海水宏基因组与其他栖息地宏基因组的比较表明，+ssRNA病毒通常是水生环境中最常见的RNA病毒类型，但文库制备的偏差仍然是这一观察结果的可能解释。海洋浮游生物占了地球上大部分的光合作用和呼吸作用，它们在全球范围内影响着碳的循环和营养物质的分布。尽管病毒对浮游生物的生态和进化至关重要，但海洋中的大多数病毒及其宿主的身份是未知的。这份报告是研究海洋中含rna病毒遗传多样性的为数不多的报告之一。这些数据扩大了已知的病毒多样性范围，并对海洋中RNA病毒的物理特性和遗传组成有了新的认识。
Viruses have a profound influence on the ecology and evolution of plankton, but our understanding of the composition of the aquatic viral communities is still rudimentary. This is especially true of those viruses having RNA genomes. The limited data that have been published suggest that the RNA virioplankton is dominated by viruses with positive-sense, single-stranded (+ss) genomes that have features in common with those of eukaryote-infecting viruses in the order Picornavirales (picornavirads). In this study, we investigated the diversity of the RNA virus assemblages in tropical coastal seawater samples using targeted PCR and metagenomics. Amplification of RNA-dependent RNA polymerase (RdRp) genes from fractions of a buoyant density gradient suggested that the distribution of two major subclades of the marine picornavirads was largely congruent with the distribution of total virus-like RNA, a finding consistent with their proposed dominance. Analyses of the RdRp sequences in the library revealed the presence of many diverse phylotypes, most of which were related only distantly to those of cultivated viruses. Phylogenetic analysis suggests that there were hundreds of unique picornavirad-like phylotypes in one 35-liter sample that differed from one another by at least as much as the differences among currently recognized species. Assembly of the sequences in the metagenome resulted in the reconstruction of six essentially complete viral genomes that had features similar to viruses in the families Bacillarna-, Dicistro-, and Marnaviridae. Comparison of the tropical seawater metagenomes with those from other habitats suggests that +ssRNA viruses are generally the most common types of RNA viruses in aquatic environments, but biases in library preparation remain a possible explanation for this observation. Marine plankton account for much of the photosynthesis and respiration on our planet, and they influence the cycling of carbon and the distribution of nutrients on a global scale. Despite the fundamental importance of viruses to plankton ecology and evolution, most of the viruses in the sea, and the identities of their hosts, are unknown. This report is one of very few that delves into the genetic diversity within RNA-containing viruses in the ocean. The data expand the known range of viral diversity and shed new light on the physical properties and genetic composition of RNA viruses in the ocean.