Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.
Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
Appl Environ Microbiol. 2021 May 11;87(11). doi: 10.1128/AEM.02704-20.
Marine microbes, including viruses, are an essential part of the marine ecosystem, forming the base of the food web and driving biogeochemical cycles. Within this system, the composition of viral assemblages changes markedly with time, and some of these changes are repeatable through time; however, the extent to which these dynamics are reflected within versus among evolutionarily related groups of viruses is largely unexplored. To examine these dynamics, changes in the composition of two groups of ecologically important viruses and communities of their potential hosts were sampled every 2 weeks for 13 months at a coastal site in British Columbia, Canada. We sequenced two marker genes for viruses-the gene encoding the major capsid protein of T4-like phages and their relatives () and the RNA-dependent RNA polymerase () gene of marnavirus-like RNA viruses-as well as marker genes for their bacterial and eukaryotic host communities, the genes encoding 16S rRNA and 18S rRNA. There were strong lagged correlations between viral diversity and community similarity of putative hosts, implying that the viruses influenced the composition of the host communities. The results showed that for both viral assemblages, the dominant clusters of phylogenetically related viruses shifted over time, and this was correlated with environmental changes. Viral clusters contained many ephemeral taxa and few persistent taxa, but within a viral assemblage, the ephemeral and persistent taxa were closely related, implying ecological dynamics within these clusters. Furthermore, these dynamics occurred in both the RNA and DNA viral assemblages surveyed, implying that this structure is common in natural viral assemblages. Viruses are major agents of microbial mortality in marine systems, yet little is known about changes in the composition of viral assemblages in relation to those of the microbial communities that they infect. Here, we sampled coastal seawater every 2 weeks for 1 year and used high-throughput sequencing of marker genes to follow changes in the composition of two groups of ecologically important viruses, as well as the communities of bacteria and protists that serve as their respective hosts. Different subsets of genetically related viruses dominated at different times. These results demonstrate that although the genetic composition of viral assemblages is highly dynamic temporally, for the most part the shuffling of genotypes occurs within a few clusters of phylogenetically related viruses. Thus, it appears that even in temperate coastal waters with large seasonal changes, the highly dynamic shuffling of viral genotypes occurs largely within a few subsets of related individuals.
海洋微生物，包括病毒，是海洋生态系统的重要组成部分，构成了食物网的基础，并推动着生物地球化学循环。在这个系统中，病毒组合的组成随时间显著变化，其中一些变化是可重复的；然而，这些动态在进化上相关的病毒群体内部和群体之间的反映程度在很大程度上尚未得到探索。为了研究这些动态，我们在加拿大不列颠哥伦比亚省的一个沿海地点每隔两周采样一次，持续 13 个月，以研究两组具有重要生态意义的病毒及其潜在宿主群落的组成变化。我们对两种病毒的标记基因进行了测序-编码 T4 样噬菌体及其亲缘病毒的主要衣壳蛋白的基因（）和类似于 marnavirus 的 RNA 病毒的 RNA 依赖性 RNA 聚合酶（）基因，以及它们的细菌和真核宿主群落的标记基因，编码 16S rRNA 和 18S rRNA 的基因。病毒多样性与假定宿主群落的相似性之间存在强烈的滞后相关性，这意味着病毒影响了宿主群落的组成。结果表明，对于这两种病毒组合，时间推移时，进化上相关的病毒的主要聚类发生了转移，这与环境变化有关。病毒聚类包含许多短暂的分类群和少数持久的分类群，但在一个病毒组合内，短暂的和持久的分类群密切相关，这意味着这些聚类内部存在生态动态。此外，这些动态发生在调查的 RNA 和 DNA 病毒组合中，这意味着这种结构在自然病毒组合中很常见。病毒是海洋系统中微生物死亡率的主要因素，但对于与它们感染的微生物群落相关的病毒组合组成的变化知之甚少。在这里，我们每隔两周从沿海海域采集水样，持续 1 年，并使用标记基因的高通量测序来跟踪两组具有重要生态意义的病毒以及作为其各自宿主的细菌和原生动物群落的组成变化。不同的遗传相关病毒子集在不同时间占主导地位。这些结果表明，尽管病毒组合的遗传组成在时间上具有高度动态性，但在大多数情况下，基因型的改组发生在少数几个进化上相关的病毒聚类内。因此，即使在具有季节性变化大的温带沿海水域，病毒基因型的高度动态改组也主要发生在少数几个相关个体的几个亚群内。
