Long-term stability and Red Queen-like strain dynamics in marine viruses
Long-term stability and Red Queen-like strain dynamics in marine viruses
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DOI：
10.1038/s41564-019-0628-x
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发表时间：
2020-02-01
影响因子：
28.3
通讯作者：
Fuhrman, Jed A.
中科院分区：
文献类型：
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作者：
Ignacio-Espinoza, J. Cesar;Ahlgren, Nathan A.;Fuhrman, Jed A.
近地表海洋病毒群落的宏基因组测序显示，在过去的5年中，尽管较小的种群变异更具变异性，但总体群落随时间的推移保持稳定，这与红皇后样动态一致。感染微生物的病毒在数量上主导海洋微生物群落，影响范围从宿主进化到全球生物地球化学循环（1，2）。然而，病毒群落的动态，必要的概念和机制模型的发展，仍然难以评估。在这里，我们通过分析近表面0.02-0.2 μ m样本的宏基因组描述了病毒群落的长期稳定性，这些样本来自圣佩德罗海洋时间序列（3），在5年内每月采样。在19，907个组装的病毒重叠群（>5 kb，平均15 kb）中，在每个样品中发现97%（通过> 98%ID宏基因组读段募集）具有范围超过7个数量级的相对丰度，其中等级丰度的有限时间重新排序沿着而丰度变化很小。病毒群落组成的季节性变化叠加在整体稳定性，最大的社区相似性发生在12个月的时间间隔。尽管具有98%序列同一性的病毒基因型簇具有稳定性，但病毒序列显示出单核苷酸多态性（SNP）的短暂变化和较小群体变异的恒定转换，每个变化在几个月内上升和下降，让人想起红皇后动力学（4）。从已知的病毒-宿主相互作用的角度来解释种群内变异的上升和下降（5），这与波动选择作用于微多样性菌株云的假设一致，并且这种连续性与不断变化的病毒-宿主防御和反防御有关。这导致了病毒与宿主的长期共存，而这种共存是由不断变化的微小变体促成的。
Metagenomic sequencing of near-surface marine viral communities sampled monthly over 5 years revealed that overall communities were stable over time, although minor population variants were more variable, which is consistent with Red Queen-like dynamics.Viruses that infect microorganisms dominate marine microbial communities numerically, with impacts ranging from host evolution to global biogeochemical cycles(1,2). However, virus community dynamics, necessary for conceptual and mechanistic model development, remains difficult to assess. Here, we describe the long-term stability of a viral community by analysing the metagenomes of near-surface 0.02-0.2 mu m samples from the San Pedro Ocean Time-series(3) that were sampled monthly over 5 years. Of 19,907 assembled viral contigs (>5 kb, mean 15 kb), 97% were found in each sample (by >98% ID metagenomic read recruitment) to have relative abundances that ranged over seven orders of magnitude, with limited temporal reordering of rank abundances along with little change in richness. Seasonal variations in viral community composition were superimposed on the overall stability; maximum community similarity occurred at 12-month intervals. Despite the stability of viral genotypic clusters that had 98% sequence identity, viral sequences showed transient variations in single-nucleotide polymorphisms (SNPs) and constant turnover of minor population variants, each rising and falling over a few months, reminiscent of Red Queen dynamics(4). The rise and fall of variants within populations, interpreted through the perspective of known virus-host interactions(5), is consistent with the hypothesis that fluctuating selection acts on a microdiverse cloud of strains, and this succession is associated with ever-shifting virus-host defences and counterdefences. This results in long-term virus-host coexistence that is facilitated by perpetually changing minor variants.