Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth
Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth
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DOI：
10.1038/s41396-021-01150-2
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发表时间：
2021-11-13
期刊：
影响因子：
11
通讯作者：
Martinez-Garcia, Manuel
中科院分区：
文献类型：
--
作者：
Martinez-Hernandez, Francisco;Diop, Awa;Martinez-Garcia, Manuel
病毒遗传微多样性驱动适应性、致病性和物种形成，并对菌株和物种水平上发生的病毒-宿主军备竞赛产生严重影响，最终影响微生物群落结构和生物地球化学循环。尽管大多数努力都集中在病毒的宏观多样性上，但人们对地球上具有重要生态意义的病毒的微观多样性知之甚少。最近，单病毒基因组学发现了温带和热带水域中假定最丰富的海洋病毒：未培养的双链 DNA 病毒 vSAG 37-F6，感染最丰富的海洋细菌 Pelagibacter。在这项研究中，我们报告了在单个海洋样本中同时存在多达大约 1,500 种不同的病毒株（>95% 核苷酸同一性）和大约 30 种相关物种（80-95% 核苷酸同一性）。病毒的微多样性在空间和时间上得以维持，大多数等位基因是同义突变的结果，没有任何明显的适应性优势来应对宿主翻译密码子偏差和效率。用于根据生物物种概念 (BSC) 界定物种的基因流分析揭示了重组对 vSAG 37-F6 病毒和 Pelagibacter 物种形成的影响。数据表明，这种巨大的病毒微多样性在某种程度上反映了宿主物种的多样性，因为在分析的 926 个 Pelagibacter 基因组中，大约 50% 被发现属于独立的 BSC 物种，这些物种之间不显着参与基因流动。这种进化成功的病毒的宿主范围表明，单一病毒物种可以感染多种 Pelagibacter BSC 物种，这表明该病毒不仅跨越正式的 BSC 屏障，而且还跨越生物群落，因为在淡水中发现了病毒祖先。
Viral genetic microdiversity drives adaptation, pathogenicity, and speciation and has critical consequences for the viral-host arms race occurring at the strain and species levels, which ultimately impact microbial community structure and biogeochemical cycles. Despite the fact that most efforts have focused on viral macrodiversity, little is known about the microdiversity of ecologically important viruses on Earth. Recently, single-virus genomics discovered the putatively most abundant ocean virus in temperate and tropical waters: the uncultured dsDNA virus vSAG 37-F6 infecting Pelagibacter, the most abundant marine bacteria. In this study, we report the cooccurrence of up to approximate to 1,500 different viral strains (>95% nucleotide identity) and approximate to 30 related species (80-95% nucleotide identity) in a single oceanic sample. Viral microdiversity was maintained over space and time, and most alleles were the result of synonymous mutations without any apparent adaptive benefits to cope with host translation codon bias and efficiency. Gene flow analysis used to delimitate species according to the biological species concept (BSC) revealed the impact of recombination in shaping vSAG 37-F6 virus and Pelagibacter speciation. Data demonstrated that this large viral microdiversity somehow mirrors the host species diversity since approximate to 50% of the 926 analyzed Pelagibacter genomes were found to belong to independent BSC species that do not significantly engage in gene flow with one another. The host range of this evolutionarily successful virus revealed that a single viral species can infect multiple Pelagibacter BSC species, indicating that this virus crosses not only formal BSC barriers but also biomes since viral ancestors are found in freshwater.