Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to constitute the most abundant and ecologically relevant group of phages that can integrate their genome into the host chromosome, it is becoming increasingly clear that other prophages are widespread. Here, we show that prophages derived from filamentous and tailless phages with genome sizes below 16 kb make up the majority of prophages in marine bacteria of the genus Vibrio. To estimate prophage prevalence unaffected by database biases, we combined comparative genomics and chemical induction of 58 diverse Vibrio cyclitrophicus isolates, resulting in 107 well-curated prophages. Complemented with computationally predicted prophages, we obtained 1,158 prophages from 931 naturally co-existing strains of the family Vibrionaceae. Prophages resembling tailless and filamentous phages predominated, accounting for 80% of all prophages in V. cyclitrophicus and 60% across the Vibrionaceae. In our experimental model, prophages of all three viral realms actively replicated upon induction indicating their ability to transfer to new hosts. Indeed, prophages were rapidly gained and lost, as suggested by variable prophage content between closely related V. cyclitrophicus. Prophages related to filamentous and tailless phages were integrated into only three genomic locations and restored the function of their integration site. Despite their small size, they contained highly diverse accessory genes that may contribute to host fitness, such as phage defense systems. We propose that, like their well-studied tailed equivalent, tailless and filamentous temperate phages are active and highly abundant drivers of host ecology and evolution in marine Vibrio, which have been largely overlooked.

中文翻译：

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 弧菌中的噬菌体


尽管 Caudovicetes 类的尾部噬菌体（噬菌体）被认为构成了最丰富和生态相关的噬菌体组，可以将其基因组整合到宿主染色体中，但越来越明显的是，其他原噬菌体也广泛存在。在这里，我们表明，来自基因组大小小于 16 kb 的丝状和无尾噬菌体的原噬菌体构成了弧菌属海洋细菌中的大部分原噬菌体。为了估计不受数据库偏倚影响的原噬菌体流行率，我们将 58 种不同的环状弧菌分离株的比较基因组学和化学诱导相结合，产生了 107 个精心策划的原噬菌体。辅以计算预测的原噬菌体，我们从 1,158 种天然共存的弧菌科菌株中获得了 931 个原噬菌体。类似于无尾和丝状噬菌体的原噬菌体占主导地位，占 V. cyclitrophicus 所有原噬菌体的 80%，占弧菌科的 60%。在我们的实验模型中，所有三个病毒领域的原噬菌体在诱导时都积极复制，表明它们能够转移到新的宿主。事实上，原噬菌体迅速获得和丢失，正如密切相关的 V. cyclitrophicus 之间可变的原噬菌体含量所表明的那样。与丝状和无尾噬菌体相关的原噬菌体仅整合到三个基因组位置，并恢复了其整合位点的功能。尽管它们的体积小，但它们包含高度多样化的辅助基因，这些基因可能有助于宿主的适应性，例如噬菌体防御系统。我们提出，与它们经过充分研究的尾巴等价物一样，无尾和丝状温带噬菌体是海洋弧菌宿主生态学和进化的活跃且高度丰富的驱动力，而这些驱动力在很大程度上被忽视了。