A domesticated phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria

Bacteria have repeatedly repurposed the machinery of their viruses
(bacteriophage) to kill strains of neighboring bacteria. These
bacteriophage (phage)-derived elements are strain-specific in their
killing activity, and this specificity has been proposed to drive
bacterial population dynamics. Direct evidence of the impact of
phage-derived elements on natural populations over time is limited. Here
we identified viral sequences in a metapopulation of wild plant-associated
Pseudomonas spp. genomes. We discovered that the most abundant viral
cluster does not encode an intact phage but instead encodes a tailocin: a
phage-derived element that bacteria use to kill bacterial competitors.
Each pathogenic Pseudomonas sp. strain carries one of a few distinct
tailocin variants, which target variable polysaccharides in the outer
membrane of co-occurring pathogenic strains. Analysis of historic
herbarium samples from the past 170 years revealed that the same tailocin
and receptor variants have persisted in the Pseudomonas populations for at
least two centuries, suggesting the continued use of a defined set of
tailocin haplotypes and receptors. These results indicate that tailocin
genetic diversity can be mined to develop targeted "tailocin
cocktails" for microbial control.

细菌已反复重新利用其病毒（bacteriophage，噬菌体）的机制来杀伤邻近的细菌菌株。这些源自噬菌体的元件在杀伤活性上具有菌株特异性，且这种特异性被认为可驱动细菌种群的动态变化。目前关于噬菌体衍生元件随时间推移对自然种群产生影响的直接证据仍较为匮乏。在此研究中，我们从与野生植物关联的假单胞菌（Pseudomonas）属基因组集合种群（metapopulation）中鉴定出了病毒序列。我们发现，丰度最高的病毒簇并不编码完整的噬菌体，而是编码一种尾素（tailocin）：一种源自噬菌体的元件，细菌可利用其杀伤细菌竞争者。每一株致病假单胞菌菌株均携带数种不同尾素变体中的一种，这些变体可靶向共存致病菌株外膜中的可变多糖。对过去170年间的植物标本馆历史样本进行分析后发现，相同的尾素与受体变体已在假单胞菌种群中存续至少两个世纪，这表明一组明确的尾素单倍型与受体得到了持续应用。本研究结果表明，可通过挖掘尾素的遗传多样性，开发用于微生物防控的靶向性"tailocin cocktails"（尾素鸡尾酒）。