ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, Zürich, Switzerland.
Institute of Natural Resource Sciences, Zürich University of Applied Sciences, Campus Grüental, Wädenswil, Switzerland.
Evolution. 2021 Feb;75(2):515-528. doi: 10.1111/evo.14153. Epub 2021 Jan 6.
Understanding the role of horizontal gene transfer (HGT) in adaptation is a key challenge in evolutionary biology. In microbes, an important mechanism of HGT is prophage acquisition (phage genomes integrated into bacterial chromosomes). Prophages can influence bacterial fitness via the transfer of beneficial genes (including antibiotic-resistance genes, ARGs), protection from superinfecting phages, or switching to a lytic lifecycle that releases free phages infectious to competitors. We expect these effects to depend on environmental conditions because of, for example, environment-dependent induction of the lytic lifecycle. However, it remains unclear how costs/benefits of prophages vary across environments. Here, studying prophages with/without ARGs in Escherichia coli, we disentangled the effects of prophages alone and adaptive genes they carry. In competition with prophage-free strains, benefits from prophages and ARGs peaked in different environments. Prophages were most beneficial when induction of the lytic lifecycle was common, whereas ARGs were more beneficial upon antibiotic exposure and with reduced prophage induction. Acquisition of prophage-encoded ARGs by competing strains was most common when prophage induction, and therefore free phages, were common. Thus, selection on prophages and adaptive genes they carry varies independently across environments, which is important for predicting the spread of mobile/integrating genetic elements and their role in evolution.
理解水平基因转移 (HGT) 在适应中的作用是进化生物学的一个关键挑战。在微生物中，HGT 的一个重要机制是噬菌体的获得（噬菌体基因组整合到细菌染色体中）。噬菌体可以通过转移有益基因（包括抗生素抗性基因，ARGs）、保护免受超感染噬菌体的侵害，或转变为溶原周期来影响细菌的适应性，从而释放出对竞争菌株具有感染力的游离噬菌体。我们期望这些效应取决于环境条件，因为例如溶原周期的环境依赖性诱导。然而，噬菌体的成本/收益如何在不同环境中变化仍不清楚。在这里，我们在大肠杆菌中研究了带有/不带有 ARGs 的噬菌体，从而分离出噬菌体本身及其携带的适应性基因的影响。在与无噬菌体菌株的竞争中，噬菌体和 ARGs 的益处在不同的环境中达到峰值。当溶原周期的诱导很常见时，噬菌体的作用最大，而在抗生素暴露和减少噬菌体诱导时，ARGs 的作用更大。竞争菌株通过获取噬菌体编码的 ARGs 最为常见，当噬菌体诱导，因此游离噬菌体普遍存在时。因此，噬菌体及其携带的适应性基因在不同环境中的选择是独立的，这对于预测移动/整合遗传元件的传播及其在进化中的作用非常重要。
