Unravelling tripartite species co-evolution under environmental change: can prophages accelerate bacterial virulence evolution?

两个相互作用的物种之间的适应和反适应可以非常快，使物种相互作用成为研究当代时间尺度上快速共适应的理想选择。虽然理论模型和实证研究都处理双重相互作用，但包括两个以上物种相互作用的数据很少。然而，在自然情况下，如果不是所有物种，大多数物种都与不止一个物种相互作用。此外，人为影响正在改变选择制度，对物种相互作用具有广泛的影响。因此，迫切需要在适当的背景下研究所有相关物种和非生物因素的物种相互作用。在第一阶段，我们建议使用一个由管鱼syngnathestyphle（即最终动物宿主）、弧菌属细菌及其相关的温带噬菌体（即感染弧菌的小病毒）组成的已建立的模型系统，研究宿主-寄生虫三方相互作用中的快速进化适应。有了融入细菌基因组的能力，温带噬菌体变成了一种原噬菌体，可以为其细菌宿主（当时被称为溶原）提供有益的基因，例如可以增加细菌基因组可塑性并最终提高细菌适应性的毒力基因。在第一阶段，我们可以证明环境变化，如降低和因此压力盐度条件改变感染动力学以及细菌和温带噬菌体之间的共同进化轨迹。利用弧菌sp.和温带噬菌体之间的共同进化实验，我们观察到细菌对噬菌体的抗性进化方面的快速适应。在压力盐度下，溶原比噬菌体抗性突变体更受青睐，而在环境盐度下，溶原过于昂贵，迅速灭绝。我们现在建议(1)对这些群体中选定的溶原和突变体进行全基因组测序，以确定潜在的基因组变化和原噬菌体整合到细菌染色体中的机制（随机与位点特异性），以及细菌在依赖环境变化的情况下进化出对温带噬菌体的抗性。(2)研究一个额外的生物相互作用伙伴，真核宿主及其免疫系统如何限制或促进弧菌与噬菌体的共同进化，以及它如何最终加速弧菌的毒力进化。为了做到这一点，我们将使用两个不同的连续传代实验，在这些实验中，我们跟踪噬菌体-细菌在真核宿主内的共同进化。获得的结果将揭示细菌和温带噬菌体之间共同进化过程的基本机制，并将为快速毒力进化以及如何被噬菌体和环境变化加速提供新的见解。

Adaptation and counter-adaptation between two interacting species can be very fast, making species interactions ideal to study rapid coadaptation on contemporary time scales. While both theoretical models and empirical studies deal with dual interactions, data including interactions of more than two species are scarce. However, in a natural scenario, most if not all species interact with more than one species. In addition, anthropogenic influences are changing selection regimes with broad implications on species interactions. Therefore, studies that address species interactions in an appropriate context with all relevant species and abiotic factors involved are urgently needed.During phase I we suggested studying rapid evolutionary adaptation in a three-way host-parasite interaction using an established model system consisting of pipefish Syngnathus typhle (i.e the final animal host), bacteria of the genus Vibrio, and it’s associated temperate phages (i.e. small viruses that infect Vibrio bacteria). With the ability to integrate into the bacterial genome, a temperate phage becomes a prophage that can provide its bacterial host (which is then called a lysogen) with beneficial genes, for instance virulence genes that may increase bacterial genome plasticity and ultimately bacterial fitness.During phase I we could demonstrate that environmental changes, such as reduced and thus stressful salinity conditions alter infection dynamics as well as co-evolutionary trajectories between bacteria and temperate phages. Using a co-evolution experiment between Vibrio sp. and a temperate phage we observed rapid adaptation in terms of bacterial resistance evolution against the phage. At stressful salinities lysogens were favoured over phage resistant mutants, whereas at ambient salinities lysogens were too costly and rapidly went extinct.We now propose (1) to perform whole genome sequencing on selected lysogens and mutants from those populations to identify the underlying genomic changes and mechanisms by which prophages integrate into the bacterial chromosome (random vs. site specific) and by which bacteria evolve resistance against temperate phages in dependence of environmental change. And (2) to investigate how an additional biotic interaction partner, the eukaryotic host and its immune system might constrain or promote Vibrio-phage co-evolution, and how it may ultimately accelerate Vibrio virulence evolution. To do so, we will use two different serial passage experiments, in which we follow phage-bacteria co-evolution inside the eukaryotic host. The obtained results will unravel basic mechanisms underlying co-evolutionary processes between bacteria and temperate phages and will provide novel insights into rapid virulence evolution and how it is accelerated by prophages and environmental change.