Data from: Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction

Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities, bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here, we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage, SBW25φ2, and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions.细菌参与构成复杂的生态互作网络，其中包含移动遗传元件（mobile genetic elements, MGEs），例如噬菌体与质粒。这类元件作为水平基因转移的载体，在微生物群落中发挥关键作用，同时也可为其细菌宿主带来重要的选择压力来源。在自然微生物群落中，细菌可能同时接触多种移动遗传元件，而不同MGE间的选择压力冲突，可能会改变细菌对每种MGE的进化响应。 本研究通过对经实验进化的细菌进行基因组测序分析，在荧光假单胞菌（Pseudomonas fluorescens）、裂解性噬菌体SBW25φ2以及接合性质粒pQBR103构成的三方互作体系中，探究了多MGE互作对细菌分子进化的影响。研究结果显示，单独存在时，质粒与噬菌体均可施加选择压力，使细菌产生与无MGE胁迫下进化的细菌种群截然不同的进化响应；但当二者共存时，质粒与噬菌体将对细菌施加相互冲突的选择压力，限制了两两互作体系中观察到的进化响应模式。 本研究结果表明，仅依据单一选择压力下的进化响应，难以准确预测多选择压力下的进化响应，这凸显了相关研究的潜在挑战。若要理解包含多种微生物与MGE的复杂群落中的进化过程，我们需要突破两两互作研究的局限。