resequencing of soil adapted Pseudomonas fluorescens. resequencing of soil adapted Pseudomonas fluorescens

Local adaptation can influence how species affect community composition, yet data quantifying the relative importance of local adaptation compared with species presence is lacking. To address this, we followed the dynamics of a natural bacterial soil (compost) community exposed to elevated temperatures over two months where adaptation and presence per se of a focal species was manipulated. Specifically, we inoculated the natural compost community with either: 1) the ancestral bacterium Pseudomonas fluorescens SBW25; or 2) SBW25 that had been locally adapted to these conditions for 48 days (apparent from a large fitness increase and correlated genomic changes); or 3) no SBW25. We detected large differences in community composition between treatments, with the effect of adaptation as great as the effect of the presence of SBW25 per se. Local adaptation, however, had a much smaller relative effect than species presence on community population dynamics, and neither treatments significantly affected community diversity metrics. These affects were robust to strong additional selection pressures imposed on the focal species, with the magnitude of effect of SBW25 on the community little affected when its densities were reduced by the presence of lytic virus. Our results show that contemporaneous adaptive evolution can play as great a role as species presence in structuring natural microbial communities. Our conclusions are likely to be particularly relevant to situations where a few species may have an evolutionary head start following colonisation of novel habitats or large perturbations, including the plant rhizosphere in agricultural systems and the gut microbiome exposed to antibiotics.

局部适应性（local adaptation）可影响物种对群落组成的塑造作用，但目前尚缺乏量化局部适应性相较于物种存在的相对重要性的研究数据。为填补这一研究空白，我们追踪了暴露于高温环境达两个月的天然土壤堆肥细菌群落的动态变化，并对焦点物种（focal species）的适应性及其自身存在与否进行了操控处理。具体而言，我们向天然堆肥群落分别实施以下三种接种处理：1）祖先型细菌荧光假单胞菌（Pseudomonas fluorescens）SBW25；2）已在该环境中完成48天局部适应性演化的SBW25（其适应性演化可通过显著的适合度提升及相关基因组变化得到验证）；3）不接种任何SBW25。我们发现不同处理组间的群落组成存在显著差异，且局部适应性的影响程度与SBW25自身存在的影响程度相当。然而在群落种群动态方面，局部适应性的相对影响远小于物种存在的影响，且所有处理均未对群落多样性指标产生显著影响。上述效应在施加于焦点物种的额外强选择压力下仍保持稳健：当裂解性病毒（lytic virus）的存在导致SBW25的种群密度降低时，其对群落的影响幅度并未发生显著变化。本研究结果表明，同步发生的适应性演化在塑造天然微生物群落结构方面，可发挥与物种存在相当的作用。我们的结论尤其适用于以下场景：少数物种在定植新生境或遭遇大规模扰动后可获得演化先发优势，包括农业系统中的植物根际（rhizosphere）以及暴露于抗生素的肠道微生物组（gut microbiome）。