In an era of pervasive anthropogenic ecological disturbances, there is a pressing need to understand the factors that constitute community response and resilience. A detailed understanding of disturbance response needs to go beyond associations and incorporate features of disturbances, species traits, rapid evolution and dispersal. Multispecies microbial communities that experience antibiotic perturbation represent a key system with important medical dimensions. However, previous microbiome studies on this theme have relied on high-throughput sequencing data from uncultured species without the ability to explicitly account for the role of species traits and immigration. Here, we serially passage a 34-species defined bacterial community through different levels of pulse antibiotic disturbance, manipulating the presence or absence of species immigration. To understand the ecological community response measured using amplicon sequencing, we combine initial trait data measured for each species separately and metagenome sequencing data revealing adaptive mutations during the experiment. We found that the ecological community response was highly repeatable within the experimental treatments, which could be attributed in part to key species traits (antibiotic susceptibility and growth rate). Increasing antibiotic levels were also coupled with an increasing probability of species extinction, making species immigration critical for community resilience. Moreover, we detected signals of antibiotic-resistance evolution occurring within species at the same time scale, leaving evolutionary changes in communities despite recovery at the species compositional level. Together, these observations reveal a disturbance response that presents as classic species sorting, but is nevertheless accompanied by rapid within-species evolution.

在一个普遍存在的人为生态干扰时代，迫切需要了解构成社区响应和复原力的因素。对干扰响应的详细了解需要超越关联，并包括干扰，物种特征，快速进化和扩散的特征。经历抗生素干扰的多物种微生物群落是具有重要医学意义的关键系统。但是，以前有关该主题的微生物组研究依赖于未培养物种的高通量测序数据，而无法明确说明物种特征和移民的作用。在这里，我们通过不同水平的脉冲抗生素干扰对34种定义的细菌群落进行了连续传代，操纵物种移民的存在与否。为了了解使用扩增子测序测得的生态群落响应，我们将分别测量每种物种的初始性状数据与在实验过程中揭示适应性突变的元基因组测序数据结合在一起。我们发现，在实验处理中，生态群落的响应是高度可重复的，这可能部分归因于关键物种的性状（抗生素敏感性和生长速率）。抗生素水平的提高还伴随着物种灭绝的可能性增加，这使得物种迁移对于社区的适应能力至关重要。此外，我们检测到在同一时间范围内物种内部发生的抗生素抗性进化信号，尽管物种组成水平有所恢复，但仍留下了群落的进化变化。总之，这些观察结果揭示了一种干扰反应，表现为经典的物种分类，但同时伴随着物种内部的快速进化。