The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.

可靠的混合文化生物技术过程的发展取决于了解微生物生态系统如何响应干扰。在这里，我们揭示了来自生物废水处理厂的含油微生物种群中广泛的表型可塑性和生态位互补性。我们每周14个月对原位样品进行元组学分析（元基因组学，元转录组学，元蛋白质组学和代谢组学）。基于1,364个从头基因组组装的新基因组，我们发现了四种不同的基本生态位类型。在整个时间序列中，我们观察到群落结构发生了重大的瞬时变化，这与底物可用性的变化相吻合。功能组学数据揭示了社区成员之间基因表达和底物用途的广泛差异。异位生物反应器实验证实，在脉冲干扰后的五小时内会发生反应，这表明特定人群可以快速适应。我们的结果表明，社区的抵抗力和恢复力是表型可塑性和生态位互补性的函数，并为未来的生态工程工作奠定了基础。