Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR–Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid–host and phage–host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant ‘Candidatus Microthrix parvicella’ population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.

病毒和质粒（侵入性移动遗传元件 (iMGE)）在塑造微生物群落方面发挥着重要作用，但它们与基于 CRISPR 的免疫的动态相互作用仍未解决。我们使用集成元组学分析了生物废水处理厂的微生物群落中跨越一年半的世代解析 iMGE 宿主动态。我们鉴定了 31 个细菌宏基因组组装的基因组，编码完整的 CRISPR-Cas 系统及其相应的 iMGE。 CRISPR 靶向质粒的数量是噬菌体对应物的至少五倍，凸显了 CRISPR 介导的质粒防御的重要性。我们的时间序列数据的线性模型表明，质粒丰度随时间的变化比噬菌体更能解释观察到的群落动态。群落规模的基于 CRISPR 的质粒-宿主和噬菌体-宿主相互作用网络揭示了 CRISPR 介导的相互作用的增加，同时伴随着占主导地位的“ Candidatus Microthrix parvicella”种群的减少。原型间隔子富含针对参与 iMGE 传递的基因的序列。了解影响特定种群适应性的因素对于制定不良物种的控制策略以及预测或解释整个群落的表型是必要的。