The ecological behavior of bacteriophages (phages), the most abundant biological entity in wastewater treatment systems, is poorly understood, especially that of temperate phages. Here, the temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue was investigated using coupled sludge metagenomic and viromic analyses. The lysogenic fragments (prophages) identified were widely distributed in the reconstructed metagenome-assembled genomes (61.7%, n = 227). However, only 12.3% of the identified prophages experienced lysogenic-lytic switching, and the abundance contribution of prophages to free virus communities was only 0.02–0.3%, indicating low activity of temperate phages. Although the sludge community changed dramatically during reactor operation, no massive prophage induction events were detected. Statistical analyses showed strong correlations between sludge concentration and free virus and temperate phage communities, suggesting microbial density-dependent virus dynamics in the sludge microbiota.

噬菌体（噬菌体）是废水处理系统中最丰富的生物实体，其生态行为知之甚少，尤其是温带噬菌体。在这里，使用耦合污泥宏基因组和病毒组学分析研究了实验室规模的活性污泥反应器中存在污泥膨胀问题的裂解和温带噬菌体的时间动力学。鉴定出的溶源性片段（原噬菌体）广泛分布在重建的宏基因组组装基因组中（61.7%，n = 227）。然而，只有 12.3% 的已识别预噬菌体经历了溶原-裂解转换，并且预噬菌体对游离病毒群落的丰度贡献仅为 0.02-0.3%，表明温带噬菌体的活性较低。尽管在反应器运行期间污泥群落发生了巨大变化，但没有检测到大量的前噬菌体诱导事件。统计分析表明，污泥浓度与游离病毒和温带噬菌体群落之间存在很强的相关性，表明污泥微生物群中的微生物密度依赖性病毒动力学。