Symbiotic bacteriophages exhibit multiple adaptive strategies in activated sludge flocs and contribute to floc stability

[Display omitted] •Activated sludge contains large amounts of novel and diverse phages.•Phages infect dominant prokaryotes in lysogenic mode as adaptive strategies.•Generalist prokaryotes and polyvalent phages enhance microbiome connectivity.•Antiviral systems can tolerate lysogenic phage infection but not lytic infection.•Symbiotic phage communities harbor AMGs that could improve floc stability. Despite the importance of phages for the dynamics and functions of microbial communities, it remains largely unexplored how symbiotic phages adapt in activated sludge systems and influence microbial aggregate stability, which is critical for clarification and reliable performance. Based on 12,127 phage contigs recovered from 12 activated sludge microbiomes, the symbiotic phages exhibited broad host ranges and infected dominant prokaryotes in activated sludge. Moreover, these phage communities exhibited high lysogenicity (49% to 66% lysogenic phages) and harbored diverse auxiliary metabolic genes (AMGs) that could enhance microbial aggregate stability, such as genes coding for lipopolysaccharide, peptidoglycan, and extracellular polysaccharide biosynthesis. Additionally, prokaryotic antiviral systems were widely distributed in dominant prokaryotes, particularly the Restriction-Modification (RM) and CRISPR-Cas systems, which could mitigate potential harmful phage infections. Overall, this study reveals the contemporary beneficial relationship between phages and prokaryotic hosts in activated sludge microbiomes and the potential benefits of symbiotic phages on floc stability.