Bacteriophage diversity and interactions with bacteria in drinking water of Paris
Bacteriophages are increasingly recognized as key determinants of microbial community structure, yet their diversity, dynamics and ecological roles in drinking water distribution systems remain poorly resolved. Here, we used a genome-resolved metagenomic approach to characterize DNA bacteriophages in the Paris drinking water distribution systems operated under low residual chlorine conditions. Large volumes of distributed water were concentrated by hollow fiber ultrafiltration and subjected to shotgun sequencing. A dedicated viral pipeline combining co-assembly, multiple viral classifiers, stringent quality control, host prediction and lifestyle inference was used to reconstruct viral populations and their putative interactions with co-occurring bacteria. We identified a taxonomically and functionally diverse core DNA phage community that persisted over several months across 300 L samples, despite temporal variation in environmental parameters. The core phageome was dominated by Caudoviricetes double-stranded DNA phages, but also included numerous unclassified viral populations, highlighting the extent of uncharted viral diversity in drinking water. Host predictions linked many of these core phages to the dominant bacterial orders previously described in DWDS, revealing tight and recurrent phage-host associations within the distribution network. Lifestyle inference suggested that temperate and chronic infections were prevalent, and genome annotation revealed auxiliary metabolic, stress related and antiviral defense genes that might enhance host persistence under oligotrophic and mildly disinfected conditions.Together, these results supported a model in which a persistent DNA phage backbone contributes to the regulation and resilience of core bacterial communities in low-chlorine drinking water distribution systems. By integrating high-volume concentration with genome-resolved viral ecology, this study advances our understanding of the drinking water phageome and its potential role in maintaining biological stability.