Nitrification control and early microbiome-resistome transitions during permanent conversion from chloramine to free chlorine in a full-scale drinking water distribution system.

Chloramine is widely used in drinking water distribution systems (DWDSs), but ammonia recycling can promote nitrification and disinfectant residual loss. As source water ammonia is controlled, permanent conversion to free chlorine may replace repeated temporary chlorine burns, yet its nitrogen control performance and microbiome-resistome consequences remain unresolved. We analyzed early responses of 16 bulk water metagenomes from four sites at chloramine baseline and free chlorine days 1, 5 and 8, with nitrification-related water quality monitored for 8 months. Conversion achieved nitrogen control benefits, with nitrite lower after conversion at multiple time points (p < 0.05), dominant nitrifying genera suppressed to <0.1%, and ammonia oxidation and hydroxylamine oxidation potentials decreasing from 125.84 to 2.77 TPM and from 20.35 to 0.45 TPM. Community restructuring was site-specific (PERMANOVA stage R2 = 0.297, p = 0.001; site R2 = 0.311, p = 0.002). Despite improved nitrification control, 21-50% of each site's baseline ARGs remained detectable after conversion. SEM linked chlorine speciation to community shift (β = 0.695) and ARG/16S shift (β = -0.344), while community shift and MGE/16S shift showed positive paths to ARG/16S shift (β = 0.426 and 0.819). The pathways suggest that the shift toward free chlorine was a potential driver of early microbiome-resistome reorganization. These early responses are consistent with succession from chloramine-resistant communities toward free chlorine-resistant, MGE-associated hosts that may facilitate ARG redistribution. Permanent conversion is a viable nitrification control option, but evaluation should include microbiome and resistome monitoring beyond residual and nitrification indicators.