Comammox biogeography subject to anthropogenic interferences along a high-altitude river

•Comammox clade B was widespread and more abundant than clade A along a plateau river.•Freshwater- and drinking water treatment plant-identified taxa dominated the comammox.•Comammox contributed more abundances and activities to nitrifiers at suburban reach.•Higher nitrate, nitrite or antibiotic contents limited comammox niches in nitrifiers.•Lincosamides, quinolones or macrolides were the major antibiotic predictors.