How nutrient loading leads to alternative stable states in microbially mediated N-cycle pathways: A new insight into bioavailable nitrogen removal in urban rivers

•Bistability in microbial-mediated N-cycle pathway in rivers was proved.•Reducing nutrient loading shifted N-cycle pathway to a desirable state.•The desirable pathway state characterized by high ammonification and nitrification.•The improvement of microbiota status promoted shifts to the desirable pathway state.•Alternative stable states theory can guide bioavailable N removal in urban rivers. Excessive nutrients have disrupted pathways of microbial-mediated nitrogen (N) cycle in urban rivers and caused bioavailable N to accumulate in sediments, while remedial actions sometimes fail to recover degraded river ecosystems even when environmental quality has been improved. It is not sufficient to revert the ecosystem to its original healthy state by restoring the pre-degradation environmental conditions, as explained by alternative stable states theory. Understanding the recovery of disrupted N-cycle pathways from the perspective of alternative stable states theory can benefit effective river remediation. Previous studies have found alternative microbiota states in rivers; however, the existence and implications of alternative stable states in microbial-mediated N-cycle pathway remain unclear. Here, high-throughput sequencing and N-related enzyme activities measurement were combined in the field investigation to provide empirical evidence for the bi-stability in microbially mediated N-cycle pathways. According to the behavior of bistable ecosystems, the existence of alternative stable states in microbial-mediated N-cycle pathway have been shown, and nutrient loading, mainly total nitrogen and total phosphorus, were identified as key driver of regime shifts. In addition, potential analysis revealed that reducing nutrient loading shifted the N-cycle pathway to a desirable state characterized by high ammonification and nitrification, probably avoiding the accumulation of ammonia and organic N. It should be noted that the improvement of microbiota status can facilitate the recovery of the desirable pathway state according to the relationship between microbiota states and N-cycle pathway states. Keystone species, including Rhizobiales and Sphingomonadales, were discerned by network analysis, and the increase in their relative abundance may facilitate the improvement of microbiota status. The obtained results suggested that the nutrient reduction should be combined with microbiota management to benefit the bioavailable N removal in urban rivers, therefore providing