The bloom of heterotrophic bacteria resulting from the presence of organic matter in wastewater streams can potentially affect the growth and activity of autotrophic ammonia-oxidizing bacteria (AOB), which are important for the operation of nitritation reactors. The present study evaluated the interactions between acetate-induced heterotrophs and the nitrosifying community using network analysis and the culture-dependence method. Bacterial succession as well as shifts in the community structure occurred as a result of the bloom of heterotrophs. The acetate-induced heterotrophs enhanced reactor productivity and stability, thus increasing the ammonium removal efficiency in comparison to that of the control reactor from day 270 onward (88.9 ± 10.0 vs 60.0 ± 10.9%, P < 0.01). Interestingly, the sludge nitritation rates in the acetate-amended reactor (125.6 ± 33.1 mg-N/(L h)) were much higher than those in the control reactor (81.7 ± 22.4 mg-N/(L h), P < 0.01) at stages IV and V, implying that the induced heterotrophs can enhance nitritation. The sequencing data showed that the presence of acetate decreased potential competition and led to increased niche differentiation among various bacteria, e.g., some of the acetate-induced members of the community favored the proliferation of AOB. Network analysis revealed that the operational taxonomic units (OTUs) belonging to the genus Arenimonas or Thauera interacted with the OTU of the genus Nitrosomonas differently. Furthermore, batch tests showed that the roles of heterotrophic isolates in nitiritation were species- or strain-dependent. These findings provide new insights into the elusive effects of organic matter-induced heterotrophs on AOB.