The controversial arguments on the true substrate in nitritation kinetics might be due to the cells' dual substrate-transport system. Our experiments revealed that, under ammonia-rich environments, it diffused into the membrane (ammonia was the direct substrate); but, under oligotrophic, ammonium ion was actively transported (ammonium was the direct substrate). Facilitating this change-over, the bacterial composition in the sludge was altered, although the predominant was Nitrosomonas eutropha in most of the six chemostats. Also, the substrate affinity constant (K-s) fell resulting in partial compensation for the reduced availability of substrate. When the environmental ammonia concentration was lower than the cytoplasmic one, a backward diffusion appeared to take place, which probably had the cells accelerate its energy-consuming ammonium transport. The % ammonium oxidizing bacteria (AOB) to the total number of bacteria in the sludge remarkably decreased when cells were grown under oligotrophic environments. This could be evidence of the cellular energy dissipation caused by ammonia loss and recovery. Intracellular total ammonium nitrogen (TAN) accumulations were observed, which gradually increased from a basal value of similar to 1 M (for AOB grown under copious environments) to much higher values (grown under oligotrophic environment). It did not affect the reaction kinetics but potentially served as a reserve against famine.