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Anammox is an environmental-friendly and cost-effective technology for nitrogen removal. This study provides the nitrogen removal profiles, physiological traits of anammox bacteria culture under the substrate deficiency conditions at the optimal cultivation temperature 35°C. The determined period of starvation tolerance was 4 weeks in the absence of nitrite, 5 weeks in the absence of ammonium, as well as 7 weeks for the absence of these two substrates at 36°C, pH 7–8 and anaerobic conditions. The physiological traits of bacteria consortium were identified through flow cytometry (FCM) analysis, and the ordinal change of increased RNA synthesizing amounts, phosphatidylserine exposure and bacteria death occurred under starvation stress. In addition, the starvation induced the increased protein content in extracellular polymeric substances and the poorer bacteria settling capacity. This study helps to develop a better understanding of anammox process in engineering environment. [ABSTRACT FROM AUTHOR]