To study the influence of substrate on completely autotrophic nitrogen removal over nitrite (CANON) process, two membrane bioreactors (MBR) with identical setup but fed with different substrate levels (R1 with low ammonia, R2 with high ammonia), were adopted in this study. The nitrogen removal performance, bioactivity, biodiversity and distribution of the functional microorganisms in two reactors were investigated. Both the aerobic ammonia-oxidizing bacteria (AerAOB) and anaerobic ammonia-oxidizing bacteria (AnAOB) in R2 showed higher bioactivity than those in R1, while nitrite-oxidizing bacteria (NOB) showed the contrary result. Nitrosomonas and Candidatus Kuenenia stuttgartiensis were detected as predominant functional microbes in the two reactors while Nitrobacter only existed in R1. High influent ammonia possibly led to the higher biodiversity of AerAOB and the more densely packed distribution. Meanwhile, this study has demonstrated the feasibility of increasing ammonia for rapid start-up, and decreasing HRT for high-rate nitrogen removal in CANON process. (C) 2013 Elsevier Ltd. All rights reserved.