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.