A laboratory-scale completely autotrophic nitrogen removal over nitrite (Canon) biofilm reactor was applied to remove nitrogen and organic carbon from swine digester liquor for 150 d. A stable nitrogen removal rate was reached after a three-week adaptation period. The nitrogen loading rate of influent were 0.20 +/- 0.04, 0.26 +/- 0.04, 0.26 +/- 0.07 kg N m(-3) d(-1) in period I, II and III, respectively. Nitrogen removal rates reached 0.096, 0.133 and 0.104 kg N m(-3) d(-1) when the C/N ratios of liquor were maintained at 0.81, 0.65, and 1.24, respectively. The Canon process was better than the denitrification process for nitrogen elimination when the C/N ratio of the influent was controlled below 0.8. PCR-DGGE analysis showed a decrease in microbial diversity of Planctomycetes during long-term operation. In contrast, the aerobic ammonium-oxidizing bacteria species were resistant to the changes due to replacement of synthetic wastewater with swine digester liquor. (C) 2012 Elsevier Ltd. All rights reserved.