BACKGROUND: In this study, the inductive effect of salinity on nitrite accumulation in a down-flow hanging sponge (DHS) reactor, developed as a novel and cost-effective wastewater treatment process, was evaluated by conducting a long-term continuous experiment lasting more than 1400 days. RESULTS: The influent salinity was controlled by adding NaCl at concentrations ranging from 0 to 25 g Cl- L-1. The effluent nitrite increased with increases in salinity, i.e. the fraction of nitrite to total nitrogen in the effluent increased from 1.6% at 0 g Cl- L-1 to 87.6% at 25 g Cl- L-1. Fluorescence in situ hybridization (FISH) analysis revealed that as salinity increased, the nitrifying bacterial community in the DHS changed markedly at the species level. In particular, the dominant nitrite-oxidizing bacteria changed from Nitrospira-sublineage I at 0 g Cl- L-1 to Nitrobacter spp. at 15 g Cl- L-1. At 25 g Cl- L-1, no nitrite-oxidizing bacteria were detected. CONCLUSION: Our findings suggest that the DHS reactor is suitable for cost-effective nitrite production processes and that salinity control using NaCl is an effective method for inducing nitrite accumulation. Copyright (c) 2012 Society of Chemical Industry