A method for collecting bacterial cells comprising the steps of: feeding water to be treated containing ammonium and nitrite to an anaerobic ammonium oxidation vessel to denitrify ammonium and nitrite by anaerobic ammonium oxidizing bacteria; and feeding the denitrified treated water to an acclimatization vessel or returning the water through the acclimatization vessel to the anaerobic ammonium oxidation vessel to collect anaerobic ammonium oxidizing bacteria in the treated water as immobilized microorganisms attached to an immobilizing material in the acclimatization vessel.