A novel anammox bacteria Candidatus Brocadia caroliniensis, having Accession Deposit Number NRRL B-50286 and the characteristics of oxidizing ammonia and releasing di-nitrogen under anaerobic conditions, has been discovered. It was isolated from livestock manure sludge at the USDA-ARS laboratory in Florence, South Carolina. Compared to conventional biological nitrogen removal methods, the anammox process can save more than 50% of the oxygen supply. This leads to a significant decrease in operational costs. We describe development work done to isolate, enrich, characterize and preserve the novel anammox bacteria Candidatus Brocadia caroliniensis. It can be used for effective treatment of wastewater having undesirable levels of ammonia, including agricultural, industrial, or municipal wastewaters. It is capable of long-term storage and reactivation after lyophilization; this protocol was used for its successful deposit with an internationally depositary authority under the provisions of the Budapest Treaty of the UN.