A system and method of treating wastewater having at least one undesirable biological species is provided. In accordance with embodiments, a wastewater treatment system is provided comprising a main biological treatment train including at least one first unit operation configured to perform an anaerobic ammonium oxidation process, and at least one subsystem configured to increase a concentration of anammox bacteria in the at least one first unit operation, the treatment system arranged to reduce the concentration of total nitrogen in the wastewater.