The present invention describes a method of optimizing CO2 concentration to increase the specific growth rate of Anammox bacteria and methanogens in wastewater and sludge treatment, as well as novel systems and methods of treating wastewater and sludge. The specific growth rate or doubling time of the Anammox bacteria and methanogens were determined to be sensitive to dissolved CO2 concentration. Optimizing dissolved CO2 concentration increases the specific growth rate of the Anammox bacteria, which may be used as an alternative biological nitrogen removal process for the treatment of domestic wastewater. In the method and system of treating sludge, the CO2 stripper returns biogas with low CO2 concentration to the headspace of an anaerobic digester in order to lower the headspace CO2 concentration and therefore, the soluble CO2 concentration. The lower soluble CO2 concentration increases the specific growth rate of the methanogens for a more efficient anaerobic digestion process.