A method and a facility for the treatment of waste from concentrated animal feed operations are disclosed. The method includes receiving manure at a central location, digesting the manure and producing therefrom combustible gases, solid matter and water containing dissolved organic pollutants. The combustible gases are used to provide energy and the water is separated from the solid matter. The solid matter is dried to produce a useful bedding material and the water is treated using an activated sludge aeration system to reduce the dissolved organic pollutants to carbon dioxide, bacteria and water. The facility includes various means for executing the method and includes an ultrasonic treatment station for disrupting bacteria cell walls to improve digestion efficiency.