TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preferred Components: The biogas apparatus comprises: at least one anaerobic digester having microorganisms for processing the thin stillage, where the pH of the digester is controlled by the addition of a neutralizing agent; a main anaerobic digester and a secondary anaerobic digester in series; and a recuperative heat exchanger for cooling the thin stillage prior to entering the digester and for reheating the biogas effluent prior to being recycled to the pretreatment apparatus. The neutralizing agent is ammonia, where the microorganisms are adapted for an ammonia environment. The nitrogen from the ammonia is added as the neutralizing agent and additional ammonia generated by digestion of the organic acids is recycled via the biogas effluent as a nutrient for the yeast in fermentation thus reducing or eliminating the need for a separate addition of ammonia to the fermentor. A second or third portion of the thin stillage is recycled directly as backset from the separator to the pretreatment apparatus, where an increase in the amount of backset obtained by recycling the biogas effluent from the biogas apparatus reduces the amount of fresh water supplied to the pretreatment apparatus or an increase in the amount of backset obtained by recycling the biogas effluent from the biogas apparatus reduces the amount of the second portion of the thin stillage recycled directly as backset and reducing the amount of solids returned to the pretreatment apparatus so that more raw plant materials can be added to the pretreatment apparatus. The integrated system further comprises: an evaporator for concentrating a first or third portions of the thin stillage into syrup by boiling off vapor from the thin stillage, where a portion of the syrup is further provided to the biogas apparatus for processing into biogas and biogas effluent and the syrup and the first portion of thin stillage being provided to the biogas apparatus in any ratio and the backset further comprises the vapor boiled off from the thin stillage, where an increase in the amount of backset obtained by recycling the biogas effluent from the biogas apparatus reduces the third portion of the thin stillage that must be concentrated by the evaporator and reducing the energy loading of the evaporator and a reduction in the third portion of the thin stillage reduces the amount of the syrup; and a dryer for drying the wet distillers grains and the syrup, where an increase in the amount of backset obtained by recycling the biogas effluent from the biogas apparatus reduces the energy loading of the dryer by reducing the amount of the syrup that must be dried, or eliminates the syrup load-out from the system. The anaerobic digester comprises a main anaerobic digester and a secondary anaerobic digester in series. The biogas apparatus further comprises a recuperative heat exchanger for cooling the thin stillage prior to entering the digester and for reheating the biogas effluent prior to being recycled to the ethanol production system. A third portion of the thin stillage is recycled directly as backset from the separator to the pretreatment apparatus, where an increase in the amount of backset obtained by recycling the biogas effluent from the biogas apparatus reduces the amount of fresh water supplied to the pretreatment apparatus.