Digestion systems can be configured with different levels of complexity:

• One-stage or single-stage

• Two-stage or multistage

A single-stage digestion system is one in which all of the biological reactions occur within a single sealed reactor or holding tank. Utilizing a single stage reduces construction costs; however, it facilitates less control of the reactions occurring within the system. Acidogenic bacteria, through the production of acids, reduce the pH of the tank. Methanogenic bacteria, as outlined earlier, operate in a strictly defined pH range. Therefore, the biological reactions of the different species in a single stage reactor can be in direct competition with each other. Another one-stage reaction system is an anaerobic lagoon. These lagoons are pond-like earthen basins used for the treatment and long-term storage of manures. Here, the anaerobic reactions are contained within the natural anaerobic sludge contained in the pool.

In a two-stage or multistage digestion system different digestion vessels are optimized to bring maximum control over the bacterial communities living within the digesters. Acidogenic bacteria produce organic acids and grow and reproduce more quickly than methanogenic bacteria. Methanogenic bacteria require stable pH and temperature in order to optimize their performance.

Typically hydrolysis, acetogenesis and acidogenesis occur within the first reaction vessel. The organic material is then heated to the required operational temperature (either mesophilic or thermophilic) prior to being pumped into a methanogenic reactor. The initial hydrolysis or acidogenesis tanks prior to the methanogenic reactor can provide a buffer to the rate at which feedstock is added. It should be noted that it is not possible to completely isolate the different reaction phases and often there is some biogas that is produced in the hydrolysis or acidogenesis tanks.