## 2 Common Substrates Used in Anaerobic Digestion  
Animal manures are residues characterized by high nitrogen (N) and organic content. Ammonia is released during the degradation of proteins, reaching a high concentration in the reactor that may inhibit methanogens. This reason explains this fact for the extended application of co-digestion in livestock farms. The high ammonia content reached in reactors also affects the equilibrium between different chemical species such as carbonates and volatile fatty acids (VFAs) derived from the sequential transformation of organics. Ammonia in the digester liquor is present as free ammonia (NH\({}_{3}\)) and ionized ammonium (NH\({}_{4}\)\({}^{+}\)), with the first being considered the most toxic form [26]. The buffering system created by the presence of these compounds produces an environment where pH is kept at levels higher than 6.4 units, ensuring suitable acid-base environments for methanogens [27]. Sewage sludge is another common waste traditionally treated by anaerobic digestion. The treatment of urban wastewaters leads to a rejected stream with a high organic content and a significant amount of water. Sludge obtained from the primary settler receives the denomination of primary sludge. The aerobic treatment of wastewater by the waste-activated sludge process also gives rise to a sludge stream mainly containing microbial biomass. The rapid growth of this biomass makes the extraction from the biological system imperative, thus producing a secondary sludge or a waste-activated sludge (WAS). Large-scale wastewater treatment plants (WWTPs) generally have a sludge line dedicated to the exclusive treatment of sewage sludge, which is composed of a mixture of the above streams. Thus, the digestibility of sludge depends on the characteristics of WAS, which is recognizedas having a limited degradation because cellular material needs to be hydrolyzed prior to the release of its internal content to make it accessible to the anaerobic microflora. Anaerobic digestion of food wastes or the organic fraction of municipal solid wastes (OFMSW) has gained popularity in recent years, with several plants being installed for treating this material in urban waste treatment centers. Source-sorted separated material is usually preferred for its higher quality due to the lower presence of inert components. On the other hand, mechanically separated food waste generates a lower quality material, needing several additional pieces of equipment to handle the slurry produced. In this latter case, grit and contaminants contained in the feed need to be removed before introducing the slurry into the digester. In addition to these inconveniences, the seasonal fluctuation of this type of waste should be noted, which highly influences biogas production [28]. The presence of heavy metals is another factor that may also add complexity to pre-treatment operations. The difficulty encountered when attempting the removal of inert materials and the risk of obtaining digestate with undesirable levels of toxic compounds make this digested slurry not suitable for agronomic use. The application of anaerobic digestion to the conversion of crop wastes and agro-industrial wastes is another field where this technology finds excellent results. However, when considering this type of substrate, the seasonal availability should be carefully evaluated along with the lignocellulosic content and high C/N ratio, which translates into excessively long digestion times and incomplete degradation. In addition, the low nitrogen levels and the lack of enough trace nutrients may hinder the successful performance and proper development of the anaerobic microflora. Given the different characteristics of these individual substrates, co-digestion of the above materials becomes the obvious solution for balancing nutrients and reducing the disadvantages associated with mono-digestion.