The process of anaerobic digestion (AD) has been extensively studied in natural and engineered ecosystems for more than a century. In natural habits, the anaerobic degradation of organic matter takes place in sediments, waterlogged soils and animal intestinal tracts, in which the oxygen access is restricted; whilst in engineered environments it refers to the biotechnological process by which organic matter (i. e., organic waste, wastewater and/or a renewable resource) is degraded in the absence of oxygen for the commercial production of biogas that can be used as an eco-friendly energy source [109], thereby representing an important asset in times of decreasing fossil fuel supplies. According to [4], the anaerobic digestion from swine, bovine and poultry slurries resulted in the production of biogas at average rates of 0.30, 0.25 and 0.48 L/g volatile solids, respectively. Another valuable co­product derived from this process is the anaerobic digested slurry, which can be applied as an organic amendment into soil either in agricultural and non-agricultural lands [110](section 3.1). It is for this reason along with the production of biogas and the reduction in greenhouse gas emissions [10] that anaerobic digestion is becoming increasingly popular as a methodological alternative for manure recycling, which in turn has increased the number of farm-scale anaerobic bioreactors up to 4200 in central and northern Europe [111].

Bacteria represent over 80% of the total diversity in anaerobic digesters [112], and they are mainly composed by the phyla Firmicutes, Proteobacteria and Bacteroidetes; whereas most of the archaeal representatives belong to the phylum Euryarchaeota, which includes all the known methanogens. Anaerobic eukaryotes — particularly, fungi and protozoa — have received less attention probably because they are slower growers than bacteria and, as such, their abundance is lower in anaerobic reactors. As occurs with composting, anaerobic digestion may be described as a four-phase microbiologically driven process. Briefly, the first and rate limiting step of the anaerobic food chain is the depolymerization and hydrolysis of complex biopolymers, such as polysaccharides, lipids, proteins and nucleic acids into their corresponding structural units (sugars, fatty acids, amino acids, purines and pyrimidines) through the joint action of a complex community of fibrolytic bacteria and fungi, which produce extracellular hydrolitic enzymes (i. e., cellulases, xylanases, proteases, lipases) responsible for the disassembling of such polymers. Since polysaccharides, mainly cellulose, are the most abundant structural and storage compounds of biomass, their hydrolysis is considered as the most determinant enzymatic process regarding the efficiency of anaerobic reactors. The rate and efficiency of cellulose hydrolysis depends greatly on the particular microbial species composition involved [113], and under anaerobic conditions it proceeds slowly due to the heterogeneity of forms in which cellulose is present in nature and to the complexity of the hemicelluloses and lignin matrices in which it is embedded [113]. Similarly, protein hydrolysis to peptides and amino acids takes place slowly, whilst lipid hydrolysis into glycerol and long-chain fatty acids occurs rapidly compared to their subsequent fermentation or p-oxidation. As mentioned above, bacterial populations are more abundant and diverse and, hence, they are responsible for the majority of hydrolytic reactions, being Clostridium, Acetivibrio, Bacteroides, Selenomonas or Ruminococcus common examples of hydrolytic bacteria found in anaerobic reactors [112,114].

The monomeric compounds released after the hydrolysis of biopolymers can be taken up by microbial cells, in which they are either fermented or anaerobically oxidised into alcohols, short-chain fatty acids, CO2 and molecular hydrogen (H2). This step is known as fermentation (acidogenesis) and usually occurs through the production of an energy-rich intermediate that is used to synthesise ATP, rendering a fermentation product that is excreted out of the cell. Since these products are typically acidic substances, the fermentative reactions are accompanied by a decrease in the extracellular pH. This fact along with the increase in short-chain fatty acids represents the most common reasons for reactor failure. Thus, for maintaining the pH balance of the system, it is of great importance to bear in mind the equilibrium between fermentative-acidogenic bacteria and acid scavenging microbes. Typically, the bacteria from the same group that hydrolyze biopolymers take up and ferment the resulting monomers. For instance, Clostridium sp. and enteric bacteria are common sugar fermenters in anaerobic reactors. Streptococcus sp. and Lactobacillus sp. also ferment sugars, producing lactate or lactate and ethanol, plus CO2 and molecular hydrogen [114]. Fermentation of amino acids and purines and pyrimidines in anaerobic environments is mainly carried out by species of Clostridium [115].

Then, during acetogenesis, the fermentation products are mainly oxidised to acetate, formate, CO2 and H2 by acetogenic bacteria, most of them belonging to the low G+C branch of Firmicutes [116]. Certain acetogenic reactions are thermodynamically unfavourable under standard conditions, which make necessary a syntrophic relationship between the acetogen and a H2-consuming methanogens in order to degrade the substrate and, in turn to obtain a net energy gain [117]. Finally, the last and most sensitive step during the anaerobic digestion of organic matter is the methanogenesis, i. e. the formation of methane from acetate, H2/CO2 and methyl compounds by the action of methanogenic organisms belonging to the phylum Euryarchaeota [118]. The orders Methanobacteriales, Methanococcales, Methanomicrobiales and Methanosarcinales include known methanogens commonly found in aerobic reactors. Members of the first three orders use CO2 and H2 as an electron acceptor and donor, respectively. Some species from these orders can also use formate and/or secondary alcohols (i. e., isopropanol or ethanol), but they cannot use acetate or C1 compounds such as methanol and methylamines (with the exception of the genus Methanosphaera from the order Methanobacteriales). However, Methanosarcinales are more diverse metabolically, and they can use acetate, hydrogen, formate, secondary alcohols and methyl compounds as energy sources. It is believed that the predominance of hydrogenotrophic or acetotrophic methanogens depends on the levels of their substrates and their tolerance to diverse inhibitors, including ammonia, hydrogen sulphide, or volatile fatty acids [119]. The aforementioned steps involved in the anaerobic digestion are explained in more detail by [109].