## 5 Substrate Composition and Microbial Communities  
Numerous authors reported that the diversity of microbial communities involved in AD is correlated with the type of biomass. For example, [PERSON] et al. [122] evaluated the influence of different agricultural waste materials, such as chicken manure combined with cattle manure, cattle manure alone or in combination with maize straw or distiller grains, and Jatropha (an energy plant widely used for commercial production of biodiesel) press cake on the composition of the microbial communities involved in AD at laboratory scale. As control substrate, cattle manure combined with maize silage, was used. Bacterial communities involved in the AD of the control substrate were rather stable and similar to each other. Conversely, in bioreactor fed with special biomass, such as chicken manure or Jatropha press cake, different communities indicating partial ammonia inhibition or other inhibiting factors were found. AD of chicken manure is based on syntrophic acetate oxidation as the aceticlastic methanogenesis is inhibited by dominant acetate-consuming process. However, the use of Jatropha as substrate led to the enrichment of fiber degrading microorganisms belonging to the genera Actinomyces and Fibobacter. The most abundant bacterial phyla were the Firmicutes (mainly Clostridia) and the Bacteroidetes, whereas the archaeal communities were dominated by methanogenic Euryarchaeota belonging to the orders Methanomicrobiales and Methanosarcinales. In all digesters, different Clostrtial phylotypes were found with variable proportions. However, the highest prevalence of these species was observed in biogas plants fed with vegetable biomass. In particular, Clostridium thermocellum and C. stercorarium were found to be the major microorganisms involved in the hydrolysis of plant biomass [123]. C. thermocellum was studied in detail for cellulosomes architecture and cellulose metabolism. In fact, cellulosomes are involved in the AD of recalcitrant cellulose, with the release of compounds necessary for the growth of acetogens and methanogens. Another Clostrtial family frequently found in all the bioreactors, in particular in the reactors fed with maize straw or Jatropha press cake, was Ruminococcaceae. The functional role of this group seems to be mainly the cellulolytic digestion of plant fibers based on the production of a cellulosome enzyme complexes and cellulose adhesion proteins [124]. [PERSON] et al. [125] used a metagenomic analysis to study the complex interaction among microbial communities involved in biogas production with the aim to understand the role played by microbes that are unknown or undetermined in the available databases. These authors noted that in an anaerobic fermenter fed with plant biomass and pig manure slurry, members of the Firmicutes and Bacteroides phyla were mainly responsible for hydrolysis and secondary fermentation. In particular, many Clostridium species, possessing cellulolytic and H\({}_{2}\)-producing activities (both essential properties for the efficient biomass degradation), were identified. In the Archaea domain, the most abundant order was Methanomicrobiales that, during methanogenesis, used CO\({}_{2}\) as a carbon source and H\({}_{2}\) as an electron donor, suggesting that hydrogenotrophic pathway, leading to CH\({}_{4}\) formation, may be more significant than previously recognized [126]. Methanoculleus marisnigri was the principal species among the Archaeal habitants, confirming the results obtained in anaerobic digesters operating under different conditions [127]. These findings showed that an optimized balance between H\({}_{2}\) producers and consumers was a critical parameter for the efficiency of the biogas microbial community [125]. A study on the microorganisms involved in AD of fruit and vegetable waste obtained from the central food distribution market in Mexico City [10], showed that the bacterial sequences were distributed among three major phyla: Firmicutes (89.5%), Actinobacteria (6.9%), and Bacteroidetes (2.3%).