# Structure of Microbial Communities When Complementary
## 3 Results and Discussion
### Molecular Characterization of Microbial Communities
Proteobacteria, Firmicutes, and Bacteroidetes are likely abundant in all anaerobic digestion systems and have been referred to by several authors (e.g., [49; 52]). Furthermore, these phyla contain several species that are known to participate in one or more phases of the general anaerobic process. It was interesting to note that, although the samples came from pig effluents, no bacterial sequences (0%) were assigned to _Enterobacteriales_, indicating that the presence of common enteric pathogens was excluded from these anaerobic digestion reactors. \begin{table}
\begin{tabular}{c c c} \hline \hline \multirow{2}{*}{**Sample**} & \multicolumn{2}{c}{**Relative Abundance (\%)**} \\ \cline{2-3}  & **Bacteria** & **Archaea** \\ \hline PE IN & 99.73 & 0.26 \\ PE OUT & 99.87 & 0.13 \\
70P + 300 IN & 99.71 & 0.28 \\
70P + 300 OUT & 99.92 & 0.08 \\ \hline \hline \end{tabular}
\end{table} 
Table 10: Relative abundance of bacteria and archaea domains. Figure 2: Alpha rarefaction curves for the occurrence with which OTUs were detected at each sample. Relative abundance of bacterial and archaea groups was determined in terms of the percentage of total number of sequences in each sample. The predominant populations in PE (IN) were, respectively, Firmicutes (65%), Bacteroidetes (16%), \(\delta\)-Proteobacteria (7%), and Actinobacteria (3%). In those samples, _Clostridiales_ (57%, Figure 4a) mainly constituted most of the Firmicutes, _Bacteroidales_ (15%, Figure 4b) mainly constituted Bacteroidales (1.8%, Figure 4c) mainly constituted Proteobacteria, and _Corynebacteriales_ (1.8%, Figure 4d) mainly constituted Actinobacteria. After anaerobic digestion of PE effluent, the predominance of the phylum Firmicutes increased in the bacterial population to 94% of the total microbiota, and Actinobacteria increased by about 29% (Figure 4a). Syngepistetes suffered a decrease of 51%, Proteobacteria, 83%, and the remaining phyla, more than 90% of respective initial values. A similar behavior was observed in the 70P + 30O mixture, but with a more pronounced increase in phyla Firmicutes and Actinobacteria, and a smaller reduction in the phyla Synergistetes and Proteobacteria. The Actinobacteria populations in both essays were mostly represented by _Corynebacteriales_ (Figure 4d), which has the capacity for nitrate reduction and assimilation that enables its growth under anaerobic conditions [53]. At the end of digestion, the Firmicutes' populations in both essays were mostly represented by _Clostridiales_ (85% in PE and 62% in 70P + 30O, Figure 4a), whose order consisted mainly of members of the families _Lachospiraceae_ (8% in PE and 9% in 70P + 30O, data not shown), _XI_ (60% in PE and 32% in 70P + 30O, data not shown), and _Ruminococcaceae_ (24% in PE and 42% in 70P + 30O, data not shown). Most of strains in Firmicutes, including _Ruminococcaceae_, might hydrolyze cellulose, glucose, starch, and proteins, into small molecular organic acids as acetate, highly contributing for improvement of the methane production yield [54; 55]. It is worth noting the increase to 26% of _Bacillus_ in the microbial community in the sample 70P + 30O, whose order consisted mainly of members of the family _Planococcaceae_ (87% in PE and 99% in 70P + 30O, data not shown), known as good carbohydrate-utilizing species [54]. The other populations, more specifically Bacteroidetes, known to be proteolytic bacteria, became almost non-existent, suggesting that these two phyla might compete for the same resources and energy. They are known for their ability to degrade complex and recalcitrant organic matter such as proteins, lipids, and cellulose as well as simpler compounds such as amino acids and sugars, using hydrolytic enzymes [52]. Moreover, the  
Figure 3: Relative abundance of Bacteria phyla.