Soil microorganisms found in agricultural residues and the so-called efficient microorganisms (EM) are attractive for their potential applications and benefits in the bioremediation of complex ecosystems. However, the knowledge about Who is doing what?, as well as the trophic interaction in those communities that explain its benefits are limited; a better understanding of this microbiome is needed to explain its benefits. The objective of this research was to characterize the microorganisms isolated from two soil communities and the efficient microorganisms obtained in laboratory (EM16 consortium), taking into account physico-chemical characteristics, diversity, quantification, and taxonomic identification through microbiological and molecular techniques. A microbiological analysis was performed according to the morphological characteristics of the colonies as well as the study of the dynamics and taxonomic identification of the microbial populations through the TRFLP and Ion Torrent techniques. The diversity, dynamics, and taxonomic identification achieved in these studies showed the prospects for using these soil EM in bioremediation, considering the diverse metabolic pathways that these species have and their symbiotic interactive potential for biodegradation of lignocellulosic-resilient compounds. This study provides the first molecular characterization of the EM (EM16 consortium) and soil isolates from agricultural residues (sugarcane crop and bamboo field). The results suggest that the use of microbiological and molecular tools in a polyphasic approach allows the complete characterization of non-cultivable microorganisms that could contribute to sustainable environmental management and crop production.

The degradation of agricultural residues by anaerobic digestion and their bioconversion to methane is still hampered by the search for pretreatment strategies due to the lignocellulosic content that limits the efficiency of the process. Adding an enriched microbial consortium could be an alternative for the biological treatment of lignocellulosic biomass. During the degradation process, it is necessary to study the dynamics and structure of the microbial community. The objective of this study was to evaluate the addition of an enriched microbial consortium, and its effect on the methane-producing prokaryotic community during the anaerobic digestion of rice straw. The consortium was characterized by diversity, microbial community dynamics, and taxonomic identification. The rice straw anaerobic digestion was bioaugmented using the microbial consortium in 10 L semi-continuous stirred tank reactors (35 ± 2°C) for 70 days of operation at increasing organic loading rates up to 1.8 g VS L-1 d-1. Relative to the control reactor, higher and more stable methane production was obtained with the biological treatment strategy. The metagenomic method allowed identification down to the genus and species level of microbial consortium and the prokaryotic community within the reactors. From the knowledge of the diversity and dynamics of the microbial community, possible preferential metabolic pathways were presumed. The enhanced anaerobic degradation of rice straw by the microbial consortium and its effect on the methane-producing microbial community demonstrated that it could be used as a bioproduct for the treatment of agricultural waste for energy purposes.