From taxonomy to metabolism: Exploring the Methane Production Potential of Anaerobic Microbiomes

Anaerobic digestion is a sustainable strategy for the treatment of organic waste, notable for its ability to produce biogas and reduce environmental impact. This study addresses the challenges of understanding the complex dynamics of microbial communities in this process using an approach that integrates metagenomic analyses and genome-scale metabolic modelling (GEM). Combinations of inoculants (wastewater treatment plant sludge and cattle manure) with substrates (pig manure, poultry manure and food waste) were evaluated under different conditions and their impact on microbial composition, metabolic dynamics and methane production was analysed.

Reconstruction of microbial communities from MAGs (genomes assembled from metagenomes) was a major challenge due to the complexity and diversity of the environmental samples. Nevertheless, high quality genomes were obtained, allowing the characterisation of key methanogenic archaea and fermentative bacteria. These results highlight the importance of syntrophic interactions in methane production and substrate degradation.

Metabolic modelling with GEMs facilitated the simulation of processes such as methanogenesis and the production of intermediate metabolites (acetate, lactate and butyrate). The models predicted clear differences in metabolic performance according to inoculum and substrate combinations, showing an increase in methane production under certain co-digestion conditions. Furthermore, temporal analysis revealed how communities evolve to maximise metabolic efficiency throughout the process.

This study highlights the importance of reconstructing microbial communities from MAGs as a tool for understanding and optimising anaerobic digestion. The results highlight the critical role of microbial interactions in process efficiency, providing a basis for improving biogas production and designing more sustainable and efficient waste treatment systems.

Keywords: Anaerobic digestion, microbial communities, metagenome-assembled genomes (MAGs), genome-scale metabolic models, methane production, Co-digestion, Syntrophic interactions, waste treatment optimization