Unraveling microbial activities and interactions in the syngas biomethanation process: a multi-omics approach

Syngas biomethanation is a bioprocess harnessing microbes to synthesize methane (CH4), through the conversion of carbon monoxide (CO), carbon dioxide (CO2) and hydrogen (H2). The gaseous carbon conversion occurs through species-specific metabolic pathways relying on collaboration and coordination between multiple functional guilds. Methanogenic archaea engage in either competition or syntrophy with acetogenic and hydrogenogenic bacteria respectively, to transform syngas streams into energy-rich biomethane under anaerobic conditions. This study aimed to elucidate the metabolism and community dynamics underlying syngas biomethanation by exposing a microbial inoculum to varying syngas compositions. Genome-centric metagenomics and metatranscriptomics were employed to reconstruct 69 metagenome-assembled genomes (MAGs), identify metabolic potential, and assess gene expression patterns. Methanothermobacter thermautotrophicus dominated the microbiome across all conditions, supported by the syntrophic bacterium Coprothermobacter proteolyticus. Syngas composition significantly influenced CH4 output, with a mixture of 77% H2, 9% CO and 14% CO2 yielding best productivity. Functional analyses revealed that key genes involved in methanogenesis and CO/CO2 conversion, including those catalyzing the Wood-Ljungdahl pathway, were differentially expressed across conditions. Results suggest a remarkable metabolic flexibility and niche adaptation within the microbiome. This study provides new insights into the microbial and enzymatic mechanisms driving syngas biomethanation, advancing our understanding of this bioenergy process and its potential for sustainable energy applications.