Syngas biomethanation, the process of converting carbon monoxide, carbon dioxide, and hydrogen into renewable methane, depends on carefully balanced microbial interactions. A new study demonstrates that an oversupply of hydrogen disrupts this balance, significantly reducing methanogenesis efficiency and triggering major shifts in microbial metabolism and viral dynamics within the microbiome. These findings provide critical molecular-level insights for optimizing industrial-scale renewable methane production from biomass-derived syngas.
Researchers from the University of Padua detailed their investigation in a 2025 early-access study published in Environmental Science and Ecotechnology (DOI: 10.1016/j.ese.2025.100637). Using genome-resolved metagenomics, metatranscriptomics, and virome profiling, the team monitored thermophilic anaerobic microbiomes as syngas composition shifted from optimal ratios to hydrogen-rich conditions. The work was supported by the European Union LIFE+ program and Horizon 2020 research and innovation program.
Under near-optimal gas ratios, methane yield improved and the dominant methanogen, Methanothermobacter thermautotrophicus, maintained stable gene expression. However, when hydrogen supply exceeded stoichiometric demand, methane production declined. Transcriptome analysis revealed strong metabolic repression, with key methanogenesis genes—including mcr, hdr, mvh, and enzymes in the CO₂-to-CH₄ reduction pathway—significantly downregulated.
Simultaneously, M. thermautotrophicus activated antiviral defense systems, upregulating CRISPR-Cas, restriction-modification genes, and stress markers like ftsZ. Virome mapping identified 190 viral species, including phages linked to major methanogens and acetogens. Some viruses showed reduced activity, suggesting defense-driven suppression, while others exhibited active replication patterns. This highlights a previously overlooked ecological dimension in biomethanation efficiency.
In contrast, several acetogenic taxa, including Tepidanaerobacteraceae, enhanced expression of Wood–Ljungdahl pathway genes (cdh, acs, cooF, cooS) to boost carbon monoxide and carbon dioxide fixation, acting as alternative electron sinks. This metabolic reprogramming indicates a shift from methanogenesis to carbon-fixation-dominant metabolism under hydrogen excess.
The authors emphasize that hydrogen excess creates a regulatory bottleneck, pushing methanogens into a stress mode while enabling acetogens to take over carbon metabolism. They note that viral interactions play a major role in shaping community stability, with CRISPR-Cas activation and phage suppression indicating a defensive state that must be considered in bioreactor design.
This research provides molecular evidence that hydrogen oversupply can destabilize methane production, underscoring the necessity for precise gas-ratio control in industrial reactors. Understanding how microbial populations reprogram under stress can guide the engineering of more resilient biomethanation systems, enabling consistent biomethane yields even with variable feedstocks. The insights into phage-microbe interactions further suggest potential for virome-aware reactor management strategies, including microbial community design, phage monitoring, or antiviral interventions. These findings support the future development of carbon-neutral gas-to-energy technologies and scalable waste-to-resource platforms, advancing the transition to circular energy systems.
