Excess Hydrogen Disrupts Microbial Balance in Syngas Biomethanation, Triggering Metabolic Shifts and Viral Defense Responses

Syngas biomethanation, which converts CO/CO₂/H₂ into renewable methane, depends on coordinated microbial interactions, but new research shows that excess hydrogen disrupts this balance, reducing methanogenesis efficiency and triggering major shifts in microbial metabolism and viral dynamics. Under hydrogen-rich conditions, the key methanogen Methanothermobacter thermautotrophicus downregulates methane-producing pathways while activating defense systems such as CRISPR-Cas and restriction-modification mechanisms, while acetogenic bacteria intensify carbon fixation through the Wood–Ljungdahl pathway as alternative electron sinks. The findings, detailed in a 2025 early-access study (DOI: 10.1016/j.ese.2025.100637) in Environmental Science and Ecotechnology, uncover a previously unclear mechanism of thermodynamic stress and microbiome-virus interplay, offering guidance for optimizing microbial consortia in syngas-to-methane conversion.

Biomethanation provides an energy-efficient, low-carbon alternative to thermochemical gas conversion, turning biomass-derived syngas into biomethane for circular energy systems, with performance relying on balanced microbial metabolism where hydrogenotrophic methanogens reduce CO₂ using H₂, supported by acetogens and syntrophic partners. However, syngas composition fluctuates during industrial operation, and the metabolic response to hydrogen excess was poorly understood, as traditional studies observed performance drops at high H₂ supply but lacked molecular-level mechanistic explanation regarding microbial regulation and viral interactions. Researchers from the University of Padua used genome-resolved metagenomics, metatranscriptomics, and virome profiling to monitor microbiomes as syngas composition shifted from optimal ratios to hydrogen-rich conditions, revealing stress-driven metabolic reorganization and highlighting phage dynamics as a significant ecological dimension in biomethanation efficiency.

The study cultivated thermophilic anaerobic microbiomes under three syngas compositions and applied multi-omics analysis to track responses before and after hydrogen increase. Under near-optimal gas ratios, methane yield improved and Methanothermobacter thermautotrophicus maintained stable gene expression, but when hydrogen supply exceeded stoichiometric demand, methane production declined and transcriptome analysis showed strong metabolic repression, with key methanogenesis genes—including mcr, hdr, mvh, and enzymes in CO₂-to-CH₄ reduction—significantly downregulated. Simultaneously, M. thermautotrophicus activated antiviral defense systems, upregulating CRISPR-Cas, restriction-modification genes, and stress markers such as ftsZ, while virome mapping identified 190 viral species, including phages linked to major methanogens and acetogens, with some viruses showing reduced activity suggesting defense-driven suppression and others exhibiting active replication patterns.

In contrast, several acetogenic taxa—including Tepidanaerobacteraceae—enhanced expression of Wood–Ljungdahl pathway genes (cdh, acs, cooF, cooS) to boost CO/CO₂ fixation and act as electron sinks, indicating a shift from methanogenesis to carbon-fixation-dominant metabolism when hydrogen is excessive. The authors emphasize that hydrogen excess creates a regulatory bottleneck, pushing methanogens into stress mode while enabling acetogens to take over carbon metabolism, and note that viral interactions—previously overlooked in biomethanation—play a major role in shaping community stability, with CRISPR-Cas activation and phage suppression indicating a defensive state that suggests virome dynamics must be considered in bioreactor design.

This research provides molecular-level evidence that hydrogen oversupply can destabilize methane production, highlighting the need for gas-ratio control in industrial reactors, as understanding how microbial populations reprogram under stress can guide engineering of more resilient biomethanation systems for 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, supporting future development of carbon-neutral gas-to-energy technologies and scalable waste-to-resource platforms.