Farmed ruminants are the largest source of anthropogenic methane emissions globally and a major target of methane mitigation efforts. Most methane emitted is produced by methanogenic archaea that use molecular hydrogen (H2) as their primary energy source. It is conventionally thought that H2 is produced by fermentative bacteria, ciliates, and fungi in the rumen, whereas hydrogenotrophic methanogens are the overwhelming H2 sink. In this work, we tested these concepts by performing a system-wide analysis of H2 metabolism in ruminants. We used genome, metagenome, and metatranscriptome datasets to resolve which microorganisms, hydrogenases, and metabolic processes mediate H2 production and consumption. In addition, we compared metatranscriptome datasets from low and high methane yield sheep to infer whether ruminal H2 supply controls methane emissions. 

Results
Analysis of the 410 bacterial and archaeal genomes from rumen isolates indicated that H2 metabolism is a widespread and diverse trait among rumen microorganisms. 60% of the genomes encoded the capacity for H2 metabolism via 23 different subgroups of hydrogenases. Analysis of metagenome and metatranscriptome datasets indicated that H2 metabolism is a complex and tightly regulated process within the rumen. Carbohydrate-degrading bacteria and eukaryotes, including uncharacterized clostridial orders and families, are the primary mediators of H2 production. A range of H2 uptake pathways were also expressed at moderate to high levels, including methanogenesis (Methanobrevibacter) acetogenesis (Blautia, Acetitomaculum), fumarate reduction (Selenomonas), and nitrate ammonification (Selenomonas). While metagenome profiles between low and high methane yield sheep were strikingly similar, there were major significant differences in the expression levels of hydrogenase classes and terminal reductases between low and high methane yield sheep. Whereas H2-producing processes were unchanged, genes mediating hydrogenotrophic acetogenesis, fumarate reduction, and nitrite reduction were highly and significantly upregulated in low methane yield sheep.

Summary
We conclude that H2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognized. There is evidence that alternative hydrogenotrophs, including acetogens and selenomonads, can prosper in the rumen and effectively compete with methanogens for H2 in low methane yield ruminants. These findings suggest that strategies to increase flux through alternative H2 uptake pathways, including through animal selection, dietary supplementations, and methanogenesis inhibitors, may lead to sustained methane mitigation. 
