Researchers have uncovered a driver of methane emissions in livestock: a newly identified organelle, the hydrogenobody, which fuels methane production in the guts of livestock. The findings provide a cellular and molecular explanation for how single-celled organisms known as rumen ciliates, that live in the stomachs of animals like cows, contribute to methane emissions from these animals, offering a potential new target for tackling agricultural contributions to climate change. Methane is a highly potent greenhouse gas. A substantial fraction of human-caused methane emissions – particularly from ruminant livestock such as cattle and sheep – originates from microbial processes in the animals’ digestive systems. Within the rumen, a complex community of microbes supports digestion but also generates methane, with methanogenic archaea acting as the direct producers and rumen ciliates playing an important but still poorly understood role in amplifying these emissions. Despite extensive multi-omics research on the rumen microbiome, ciliates have remained understudied due to limited genomic resources, leaving key mechanisms unresolved.

To address this, Fei Xie and colleagues constructed a rumen ciliate genome (RCG) catalog comprising 450 genomes across multiple ruminant hosts and used it to analyze 1877 multi-omics datasets, alongside direct measurements from dairy cows. This large-scale integration linked ciliate abundance and activity to methane emissions and enabled validation in a real-world livestock setting. Xie et al. also discovered and experimentally confirmed a previously unknown organelle in rumen ciliates, the hydrogenobody (HB), which produces hydrogen while also regulating oxygen within the cell. By generating hydrogen and removing oxygen, the HB effectively supports methanogenic archaea while maintaining localized anaerobic conditions within the rumen. Moreover, its abundance varies with ciliate size and surface structure, indicating that different species occupy distinct ecological niches tied to micro-scale oxygen conditions. Notably, ciliates with higher HB abundance are associated with greater methane production, identifying them as potential targets for mitigation strategies aimed at reducing livestock emissions without broadly disrupting essential digestive functions.

The enzyme RNA polymerase reads a DNA template to build RNA one nucleotide at a time, but how it performs its core chemistry is unresolved. New cryo-EM structures capture the enzyme in intermediate states, showing for the first time that RNA polymerase catalyzes reactions through the precise alignment of substrates and using a coordinated chain of water molecules that act as a proton shuttle. Because this mechanism is conserved across all life, the findings provide a universal blueprint for gene expression and explain how certain mutations disrupt transcription.