Over the last decade, metagenomics has changed the face of microbial ecology. Metagenomics bypasses traditional culture-dependent approaches and holds the promise of genome-level insights into the mostly uncharted microbial world. However, for most environments it was not possible to obtain genomes from these data because the complexity of the microbial communities under consideration and limited throughput of the sequencing technology precluded assembly. Recent advances in high-throughput sequencing and development of new tools for analyzing metagenomic data are driving the evolution of this nascent field.

We are currently applying these new bioinformatics approaches to metagenomic data from a range of different habitats, which is revealing new key populations involved in methane cycling. For example, in relatively low diversity microbial communities from deep coal-associated aquifers, we have discovered a novel archaeal lineage outside of the Euryarchaeota that contains a near complete complement of genes for methanogenesis, including the methyl-coenzyme M reductase (mcr). These novel mcrA genes have previously gone undetected in nature because of their divergence to commonly used primers. Using these novel genes we could identify other divergent mcr genes in metagenomic data from several high methane flux environments, suggesting that this metabolism may be present in many other archaeal phyla. Our findings show that methane metabolism is widespread across the archaea, which has important implications for the carbon cycle and fundamentally changes our understanding of the evolutionary history of methane metabolism.