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 has not been possible to obtain genomes from metagenomics data because the complexity of the microbial communities under consideration and limited throughput of the sequencing technology precluded assembly. The primary way to extract biologically meaningful information from these largely unassembled datasets was to use “gene-centric” approaches that explored the distribution and abundance of genes and gene families between different environments. However, recent advances in high-throughput sequencing and development of new tools for analyzing metagenomic data are driving the evolution of this field.
Anaerobic archaea are major contributors to global methane cycling. Methanogenic archaea are estimated to produce one billion tons of methane per year with an equal amount estimated to be oxidized by archaeal methanotrophs. All previously described archaeal methane metabolizing microorganisms belong to the phylum Euryarchaeota and share a core set of bidirectional enzymes responsible for their respective metabolisms. This restricted phylogenetic distribution has led to the hypothesis that archaeal methane metabolism originated within the Euryarchaeota, although an origin outside this phylum has also been proposed. My research team is applying metagenomic techniques to recover a large number of archaeal genomes from many previously uncultivated archaeal lineages and from increasingly complex environments. This has greatly expanded our understanding of the metabolic capabilities of the Archaea and challenges our understanding of the diversity and evolution of microorganisms involved in methane cycling.