Whoever smelt it, dealt it: a metagenomic view of the seedy underworld of microbial methane cycling
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. 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 these lineages and changing our understanding of the diversity and evolution of microorganisms involved in methane cycling.
Associate Professor Gene Tyson is a microbial ecologist whose research applies culture-independent molecular approaches to understand the structure and function of microbial communities in the environment. During Gene’s dissertation research (University of California, Berkeley) he was the lead author on one of the first studies to use metagenomics. In this work he investigated the metabolic potential and population diversity of microbial communities involved in acid mine drainage (AMD) generation, and demonstrated, for the first time, that metagenomic data could be used to reconstruct near complete genomes directly from environmental samples.
Associate Professor Tyson’s group at the University of Queensland, is now using the metagenomic and metatranscriptomic approaches he helped pioneer, to investigate microbial communities in a wide range of different communities in both engineered systems and natural environments. His group is continuing to develop new ways to analyze omic data by leading efforts in error correction for high-throughput sequencing platforms, single cell sequencing and deep spatio-temporal metagenomics