What is Ecogenomics?

A whole range of culture-independent technologies have emerged in recent years that are revolutionizing our understanding of the microbial biosphere. Chief amongst these are sequence-based methods that rely on cheap high-throughput sequencing of DNA and RNA extracted directly from environmental samples (metagenomics and metatranscriptomics respectively). Similarly, mass spectrometry-based identification of peptides and small molecules has reached the stage that it is now possible to identify many proteins (metaproteomics) and metabolites (metabolomics) in environmental samples. In parallel, cell sorting and whole genome amplification methods are making single cell genomics a reality, providing a natural complement to ‘whole’ community characterization methods. One other important experimental approach, also advancing rapidly, is cell imaging that provides a high-resolution spatial framework on which to overlay molecular data. All of these techniques can be combined into an integrated ecological framework using computational advances and new modelling approaches, which we collectively define as ‘ecogenomics’.