Maths on microbes: adding microbial ecophysiology to metagenomics

Microbial ecology has shifted in the last 30 years from a field strongly depending on culturing and microscopy to a discipline dominated by cultivation-independent molecu-lar analysis. Nowadays, metagenomics (for simplicity, I include in metagenomics also high-throughput sequenc-ing of phylogenetic and functional marker genes) allows unprecedented insight into the composition and functional potential of microbial communities, while metatranscrip-tomics, metaproteomics and metabolomics inform on the expression of functional potential. Yet it is easy to lose sight of the forest for the trees: certainly for engineered systems, like waste water treatments and bioremediation, one is in the end more interested in what all species together do than what their individual identities and activities are.