Genome-centric metagenomics: the next step in microbial ecophysiology

So far, progress of microbial physiology has depended on the use of pure cultures. Study of a microbial strain in pure culture was essential to obtain unambiguous results about metabolism, regulation or cell biology, especially when a genetic system or a complete genome sequence was available. Unfortunately, it is also all but impossible to interpret results from physiological studies in ecological context. Indeed, for many highly interesting model organisms, meaningful definition of an ecological niche has defied decades of intensive study. Advances in next generation DNA and RNA sequencing, community proteomics, and metabolomics, in combination with advances in computational procedures are now enabling detailed physiological study of specific bacteria in the context of their natural community. This approach is currently under rapid development and used both directly with natural habitats or on habitats engineered in the laboratory. It provides information about how different bacteria interact, exchange and compete for nutrients, co-factors and metabolites. Finally we will be able to link physiology to ecological fitness! From a metagenomics perspective, what sets the approach apart from previous approaches is that it is not gene-centric, focused on abundances of individual functional genes, but genome-centric. Now the aim has become to extract more or less complete provisional whole genome sequences of the interacting populations. This research topic aims to generate an overview of current developments in computational approaches to enable extraction of provisional whole genome sequences and to provide examples of how genome-centric metagenomics can be combined with conventional physiological or biogeochemical techniques to link microbial physiology and ecology.