Metaproteomics: a new approach for studying functional microbial ecology
Résumé
Establishing the link between microbial diversity and ecosystem functioning constitutes one of the fundamental questions in microbial ecology. However, microbial biodiversity cannot be resolved in a single manner and the question arises about which of the genetic and/or taxonomic and/or functional components of biodiversity are the most relevant in such a problematic. To date, most researches in this field has focused on genetic diversity and few investigations have examined functional diversity, resulting in a poor understanding of the manner in which genetic and taxonomic diversity affect functional diversity or ecosystem properties. This can be explained by paucity of methods allowing an in situ and without a priori functional analysis of indigenous microbial communities. This statement recently stimulated the development of new approaches allowing the characterization of microbial metaproteome (i.e. all the proteins synthesized at the scale of the community at a given moment) extracted from environmental samples. Since proteins, and more precisely enzymes, are involved in biotransformation processes, metaproteome analysis constitutes a suitable way to characterize the dynamics of microbial functions in a holistic way. Our presentation deals with interest and expected outcomes of the development of the metaproteomic approach for the functional analysis of microbial communities in their habitat. Different applications will be presented, highlighting the specificity and the sensitivity of the approach to characterize modifications of the functional structure and of the physiology of indigenous bacterial communities in response to metallic pollutions or organic matter inputs. Results presented show that, depending on soil characteristics, bacterial communities with similar genetic structures can harbour different functional structures and thus be potentially of different ecological significance for soil functioning. However, since they do not necessarily evolve in the same way, the simultaneous characterisation of genetic and the functional structures appears warranted to highlight fine and qualitative modifications in bacterial communities induced by variations in surrounding environmental conditions.