Eco-systems biology of microbial communities: integration of biomolecular information from unique samples

In microbial ecology, high-resolution molecular approaches are essential to characterize the vast organismal and functional diversity and to understand the interactions between environmental factors and microbial communities (MCs). Molecular eco-systems biology based on the integration of genomics and functional omics, allows conclusive links to be drawn between genetic potential and function. However, the field faced major challenges arising from the heterogeneity and dynamics of MCs. Hence, to facilitate meaningful data integration, analysis and modeling, it is crucial to obtain standardised, reproducible and simultaneous measurements of multiple features from a unique sample. We have developed a new methodological framework for the isolation of high-quality DNA, large and small RNA, proteins and metabolites fractions from undivided MC samples. The methodology is based on cryogenic sample preservation and cell lysis. Metabolites are first extracted using organic solvents, followed by sequential isolation of biomacromolecules using chromatographic spin column technology. The methodology was validated by comparison to commonly used dedicated methods and its broad applicability was demonstrated on MCs of biotechnological, environmental and medical interest. Applying this method to sewage plant MCs has allowed us to determine community-level keystone genes and to probe the functional relevance of the population-level composite genomes, leading to the identification of key players of the community. This methodological framework lays the foundation for standardized molecular eco-systems biology and offers exciting prospects for elucidating the genetic blueprints and the functional relevance of specific populations within MCs, particularly in relation to environment-driven demography changes leading to catastrophic bifurcations