Global change due to human activities causes an increasing number of disturbed ecosystems and poses a challenge to humanity because human life on earth depends on the stability of ecosystem services. Microorganisms are main drivers of element cycling, they contribute largely to the global organic carbon budget and are therefore a fundament for all biological processes and relevant for ecosystem services. They furthermore represent model organisms to test ecological theory, as they are small and have short generation times what facilitates the generation of comprehensive datasets for statistical evaluation. Earlier research points to the following mechanisms that support stability of community functioning in fluctuating environments: first, the tolerance of individual community members against environmental change impacts also the community-level robustness and the classification of individual community members along the generalist-specialist continuum may be a valuable tool to evaluate the vulnerability of a whole community in a disturbed environment. Secondly, there has been a long debate about the link of community structures, such as diversity patterns but also the architecture of species interactions to the vulnerability of these communities to environmental change. The genomic material of microbial communities represents a blueprint of their functioning and should contain the information about the tolerance of individual community members and concerning the above mentioned community structures.We use metagenome data from two aquatic sites that are contrasting concerning their environmental variability and their trophic status to explore parameters that can be delineated from metagenome data to characterize the community performance in response to environmental change.