Microbial community structure is the result of environmental conditions that vary significantly and frequently. In laboratory conditions, associations from two microorganisms to complex microbial communities are used to mimic real ecosystems and their functions. Nevertheless, the composition of individual members of complex ecosystems and their relationships, as well the environmental conditions needed to re-create microcosms and their associated activities, are hard to reproduce. The present chapter gives a laboratory-based methodological approach to study structure-function relationships. The results obtained from a systematic study of various ecosystems and the extent of environmental conditions that dictate the structure of communities and the link with ecosystem function are discussed. We also comment on, to what extent the results obtained in laboratory conditions are transposable to natural ecosystems. Finally, three specific case-studies related to cheese ripening are developed to illustrate how microbial ecology can be integrated into food microbiology for better quality and safety of smear cheeses.