The transition to a complete sustainable economy demands not only for a CO2-neutral energy production, but also for closed loops in material processing. This challenge cannot be met by chemical conversion alone, but has to integrate biotechnology process steps, too. It further development depends on the knowledge and exploration of natural microbial resources, which are an invaluable, but widely non-discovered natural treasure, up to now. Conventional cultivation methods are limited in their ability to make the huge unknown variety of natural microbial communities accessible. In particular, methods for high sample throughput and massive parallel cultivation and testing of larger parameter spaces are needed. Droplet-based microfluidics allows the parallelization of tiny cultivation volumes for large sets of microorganisms. It is possible to investigating the formation of microbial colonies by dilution of unknown communities down to the single-cell level using the principle of “stoachastic confinement”, on the one hand, and for analysing the response of microbial populations on environmental pollutions, drugs or even special substrates, on the other hand. The so-called “segmented flow technique” is particular suited for studying the concentration-dependent microbial response on concentration of special components, supplies highly-resolved dose/response functions and maps of combinatorial effects of toxins. These techniques have been applied for investigating soil samples from special environments, as mining areas, smelting places and archaeological sites. In result, very different soil bacterial communities have been detected and characterized in their chemical response behaviour, new interesting species can be found and new bacterial strains of known species with unknown special physiological properties have been isolated.