Microfluidic systems have a tremendous potential for the miniaturization and automation of bio-chemical assays. Cells or genes can be encapsulated in droplets that are manipulated, fused, analysed and sorted at high-throughput. Such systems are extremely powerful for the selection of microorganisms. To go further, I propose now to develop new types of microreactors for biotechnological assays, combining microfluidics and encapsulation. I propose to generalize droplet production to other encapsulation procedures based on SOFt-Interfaces (surfactant-laden interfaces, particle-laden interfaces, soft polymer shells, biofilms...). First, I will characterize the mechanical properties of soft interfaces using interfacial rheology methods and I will develop novel microfluidic methods for the quantitative measurements of the mechanics of microcapsules. Next, I will use microfluidics as a tool to characterize the chemical stability of the microreactors and to induce the release of the contents of the capsules by external forcing. Finally, I propose to use these new types of microreactors in order to control the adhesion of cells inside the microcontainer to develop new high-throughput screening systems for adherent cells. I also envision a novel type of self-sorting microreactor. Based on the recent developments of self-propelled droplets, I will design a system where the droplets containing the object of interest (for example a cell) would sort themselves, by controlling droplet propulsion with an enzymatic reaction. Sorting of microorganisms based on a specific activity is of considerable interest for applications in diagnostics, or selection of organisms for specific tasks. Such self-sorting microreactors would have a huge potential as a new approach to select efficient microorganisms in an automated manner. Such systems can also be seen in the frame of synthetic biology as new microorganisms capable of motion which can be assembled in a bottom-up approach.