Biofilms, a natural form of immobilized whole cells, are currently being investigated as a robust biocatalyst for the production of chemicals. Fluidic conditions and reactor geometry severely influence biofilm growth, development, and reaction performance. However, there is a missing link between the in situ characterization of biofilms on microscale setups and macroscale reactors because of the difference in reactor geometry and fluidic conditions. In this protocol, we describe the assembly and operation of flow cell and flow reactor setups with identical system geometry and segmented flow conditions to link biofilm characterization to reactor performance. The flow cell setup enables the in situ characterization of biofilm growth, structural development, and cell viability by utilizing confocal laser scanning microscopy (CLSM). Whereas, the laboratory scale flow reactor allows the determination of overall biofilm dry mass, catalytic activity, and final product titer during biocatalysis. Finally, CLSM image acquisition and the following data analysis are briefly described.
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