Virtually all microbial communities on our planet are dominated by a great diversity of uncultured microorganisms, which cannot be studied by traditional approaches in microbiology. In their habitats, microbes often coexist in spatially complex assemblies colonising sediments, soils, roots, teeth, the gut, and many other environments with an intricate three-dimensional architecture. Within these consortia, microbes are influenced by numerous abiotic factors (e.g., fluctuations in nutrient concentrations) and involved in a plethora of biotic interactions.

To understand this complex microbial life, we must look directly at single cells and the microscopically small niches where they thrive and interact with other organisms. Only then can we decipher the in situ metabolic activities and symbioses of uncultured microbes. However, single-cell microbiology is an enormous methodological challenge if we consider the tiny size of a microbial cell and the ultra-low amounts of substrates that are taken up, utilised, and exchanged by single cells.