Microbial communities play a crucial role in bioprocesses aimed at bioenergy recovery, bioproduction and nutrient recovery. Current monitoring focuses mainly on compositional analyses, which do not consider 3-dimensional microbial organisation. Hence, a novel approach for direct microbial community engineering is essential to explore opportunities in the bio-based economy. This project aims to acquire and apply fundamental insights in microbial 3D organisation and activity. Anaerobic granules will be used, because of their unique organisation, targeted towards renewable energy recovery from organic waste. Synthetic granules will be created with a pre-defined microbial composition and organisation for tailor-made applications. Natural granules will be combined with synthetic granules for process engineering. Novel on-line techniques for microbial organisation and activity monitoring will be developed and validated. The successful integration of these objectives will result in fundamental knowledge, and enable hypothesis-driven research of the microbial 3D organistion and activity in anaerobic granules and beyond.