Abstract Microbes in Nature rarely exist in isolation. How stable, functional microbial communities establish, however, is not fully understood. Studies on synthetic communities, ‘constructed’ from few species, have shown metabolic interactions can readily emerge among microbes and can allow for their stable co-existence. The extent and stability of metabolic interactions within natural communities, however, is more difficult to study, especially over time. In this talk, I will explain our attempts to adapt and maintain a natural community in the laboratory for long-term study of species composition, metabolic interactions, and stability. We have ‘adapted’ a freshwater community to the lab under lack of carbon source and application of a 12hr light-dark cycle. This resulted in a microbial community of 17 species, including a filamentous, gliding cyanobacteria. We found that this community maintains species composition stably over a 2-year period of serial passaging. We found evidence for carbon and vitamin sharing among members of this community and genetic capacity of sulfur cycling and anoxygenic photosynthesis functions. We have also found that this system results in reproducible spatial structure formation, including cm-scale granules. We show that these granules harbour anoxic microenvironments, which could sustain some of the genetically encoded anoxic functions. The formation of structural organisation is underpinned by the gliding motility of the filamentous cyanobacteria and we find that the collective motility of many filaments leads to emergent behaviours underpinning iron acquisition. Our findings show that structural organisation driven by one species can significantly shape microenvironments and determine assembly, stability, and function of a larger microbial community. The presented system can act as a model for understanding the formation of cyanobacterial mats and granules found in Nature and how they function to underpin biogeochemical cycling of key compounds. At the same time, the presented (or similar) mid-complexity system can be adapted to biotechnological applications in carbon capture, and sunlight to chemical conversion.