Heterocysts are specialized cells in filamentous cyanobacteria that differ significantly from vegetative cells. Structurally, heterocysts are generally larger and have a thicker, multi-layered cell envelope, which limits oxygen diffusion. They possess diminished pigmentation, lack Photosystem II (thus, no oxygenic photosynthesis), and their thylakoid membranes are often less organized centrally. Vegetative cells, conversely, are smaller, actively photosynthetic, and lack the specialized envelope.

Heterocyst formation is primarily controlled by the availability of fixed nitrogen in the environment. When nitrogen sources like ammonium or nitrate are scarce, it triggers a cascade of genetic events. Key regulatory genes like ntcA and hetR are activated, initiating the differentiation process. Oxygen levels also play a crucial role, as the nitrogen-fixing enzyme, nitrogenase, is highly oxygen-sensitive.

The main function of heterocysts is atmospheric nitrogen fixation, converting inert nitrogen gas (N₂) into usable ammonia (NH₃). To achieve this, their thick walls and modified photosynthetic apparatus (retaining only Photosystem I for ATP production) create a micro-anaerobic environment essential for nitrogenase activity. They supply fixed nitrogen compounds to the adjacent vegetative cells, which in turn provide carbohydrates to the heterocysts, illustrating a remarkable cellular division of labor.