Autotrophic microorganisms generally refer to microorganisms that use carbon dioxide as the main or only carbon source and inorganic nitride as the nitrogen source to obtain energy through bacterial photosynthesis or chemical synthesis. Therefore, there are generally chemoautotrophic type and photoautotrophic type. Among them, photoautotrophic microorganisms can synthesize photosensitive proteins, some bacteria use bacterial chlorophyll, and some use protein similar to rhodopsin.

In the process of assimilation, heterotrophic microorganisms can not directly use inorganic substances to make organic substances, but can only convert ready-made organic substances absorbed from the outside into their own components and store energy.

There are many kinds of heterotrophic microorganisms, generally saprophytic and parasitic, which feed themselves by degrading organic matter.

In short, the biggest difference between autotrophs is their dependence on organic matter and their different internal structures because of their different functions.