Microorganisms play a crucial role in the global carbon and nitrogen cycles, exerting a significant impact on greenhouse gas (GHG) emissions. These microorganisms, mainly bacteria and archaea, mediate key biogeochemical processes such as carbon fixation, methane production (methanogenesis), nitrification and denitrification, which contribute directly to the atmospheric concentration of GHGs. In terrestrial and aquatic environments, microbes can both mitigate and aggravate GHG emissions, depending on environmental conditions, substrate availability, and microbial community composition. By exploring their ecological roles in various environments present chapter highlights the importance of microbial activities in regulating atmospheric GHG levels.