Microbes are involved in many processes, including the carbon and nitrogen cycles, and are responsible for both using and producing greenhouse gases such as carbon dioxide and methane. Microbes can have positive and negative responses to temperature, making them an important component of climate change models. Microbes play an important role in climate because they release carbon dioxide into the atmosphere when they eat. Bacteria and their main predators, protists, account for more than 40 times the biomass of all animals on Earth. As a result, they have a huge effect on carbon dioxide emissions. Climate change increases the activities of pathogens and heterotrophic microorganisms, shifting of beneficial microbes from one ecological niche to another. Precipitation is an important regulator of activities of plant and microbiomes.

Cyanobacteria established Earth's oxygenated atmosphere in geologic time and continue to fix carbon and liberate oxygen gas.

There is no "the microbiome" - there are untold numbers of microbiomes, esp. with the concept expanded to otherwise inanimate realms.