There are three main nutrient cycles that bacteria use. They are the carbon cycle, nitrogen cycle, and sulfur cycles.  In the carbon cycle, CO2 is removed from the atmosphere by photosynthesis of land plants and return through the respiration of land animals. The nitrogen cycle is an essential element for life and includes nitrogen fixation and denitrification. During nitrogen fixation nitrogen in the atmosphere is converted into ammonium. During denitrification, NO3- is reduced to N2, NO, or N2O. During the sulfur cycle mineralization of organic sulfur into inorganic form occurs, followed by the oxidation of hydrogen sulfide. Then sulfate is reduced into sulfide, and the sulfide in incorporated into organic materials.

Humans have a large impact on microbial nutrient cycles by adding and removing components of the of the cycles in large amounts. CO2 is responsible for global warming. It has increased in the atmosphere by 40% since the industrial revolution. Human impact on nitrogen cycles includes the production of nitrogenous fertilizers. These fertilizers create a nitrogen amount equivalent to the amount of fixed nitrogen entering the biosphere.