Within in most ecosystems nitrogen is primarily stored in living and dead organic matter . This organic nitrogen is converted into inorganic forms when it re-enters the biogeochemical cycle via decomposition . This process is known as mineralization and it is carried out by a variety of bacteria , actinomycetes , and fungi . Nitrogen in the form of ammonium can be absorbed onto the surfaces of clay particles in the soil. The ion of ammonium has a positive molecular charge is normally held by soil colloids .
Ammonium is released from the colloids by way of cation exchange .
Both of these processes involve chemical oxidation and are known as nitrification . However, nitrate is very soluble and it is easily lost from the soil system by leaching . Some of this leached nitrate flows through the hydrologic system until it reaches the oceans where it can be returned to the atmosphere by denitrification . Denitrification is also common in anaerobic soils and is carried out by heterotrophic bacteria . Both of these gases then diffuse into the atmosphere.