Nitrate ions are very soluble and leach through the soil. In natural ecosystems, the nitrate levels are restored through recycling of nitrogen-containing compounds. In agricultural ecosystems, the level of nitrate can be further increased by the use of fertilisers.
When plant and animals die, the process of decomposition begins, in a series of steps by which microorganisms replenish the nitrate levels in the soil.
Ammonification is the production of ammonia from organic ammonium containing compounds such as urea and proteins. Saprobiotic microorganisms feed on these materials releasing ammonia in the form of ammonium ions in the soil.
Nitrifying bacteria oxidise ammonium ions into nitrite ions which are further oxidised to nitrate ions. Nitrifying bacteria need oxygen to carry out these conversion and so they need a soil that has many air spaces which is achieved by ploughing to keep soil structure light and aerated.
This is a process by which nitrogen gas is converted into nitrogen containing compounds.
Free-living nitrogen-fixing bacteria reduce gaseous nitrogen to ammonia which they then use to manufacture amino acids, releasing nitrogen compounds when they decay.
Mutualistic nitrogen-fixing bacteria live in nodules on the roots of plants. They form a mutualistic bond with the plants and provide the plant with nitrogen compounds and the plant provides them with carbohydrates.
When soils become waterlogged, and therefore short of oxygen, the type of microorganism present changes. Fewer aerobic nitrifying and nitrogen-fixing bacteria are found and there is an increase in anaerobic denitrifying bacteria. These convert soil nitrates into gaseous nitrogen reducing the availability of nitrogen-containing compounds for plants. For land to be productive it must be kept well aerated to prevent the build up of denitrifying bacteria.