Nitrification

The use of nitrogen-containing fertilizers in agriculture has a strong influence on nitrification and on the nitrogen cycle more broadly. Rates of fertilization in intensive agricultural systems often exceed 500 kg of nitrogen per hectare per year. Much of the nitrogen addition occurs as ammonia or ammonium which is the substrate for nitrification, so this process can occur very rapidly, and nitrate may be present in large concentrations.

If soils with large nitrate concentrations become wet and anaerobic conditions develop, the rate of denitrification is greatly increased. Denitrification represents a loss of fixed nitrogen capital, and the emitted nitrous oxide (N₂O) may contribute to an enhancement of Earth's greenhouse effect.

If the availability of nitrate overwhelms the ability of the plant crop and soil microbes to assimilate this nutrient, some of the nitrate will leach from the site into groundwater and surface waters such as streams and rivers. This can contribute to the increased productivity of surface waters through eutrophication. In addition, large concentrations of nitrate in groundwater are of great concern for several reasons. Nitrate can react with amino compounds to form nitrosamines, which are poisonous and carcinogenic. Nitrate itself is not particularly toxic, but it can be chemically reduced in the gut of animals to form toxic nitrite. This reaction occurs especially rapidly in the relatively alkaline gut of infant humans, so they are especially sensitive to nitrite poisoning if they drink well waters with large concentrations of nitrate. Nitrite combines with hemoglobin in the blood, forming a relatively stable complex that is therefore not available to transport oxygen and carbon dioxide and resulting in a toxic condition known as the "blue baby" syndrome. Cattle and sheep can also be poisoned by excessive exposures to nitrate, because nitrites are also readily formed by bacteria in their rumen.