Nitrogen use in the soil

The nitrogen fixed by the symbiotic and non-symbiotic bacteria eventually becomes part of the fresh and decaying organic matter in the soil. Most (over 95%) of the soil nitrogen at any one time is in the organic matter, and only a very small percentage (<5%) of this is converted for the use of plants in any one year. Thus turnover of the nitrogen content of organic matter is very slow but vitally important in any one year.

The first stage in preparing the organic nitrogen in the organic matter for use by plants is to transfer it to an inorganic form (by the process of mineralisation. In this process ammonia (NH₃) is formed, most of which quickly forms ammonium (NH₄⁺). The ammonium ion is available to plants and could be the chief way in which forests and grassland receive their supply of nitrogen. It is also an important means of supplying nitrogen to plants in poorly drained and flooded soils.

The ammonium is rapidly converted to nitrate by the process of nitrification. This is a two-stage process by which the ammonia is first converted to nitrite (NO₂) by Nitrosomonas bacteria and the nitrite then converted to nitrate (NO₃) by Nitrobacter bacteria. Nitrification converts the nitrogen to a form that can be used by many plants. Along with the ammonium ions these are the two forms of nitrogen most readily taken up by the natural flora and agricultural crops such as wheat, barley, oats. The rice plant takes up most of its nitrogen in the ammonium form because the 'anaerobic' waterlogged conditions under which paddy rice grows inhibit the nitrification of ammonium.