The nitrogen cycle in agricultural soils

Why nitrogen needs a cycle

About 78 per cent of air by volume is nitrogen gas, N₂. Its triple bond makes it unusable to plants and animals. A crop takes up nitrogen almost entirely as two small ions dissolved in the soil water: ammonium (NH₄⁺) and nitrate (NO₃^-).

Nitrogen in a soil is therefore always in one of three pools:

• Organic nitrogen in crop residues, manure, microbial cells and humus. This is by far the largest pool in most soils, often more than 95 per cent of the total, but plants cannot use it until microbes break it down.
• Mineral nitrogen, the ammonium and nitrate a root can absorb. It is small, it changes from week to week, and it is the pool that fertiliser adds to.
• Gaseous nitrogen: N₂ in the soil air, and the gases lost from it (ammonia, nitrous oxide).

Getting nitrogen into the soil: fixation

Fixation means converting N₂ into ammonia. Three routes matter.

Biological fixation. Certain bacteria and archaea carry the enzyme nitrogenase, which reduces N₂ to ammonia. The reaction is expensive: about 16 molecules of ATP for every molecule of N₂ fixed. Nitrogenase is also destroyed by oxygen, so fixing organisms protect it in different ways.

• Symbiotic fixation in the root nodules of legumes, by rhizobia (Rhizobium, Bradyrhizobium, Mesorhizobium and related genera). The plant supplies sugars; the nodule supplies ammonia. Inside the nodule, leghaemoglobin binds oxygen tightly, which is why an active nodule is pink or red inside.
• Associative and symbiotic fixation by cyanobacteria, such as Anabaena living inside the small water fern Azolla, used for centuries in paddy rice in East and South-East Asia.
• Free-living fixation by bacteria such as Azotobacter (aerobic) and Clostridium (anaerobic), which adds far less.

A healthy legume crop commonly fixes tens to a few hundred kilograms of nitrogen per hectare in a season, depending on species, inoculation, soil nitrate and moisture. A legume growing in soil rich in nitrate fixes less, because it can take up the nitrate more cheaply.

Industrial fixation. The Haber–Bosch process combines N₂ with hydrogen over an iron catalyst at high temperature and pressure to make ammonia, the starting point of nearly all nitrogen fertiliser. It now fixes roughly as much nitrogen each year as all natural land ecosystems together.

Lightning adds a little, as nitrogen oxides in rain.

Turning organic nitrogen into plant food: mineralisation

When microbes decompose residues, manure and humus, they release nitrogen as ammonium. This is mineralisation, and the first step, from organic amino groups to ammonium, is often called ammonification. It is carried out by a huge range of bacteria and fungi, and it runs faster in warm, moist, well-aerated soil.

The reverse process is immobilisation: microbes take mineral nitrogen out of the soil solution to build their own cells. Which one wins depends on the carbon-to-nitrogen ratio (C:N) of what they are eating.

So a crop sown into freshly incorporated straw can turn yellow, while a legume green manure (low C:N) behaves like a fertiliser. Immobilised nitrogen is not lost; it returns as the microbes die and decompose.

Ammonium to nitrate: nitrification

In most aerated agricultural soils, ammonium does not stay ammonium for long. Two groups of microbes oxidise it, using it as their energy source:

1. Ammonia oxidisers (bacteria such as Nitrosomonas, and ammonia-oxidising archaea) convert ammonium to nitrite (NO₂^-).
2. Nitrite oxidisers (bacteria such as Nitrobacter and Nitrospira) convert nitrite to nitrate.

Some Nitrospira carry out both steps alone ("comammox", described in 2015). Nitrite rarely builds up, because the second step is normally faster.

Three consequences of nitrification appear again and again in exams:

• It acidifies the soil. Oxidising one ammonium ion releases two hydrogen ions. Years of ammonium-based fertiliser without liming lower soil pH.
• It makes nitrogen mobile. Ammonium is a cation, held on the negatively charged surfaces of clay and humus. Nitrate is an anion, repelled by those surfaces, so it moves freely with water.
• It needs oxygen. Nitrification slows sharply in waterlogged soil, in very acid soil and in cold soil. This is one reason flooded rice paddies hold nitrogen mostly as ammonium.

How the crop takes it up

Roots absorb both ions. Upland crops take up mainly nitrate, because that is what aerated soil contains; paddy rice takes up mainly ammonium. Nitrogen ends up in proteins, chlorophyll and nucleic acids, so a starved crop is pale and yellows on its older leaves first: nitrogen is mobile in the plant and is moved to new growth.

How a field loses nitrogen

Ammonia volatilisation

Urea applied to the soil surface is hydrolysed by the enzyme urease to ammonium carbonate. Around the granule the pH rises, ammonium converts to ammonia gas (NH₃), and it escapes to the air. Losses are greatest on alkaline or calcareous soils, on warm, windy days, on moist surfaces that then dry, and from surface-applied manure. Working urea into the soil, applying it just before rain or irrigation, or using urease inhibitors reduce the loss.

Denitrification

When a soil becomes waterlogged, oxygen runs out within hours to days. Many common bacteria then use nitrate instead of oxygen to respire, reducing it step by step: NO₃^- → NO₂^- → NO → N₂O → N₂. Denitrification needs three things at once: nitrate, little oxygen and available carbon for the bacteria.

The intermediate nitrous oxide (N₂O) matters far beyond the field. Over a hundred years it warms the climate about 270 times more than the same mass of carbon dioxide, and it also damages the ozone layer. Agricultural soils are the largest human source of it.

Leaching

Because nitrate is not held by soil colloids, water moving down through the profile carries it below the roots and into groundwater, drains and streams. Leaching is worst on sandy soils, under heavy rain or over-irrigation, and when nitrate is present in the soil while no crop is growing to take it up, for example after harvest. Nitrate in drinking water is regulated because of the risk to infants; the World Health Organization guideline value is 50 milligrams of nitrate per litre. In surface waters, nitrogen (with phosphorus) drives algal blooms and oxygen-depleted "dead zones".

Managing the cycle on a farm

Good nitrogen management is about keeping the mineral nitrogen pool matched to what the crop can use at each stage, so that little is left for the loss pathways. The practical rules are often summarised as applying the right source, at the right rate, at the right time, in the right place:

• Base the rate on expected yield, soil tests and credits from legumes and manure.
• Split applications to match the crop's fastest growth, and place fertiliser in the soil, not on it.
• Use legumes in rotations, and cover crops to catch nitrate after harvest.
• Avoid waterlogging and over-irrigation, which drive denitrification and leaching.
• Where approved locally, nitrification and urease inhibitors slow the steps that lead to loss.

Questions people ask

Sources

1. Brady, N. C. and Weil, R. R. The Nature and Properties of Soils, 15th edition. Pearson, 2017. Chapter 13, Nitrogen and sulfur economy of soils.
2. Robertson, G. P. and Groffman, P. M. "Nitrogen transformations." In Paul, E. A. (ed.), Soil Microbiology, Ecology and Biochemistry, 4th edition. Academic Press, 2015.
3. Daims, H. et al. "Complete nitrification by Nitrospira bacteria." Nature 528, 504–509 (2015).
4. IPCC. Climate Change 2021: The Physical Science Basis, Working Group I, Chapter 7 (global warming potentials). Cambridge University Press, 2021.
5. World Health Organization. Guidelines for Drinking-water Quality, 4th edition incorporating the first and second addenda. WHO, 2022. Nitrate and nitrite.
6. FAO. Plant nutrition for food security: a guide for integrated nutrient management. FAO Fertilizer and Plant Nutrition Bulletin 16, 2006.

Related on Laisha

More in soil science