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Biology toolbox: The role of microbes in the nitrogen cycle

Nitrogen cycle -- ammonification, nitrification, nitrogen fixation, denitrification. The role of microbes in these.
© Rebecca Hall

What is the nitrogen cycle?

The nitrogen cycle is the process by which nitrogen from the atmosphere is converted into nitrate, nitrite and ammonium. Atmospheric nitrogen is abundant but not very useful biologically, as plants cannot use nitrogen in gaseous form. Nitrogen is essential to plants as it is an important component of amino acids and chlorophyll. The nitrogen cycle is therefore key to getting nitrogen in the ecosystem into a usable form.
There are four key stages of the nitrogen cycle:
  • Nitrogen fixation
  • Ammonification
  • Nitrification
  • Denitrification
Bacteria, including symbionts, are vital at all stages.
This figure shows nitrogen cycle showing the role of microbes, plants and animals in cycling nitrogen from the atmosphere into usable nitrate in the soil. The nitrogen cycle involves gaseous nitrogen from the atmosphere being fixed into ammonia and then converted to nitrate, a usable form of nitrogen for plants. Ammonia is also formed via the decomposition of plants and animals. Bacteria are involved at all stages of the nitrogen cycle.

Figure 1. The nitrogen cycle. Gaseous nitrogen from the atmosphere is fixed into ammonia and then converted to nitrate, a usable form of nitrogen for plants. Ammonia is also formed via the decomposition of plants and animals. Bacteria are involved at all stages of the nitrogen cycle.

Nitrogen fixation

During nitrogen fixation, atmospheric nitrogen is converted into nitrates and nitrites. Plants cannot use atmospheric nitrogen until it has been fixed. The majority of nitrogen fixation is performed by bacteria, either free-living (e.g. Azotobacter) or symbiotic (e.g. Rhizobium). These bacteria live in the root nodules of legumes, including beans and peas. They express a nitrogenase enzyme that combines the gaseous, atmospheric nitrogen with hydrogen to produce ammonia. Ammonia is a useful biological molecule as it is an essential part of molecules such as amino acids. The bacteria receive carbohydrates from the legumes in return for the production of ammonia. This is therefore a mutualistic symbiotic relationship. Nitrogen can also be fixed artificially on an industrial scale. This is called the Haber Process and today it is mainly used to make fertiliser. The Haber Process combines atmospheric nitrogen with hydrogen from natural gas, producing ammonia. It involves an iron catalyst to increase efficiency and 200 atmospheres’ pressure.


Ammonia can be also be produced directly by the decomposition of plants and animals, or via the production of waste by animals. This decomposition forms organic nitrogen, which is then converted by bacteria (either aerobic or anaerobic) and fungi into ammonia. This process involves three enzymes:
  • Glutamine synthetase – Converts glutamate and ammonia into glutamine, in an ATP-dependent reaction
  • Glutamate oxoglutarate aminotransferase – Also known as glutamate synthase, this enzyme forms glutamate from glutamine and alpha-ketoglutarate
  • Glutamate dehydrogenase – Converts glutamate into alpha-ketoglutarate and ammonia


Nitrification is the process by which ammonium is converted into nitrite, and then to nitrate. The first step is the conversion of ammonium to nitrite. This is performed by different species of bacteria including Nitrosomonas. These bacteria are widespread in soil, and use electrons from ammonia to generate energy. Species such as Nitrobacter perform the second nitrification step, converting nitrite in the soil into nitrate. Nitrobacter is an obligate aerobe, meaning it needs oxygen to survive.


Denitrification completes the nitrogen cycle. Here, nitrate is converted back into nitrogen gas. This stage of the nitrogen cycle is anaerobic, meaning it is performed in the absence of oxygen. When soils become waterlogged, the amount of oxygen available in the soil decreases. This allows denitrification to occur, catalysed by facultative anaerobic bacteria. Facultative anaerobes can respire aerobically but also use anaerobic respiration when there is no oxygen available. Pseudomonas aeruginosa is one such species of denitrifying bacteria. Denitrification reduces the amount of biologically accessible nitrogen available to the plants.
You will learn about how the nitrogen cycle is important in an agricultural setting during Beasts week!
© Rebecca Hall
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