Nitrogen: essential but troublesome

Part 1: The natural nitrogen cycle

Author: Marc Siepman. Translation by Marc Siepman. The original can be found here: ‘Stikstof: essentieel maar lastig – deel 1: de natuurlijke stikstofkringloop’). Editor: Frederique Hijink.

Note: this article was written from the perspective of The Netherlands. Although the situation differs greatly from country to country, the trends are global.

Nitrogen is an essential nutrient for all life on Earth, but not all of its forms of nitrogen can be taken up by plants or animals. Nature, in all her complexity, makes sure that the amount of plant available nitrogen is always approximately the same. In part 1 I’ll explain, in a simplified way, how the natural nitrogen cycle works. In part 2 I’ll explain, again simplified, how humans have disturbed the balance and some of the disastrous effects this has.

Caterpillar of the peacock butterfly (Aglais io) on the stinging nettle (Urtica dioica). Photo: Quartl, Attribution-ShareAlike 3.0 Unported.

Various forms

The trouble with talking or writing about nitrogen is that it exists in several forms. In the two parts of this article I will discuss nitrogen gas (dinitrogen), ammonium, nitrate, ammonia and several nitrogen oxides – which are all forms of nitrogen. And then there’s organic nitrogen: nitrogen is the building block of amino acids, which are in turn the building blocks of proteins. Nitrogen can also be found in DNA and chlorophyll. Nitrogen is essential for all life of Earth.

Nitrogen gas

Nitrogen can be found in several forms all over the biosphere, predominantly as nitrogen gas. About 78% of the volume of the atmosphere is nitrogen gas. Some people think that, given this fact, nitrogen cannot be a problem; after all, it’s everywhere and you constantly breathe it in. But nitrogen gas is non-reactive, which means that this form rarely interacts with other elements. Other forms do interact, and that is where the problem lies.

The chemical formula of nitrogen gas is N2: dinitrogen, a molecule consisting of two nitrogen atoms (N), with a triple bond. This strong bond makes it hard to break, it requires a lot of energy to split the molecule into two separate atoms. Free nitrogen atoms are practically non-existent, they always bind immediately to another free nitrogen atom to form nitrogen gas.

Plants and nitrogen

Plants need nitrogen to build proteins. If a plant doesn’t receive enough nitrogen, it will pull nitrogen from the lower leaves, causing them to wilt and turn yellow. This is possible due to the fact that nitrogen is mobile: it can be transported to where it’s needed most. This is true for the plant, but also for the soil.

Trees and shrubs prefer nitrogen in the form of ammonium (NH4+), while all other plants prefer nitrate (NO3). Plants and trees can also use nitrogen from complex molecules, like amino acids and even proteins. To do so, they produce proteases: enzymes capable of breaking down proteins. This enables plants to take up these organic nitrogen sources without the help of microorganisms. The pH at which these proteases work best varies per plant.

For the most part, plants need bacteria to convert nitrogen gas to a form they can take up. This makes bacteria an indispensable actor in the nitrogen cycle.

Nitrogen-fixing bacteria

Nodules on the roots of the cowpea (Vigna unguiculata). Photo: Harry Rose, Creative Commons Attribution 2.0 Generic.

Nitrogen atoms are constantly recycled and can be found in new molecules again and again. In time, they always return to nitrogen gas. For an organism to be able to use it again, the nitrogen gas must first be converted to another form. This conversion is called nitrogen fixing. Before there was life on Earth, all nitrogen was fixed by lightning. Currently this is considered to be no more than 10%. The nitrogen-fixing bacteria, or diazotrophs, are capable of converting nitrogen gas to ammonium (NH4+), which can be taken up by plants. The bacteria use a portion for themselves and the plant (and other organisms) take up the rest.

Nitrogen-fixing bacteria contain the enzyme nitrogenase. This enzyme does the real work, but uses a lot of energy. The energy needed for this process is obtained from the host plant, in the form of carbon compounds.

Under natural conditions, approximately 75% of the nitrogen needed by plants is provided by mycorrhizal fungi, but the fungi do not fix the nitrogen themselves. They obtain it from organic sources.

Legumes team up with nitrogen-fixing bacteria, along with mycorrhizal fungi. These fungi deliver, besides nitrogen, the phosphates needed to store energy. The phosphates are freed from the soil by phoshate solubilising bacteria. A symbiosis is always way more complex than one might think.


The best known nitrogen fixing bacteria are the rhizobia species, which live in symbiosis with a certain type of plant, usually legumes (Leguminosae or Fabaceae). We know this type of bacteria exists for quite some time now: Rhizobium leguminosarum was discovered as early as 1889. Millions of rhizobia bacteria live together in root nodules that the plants produce specially for them by the plant. Examples of legumes are: clover (Trifolium spp.), black locust (Robinia pseudoacacia), peanuts (Arachis spp.), soy (Glycine max), peas (Pisum sativum), vetch (Vicia spp.) and beans (many genera) – simply anything with pods.

Whether they are in fact fixing nitrogen can be tested by cutting a root nodule in two: the inside should be pink or red. This colouration is caused by the protein leghemoglobin that is produced thanks to the symbiosis; it is, as its name indicates, closely related to hemoglobin that gives the characteristic color to our blood. If there are no nodules at all, this is likely caused by the plant not being able to find a suitable symbiont in the soil. The bacteria tend to disappear after four or so years if the plant they prefer to team up with does not grow there. If the plant can’t find its favourite strand of Rhizobium in the soil, less nitrogen will be fixed. It may then be necessary to inoculate the soil with the right bacteria.

In general there is not much leakage of nitrogen into the soil from the plant roots. Also, the plant will contain very little nitrogen once it has produced seeds. The seeds contain lots of proteins, and therefore a lot of nitrogen; for a plant to add nitrogen to the soil, it is required it dies before it starts to produce seeds (i.e. during or before flowering).

Free living nitrogen fixers

Bacteria (or archaea) that live in the root zone of any plant are not true symbionts. They carry names like Azotobacter and Azospirillum (azote is the French word for nitrogen), Beijerincka and Clostridium. It is my view that these bacteria are much more important than Rhizobia-bacteria.

Actinorhizal trees

Actinobacteria called Frankia can form a symbiosis with trees such as alder (Alnus). These bacteria are not very specialised and can live freely in the soil.

The good thing about both the symbionts and the free living bacteria is that they stop fixing nitrogen as soon as the amount of plant available nitrogen is high enough. This means that they cannot produce too much nitrogen.


Ammonium (NH4+) is the preferred form of nitrogen for trees and shrubs. In a healthy forest almost all nitrogen is present in the form of ammonium. The more a soil’s acidity exceeds pH 5, the more of the ammonium will be converted to nitrite (NO2) by bacteria like Nitrosomonas and then to nitrate (NO3) by bacteria like Nitrobacter. This process is called nitrification and the bacteria in question are of course called nitrifying bacteria.

Although it’s a natural process, there are some downsides to nitrification. For example, nitrate, the end product of nitrification, leaches into groundwater, streams or lakes a lot more readily than ammonium, causing eutrophication. I’ll get back to that in part 2.

Over time, nitrification slows down and comes to a halt, because nitrification causes the pH to go down (hydrogen ions are released in the process) – the lower the pH, the less nitrification. Also, the soil becomes more and more dominated by fungi (due to succession). The fungi exude acids that lower the pH. In a healthy forest there should be no leaching of nitrates, therefore it would be a step forward to eat more from perennial plants and trees.


To complete the nitrogen cycle, there needs to be a source of nitrogen gas. The process involved is called denitrification. Denitrifying bacteria are able to convert nitrates to nitrogen gas. They’re facultative anaerobic, which means they can survive in the presence of oxygen but they won’t thrive. These bacteria assist in their own way: they remove excess nitrates from lakes or streams. The ponds created by beaver dams contain a lot of denitrifying bacteria, which typically causes the water downstream to contain about 45% less nitrogen. Wastewater treatment plants make use of these bacteria to remove nitrates from the water.

The nitrogen cycle

By now, you will have an idea of how the nitrogen cycle works. It begins with nitrogen gas, which is fixed by specialised bacteria. The ammonium they create is either taken up by a plant or converted to nitrate and then taken up. If a plant is eaten by an organism, then this organism uses the nitrogen to build proteins. Via the droppings (or mortal remains) of the organism, the nitrogen returns to the soil, where it may be taken up again or nitrified. The last step is denitrification and the escape to the atmosphere as nitrogen gas.

Of course, the nitrogen cycle is far more complex than this. But you can see that there are a number of different mechanisms that ensure the amount of available nitrogen is balanced. In part two I’ll discuss how humans have destabilised this system and that immediate and drastic changes are needed to avert an even more dramatic loss of diversity.

Part 2 can be found here.