The nitrogen cycle is a group of biogeochemical processes that harvest the element (nitrogen) from the Earth’s reservoirs, transform it into biologically active chemical forms so that organisms in the ecosystem can consume and reap benefits before returning the element to its sources.

The chemical transformation in each nitrogen cycle step redistributes nitrogen between the environment and organisms in the ecosystem. In doing so, organisms can use naturally available nitrogen while the nitrogen content in the global environment remains unchanged. Over time, the nitrogen cycle can gradually shape and change the structure and composition of the ecosystem.

Nonetheless, human activities in the past centuries have dramatically increased nitrogen content. Moreover, the non-natural nitrogen input disturbs the global nitrogen cycle and negatively impacts the global climate and Earth’s ecosystems.

What is Nitrogen?

Nitrogen (N) is one of the fundamental elements of life on Earth, constituting a functional group in biomolecules such as proteins, nucleic acids, and chlorophylls.

It exists in various chemical forms and redox states. In living organisms, nitrogen exists as organic nitrogen (R-NH3).

Most nitrogen on Earth, however, is from inorganic sources. Small fractions are sporadically distributed in various forms on the Earth’s surface, such as in soils, ocean floors, rocks, and sediments. Most inorganic nitrogen is in the form of an inert, colorless, odorless, and tasteless gas called dinitrogen (N2) found in the atmosphere.[1]  

What Happens in the Nitrogen Cycle?

The nitrogen cycle allows organisms to consume and use nitrogen in the environment before returning it to Earth’s reservoirs.

It consists of a series of redox reactions that transform nitrogen into various chemical forms so that it is biologically available. Here, nitrogen is transferred from the environment to the organisms and moved from one location to another without increasing or reducing the size of the global nitrogen content.[1]

Hence, the amount of nitrogen in the nitrogen cycle at a specific location is viewed as a budget. The input refers to the acquisition and transformation of non-reactive nitrogen into a biologically available form, called fixed N.

The output refers to the nitrogen released to the environment. Between the input and output is the internal cycling of nitrogen, consisting of several reactions that take place in microorganisms, plants, and animals.[2,3]

Steps in the Nitrogen Cycle

The nitrogen cycle occurs when free oxygen is present (oxic condition) or when it is in short supply (anoxic condition).[1,3]

The nitrogen cycle comprises the following steps:[2]

1. Nitrogen Fixation

Nitrogen fixation is the input of nitrogen in the cycle. Here, the least reactive nitrogen form, N2, is acquired from the atmosphere and subsequently reduced to chemically reactive forms such as ammonia, nitrate, or nitrite, collectively called fixed N. Nitrogen fixation occur in the following processes:
  • Chemical processes taking place in the troposphere such as cosmic radiation and lightning provide the electrical energy that transforms the inert N2 into chemically reactive form, which is often in the form of NOx.[3]
  • Biological processes are enzymatic reactions in specialized archaea and prokaryotes, called nitrogen fixers or diazotrophs, for example, Rhizobium and Acetobacter.
    Diazotrophs fix N2 in the atmosphere, and the fixed N is subsequently transformed into ammonia so that it can be assimilated into biomolecules, as summarized in the following equation:

N2 + 8H+ + 8e  —>  2NH3 + H2

  • The reaction is endergonic and highly unfavorable due to the tremendous amount of free energy that it requires. In the laboratory, the reaction occurs at more than 400℃ and 300 bars, even with metal catalysts.

    In diazotrophs, nitrogenase complexes, consisting of enzymes nitrogenase and nitrogen-reductase, are used to fix and transform atmospheric nitrogen.

  • Anthropogenic nitrogen fixation is the non-naturally occurring fixed N from human activities such as mass combustion in transport and production industries, and soil fertilization in agricultural sectors.
    Fixed N from industrial activities are mostly oxidized nitrogen gasses such as nitric oxide (NO) and nitrogen dioxide (NO2), while those from fertilization activities are nitric oxide, nitrate (NO3), and ammonia (NH3).[3]
An illustration on how nitrogen is fixed in the nitrogen cycle
Credit: Bioninja[5]

2. Assimilation

Immediately after fixation, the fixed nitrogen is assimilated by organisms such as bacteria, fungi, algae, and plants, transforming inorganic nitrogen into organic nitrogen (R-NH3) that the organisms can use in their anabolic processes.[1,4]  

Plants and microorganisms can absorb nitrate (NO3), ammonium (NH4+), and ammonia dissolved in water. Most are found in soils, ocean beds, or acquired from nitrogen fixers.[1,2]   

In the case of nitrate, it is first reduced into nitrite (NO2), which is further reduced to ammonium. The first reaction is catalyzed by the enzyme nitrate reductase and nitrite reductases, respectively. Ammonium is subsequently incorporated into amino acids as an amino group (NH3+).[4]   

The nitrogen cycle’s central players in the nitrogen assimilation step are the enzymes glutamine synthetase (GS) and glutamate synthase, which is also named glutamine oxoglutarate aminotransferase (GOGAT).

GS catalyzes the incorporation of an amino group into glutamate, resulting in glutamine. GOGAT catalyzes the glutamine’s reversion to glutamate, a substrate for the synthesis of other amino acids, including ɑ-ketoglutarate, an intermediate in the Krebs cycle.[1,2]

3. Ammonification

Also known as mineralization, it converts organic nitrogen (R-NH3) into inorganic nitrogen such as ammonia or ammonium.[2] 

Ammonification occurs when nitrogenous compounds in plant and fungal remains, animal corpses, and excretion decompose. It results in the breakdown of proteins, amino acids, and genetic materials, subsequently hydrolyzed by proteolytic enzymes.

Ammonification in terrestrial ecosystems is largely carried out by plants, fungi, and small animals. In marine ecosystems, it is facilitated by non-photosynthetic microorganisms. The resulting ammonia is used to assimilate nitrogen-containing compounds, increasing the biomass. It can also be oxidized to nitrate during nitrification.[1,2] 

Under anoxic conditions, ammonium can be converted from nitrate or nitrite in dissimilative nitrate/nitrite reduction to ammonia (DNRA). It is present in many nitrogen-reducing bacteria and fungi in ocean sediments, ocean shores, human gastrointestinal tracts, and wastewater plants.[1,2] 

4. Nitrification

In nitrification, ammonium is oxidized to nitrate (NO3) in a series of redox reactions. It takes place at neutral to slightly alkaline pH in terrestrial and aquatic ecosystems.

The oxidation of ammonium to nitrate comprises two steps:[1,4] 

  • The oxidation of ammonium into nitrite (NO2), which converts ammonium into This results in hydroxylamine, which is oxidized into nitrite, together with the reduction of oxygen to water. Thus, the reactions in the first step can be summarized into:

2NH3 + 3O2    —>   2NO2–  + 2H+ + 2H2O

  • The oxidation of nitrite into nitrate (NO3) is coupled with the reduction of oxygen to water, which are:
    The oxidation of nitrite:

NO2  +  H2O   —>   NO3  +  2H+  +  2e

The reduction of oxygen:

O2  +  4H+  +  4e   —> 2H2O

Both are summarized into the following redox: 

2NO2  +  O2   —>   2NO3

Most aerobic microbes can perform only one step of nitrification. Only a specific group of microorganisms called Complete Ammonia Oxidizers (COMAMMOX) can carry out both nitrification steps.

5. Denitrification

In this step, nitrate (NO3) is reduced to dinitrogen (N2) and released into the atmosphere. It is the last step of the nitrogen cycle and is considered the output of the cycle.[1,4]    

When the oxygen level is insufficient, nitrate is used as the terminal electron acceptor in denitrifiers’ cellular respiration. Subsequently, nitrate is sequentially reduced to dinitrogen (N2), illustrated as follows:

NO3  —> NO2  —>  NO  —>  N2O  —>  N2

Complete reduction of nitrate involves several enzymes like nitrate reductase, nitrite reductase, nitrous oxide reductase, and nitric oxide reductase.[1]

An incomplete suite of nitrate reductase enzymes is the reason that many denitrifiers cannot fully reduce nitrate, leading to the release of the two intermediates, nitric oxide (NO) and nitrous oxide (N2O), into the atmosphere.

Nitrogen gas can come from anaerobic ammonium oxidation (ANAMMOX)

In addition to denitrification, anaerobic ammonium oxidation, or ANAMMOX, can produce dinitrogen gas (N2) that serves as the output of the nitrogen cycle.

Here, the oxidation of ammonium (NH4+) to N2 occurs in conjunction with the reduction of nitrite (NO2), as illustrated in the summarized equation:

NH4+  +  NO2   ⇌  N2 +  2H2O

ANAMMOX is carried out by autotrophic Planctomycetes species, which are found in marine sediments and wastewater plant sludge.[1,2]

Illustration on a the nitrogen cycle step, denitrification

The Importance and Impact of the Nitrogen Cycle

1. The nitrogen cycle can increase the rate of primary production

Nitrogen is considered one of the limiting factors in primary production. Atmospheric nitrogen fixation, the subsequent transformation, and the internal cycling steps enable autotrophs to use nitrogen that may not be readily accessible in the environment.

In this process, the nitrogen cycle also allows the element to be redistributed to areas where nitrogen is limited. Plants, microorganisms, and animals that participate in one of the nitrogen cycle steps can mobilize the element from nitrogen-rich to nitrogen-limited areas.

For example, degraded soils are often first colonized by legumes and actinorhizal plants that form mutualistic symbiosis relationships with nitrogen-fixing bacteria.

In this symbiosis relationship, the bacteria fix nitrogen from the atmosphere and provide it to the plants. As a result, the plants can use the fixed N to produce food, which initiates subsequent biochemical reactions that increase the soil organic matter, restoring the soil in the process.[4] Read more about soil biology here.

2. Nitrogen cycle alter the ecological structure and compositions

Several nitrogen cycle steps influence the structure and species composition of the ecosystem. Fixed N can be transformed and cycled back and forth between the environment and the organisms that interact with it, initiating several processes that can alter ecosystems. For instance,
  • Acidification of the environment from excessive soil fertilization can lead to an increase in The oxidation of ammonium to nitrate decreases the pH, which increases mineral solubility. Here, plants and microorganisms can benefit from increased nutrients, but a long-term acidification can reduce soil fertility due to increased leaching.[1,2]
  • Eutrophication describes the uncontrollable growth of aquatic autotrophs, commonly referred to as algal blooms.
    Imbalances in the rate of nitrogen fixation, ammonification, nitrification, and incomplete denitrification can lead to excessive accumulation of nitrogen in the surface and water bodies that autotrophs can assimilate and use for their growth and development. Once bloomed, the number of aquatic organisms increases due to the biomass from overgrown algae. Consequently, dissolved oxygen is used up by these organisms, leading to the formation of dead zones where aquatic organisms suffocate due to the lack of oxygen. Eventually, anaerobic bacteria will dominate, and a more suitable species may start to occupy the site.[2,3]

3. It shapes the global climate

Due to alterations in the structure and species composition of the ecosystems, the disparity in the nitrogen cycle steps can affect the global climate. How?

For example, nitrous oxide (N2O) produced from nitrification and incomplete denitrification is a greenhouse gas. The gas can be reduced to dinitrogen in the atmosphere, but excessive gas can interact with photons, transforming to nitric oxide, thus damaging the ozone layer. This reduces the ability of the Earth’s stratosphere to insulate heat while absorbing ultraviolet rays.[1,2]

4. It is the basis for wastewater treatment technologies

Molecular mechanisms of ANAMMOX and the denitrification step of the nitrogen cycle are the basis for biotechnological solutions to wastewater.

Denitrification and ANAMMOX involve the microbial conversion of ammonium and nitrate to the chemically inert dinitrogen gas, which can be released to the environment without causing immediate harm.

For this reason, either process is applied to eliminate excess nitrogen from drinking water and develop new wastewater treatment systems, which have the potential to eradicate problems arising from acidification and eutrophication.[1]    


The nitrogen cycle is a series of bio- and geo-chemical reactions that transform nitrogen and cycle it through the environment and organisms in the ecosystem. It enables organisms to acquire and use the element without depleting the global nitrogen content.

This cycle can gradually influence the life of organisms and the ecosystems they inhabit. Along the same line, human activities that overburden any nitrogen cycle steps can lead to environmental problems that devastate the ecosystems.

Nonetheless, some steps in the nitrogen cycle are applied to treat wastewater, which can be the key to addressing human-influenced environmental concerns.


  1. Gonzalez-López J and Gonzalez-Martinez A. Nitrogen Cycle Ecology, Biotechnological Applications and Environmental Impacts. CRC PRESS, 2021.
  2. Zhang X, Ward BB, and Sigman DM. 2020 Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics. Chem Rev 12: 5308-535.  
  3. Fowler D et al. 2013 The global nitrogen cycle in the twenty-first century. Phil Trans R Soc B 368: 20130164.
  4. Bothe H, Ferguson SJ, and Newton WE. Biology of the Nitrogen Cycle. Elsevier, 2007.
  5. Bioninja. 2022. Nitrogen cycle. [ONLINE] Available at: [Accessed 26 March 2022].