The microbial nitrogen-cycling network

Key Points

  • Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet. Its availability depends on diverse nitrogen-transforming reactions that are carried out by microorganisms.

  • Nitrogen-transforming microorganisms are metabolically versatile, rendering their classification as mere nitrifiers, denitrifiers and similar classes inadequate.

  • The classical nitrogen cycle consisting of distinct processes that follow each other in an orderly fashion does not exist. In nature, microorganisms form complex networks that link nitrogen-transforming reactions.

  • Microbial nitrogen-transforming networks both attenuate and exacerbate human-induced global change. They produce and consume the powerful greenhouse gas nitrous oxide, lead to eutrophication of aquatic systems and, at the same time, remove nitrogen from wastewater.

  • There are still many undiscovered nitrogen-transforming reactions that are thermodynamically feasible. The microorganisms catalysing these reactions and the involved biochemical pathways are waiting to be discovered.


Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet. By far, the largest inventory of freely accessible nitrogen is atmospheric dinitrogen, but most organisms rely on more bioavailable forms of nitrogen, such as ammonium and nitrate, for growth. The availability of these substrates depends on diverse nitrogen-transforming reactions that are carried out by complex networks of metabolically versatile microorganisms. In this Review, we summarize our current understanding of the microbial nitrogen-cycling network, including novel processes, their underlying biochemical pathways, the involved microorganisms, their environmental importance and industrial applications.

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Figure 1: Microbial transformations of nitrogen compounds.
Figure 2: Enzymes catalysing four key nitrogen-cycling reactions.
Figure 3: Potential nitrogen-transforming microbial networks in different ecosystems.


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The authors thank W. Mohr and J. Milucka (Max Planck Institute for Marine Microbiology, Bremen, Germany) for discussions. This work was supported by the Max Planck Society (MPG) and the European Research Council Grant 640422 to B.K.

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M.M.M.K., H.K.M. and B.K. researched data for the article, made substantial contributions to discussions of the content, wrote the article and reviewed and edited the manuscript before submission.

Corresponding author

Correspondence to Marcel M. M. Kuypers.

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The authors declare no competing financial interests.

PowerPoint slides



The electron-donating compounds in a redox reaction.

Oxygenic phototrophs

Organisms that obtain energy from light and use water as the electron donor, forming molecular oxygen and sugar as products.


Special cells in animals that contain endosymbiotic bacteria.


The phylum that contains the ammonia-oxidizing archaea.


The propensity of organisms to grow in acidic environments (pH <6).


Organisms that oxidize methane to conserve energy.


A candidate bacterial phylum, named after the Nullarbor Caves in Australia, that contains 'Candidatus Methylomirabilis oxyfera', which is the first organism discovered that performs methane oxidation coupled to oxygenic denitrification.


A reaction that requires energy input.


A bacterial phylum with only a few described species, some of which appear to be important in the methane cycle.

Anoxygenic phototrophs

These microorganisms obtain energy from light and use compounds such as hydrogen sulfide instead of water as an electron donor and thus do not produce molecular oxygen.


An increased input of nutrients that leads to excessive growth of algae or cyanobacteria.

Proton motive force

Proton dislocation creates a difference of charge and pH between two sides of a cell membrane and thereby generates an electrochemical potential, which is used for energy conservation.

Anaerobic sludge digesters

Bioreactors in which excess microbial biomass (sludge) produced during wastewater treatment is anaerobically converted to carbon dioxide, methane, ammonium and reduced sulfur compounds.

Primary nitrite maxima

The peak in nitrite concentrations at the base of the euphotic zone.

Nitric oxide dismutation

Two molecules of nitric oxide are disproportionated into one molecule of molecular oxygen and one molecule of dinitrogen gas.


A chemical reaction in which two reactants containing the same element with a different oxidation state react to create a product with a single oxidation state.


A bacterial organelle found in anaerobic ammonium oxidizing (anammox) bacteria that is the only known prokaryotic membrane-bound structure that is equally divided into daughter cells upon cell division.


A reaction that results in the release of free energy.


A chemical reaction in which a reactant is split into two species containing the same element with different oxidation states, one more oxidized and the other more reduced than the reactant.

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Kuypers, M., Marchant, H. & Kartal, B. The microbial nitrogen-cycling network. Nat Rev Microbiol 16, 263–276 (2018).

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