The nitrogen cycle is among the most important biogeochemical cycles on Earth, and it is driven almost entirely by microorganisms. Without the biological nitrogen fixation performed by soil bacteria, the global food system would collapse: atmospheric nitrogen (N2, the most abundant gas in the atmosphere at 78 per cent) is biologically unavailable to plants and animals. Bacteria convert it to biologically usable forms (nitrate, ammonium, amino acids). Understanding the nitrogen cycle, the microorganisms that drive each step, and the environmental and agricultural significance of each transformation is essential knowledge in environmental microbiology, agricultural science, and climate science.
The Key Steps of the Nitrogen Cycle
Nitrogen fixation: the conversion of atmospheric N2 to ammonium (NH4+), the primary input of new nitrogen to the biological cycle. Only a small group of prokaryotes (diazotrophs) possess nitrogenase, the enzyme complex capable of breaking the extremely stable N2 triple bond under ambient conditions.
Free-living diazotrophs: Azotobacter (aerobic, soil), Clostridium pasteurianum (anaerobic, soil), Cyanobacteria (Anabaena, Nostoc: fix nitrogen in heterocyst cells under aerobic conditions). These organisms fix nitrogen independently of plants and contribute to the general nitrogen fertility of soil.
Symbiotic diazotrophs: the most agriculturally significant nitrogen fixers are Rhizobium, Bradyrhizobium, Mesorhizobium, and related alpha-Proteobacteria that form symbiotic nitrogen-fixing nodules on legume roots (soybeans, clover, alfalfa, peas, beans). In the nodule, the plant provides carbon (photosynthate) and the Rhizobium provides fixed nitrogen. Legume-Rhizobium symbiosis is estimated to fix approximately 40 million tonnes of nitrogen per year globally, the equivalent of approximately 80 million tonnes of nitrogenous fertiliser.
Frankia: another genus of nitrogen-fixing bacteria forming actinorhizal symbioses with non-legume plants (Alnus/alder, Casuarina, Ceanothus), important for reforestation and revegetation.
Ammonification (mineralisation): dead organic matter (proteins, nucleic acids, urea) is decomposed by heterotrophic bacteria and fungi, releasing ammonium (NH4+). This is the primary mechanism by which nitrogen in organic matter is returned to the inorganic pool for plant uptake. Key organisms: Bacillus, Pseudomonas, Clostridium, Streptomyces (and many fungi: Aspergillus, Penicillium, Rhizopus).
Nitrification: the two-step aerobic oxidation of ammonium to nitrite and then to nitrate. This is a chemoautotrophic process: the bacteria obtain energy from the oxidation of nitrogen compounds rather than from organic carbon.
Step 1 (nitritation): NH4+ to NO2- (nitrite), performed by ammonia-oxidising bacteria (AOB: Nitrosomonas europaea being the most studied) and ammonia-oxidising archaea (AOA: Thaumarchaeota, which are now recognised as quantitatively dominant in many soil environments).
Step 2 (nitratation): NO2- to NO3- (nitrate), performed by nitrite-oxidising bacteria (NOB: Nitrospira, Nitrobacter). Recently discovered "comammox" Nitrospira strains perform both steps simultaneously (complete ammonia oxidation).
Nitrification converts ammonium (cationic, adsorbed to negatively charged soil particles) to nitrate (anionic, mobile in soil water), increasing the risk of nitrogen leaching from agricultural soils into waterways (contributing to eutrophication).
Denitrification: the anaerobic reduction of nitrate and nitrite to gaseous nitrogen (N2O, NO, and N2), returning fixed nitrogen to the atmosphere. Performed by facultative anaerobic heterotrophs (Pseudomonas denitrificans, Paracoccus denitrificans, Bacillus licheniformis, Thiobacillus denitrificans) under anaerobic or low-oxygen conditions, using nitrate as an electron acceptor instead of oxygen.
Denitrification is the primary nitrogen loss pathway from agricultural soils and contributes to greenhouse gas emissions (N2O is a potent greenhouse gas with a global warming potential 273 times that of CO2 over 100 years, and is also the dominant ozone-depleting substance emitted in the current century).
Anaerobic ammonium oxidation (Anammox): discovered in 1999, Anammox is the anaerobic oxidation of ammonium with nitrite as electron acceptor, producing N2 directly. Performed by Planctomycetes (Candidatus Brocadia, Kuenenia, etc.). Anammox is now recognised as responsible for approximately 50 per cent of global oceanic nitrogen loss and is increasingly used in wastewater treatment for energy-efficient nitrogen removal.
Soil Microbiome and Antibiotic Discovery
Soil Streptomyces species have been the source of most clinically used antibiotics: streptomycin, tetracycline, erythromycin, chloramphenicol, vancomycin, rifampicin, and the aminoglycosides were all isolated from Streptomyces. The discovery era (1940s to 1960s) was driven by systematic screening of soil Streptomyces isolates. Over 50 per cent of all natural product antibiotics and most antifungals originate from soil actinobacteria.
Modern metagenomics is reviving this discovery tradition: sequencing of soil metagenomes reveals enormous biosynthetic gene cluster diversity encoding novel natural products that cannot be cultured using standard laboratory methods. The "uncultured majority" of soil bacteria (estimated at 99 per cent of all soil bacterial species have never been grown in laboratory culture) represents an untapped reservoir of potential new antibiotics.
Frequently Asked Questions
What is nitrogen fixation?
Nitrogen fixation is the biological conversion of atmospheric N2 to ammonium (NH4+), making nitrogen available to living organisms. It requires the enzyme nitrogenase and is performed exclusively by prokaryotes (diazotrophs), including free-living soil bacteria (Azotobacter, Clostridium, cyanobacteria) and symbiotic bacteria in plant root nodules (Rhizobium with legumes, Frankia with actinorhizal plants).
What is the Rhizobium-legume symbiosis?
Rhizobium species (and related genera: Bradyrhizobium, Mesorhizobium, Sinorhizobium) form symbiotic nitrogen-fixing root nodules on legume plants (soybeans, clover, peas, beans, alfalfa). The bacteria fix atmospheric N2 to ammonium, which the plant uses for protein synthesis. The plant provides carbon compounds (photosynthate) to the bacteria. This symbiosis contributes approximately 40 million tonnes of fixed nitrogen per year globally.
What is nitrification?
Nitrification is the two-step aerobic microbial oxidation of ammonium (NH4+) to nitrite (NO2-) by ammonia-oxidising bacteria/archaea (Nitrosomonas, Thaumarchaeota), and then nitrite to nitrate (NO3-) by nitrite-oxidising bacteria (Nitrospira, Nitrobacter). Nitrification makes nitrogen more available to plants (as nitrate) but also increases the risk of nitrogen leaching from soils into waterways.
What is denitrification?
Denitrification is the anaerobic reduction of nitrate and nitrite to gaseous nitrogen (N2O, NO, N2) by facultative anaerobic bacteria, under conditions of low oxygen. It is the primary mechanism returning fixed nitrogen to the atmosphere. Denitrification causes nitrogen losses from agricultural soils and produces nitrous oxide (N2O), a potent greenhouse gas.
What is nitrous oxide (N2O) and why is it important?
Nitrous oxide is a greenhouse gas produced by soil denitrifying bacteria and nitrifiers (as a by-product). It has a global warming potential 273 times greater than CO2 over 100 years and is the dominant ozone-depleting substance currently emitted by human activities. Agricultural nitrogen fertiliser application is the largest global source of N2O emissions, making the nitrogen cycle a key concern in climate change.
What are ammonia-oxidising archaea (AOA) and why are they important?
AOA (Thaumarchaeota) were discovered in 2005 and are now recognised as quantitatively dominant over bacterial ammonia oxidisers (AOB) in most soil environments, particularly in nutrient-poor (oligotrophic) soils and marine environments. They have a very high affinity for ammonium, allowing them to nitrify at very low ammonium concentrations. AOA are estimated to be among the most abundant organisms on Earth.
What is Anammox?
Anaerobic Ammonium Oxidation (Anammox) is the microbial process by which ammonium is oxidised with nitrite as the electron acceptor under anaerobic conditions, producing N2 gas. Performed by Planctomycetes. Anammox is estimated to be responsible for 40 to 50 per cent of nitrogen loss from oceanic oxygen minimum zones and is increasingly used in wastewater treatment as an energy-efficient nitrogen removal process (requiring no aeration or carbon source).
What are mycorrhizal fungi and how do they relate to soil microbiology?
Mycorrhizal fungi form symbiotic associations with plant roots, extending the root's effective surface area by orders of magnitude through their hyphal network. Arbuscular mycorrhizal fungi (AMF, Glomeromycota) are the most widespread, forming symbioses with approximately 70 to 80 per cent of terrestrial plant species. They improve plant access to phosphorus (which is relatively immobile in soil), nitrogen, and water, in exchange for carbon from the plant. The mycorrhizal network connects individual plants and mediates resource sharing in ecosystems.
Why is soil the source of most antibiotics?
Soil-dwelling Streptomyces and other actinobacteria produce antibiotics as secondary metabolites in the context of microbial competition in soil. Competition for space and nutrients is intense, and antibiotic production provides a competitive advantage against microbial competitors. Systematic screening of soil Streptomyces in the 1940s to 1960s led to the discovery of most of the antibiotic classes in clinical use today. Soil remains an important source of novel antibiotic discovery through culture-independent metagenomic approaches.
What is the connection between the nitrogen cycle and water quality?
Nitrate leached from agricultural soils into rivers, lakes, and coastal waters causes eutrophication: algal blooms, oxygen depletion (hypoxia), and death of aquatic organisms. Excessive ammonium in drinking water is toxic. The EU Nitrates Directive and US Clean Water Act regulate nitrate concentrations in water bodies. In agricultural management, nitrogen use efficiency (maximising crop uptake relative to application) and precision agriculture approaches aim to reduce nitrate leaching.