The Nitrogen Cycle

How it works and how we've changed it

Without the nitrogen cycle, there would be no life as we know it. Plants can’t grow without nitrogen. And if plants don’t grow, neither do we. Nitrogen is the fourth most common element in your body. It’s in your muscles, your DNA, your food, and your breath. Every bite of food you eat, every breath you take, depends on this cycle functioning well. When it’s in balance, it feeds the world. When it’s out of balance, it poisons it. It's one of Earth’s essential life-support systems.

The nitrogen cycle is the natural process by which nitrogen moves between the atmosphere, soil, water, and living organisms. Although nitrogen gas (N₂) makes up about 78% of Earth’s atmosphere, most living things can't use it in that form. Natural processes and specialized microbes convert atmospheric nitrogen into usable forms like ammonium (NH₄⁺) and nitrate (NO₃⁻), which plants absorb through their roots. Animals, in turn, obtain nitrogen by eating plants or other animals. When organisms die or excrete waste, decomposers return nitrogen to the soil, where it can be reused or eventually converted back into nitrogen gas and released into the atmosphere.

This cycle is essential because nitrogen is a key building block of proteins, DNA, and other vital molecules. Without it, life couldn’t exist. But human activities—especially fertilizer use and fossil fuel combustion—have overloaded the nitrogen cycle, causing pollution, ecosystem damage, and climate impacts. Maintaining a balanced nitrogen cycle is vital for food production, clean water, and a stable climate.

The main nitrogen transformations—fixation, nitrification, ammonification, assimilation, denitrification, and anammox—are essential to life on Earth. These processes depend on diverse microbes, including bacteria, archaea, and fungi, which drive changes in nitrogen’s oxidation states and support the biosphere.

Plants absorb nitrogen primarily in two forms: ammonium (NH₄⁺) and nitrate (NO₃⁻). Nitrate tends to dominate in well-aerated, oxygen-rich soils because it's the end product of nitrification, a microbial process that requires oxygen. It's also more mobile in water in the soil, making it more accessible to plant roots.

Ammonium is more stable in acidic or waterlogged soils where oxygen is limited and nitrification slows down. As a result, plants adapted to such environments, like rice and many wetland species, often rely more heavily on ammonium.

Agricultural crops such as corn, wheat, and tomatoes typically use both forms but lean toward nitrate when it is available. Some forest species, including conifers, favor ammonium.

On average, plants absorb about 60–70% of their nitrogen as nitrate and 30–40% as ammonium, though this ratio varies depending on soil pH, moisture, microbial activity, and plant type. While many plants prefer nitrate, most are flexible and adjust their uptake based on what the environment provides.

But the nitrogen in the air (N₂) is unusable by plants, so microbes need to convert atmospheric nitrogen into nitrate and ammonium. There are several species and steps involved.

Fixation

N₂ → NH₃

specifically,

N₂ + 8 H⁺ + 8 e⁻ → 2 NH₃ + H₂

To "fix" nitrogen means to convert atmospheric nitrogen into biologically available nitrogen by breaking the triple bond of N₂ and turning N₂ into ammonia (NH₃). Because N₂ has a strong triple bond, breaking it requires a lot of energy (941 kJ/mol of N₂). Nitrogen fixation is an exclusive ability of certain prokaryotes. Some of these organisms live freely in the soil, while others form symbiotic relationships with plants.

Legume plants (Fabaceae family) such as peas, clover, and soybeans release chemical compounds from their roots that act as signals to attract specific nitrogen-fixing bacteria like Rhizobium. In response, these bacteria move toward the root, and a highly coordinated interaction begins that results in their entry into the root tissue and the formation of nodules—specialized structures where nitrogen fixation takes place. These bacteria fix nitrogen in exchange for carbon from the plant. Legume plants can take the form of small herbaceous plants, bushes, or huge trees such as acacia, mesquite, and locust.

I grow clover in my garden to fix nitrogen for my other plants and trees. Notice the Rhizobium root nodules.

Actinorhizal plants, like alders and bayberries, associate with Frankia bacteria. Some aquatic plants, such as Gunnera, form symbioses with cyanobacteria like Nostoc. Lichens are symbiotic organisms that often involve a fungus and a nitrogen-fixing cyanobacterium. Some contribute fixed nitrogen to ecosystems, especially in early successional or nutrient-poor environments, which allows other plants to get established.

Nitrogen-fixing bacteria and archaea vary widely. Some require oxygen, while others thrive without it. Some harness energy from light (phototrophic), while others rely on chemical reactions (chemotrophic). Despite this diversity in form and function, all of them use a shared enzyme complex called nitrogenase, which enables the conversion of atmospheric nitrogen gas (N₂) into ammonia (NH₃).

Genus (Nitrogen Fixing)	Phylogenetic Affiliation	Lifestyle
Nostoc, Anabaena	Bacteria (Cyanobacteria)	free-living, aerobic, phototrophic
Pseudomonas, Azotobacter, Methylomonas	Bacteria	free-living, aerobic, chemoorganotrophic
Alcaligenes, Thiobacillus	Bacteria	free-living, aerobic, chemolithotrophic
Methanosarcina, Methanococcus	Archaea	free-living, anaerobic, chemolithotrophic
Chromatium, Chlorobium	Bacteria	free-living, anaerobic, phototrophic
Desulfovibrio, Clostridium	Bacteria	free-living, anaerobic, chemoorganotrophic
Rhizobium, Frankia	Bacteria	symbiotic, aerobic, chemoorganotrophic

Ammonification

Organic N → NH₃

When plants and animals die, the nitrogen in their bodies, contained in proteins, nucleic acids, and other organic compounds, is converted into ammonia (NH₃) by decomposer microorganisms. These decomposers include a wide range of bacteria (Bacillus, Clostridium, Pseudomonas, Proteus, Actinomycetes) and fungi (Aspergillus, Penicillium, Mucor, Fusarium) that break down organic matter in soil and aquatic environments.

These organisms digest proteins, nucleic acids, and other nitrogen-containing compounds from dead plants, animals, and waste, releasing ammonia (NH₃). The released ammonia often becomes ammonium (NH₄⁺) in the presence of water. Without ammonification, nitrogen would remain locked in dead organic material, unavailable to living organisms. It also prevents corpses and feces from piling up everywhere, so that's good.

Note: Soil pH affects nitrogen uptake by shifting the balance between ammonium (NH₄⁺), which plants can absorb, and ammonia (NH₃), which is less accessible and can be toxic. In acidic to neutral soils, nitrogen stays mostly in the usable ammonium form, while in alkaline soils, more nitrogen converts to ammonia, reducing availability and increasing loss to the air.

Nitrification

NH₃ → NO₂⁻ → NO₃⁻

NH₃ + O₂ + 2 e⁻ → NH₂OH + H₂O

NH₂OH + H₂O → NO₂⁻ + 5 H⁺ + 4 e⁻

then,

NO₂⁻ + ½ O₂ → NO₃⁻

Once N₂ is fixed into ammonia, plants still can't use it. The ammonia then needs to be converted into nitrate (NO₃⁻) in a two-step process called nitrification. In the first step, ammonia-oxidizing bacteria and archaea convert ammonia to nitrite (NO₂⁻) using the enzymes ammonia monooxygenase and hydroxylamine oxidoreductase. This process releases only a small amount of energy, so these microbes grow slowly. They are also autotrophs, using ammonia as an energy source to fix carbon dioxide.

The actual substrate for microbial oxidation is ammonia (NH₃), not ammonium (NH₄⁺). However, in most soils and natural environments, NH₄⁺ is the dominant form due to its stability in water. These two forms exist in equilibrium, and microbes rely on the small amount of NH₃ that is naturally released from NH₄⁺, depending on the pH. The key enzyme that initiates nitrification—ammonia monooxygenase—acts specifically on NH₃. So while ammonium is the more abundant form in the environment, it's the NH₃ derived from it that microbes use to begin the conversion to nitrite.

The second step is performed by nitrite-oxidizing bacteria, which convert nitrite (NO₂⁻) to nitrate (NO₃⁻). Genera such as Nitrospira, Nitrobacter, and Nitrococcus carry out this low-energy process, also resulting in slow growth. For complete nitrification, both ammonia oxidation and nitrite oxidation must occur. Now the nitrate is available to be used by plants.

Ammonia- and nitrite-oxidizing microbes are widespread in oxygen-rich environments and have been well-studied in ecosystems like soils, estuaries, lakes, and oceans. Beyond their natural roles, they are crucial in wastewater treatment systems, where they help prevent pollution by removing excess ammonium. Maintaining stable populations of these microbes is a major focus in managing effective treatment processes. They also support healthy aquarium environments by breaking down harmful ammonium produced by fish waste.

Assimilation

NO₃⁻ or NH₄⁺ → Organic N

Nitrogen assimilation is the process by which plants and other organisms incorporate inorganic nitrogen, mainly in the form of ammonium (NH₄⁺) or nitrate (NO₃⁻), into organic molecules like amino acids, proteins, and nucleic acids that they need to grow. Plants typically take up nitrate from the soil and first reduce it to nitrite (NO₂⁻) and then to ammonium inside their cells. This ammonium is then combined with carbon compounds to form amino acids through enzymes like glutamine synthetase and glutamate synthase.

So why do plants bother taking up nitrate at all, instead of just absorbing ammonium? There are a few reasons. In well-aerated soils, much of the ammonium produced by decomposition is quickly converted into nitrate by nitrifying bacteria, making nitrate the more abundant form of nitrogen in many environments, especially in temperate and agricultural soils. Nitrate is also more mobile in soil water than ammonium, allowing it to travel easily with water and reach plant roots more effectively, particularly those with deeper or wider root systems. Ammonium binds tightly to negatively charged soil particles, making it less mobile and less accessible. Additionally, high concentrations of ammonium can be toxic to plants, disrupting cellular pH and metabolism, so many plants prefer a balanced uptake of both forms.

Through assimilation, nitrogen becomes part of plants' living tissue, supporting growth, reproduction, and metabolism. When animals eat the plants, nitrogen enters their bodies and becomes part of new organic structures within them.

Denitrification

NO₃⁻ → NO₂⁻ → NO + N₂O → N₂

and

2 NO₃⁻ + 10 e⁻ + 12 H⁺ → N₂ + 6 H₂O

When soils are low in oxygen, some bacteria switch from using oxygen to using nitrate as their electron acceptor. Denitrification is the anaerobic process by which nitrate (NO₃⁻) is converted into nitrogen gas (N₂), returning nitrogen to the atmosphere and reducing its availability in ecosystems. It primarily occurs in low-oxygen environments, such as soils, sediments, and anoxic zones in aquatic systems. It is carried out primarily by prokaryotes, such as species in the genera Bacillus, Paracoccus, and Pseudomonas, that use organic carbon for energy.

While denitrification can lead to the loss of valuable nitrogen from agricultural soils, it plays a useful role in wastewater treatment by removing excess nitrate and helping to prevent downstream problems like algal blooms. Intermediate gases, such as nitrous oxide (N₂O), an air pollutant and greenhouse gas 300 times as potent as CO₂, can also be produced during this process.

Anammox (Anaerobic Ammonia Oxidation)

NH₄⁺ + NO₂⁻ → N₂ + 2H₂O

This is a shortcut found in some low-oxygen places, especially in aquatic systems. Prokaryotes, belonging to the Planctomycetes phylum of Bacteria, combine ammonium and nitrite directly into nitrogen gas and water. It’s a relatively recent discovery and important in understanding how nitrogen cycles in oceans.

DNRA (Dissimilatory Nitrate Reduction to Ammonium)

NO₃⁻ → NO₂⁻ → NH₄⁺

In some anaerobic environments, microbes don’t make nitrogen gas. They reduce nitrate to ammonium instead. This keeps nitrogen in the system, recycling it in a usable form.

Lightning

Lightning provides enough energy to break the strong triple bond in nitrogen gas (N₂), forming nitric oxide (NO), which reacts with oxygen to eventually form nitrate (NO₃⁻). This nitrate dissolves in rainwater and enters soils.

Lightning accounts for roughly 5-10 million metric tons of nitrogen fixation per year, or about 5-10%. Microbial fixation accounts for approximately 90-140 million metric tons, or 90-95% of natural nitrogen fixation, according to the Ecological Society of America.

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Human Influence

Humans have dramatically altered the nitrogen cycle (much more than the carbon cycle), primarily through the industrial production and widespread use of synthetic nitrogen fertilizers. The most significant development was the invention of the Haber-Bosch process in the early 20th century, which captures inert atmospheric nitrogen gas (N₂) and converts it into ammonia (NH₃) using high temperatures, high pressure, and a catalyst—usually using natural gas as an energy source and a feedstock to produce the necessary hydrogen. Ammonia is then used to create nitrogen-rich fertilizers such as urea, ammonium nitrate, and ammonium sulfate. This breakthrough allowed humans to artificially "fix" nitrogen at an industrial scale, bypassing the slow, energy-intensive microbial processes that had governed nitrogen availability for billions of years.

Today, the world adds 110 million metric tons of this synthetic nitrogenous fertilizer to agricultural land. That just about doubles the natural amount. The result has been a massive increase in reactive nitrogen in soils, far beyond what natural systems evolved to handle. Crops can grow faster and larger with this extra nitrogen, which has greatly increased food production and supported a growing global population. In fact, synthetic nitrogenous fertilizer supports half of the entire world's population (4 billion people)!

However, this abundance of nitrogen comes with ecological costs. Big ones. In agricultural soils, heavy fertilizer use can disrupt the balance of microbial life. Nitrogen-fixing bacteria often become inactive or decline in number, as plants no longer need to form symbiotic relationships to access nitrogen. This destroys the natural fertility of the soil, making crops more dependent on continued fertilizer input.

Excess nitrogen also favors fast-growing, nitrogen-loving microbes and can suppress populations of organisms that perform other critical functions, such as decomposers and mycorrhizal fungi. This reduces microbial diversity and soil health, altering nutrient cycling, organic matter breakdown, and water retention. The reduction in microbes results in a decrease in the amount of organic carbon in the soil. Estimates vary, but a loss of 1% of soil carbon can decrease the soil's ability to hold water by around 3,700 gallons per acre. That means more soil is lost to runoff, and additional irrigation water needs to be applied, further depleting aquifers.

Moreover, some microbes involved in the nitrogen cycle produce greenhouse gases like nitrous oxide (N₂O) during denitrification, especially when nitrogen levels are high. N₂O is the previously mentioned greenhouse gas, 300 times as potent as CO₂, and it also contributes to ozone depletion and the formation of photochemical smog.

Beyond soil, the surplus nitrogen often leaches into groundwater or runs off into rivers and lakes, leading to eutrophication—a condition where excess nutrients trigger algal blooms. When these blooms die and decompose, they consume oxygen in the water, creating hypoxic or "dead zones" where aquatic life cannot survive. The Gulf of Mexico and Chesapeake Bay are well-known examples of this effect.

Nitrogenous fertilizers used in agriculture get converted to nitrate in the soil. Nitrate is highly soluble and can easily leach into groundwater, especially after heavy rainfall or irrigation. Once in drinking water, high nitrate levels can pose health risks, particularly for infants, where it can cause methemoglobinemia, or “blue baby syndrome.”

Airborne nitrogen compounds, released from agriculture and fossil fuel combustion, also contribute to acid rain, smog, and nitrogen deposition, which can alter soil chemistry and plant life even in faraway ecosystems.

While synthetic nitrogen fertilizers have revolutionized agriculture, they have also introduced deep and widespread disruptions to the nitrogen cycle. These changes affect not only crop systems but also soil ecology, microbial and plant life, climate, and water and air quality. Restoring balance requires rethinking how nitrogen is managed—by reducing overuse, improving fertilizer efficiency, and supporting natural nitrogen-fixing processes in soil.

We need to rethink how we use nitrogen as a civilization. Using a finite supply of fossil fuels in an energy-intensive way to create synthetic fertilizers to put on agricultural fields that have been degraded—in part, by said fertilizers—to support ever-increasing populations (I hope it's obvious by now) is not sustainable.

Unfortunately, there is no single remedy. But a large part of the solution is undoubtedly restoring agriculture to its previous state in harmony with the natural cycles of the Earth. Regenerative agriculture and permaculture practices offer a pathway to not only sustain but also restore the land that supports us all.

If we don't rethink our linear, polluting, industrial agriculture system that has unsettled the nitrogen cycle, it's not just soil microbes that will suffer—it's your kids.

The stakes are not merely agricultural. They are human.

We must choose between a fleeting abundance and a lasting home.

Resources:

Aber, J. D., Galloway, J. N., Erisman, J. W., Seitzinger, S. P., Howarth, R. W., Cowling, E. B., & Cosby, B. J. (2003). The nitrogen cascade. BioScience, 53(4), 341–356. https://doi.org/10.1641/0006-3568(2003)053[0341:TNC]2.0.CO;2

Ecological Society of America. (2000). Human alteration of the global nitrogen cycle: Causes and consequences. Issues in Ecology, 1(1). https://www.esa.org/esa/wp-content/uploads/2013/03/issue1.pdf

Encyclopædia Britannica. (n.d.). Nitrogen cycle. In Encyclopædia Britannica. https://www.britannica.com/science/nitrogen-cycle

Galloway, J. N., Townsend, A. R., Erisman, J. W., et al. (2008). Transformation of the nitrogen cycle: Recent trends, questions, and potential solutions. Science, 320(5878), 889–892. https://doi.org/10.1126/science.1136674

Johnson, G. (2008, May 19). Reactive nitrogen: The next big pollution problem. Wired. https://www.wired.com/2008/05/reactive-nitrog/

Keim, B. (2010, December 13). Acidifying oceans could upset life's nitrogen cycles. Wired. https://www.wired.com/2010/12/ocean-nitrification/

University of Nebraska–Lincoln. (n.d.). The connection between soil organic matter and soil water. Water.unl.edu. https://water.unl.edu/article/animal-manure-management/connection-between-soil-organic-matter-and-soil-water/

Our World in Data. (n.d.). Fertilizer use by nutrient. https://ourworldindata.org/grapher/fertilizer-use-nutrient

Zehr, J. P., & Kudela, R. M. (2011). The nitrogen cycle: Processes, players, and human impact. Nature Education Knowledge, 3(10), 25. https://www.nature.com/scitable/knowledge/library/the-nitrogen-cycle-processes-players-and-human-15644632/

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Nerds Only Section:

How much energy is required to break the triple bonds of N₂ molecules to supply the nitrogen that an oak tree requires for a year?

N₂ has a very strong triple bond. The N₂bond dissociation energy is approximately 941 kJ/mol of N₂.

(This is the energy required to break one mole of N₂ molecules into individual nitrogen atoms.)

Estimates vary, but for a mature oak tree, total annual nitrogen uptake is roughly 50 to 100 grams of nitrogen (N) per year, depending on soil fertility, age, and growth stage. Let’s use 75 grams of nitrogen per year as a mid-range value.

Atomic weight of nitrogen (N) ≈ 14 g/mol

So 75 g N ÷ 14 g/mol = 5.36 mol N

But atmospheric nitrogen is N₂, meaning each molecule contains 2 nitrogen atoms.

So: 5.36 mol N = 2.68 mol N₂ required

Now we apply the bond dissociation energy:

941 kJ/mol × 2.68 mol = 2,522 kJ

So, to supply a mature oak tree with 75 g of nitrogen purely by breaking atmospheric N₂, you would need about 2,522 kilojoules of energy per year.

That's about 700 Wh. Which equates to a continuous average power requirement of 0.08 watts dedicated only to breaking N₂ bonds. That may not seem like much in human terms, but for microbes fixing nitrogen biologically it's metabolically expensive.