Earth CyclesThe Nitrogen Cycle: Of Microbes and Men

by John Harrison, Ph.D.

Did you know?

Did you know that all organisms need nitrogen to survive? While the atmosphere is full of nitrogen, it is in a form that can’t be used by living things. Processes within the nitrogen cycle convert nitrogen from the atmosphere into a form that plants and animals can use. Humans alter and influence the nitrogen cycle, primarily through the use of fertilizers, which can have serious environmental consequences.


Although the majority of the air we breathe is N2, molecular nitrogen cannot be used directly to sustain life. This module provides an overview of the nitrogen cycle, one of the major biogeochemical cycles. The five main processes in the cycle are described. The module explores human impact on the nitrogen cycle, resulting in not only increased agricultural production but also smog, acid rain, climate change, and ecosystem upsets.

Terms you should know
  • fertilizer = a substance added to soil to help plants grow
  • microbial = relating to microorganisms such as bacteria
  • species = a distinct type of plant or animal; a related group of living things that can produce offspring
Table of contents

Nitrogen (N) is an essential component of DNA, RNA, and proteins, the building blocks of life. All organisms require nitrogen to live and grow. Although the majority of the air we breathe is N2, most of the nitrogen in the atmosphere is unavailable for use by organisms. This is because the strong triple bond between the N atoms in N2 molecules makes it relatively inert, or unreactive, whereas organisms need reactive nitrogen to be able to incorporate it into cells. In order for plants and animals to be able to use nitrogen, N2 gas must first be converted to more a chemically available form such as ammonium (NH4+), nitrate (NO3-), or organic nitrogen (e.g. urea - (NH2)2CO). The inert nature of N2 means that biologically available nitrogen is often in short supply in natural ecosystems, limiting plant growth.

Nitrogen is an incredibly versatile element, existing in both inorganic and organic forms as well as many different oxidation states. The movement of nitrogen between the atmosphere, biosphere, and geosphere in different forms is called the nitrogen cycle (Figure 1), one of the major biogeochemical cycles. Similar to the carbon cycle, the nitrogen cycle consists of various reservoirs of nitrogen and processes by which those reservoirs exchange nitrogen (arrows) (see The Carbon Cycle module for more information).

Figure 1: The nitrogen cycle. Yellow arrows indicate human sources of nitrogen to the environment. Red arrows indicate processes in which microorganisms participate in the transformation of nitrogen. Blue arrows indicate physical forces acting on nitrogen. And green arrows indicate natural processes affecting the form and fate of nitrogen that do not involve microbes.

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Processes in the nitrogen cycle

Five main processes cycle nitrogen through the biosphere, atmosphere, and geosphere: nitrogen fixation, nitrogen uptake through organismal growth, nitrogen mineralization through decay, nitrification, and denitrification. Microorganisms, particularly bacteria, play major roles in all of the principal nitrogen transformations. Because these processes are microbially mediated, or controlled by microorganisms, these nitrogen transformations tend to occur faster than geological processes like plate motion, a very slow, purely physical process that is a part of the carbon cycle. Instead, rates are affected by environmental factors that influence microbial activity, such as temperature, moisture, and resource availability.

Comprehension Checkpoint

Processes within the nitrogen cycle progress at a _______ rate than geological processes like plate motion.

Figure 2: Part of a clover root system bearing naturally occurring nodules of Rhizobium, bacteria that can transform atmospheric nitrogen through the process of nitrogen fixation. Each nodule is about 2-3 mm long. Image courtesy of image © The Microbial World

Nitrogen fixation

N2 arrow-right NH4+

Nitrogen fixation is the process wherein N2 is converted to ammonium, or NH4+. This is the only way that organisms can attain nitrogen directly from the atmosphere; the few that can do this are called nitrogen fixing organisms. Certain bacteria, including those among the genus Rhizobium, are able to fix nitrogen (or convert it to ammonium) through metabolic processes, analogous to the way mammals convert oxygen to CO2 when they breathe. Nitrogen fixing bacteria often form symbiotic relationships with host plants. This symbiosis is well-known to occur in the legume family of plants (e.g., beans, peas, and clover). In this relationship, nitrogen fixing bacteria inhabit legume root nodules (Figure 2) and receive carbohydrates and a favorable environment from their host plant in exchange for some of the nitrogen they fix. There are also nitrogen fixing bacteria that exist without plant hosts, known as free-living nitrogen fixers. In aquatic environments, blue-green algae (really a bacteria called cyanobacteria) are an important free-living nitrogen fixer.

In addition to nitrogen fixing bacteria, high-energy natural events such as lightning, forest fires, and even hot lava flows can cause the fixation of smaller, but significant, amounts of nitrogen. The high energy of these natural phenomena can break the triple bonds of N2 molecules, thereby making individual N atoms available for chemical transformation.

Within the last century, humans have become as important a source of fixed nitrogen as all natural sources combined. Burning fossil fuels, using synthetic nitrogen fertilizers, and cultivation of legumes all fix nitrogen. Through these activities, humans have more than doubled the amount of fixed nitrogen that is pumped into the biosphere every year (Figure 3), the consequences of which are discussed below.

Figure 3: Recent increases in anthropogenic N fixation in relation to “natural” N fixation. Modified from Vitousek, P. M.. and Matson, P. A. (1993). Agriculture, the global nitrogen cycle, and trace gas flux. The Biogeochemistry of Global Change: Radiative Trace Gases. R. S. Oremland. New York, Chapman and Hall: 193-208.

Nitrogen uptake

NH4+ arrow-right Organic N

The ammonium (NH4+) produced by nitrogen fixing bacteria is usually quickly taken up by a host plant, the bacteria itself, or another soil organism and incorporated into proteins and other organic nitrogen compounds, like DNA. When organisms nearer the top of the food chain (like us!) eat, we are taking up nitrogen that has been fixed initially by nitrogen fixing bacteria.

Nitrogen mineralization

Organic N arrow-rightNH4+

After nitrogen is incorporated into organic matter, it is often converted back into inorganic nitrogen by a process called nitrogen mineralization, otherwise known as decay. When organisms die, decomposers (such as bacteria and fungi) consume the organic matter and lead to the process of decomposition. During this process, a significant amount of the nitrogen contained within the dead organism is converted to ammonium. Once in the form of ammonium, nitrogen is available for use by plants or for further transformation into nitrate (NO3-) through the process called nitrification.


NH4+ arrow-right NO3-

Some of the ammonium produced by decomposition is converted to nitrate (NO3-) via a process called nitrification. The bacteria that carry out this reaction gain energy from it. Nitrification requires the presence of oxygen, so nitrification can happen only in oxygen-rich environments like circulating or flowing waters and the surface layers of soils and sediments. The process of nitrification has some important consequences. Ammonium ions (NH4+) are positively charged and therefore stick (are sorbed) to negatively charged clay particles and soil organic matter. The positive charge prevents ammonium nitrogen from being washed out of the soil (or leached) by rainfall. In contrast, the negatively charged nitrate ion is not held by soil particles and so can be washed out of the soil, leading to decreased soil fertility and nitrate enrichment of downstream surface and groundwater.


NO3- arrow-right N2+ N2O

Through denitrification, oxidized forms of nitrogen such as nitrate (NO3-) and nitrite (NO2-) are converted to dinitrogen (N2) and, to a lesser extent, nitrous oxide gas (NO2). Denitrification is an anaerobic process that is carried out by denitrifying bacteria, which convert nitrate to dinitrogen in the following sequence:
NO3- arrow-right NO2- arrow-right NO arrow-right N2O arrow-right N2.
Nitric oxide and nitrous oxide are gases that have environmental impacts. Nitric oxide (NO) contributes to smog, and nitrous oxide (N2O) is an important greenhouse gas, thereby contributing to global climate change.

Once converted to dinitrogen, nitrogen is unlikely to be reconverted to a biologically available form because it is a gas and is rapidly lost to the atmosphere. Denitrification is the only nitrogen transformation that removes nitrogen from ecosystems (essentially irreversibly), and it roughly balances the amount of nitrogen fixed by the nitrogen fixers described above.

Comprehension Checkpoint

Which process returns nitrogen gas to the atmosphere?

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Human alteration of the N cycle and its environmental consequences

Early in the 20th century, a German scientist named Fritz Haber figured out how to short circuit the nitrogen cycle by fixing nitrogen chemically at high temperatures and pressures, creating fertilizers that could be added directly to soil. This technology has spread rapidly over the 20th century, and, along with the advent of new crop varieties, the use of synthetic nitrogen fertilizers led to an enormous boom in agricultural productivity. This agricultural productivity has helped us to feed a rapidly growing world population, but the increase in nitrogen fixation has had some negative consequences as well. While the consequences are perhaps not as obvious as an increase in global temperatures (see our Data Analysis and Interpretation module) or a hole in the ozone layer (see The Practice of Science module), they are just as serious and potentially harmful for humans and other organisms.

Why? Not all of the nitrogen fertilizer applied to agricultural fields stays to nourish crops. Some is washed off of agricultural fields by rain or irrigation water, where it leaches into surface water or groundwater and can accumulate. In groundwater that is used as a drinking water source, excess nitrogen can lead to cancer in humans and respiratory distress in infants. The US Environmental Protection Agency has established a standard for nitrogen in drinking water of 10 mg per liter nitrate-N. Unfortunately, many systems (particularly in agricultural areas) already exceed this level. By comparison, nitrate levels in waters that have not been altered by human activity are rarely greater than 1 mg/L. In surface waters, added nitrogen can lead to nutrient over-enrichment, particularly in coastal waters receiving the inflow from polluted rivers. This nutrient over-enrichment, also called eutrophication, has been blamed for increased frequencies of coastal fish-kill events, increased frequencies of harmful algal blooms, and species shifts within coastal ecosystems.

Reactive nitrogen (like NO3- and NH4+) present in surface waters and soils, can also enter the atmosphere as the smog-component nitric oxide (NO) which is a component of smog, and also as the greenhouse gas nitrous oxide (N2O). Eventually, this atmospheric nitrogen can be blown into nitrogen-sensitive terrestrial environments, causing long-term changes. For example, nitrogen oxides comprise a significant portion of the acidity in acid rain which has been blamed for forest death and decline in parts of Europe and the northeastern United States. Increases in atmospheric nitrogen deposition have also been blamed for more subtle shifts in dominant species and ecosystem function in some forest and grassland ecosystems. For example, on nitrogen-poor serpentine soils of northern Californian grasslands, plant communities have historically been limited to native species that can survive without a lot of nitrogen. There is now some evidence that elevated levels of atmospheric N input from nearby industrial and agricultural development have allowed invasion of these ecosystems by non-native plants. As noted earlier, NO is also a major factor in the formation of smog, which is known to cause respiratory illnesses like asthma in both children and adults.

Currently, much research is devoted to understanding the effects of nitrogen enrichment in the air, groundwater, and surface water. Scientists are also exploring alternative agricultural practices that will sustain high productivity while decreasing the negative impacts caused by fertilizer use. These studies not only help us quantify how humans have altered the natural world, but increase our understanding of the processes involved in the nitrogen cycle as a whole.

Key Concepts

  • The nitrogen cycle is the set of biogeochemical processes by which nitrogen undergoes chemical reactions, changes form, and moves through difference reservoirs on Earth, including living organisms.
  • Nitrogen is required for all organisms to live and grow because it is the essential component of DNA, RNA, and protein. However, most organisms cannot use atmospheric nitrogen, the largest reservoir.
  • The five processes in the nitrogen cycle – fixation, uptake, mineralization, nitrification, and denitrification – are all driven by microorganisms.
  • Humans influence the global nitrogen cycle primarily through the use of nitrogen-based fertilizers.

Further Reading

John Harrison, Ph.D. “The Nitrogen Cycle” Visionlearning Vol. EAS-2 (4), 2003.