The key role of microbes in nitrogen fixation. How overuse of nitrogen-containing fertilizers can cause algal blooms.

Key points

  • Nitrogen is a key component of the bodies of living organisms. Nitrogen atoms are found in all proteins and DNA\text{DNA}.
  • Nitrogen exists in the atmosphere as N2\text N_2 gas. In nitrogen fixation, bacteria convert N2\text N_2 into ammonia, a form of nitrogen usable by plants. When animals eat the plants, they acquire usable nitrogen compounds.
  • Nitrogen is a common limiting nutrient in nature, and agriculture. A limiting nutrient is the nutrient that's in shortest supply and limits growth.
  • When fertilizers containing nitrogen and phosphorous are carried in runoff to lakes and rivers, they can result in blooms of algae—this is called eutrophication.


Nitrogen is everywhere! In fact, N2\text N_2 gas makes up about 78% of Earth's atmosphere by volume, far surpassing the O2\text O_2 we often think of as "air".1^1
But having nitrogen around and being able to make use of it are two different things. Your body, and the bodies of other plants and animals, have no good way to convert N2\text N_2 into a usable form. We animals—and our plant compatriots—just don't have the right enzymes to capture, or fix, atmospheric nitrogen.
Still, your DNA\text{DNA} and proteins contain quite a bit of nitrogen. Where does that nitrogen come from? In the natural world, it comes from bacteria!

Bacteria play a key role in the nitrogen cycle.

Nitrogen enters the living world by way of bacteria and other single-celled prokaryotes, which convert atmospheric nitrogen—N2\text N_2—into biologically usable forms in a process called nitrogen fixation. Some species of nitrogen-fixing bacteria are free-living in soil or water, while others are beneficial symbionts that live inside of plants.
Photosynthetic cyanobacteria are found in most aquatic ecosystems that get sunlight, and they play a key role in nitrogen fixation.
Another type of bacteria, Rhizobium, live symbiotically in the roots of legume plants—like peas, beans, and peanuts—and provide them with fixed nitrogen.
Free-living bacteria in the genus Azotobacter are also key nitrogen fixers in terrestrial—land-based—ecosystems.
Nitrogen-fixing microorganisms capture atmospheric nitrogen by converting it to ammonia—NH3\text {NH}_3—which can be taken up by plants and used to make organic molecules. The nitrogen-containing molecules are passed to animals when the plants are eaten. They may be incorporated into the animal's body or broken down and excreted as waste, such as the urea found in urine.
Prokaryotes play several roles in the nitrogen cycle. Nitrogen-fixing bacteria in the soil and within the root nodules of some plants convert nitrogen gas in the atmosphere to ammonia. Nitrifying bacteria convert ammonia to nitrites or nitrates. Ammonia, nitrites, and nitrates are all fixed nitrogen and can be absorbed by plants. Denitrifying bacteria converts nitrates back to nitrogen gas.
Image credit: modified from Nitrogen cycle by Johann Dréo (CC BY-SA 3.0); the modified image is licensed under a CC BY-SA 3.0 license
Nitrogen doesn't remain forever in the bodies of living organisms. Instead, it's converted from organic nitrogen back into N2\text N_2 gas by bacteria. This process often involves several steps in terrestrial—land—ecosystems. Nitrogenous compounds from dead organisms or wastes are converted into ammonia—NH3\text {NH}_3—by bacteria, and the ammonia is converted into nitrites and nitrates. In the end, the nitrates are made into N2\text N _2 gas by denitrifying prokaryotes.

Nitrogen cycling in marine ecosystems

So far, we’ve focused on the natural nitrogen cycle as it occurs in terrestrial ecosystems. However, generally similar steps occur in the marine nitrogen cycle. There, the ammonification, nitrification, and denitrification processes are performed by marine bacteria and archaea.
The illustration shows the nitrogen cycle. Nitrogen gas from the atmosphere is fixed into organic nitrogen by nitrogen-fixing bacteria. This organic nitrogen enters terrestrial food webs. It leaves the food webs as nitrogenous wastes in the soil. Ammonification of this nitrogenous waste by bacteria and fungi in the soil converts the organic nitrogen to ammonium ion—NH4 plus. Ammonium is converted to nitrit—NO2 minus—then to nitrate—NO3 minus—by nitrifying bacteria. Denitrifying bacteria convert the nitrate back into nitrogen gas, which reenters the atmosphere. Nitrogen from runoff and fertilizers enters the ocean, where it enters marine food webs. Some organic nitrogen falls to the ocean floor as sediment. Other organic nitrogen in the ocean is converted to nitrite and nitrate ions, which is then converted to nitrogen gas in a process analogous to the one that occurs on land.
Image credit: Biogeochemical cycles: Figure 4 by OpenStax College, Biology, CC BY 4.0. Modification of work by John M. Evans and Howard Perlman, USGS
Some nitrogen-containing compounds fall to the ocean floor as sediment. Over long periods of time, the sediments get compressed and form sedimentary rock. Eventually, geological uplift may move the sedimentary rock to land. In the past, scientists did not think that this nitrogen-rich sedimentary rock was an important nitrogen source for terrestrial ecosystems. However, a new study suggests that it may actually be quite important—the nitrogen is released gradually to plants as the rock wears away, or weathers.2^2

Nitrogen as a limiting nutrient

In natural ecosystems, many processes, such as primary production and decomposition, are limited by the available supply of nitrogen. In other words, nitrogen is often the limiting nutrient, the nutrient that's in shortest supply and thus limits the growth of organisms or populations.
How do we know if a nutrient is limiting? Often, this is tested as follows:3^3
  • When a nutrient is limiting, adding more of it will increase growth—e.g., it will cause plants to grow taller than if nothing were added.
  • If a non-limiting nutrient is instead added, it won't have an effect—e. g., plants will grow to the same height whether the nutrient is present or absent.
For example, if we added nitrogen to half the bean plants in a garden and found that they grew taller than untreated plants, that would suggest nitrogen was limiting. If, instead, we didn't see a difference in growth in our experiment, that would suggest that some other nutrient than nitrogen must be limiting.
Nitrogen and phosphorous are the two most common limiting nutrients in both natural ecosystems and agriculture. That's why, if you look at a bag of fertilizer, you will see it contains a lot of nitrogen and phosphorous.

Human activity affects cycling of nitrogen.

We humans may not be able to fix nitrogen biologically, but we certainly do industrially! About 450 million metric tons of fixed nitrogen are made each year using a chemical method called the Haber-Bosch process, in which N2\text N_2 is reacted with hydrogen—H2\text H_2—at high temperatures.4^4 Most of this fixed nitrogen goes to make fertilizers we use on our lawns, gardens, and agricultural fields.
In general, human activity releases nitrogen into the environment by two main means: combustion of fossil fuels and use of nitrogen-containing fertilizers in agriculture. Both processes increase levels of nitrogen-containing compounds in the atmosphere. High levels of atmospheric nitrogen—other than N2\text N_2—are associated with harmful effects, like the production of acid rain—as nitric acid, HNO3\text{HNO}_3—and contributions to the greenhouse effect—as nitrous oxide, N2O\text N_2 \text O.
Also, when artificial fertilizers containing nitrogen and phosphorous are used in agriculture, the excess fertilizer may be washed into lakes, streams, and rivers by surface runoff. A major effect from fertilizer runoff is saltwater and freshwater eutrophication. In this process, nutrient runoff causes overgrowth, or a "bloom," of algae or other microorganisms. Without the nutrient runoff, they were limited in their growth by availability of nitrogen or phosphorus.
Eutrophication can reduce oxygen availability in the water during the nighttime because the algae and microorganisms that feed on them use up large quantities of oxygen in cellular respiration. This can cause the death of other organisms living in the affected ecosystems, such as fish and shrimp, and result in low-oxygen, species-depleted areas called dead zones.5^5


This article is a modified derivative of the following articles:
The modified article is licensed under a CC BY-NC-SA 4.0 license.

Works Cited

  1. "Atmosphere of Earth," Wikipedia, last modified June 9, 2016,
  2. Scott L. Morford, Benjamin Z. Houlton, and Randy A. Dahlgren, “Increased Forest Ecosystem Carbon and Nitrogen Storage from Nitrogen Rich Bedrock,” Nature 477, no. 7362 (2011): 78–81.
  3. "Haber Process," Wikipedia, last modified June 10, 2016,
  4. "Eutrophication," Wikipedia, last modified June 6, 2016,


Abedon, Stephen T. "Limiting nutrient." Biology as Poetry: Ecology.
"Azotobacter." Wikipedia. Last modified June 7, 2016.
"Atmosphere of Earth." Wikipedia. Last modified June 9, 2016.
"Eutrophication." Wikipedia. Last modified June 6, 2016.
"Haber Process." Wikipedia. Last modified June 10, 2016.
Hu, S., F. S. Chapin, III, M. K. Firestone, C. B. Field, and N. R. Chiariello. "Nitrogen Limitation of Microbial Decomposition in a Grassland Under Elevated CO2\text{CO}_2." Nature 409 (2001): 188-191.
Morford, Scott L., Benjamin Z. Houlton, and Randy A. Dahlgren. “Increased Forest Ecosystem Carbon and Nitrogen Storage from Nitrogen Rich Bedrock.” Nature 477, no. 7362 (2011): 78–81.
"Nitrogen Fixation." Wikipedia. Last modified June 10, 2016.
"Nitrous Oxide Emissions." United States Environmental Protection Agency. Last modified May 26, 2016.
"Phosphorous Cycle." Wikipedia. Last modified May 20, 2016.
Purves, William K., David E. Sadava, Gordon H. Orians, and H. Craig Heller. "Prokaryotes Are Important Players in Nutrient Cycling." In Life: The Science of Biology, 531. 7th ed. Sunderland: Sinauer Associates, 2003.
Purves, William K., David E. Sadava, Gordon H. Orians, and H. Craig Heller. "Prokaryotes Have Exploited Many Metabolic Possibilities." In Life: The Science of Biology, 529-531. 7th ed. Sunderland: Sinauer Associates, 2003.
Raven, Peter H., George B. Johnson, Kenneth A. Mason, Jonathan B. Losos, and Susan R. Singer. "Biogeochemical Cycles." In Biology, 1209-1211. 10th ed., AP ed. York: McGraw-Hill, 2014.