The nitrogen cycle

The key role of microbes in nitrogen fixation. How overuse of nitrogen-containing fertilizers can
cause algal blooms.
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Key points
 Nitrogen is a key component of the bodies of living organisms. Nitrogen
atoms are found in all proteins and \text{DNA}DNAD, N, A.

 Nitrogen exists in the atmosphere as \text N_2N2N, start subscript, 2, end

subscript gas. In nitrogen fixation, bacteria convert \text N_2N2N, start
subscript, 2, end subscript 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.

Introduction
Nitrogen is everywhere! In fact, \text N_2N2N, start subscript, 2, end
subscript gas makes up about 78% of Earth's atmosphere by volume, far
surpassing the \text O_2O2O, start subscript, 2, end subscript we often think
of as "air".^11start superscript, 1, end superscript

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 \text N_2N2N, start subscript, 2, end subscript 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 \text{DNA}DNAD, N, A 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—\text N_2N2N, start
subscript, 2, end subscript—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.
[What are some examples of nitrogen-fixing prokaryotes?]

Nitrogen-fixing microorganisms capture atmospheric nitrogen by converting

it to ammonia—\text {NH}_3NH3N, H, start subscript, 3, end subscript—
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 \text N_2N2N, start subscript, 2,
end subscript gas by bacteria. This process often involves several steps in
terrestrial—land—ecosystems. Nitrogenous compounds from dead organisms
or wastes are converted into ammonia—\text {NH}_3NH3N, H, start
subscript, 3, end subscript—by bacteria, and the ammonia is converted into
nitrites and nitrates. In the end, the nitrates are made into \text N _2N2N, start
subscript, 2, end subscript 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.^22start superscript, 2, end superscript

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:^33start superscript, 3, end superscript

 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 \text
N_2N2N, start subscript, 2, end subscript is reacted with hydrogen—\text
H_2H2H, start subscript, 2, end subscript—at high temperatures.^44start
superscript, 4, end superscript 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 \text N_2N2N, start subscript, 2, end subscript—are
associated with harmful effects, like the production of acid rain—as nitric
acid, \text{HNO}_3HNO3H, N, O, start subscript, 3, end subscript—and
contributions to the greenhouse effect—as nitrous oxide, \text N_2 \text ON2
ON, start subscript, 2, end subscript, 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.
 Image

credit: Eutrophication at a waste water outlet in the

Potomac River, Washington, D.C. by Alexandr Trubetskoy, CC BY-SA 3.0

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.^55

https://youtu.be/DsCMYyQ0NWU
 The phosphorous cycle
The slow cycling of phosphorous through the biosphere. How phosphorous-containing fertilizers can
cause aquatic dead zones.
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Key points
 Phosphorous is an essential nutrient found in the macromolecules of humans
and other organisms, including \text{DNA}DNAD, N, A.

 The phosphorous cycle is slow. Most phosphorous in nature exists in the

form of phosphate ion—\text {PO}_4^{3-}PO43−P, O, start subscript, 4, end
subscript, start superscript, 3, minus, end superscript.

 Phosphorous is often the limiting nutrient, or nutrient that is most scarce and
thus limits growth, in aquatic ecosystems.

 When nitrogen and phosphorous from fertilizer are carried in runoff to lakes
and oceans, they can cause eutrophication, the overgrowth of algae. The
algae may deplete oxygen from the water and create a dead zone.

Introduction
Is phosphorous important? That depends—do you like
having \text{DNA}DNAD, N, A, cell membranes, or bones in you body?
Hint: The answer is probably yes!

Phosphorus is an essential nutrient for living organisms. It’s a key part of

nucleic acids, like \text{DNA}DNAD, N, A and of the phospholipids that
form our cell membranes. As calcium phosphate, it also makes up the
supportive components of our bones.
In nature, phosphorus is often the limiting nutrient—in other words, the
nutrient that’s in shortest supply and puts a limit on growth—and this is
particularly true for aquatic, freshwater ecosystems.

Natural cycling of phosphorous

The phosphorous cycle is slow compared to other biogeochemical cycles
such as the water, carbon, and nitrogen cycles.^11start superscript, 1, end
superscript

In nature, phosphorous is found mostly in the form of phosphate ions—\text

{PO}_4^{3-}PO43−P, O, start subscript, 4, end subscript, start superscript, 3,
minus, end superscript. Phosphate compounds are found in sedimentary
rocks, and as the rocks weather—wear down over long time periods—the
phosphorous they contain slowly leaches into surface water and soils.
Volcanic ash, aerosols, and mineral dust can also be significant phosphate
sources, though phosphorous has no real gas phase, unlike other elements
such as carbon, nitrogen, and sulfur.

Phosphate compounds in the soil can be taken up by plants and, from there,
transferred to animals that eat the plants. When plants and animals excrete
wastes or die, phosphates may be taken up by detritivores or returned to the
soil. Phosphorous-containing compounds may also be carried in surface
runoff to rivers, lakes, and oceans, where they are taken up by aquatic
organisms.

When phosphorous-containing compounds from the bodies or wastes of

marine organisms sink to the floor of the ocean, they form new sedimentary
layers. Over long periods of time, phosphorous-containing sedimentary rock
may be moved from the ocean to the land by a geological process called
uplift. However, this process is very slow, and the average phosphate ion has
an oceanic residence time—time in the ocean—of 20,000 to 100,000 years.
 This illustration shows the phosphorus cycle. Phosphorus enters the
atmosphere from volcanic aerosols. As this aerosol precipitates to earth, it
enters terrestrial food webs. Some of the phosphorus from terrestrial food
webs dissolves in streams and lakes, and the remainder enters the soil.
Another source of phosphorus is fertilizers. Phosphorus enters the ocean via
leaching and runoff, where it becomes dissolved in ocean water or enters
marine food webs. Some phosphorus falls to the ocean floor where it becomes
sediment. If uplifting occurs, this sediment can return to land.
Image credit: Biogeochemical cycles: Figure 5 by OpenStax College, Concepts of Biology, CC BY 4.0;
modification of work by John M. Evans and Howard Perlman, USGS

Eutrophication and dead zones

Most fertilizers used in agriculture—and on lawns and gardens—contain both
nitrogen and phosphorous, which may be carried to aquatic ecosystems in
surface runoff. Fertilizer carried in runoff may cause excessive growth of
algae or other microbes that were previously limited by nitrogen or
phosphorous. This phenomenon is called eutrophication. At least in some
cases, phosphorous, not nitrogen, seems to be the main driver of
eutrophication.^22start superscript, 2, end superscript

Why is eutrophication harmful? Some algae make water taste or smell bad or
produce toxic compounds.^22start superscript, 2, end superscript Also, when
all of those algae die and are decomposed by microbes, large amounts of
oxygen are used up as their bodies are broken down. This spike in oxygen
usage can sharply lower dissolved oxygen levels in the water and may lead to
death by hypoxia—lack of oxygen—for other aquatic organisms, such as
shellfish and finfish.
Regions of lakes and oceans that are depleted of oxygen due to a nutrient
influx are called dead zones. The number of dead zones has increased for
several years, and more than 400 of these zones existed in 2008. One of the
worst dead zones is off the coast of the United States in the Gulf of Mexico.
Fertilizer runoff from the Mississippi River Basin created a dead zone of over
8,463 square miles. As you can see in the figure below, dead zones are found
in areas of high industrialization and population density around the world.
 World map shows areas where dead zones occur. Dead zones are present
along the eastern and western shore of the United States, in the North and
Mediterranean Seas, and off the east coast of Asia.
Image credit: Biogeochemical cycles: Figure 6 by OpenStax College, Concepts of Biology, CC BY 4.0;
original work: Aquatic dead zones by Robert Simmon and Jesse Allen, NASA Earth Observatory

How can eutrophication be reduced or prevented? Fertilizers, phosphorous-

containing detergents, and improperly disposed of sewage can all be sources
of nitrogen and phosphorous that drive eutrophication. Using less fertilizer,
eliminating phosphorous-containing detergents, and ensuring that sewage
does not enter waterways—e.g., from a leaky septic system—are all ways
that individuals, companies, and governments can help reduce
eutrophication.^{3,4}3,4