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The Nitrogen Cycle

All life requires nitrogen-compounds, e.g., proteins and nucleic acids.
Air, which is 79% nitrogen gas (N₂), is the major reservoir of nitrogen.
But most organisms cannot use nitrogen in this form.
Plants must secure their nitrogen in "fixed" form, i.e., incorporated in compounds such as:
- nitrate ions (NO₃⁻)
- ammonium ions (NH₄⁺)
- urea (NH₂)₂CO
Animals secure their nitrogen (and all other) compounds from plants (or animals that have fed on plants).

Four processes participate in the cycling of nitrogen through the biosphere:

nitrogen fixation
decay
nitrification
denitrification

Microorganisms play major roles in all four of these.

Nitrogen Fixation

The nitrogen molecule (N₂) is quite inert. To break it apart so that its atoms can combine with other atoms requires the input of substantial amounts of energy.

Three processes are responsible for most of the nitrogen fixation in the biosphere:

atmospheric fixation by lightning
industrial fixation
biological fixation by certain microbes — alone or in a symbiotic relationship with some plants and animals

The enormous energy of lightning breaks nitrogen molecules and enables their atoms to combine with oxygen in the air forming nitrogen oxides. These dissolve in rain, forming nitrates, that are carried to the earth.

Atmospheric nitrogen fixation probably contributes some 5– 8% of the total nitrogen fixed.

Industrial Fixation

Under great pressure, at a temperature of 600°C, and with the use of a catalyst, atmospheric nitrogen and hydrogen (usually derived from natural gas or petroleum) can be combined to form ammonia (NH₃). Ammonia can be used directly as fertilizer, but most of its is further processed to urea and ammonium nitrate (NH₄NO₃).

Biological Fixation

The ability to fix nitrogen is found only in certain bacteria and archaea.

Some live in a symbiotic relationship with plants of the legume family (e.g., soybeans, alfalfa).
Link to a discussion of symbiotic nitrogen fixation in legumes.
Some establish symbiotic relationships with plants other than legumes (e.g., alders).
Some establish symbiotic relationships with animals, e.g., termites and "shipworms" (wood-eating bivalves).
Some nitrogen-fixing bacteria live free in the soil.
Nitrogen-fixing cyanobacteria are essential to maintaining the fertility of semi-aquatic environments like rice paddies.

Biological nitrogen fixation requires a complex set of enzymes and a huge expenditure of ATP.

Although the first stable product of the process is ammonia, this is quickly incorporated into protein and other organic nitrogen compounds.

Decay

The proteins made by plants enter and pass through food webs just as carbohydrates do. At each trophic level, their metabolism produces organic nitrogen compounds that return to the environment, chiefly in excretions. The final beneficiaries of these materials are microorganisms of decay. They break down the molecules in excretions and dead organisms into ammonia.

Nitrification

Ammonia can be taken up directly by plants — usually through their roots. However, most of the ammonia produced by decay is converted into nitrates. Until recently this was thought always to be accomplished in two steps:

Bacteria of the genus Nitrosomonas oxidize NH₃ to nitrites (NO₂⁻).
Bacteria of the genus Nitrobacter oxidize the nitrites to nitrates (NO₃⁻).

These two groups of autotrophic bacteria are called nitrifying bacteria. Through their activities (which supply them with all their energy needs), nitrogen is made available to the roots of plants.

However, in 2015, two groups reported finding that bacteria in the genus Nitrospira were able to carry out both steps: ammonia to nitrite and nitrite to nitrate. This ability is called "comammox" (for complete ammonia oxidation).

In addition, both soil and the ocean contain archaeal microbes, assigned to the Crenarchaeota, that convert ammonia to nitrites. They are more abundant than the nitrifying bacteria and may turn out to play an important role in the nitrogen cycle.

Many legumes, in addition to fixing atmospheric nitrogen, also perform nitrification — converting some of their organic nitrogen to nitrites and nitrates. These reach the soil when they shed their leaves.

Denitrification

The three processes above remove nitrogen from the atmosphere and pass it through ecosystems.

Denitrification reduces nitrates and nitrites to nitrogen gas, thus replenishing the atmosphere. In the process several intermediates are formed:

nitric oxide (NO)
nitrous oxide (N₂O)(a greenhouse gas 300 times as potent as CO₂)
nitrous acid (HONO)

Once again, bacteria are the agents. They live deep in soil and in aquatic sediments where conditions are anaerobic. They use nitrates as an alternative to oxygen for the final electron acceptor in their respiration.

Anammox (anaerobic ammonia oxidation)

Under anaerobic conditions in marine and freshwater sediments, other species of bacteria are able to oxidize ammonia (with NO₂⁻) forming nitrogen gas.

NH₄⁺ + NO₂⁻ → N₂ + 2H₂O

The anammox reaction may account for as much as 50% of the denitrification occurring in the oceans.

All of these processes participate in closing the nitrogen cycle.

Are the denitrifiers keeping up?

Agriculture may now be responsible for one-half of the nitrogen fixation on earth through

the use of fertilizers produced by industrial fixation
the growing of legumes like soybeans and alfalfa.

This is a remarkable influence on a natural cycle.

Are the denitrifiers keeping up the nitrogen cycle in balance? Probably not. Certainly, there are examples of nitrogen enrichment in ecosystems. One troubling example: the "blooms" of algae in lakes and rivers as nitrogen fertilizers leach from the soil of adjacent farms (and lawns). The accumulation of dissolved nutrients in a body of water is called eutrophication.

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7 October 2016