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The Nitrogen Cycle

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

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.

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.


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.


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:

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.


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:

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 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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29 December 2015