The Nitrogen Cycle

Nitrogen is an essential component of DNA, RNA, and proteins. All organisms require nitrogen to live and grow. Six main processes cycle nitrogen through the biosphere: nitrogen fixation, nitrogen assimilation (cellular uptake and incorporation into biomass), ammonification (a decay processes that releases ammonium from biomass), nitrification (an aerobic respiratory process in which microorganisms use ammonium as an electron donor), denitrification (an anaerobic respiratory process in which microorganisms use nitrate as an electron acceptor), and anammox (anaerobic ammonium oxidation - in which microorganisms grow anaerobically using ammonium as the electron donor and nitrite as the electron acceptor). Table 1 provides a summary ofthe identities of major nitrogenous substrates found in biosphere habitats and the oxidation state of N in each. Like C, N has the potential to gain or lose as many as eight electrons (its oxidation state ranges from —3 (in ammonium) to +5 (in nitrate)). Thus, ammonium is highly reduced and serves as an excellent electron donor for chemolithotrophic microorganisms that convert it, in a stepwise fashion, to nitrate. In turn, nitrate is an excellent electron acceptor for anaerobic microorganisms (see below).

Nitrogen fixation

Chemically, nitrogen gas, N2, is the most stable form of nitrogen and requires a large input of energy during reduction to ammonia. Only a relatively small number of organisms (aerobes and anaerobes) are able to convert the nutritionally inert, atmospheric N2 to nutritionally useful ammonia. The stoichiometry of biological nitrogen fixation is: (N2 + 8H+ + 8e— ! 2NH3 + H2).

Nitrogen assimilation and ammonification

The ammonia produced by nitrogen-fixing bacteria is usually quickly incorporated into protein and other organic nitrogen compounds either by the active bacterium or its symbiotic host (in the case ofroot-nodule-based nitrogen fixation in leguminous plants are the hosts), or by another microorganism. After nitrogen is incorporated into protein of viable organisms, they eventually perish and are decomposed by other bacteria and fungi. Through simple decomposition and hydrolysis of the polymers, the organic N is converted back into inorganic ammonia (ammonification). In soil the ammonium pool is available for uptake and direct assimilation by growing microorganisms and plants into their biomass.

The remainder of biologically mediated N transformations can be categorized as oxidation-reduction reactions of compounds in waters, sediments, and soils that cycle N from one form to another. Free ammonium is also a reduced form of N that is thermodynamically unstable in the presence of molecular oxygen - subject to nitrification.


Nitrification is an aerobic process that involves the oxidation of ammonium ion (NH4+) first to nitrite (NO—) then to nitrate (NO—). Therefore, nitrification occurs only in oxygen-rich environments such as flowing waters and the surface layers of soils and sediments. Bacteria of the genera Nitrosomonas and Nitrosococcus carry out the first step of nitrification, and Nitrobacter and related chemo-lithoautotrophic bacteria carry out the second step of nitrite oxidation to nitrate.


Denitrification is an anaerobic process which converts nitrate to dinitrogen in the following sequence: NO—! NO—! NO ! N2O ! N2. This dissimilatory process (the end product is not assimilated into biomass) in which nitrate is used as final electron acceptor in anaerobic respiration is carried out by many microorganisms, such as Pseudomonas denitrificans. Many physiological types of microorganisms can use nitrate as an electron acceptor; therefore, the ability to reduce nitrate blurs the line between aerobe and anaerobes. For example, strains of Pseudomonas, Escherichia, Enterobacter, Micrococcus, Rhizobium, and Bacillus are considered aerobes, but many can grow anaerobically by reducing nitrate. Many ofthese organisms are able to reduce nitrate only to nitrite.

Denitrification can be considered an ecologically beneficial and detrimental process, depending upon when and where it occurs. Denitrification is very useful as a tertiary-water-treatment process for municipal sewage because denitrification removes nitrogen prior to water discharge into lakes and streams. However, by-products of denitrification (nitric oxide (NO) and nitrous oxide (N2O)) contribute, respectively, to smog and to greenhouse gas-based global climate change. Once produced, dinitrogen (N2) is unlikely to be reconverted to a biologically available form because it is a gas that is rapidly lost to the atmosphere. Denitrification is the only nitrogen transformation that removes nitrogen from ecosystems

(essentially irreversibly), though it roughly balances the amount of nitrogen fixed by the nitrogen fixers in most ecosystems.


Anammox is a process that has become recognized as ecologically important in the last decade. Based on geo-chemical gradients in deep ocean waters that showed zones of both nitrite and ammonium depletion, chemical oceanographers long hypothesized that chemolithauto-trophic bacteria might be able to grow on ammonium as an electron donor and nitrite as an electron acceptor. In the last decade, the anammox process has been extensively investigated at the microbiological, physiological, biochemical, and genetic level. Sites as far ranging as the Black Sea and coastal areas of both Costa Rica and Africa have been shown to be highly active in the anammox reaction - accounting for 50% or more of the total biologically produced N2 in the ocean.

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