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Nitrogen cycle
Nitrification
From Wikipedia, the free encyclopedia
Nitrification is the biological oxidation of ammonia
or ammonium to nitrite followed by the oxidation of
the nitrite to nitrate.
[1]
The transformation of
ammonia to nitrite is usually the rate limiting step of
nitrification. Nitrification is an important step in the
nitrogen cycle in soil. Nitrification is an aerobic
process performed by small groups of autotrophic
bacteria and archaea. This process was discovered
by the Russian microbiologist, Sergei Winogradsky.
Contents
1 Microbiology and ecology
2 Chemistry
3 Nitrification in the marine environment
4 Soil Conditions controlling nitrification
rates
5 See also
6 References
7 External links
Microbiology and ecology
The oxidation of ammonia into nitrite is performed by two groups of organisms, ammonia-oxidizing
bacteria (AOB) and ammonia-oxidizing archaea (AOA
[2]
).
[3]
AOB can be found among the -
proteobacteria and gammaproteobacteria.
[4]
Currently, two AOA, Nitrosopumilus maritimus and
Nitrososphaera viennensis, have been isolated and described.
[5]
In soils the most studied AOB belong to
the genera Nitrosomonas and Nitrosococcus. Although in soils ammonia oxidation occurs by both AOB
and AOA, AOA dominate in both soils and marine environments,
[2][6][7]
suggesting that
Thaumarchaeota may be greater contributors to ammonia oxidation in these environments.
[2]
The second step (oxidation of nitrite into nitrate) is done (mainly) by bacteria of the genus Nitrobacter
and Nitrospira. Both steps are producing energy to be coupled to ATP synthesis. Nitrifying organisms
are chemoautotrophs, and use carbon dioxide as their carbon source for growth. Some AOB possess the
enzyme, urease, which catalyzes the conversion of the urea molecule to two ammonia molecules and one
carbon dioxide molecule. Nitrosomonas europaea, as well as populations of soil-dwelling AOB, have
been shown to assimilate the carbon dioxide released by the reaction to make biomass via the Calvin
Cycle, and harvest energy by oxidizing ammonia (the other product of urease) to nitrite. This feature
may explain enhanced growth of AOB in the presence of urea in acidic environments.
[8]
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In most environments, organisms are present that will complete both steps of the process, yielding
nitrate as the final product. However, it is possible to design systems in which nitrite is formed (the
Sharon process).
Nitrification is important in agricultural systems, where fertilizer is often applied as ammonia.
Conversion of this ammonia to nitrate increases nitrogen leaching because nitrate is more water-soluble
than ammonia.
Nitrification also plays an important role in the removal of nitrogen from municipal wastewater. The
conventional removal is nitrification, followed by denitrification. The cost of this process resides mainly
in aeration (bringing oxygen in the reactor) and the addition of an external carbon source (e.g.,
methanol) for the denitrification.
Nitrification can also occur in drinking water. In distribution systems where chloramines are used as the
secondary disinfectant, the presence of free ammonia can act as a substrate for ammonia-oxidizing
microorganisms. The associated reactions can lead to the depletion of the disinfectant residual in the
system.
[9]
The addition of chlorite ion to chloramine-treated water has been shown to control
nitrification.
[10][11]
Together with ammonification, nitrification forms a mineralization process that refers to the complete
decomposition of organic material, with the release of available nitrogen compounds. This replenishes
the nitrogen cycle.
Chemistry
Nitrification is a process of nitrogen compound oxidation (effectively, loss of electrons from the
nitrogen atom to the oxygen atoms):
1. 2 NH
4
+
+ 3 O
2
2 NO
2
-
+ 2 H
2
O + 4 H
+
(Nitrosomonas)
2. 2 NO
2
-
+ O
2
2 NO
3
-
(Nitrobacter, Nitrospina)
3. NH
3
+ O
2
NO
2

+ 3H
+
+ 2e

4. NO
2

+ H
2
O NO
3

+ 2H
+
+ 2e

Nitrification in the marine environment

In the marine environment, nitrogen is often the limiting nutrient, so the nitrogen cycle in the ocean is of
particular interest.
[12][13]
The nitrification step of the cycle is of particular interest in the ocean because it
creates nitrate, the primary form of nitrogen responsible for "new" production. Furthermore, as the ocean
becomes enriched in anthropogenic CO
2
, the resulting decrease in pH could lead to decreasing rates of
nitrification. Nitrification could potentially become a "bottleneck" in the nitrogen cycle.
[14]
Nitrification, as stated above, is formally a two-step process; in the first step ammonia is oxidized to
nitrite, and in the second step nitrite is oxidized to nitrate. Different microbes are responsible for each
step in the marine environment. Several groups of ammonia-oxidizing bacteria (AOB) are known in the
marine environment, including Nitrosomonas, Nitrospira, and Nitrosococcus. All contain the functional
gene ammonia monooxygenase (AMO) which, as its name implies, is responsible for the oxidation of
ammonia.
[2][13]
More recent metagenomic studies have revealed that some Thaumarchaeota (formerly
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Crenarchaeota) possess AMO. Thaumarchaeotes are abundant in the ocean and some species have a 200
times greater affinity for ammonia than AOB, leading researchers to challenge the previous belief that
AOB are primarily responsible for nitrification in the ocean.
[15]
Furthermore, though nitrification is
classically thought to be vertically separated from primary production because the oxidation of nitrogen
by bacteria is inhibited by light, nitrification by AOA does not appear to be light inhibited, meaning that
nitrification is occurring throughout the water column, challenging the classical definitions of "new" and
"recycled" production.
[15]
In the second step, nitrite is oxidized to nitrate. In the oceans, this step is not as well understood as the
first, but the bacteria Nitrospina and Nitrobacter are known to carry out this step in the sea.
[15]
Soil Conditions controlling nitrification rates
Substrate availability (presence of NH
4
+
)
Aeration (availability of O2)
Well-drained soils with 60% soil moisture
pH (near neutral)
Temperature (best 20-30C) => Nitrification is seasonal, affected by land use practices
See also
f-ratio
Haber process
Nitrifying bacteria
Nitrogen fixation
Simultaneous nitrification-denitrification
References
1. ^ Nitrification Network. "Nitrification primer" (http://nitrificationnetwork.org/Introduction.php).
nitrificationnetwork.org. Oregon State University. Retrieved 21 August 2014.
2. ^
a

b

c

d
Hatzenpichler R. (2012) Diversity, physiology and niche differentiation of ammonia-oxidizing
archaea. Appl Environ Microbiol 78: 7501-7510
3. ^ Treusch, A.H., Leininger, S., Kletzin, A., Schuster, S.C., Klenk, H.P., and Schleper, C. (2005) Novel
genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in
nitrogen cycling. Environ Microbiol 7: 19851995
4. ^ Purkhold, U., Pommerening-Roser, A., Juretschko, S.,Schmid, M.C., Koops, H.-P., and Wagner, M.
(2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA
sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 66: 53685382
5. ^ Martens-Habbena, W., Berube, P. M., Urakawa, H., de la Torre, J. R., Stahl, D. A. 2009. Ammonia
oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461: 976-981.
6. ^ Wuchter, C., Abbas, B., Coolen, M.J.L., Herfort, L., van Bleijswijk, J., Timmers, P., et al. (2006)
Archaeal nitrification in the ocean. Proc Natl Acad Sci USA 103: 1231712322.
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External links
Nitrification at the heart of filtration (http://www.fishdoc.co.uk/filtration/nitrification.htm) at
fishdoc.co.uk
Nitrification (http://www.abdn.ac.uk/~mbi010/nitrification.htm) at University of Aberdeen
King's College
Nitrification Basics for Aerated Lagoon Operators (http://www.lagoonsonline.com/ripple.htm) at
lagoonsonline.com
Retrieved from "http://en.wikipedia.org/w/index.php?title=Nitrification&oldid=626932466"
Categories: Nitrogen metabolism Soil biology
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7. ^ Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G.W., Prosser, J.I., Schuster, S.C.,
Schleper, C. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:7014
pages 806-9.
8. ^ Marsh, K. L., G. K. Sims, and R. L. Mulvaney. 2005. Availability of urea to autotrophic ammonia-
oxidizing bacteria as related to the fate of 14C- and 15N-labeled urea added to soil. Biol. Fert. Soil. 42:137-
145.
9. ^ Zhang, Y, Love, N, & Edwards, M (2009), "Nitrification in Drinking Water Systems", Critical Reviews in
Environmental Science and Technology, 39(3):153-208, doi:10.1080/10643380701631739
(http://dx.doi.org/10.1080%2F10643380701631739).
10. ^ McGuire, M.J., Lieu, N.I. and Pearthree, M.S. (1999). Using Chlorite Ion to Control Nitrification,
Journal American Water Works Association. 91:10 (October) 52-61.
11. ^ McGuire, M.J., Wu, X., Blute, N.K., Askenaizer, D., and Qin, G. (2009). Prevention of nitrification using
chlorite ion: Results of a demonstration project in Glendale, Calif., Journal American Water Works
Association. 101:10 (October) 47-59.
12. ^ Zehr, J. P. and R. M. Kudela. 2011. Nitrogen cycle of the open ocean: from genes to ecosystems. Annu.
Rev. Mar Sci. 3:197-225.
13. ^
a

b
Nitrification and Denitrification: Probing the Nitrogen Cycle in Aquatic Environments B. B. Ward
Microbial Ecology Vol. 32, No. 3 (1996), pp. 247-261
14. ^ Hutchins, D. A., Mulholland, M. R., Fu, F. (2009). Nutrient cycles and marine microbes in a CO2-enriched
ocean. Oceanography. Vol. 22, pp. 128-145.
15. ^
a

b

c
Zehr, J. P. and Kudela R. M.. 2011. Nitrogen cycle of the open ocean: from genes to ecosystems.
Annu. Rev. Mar Sci. 3:197-225.
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