162 Ecological Processes | Ammonification

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Ammonification
J S Strock, University of Minnesota, Lamberton, MN, USA
ª 2008 Elsevier B.V. All rights reserved.

Introduction Ammonia and Ammonium in the Environment

Nitrogen Cycle Further Reading

Introduction proteins, and nucleic acids. Terrestrial, aquatic, and

atmospheric ecosystems receive nitrogen inputs through
This article presents a scientific overview of the process natural processes and human activities. The Earth’s
of ammonification. The first section provides a scientific atmosphere contains about 78% nitrogen. Nitrogen in
overview of the relevant components of the nitrogen the atmosphere is abundant but not in the right chemical
cycle related to ammonification. The subsequent sec- form unless it is transformed into more chemically avail-
tions emphasize important processes and mechanisms able forms. Nitrogen is introduced into terrestrial and
affecting ammonification in soil, water, and atmosphere aquatic ecosystems by biological and chemical nitrogen
ecosystems. fixation and removed again by denitrification.
A complete study of the nitrogen cycle and its interac-
tions requires contributions from biology (to understand
how nonreactive atmospheric nitrogen is ‘fixed’; molecu- Fixation
lar nitrogen (dinitrogen, N2) is reduced into oxidized Transfer of nitrogen between atmosphere and terrestrial
forms that can be assimilated by plants, by certain blue- and aquatic ecosystems begins with chemical or biological
green algae, and some genera of bacteria (e.g., Rhizobium fixation of molecular nitrogen. This process is carried out
spp.; Azotobacter spp.); chemistry (to understand how nitro- by lightning, by photochemical fixation in the atmos-
gen transformations between organic and inorganic phere, by the action of microorganisms, and industrially
components are influenced by pH, temperature, and oxi- by the Haber–Bosch process used in the manufacture of
dation–reduction status); mathematics (to model how commercial fertilizers. Nitrogen fixation is the conversion
nitrogen cycling processes vary in space and time); cli- of molecular, unreactive, dinitrogen gas (N2) to nitrogen
matology (to understand climate influences on the flow of combined with other elements, such as oxygen and
nutrients through biogeochemical cycles); hydrology (to hydrogen, into reactive forms that readily undergo
understand the dynamic cycling and pathways of nitrogen chemical reactions.
associated with water); environmental physics (to under- Ammonia (NH3) is the first product of nitrogen fixa-
stand how nitrogen losses from soil–water–atmosphere– tion. Biological nitrogen fixation is performed exclusively
plant systems affect the local, regional, and global by bacteria and related microorganisms using an enzyme
environments), and medicine (to understand nitrogen- complex termed nitrogenase. Biological nitrogen fixation
related illnesses). can be represented by the following equation, in which
two moles of ammonia are produced from one mole of
nitrogen gas, accompanied by the conversion of 16 mol-
Nitrogen Cycle ecules of adenosine triphosphate (ATP) to 16 molecules
of adenosine diphosphate (ADP) and the release of one
The nitrogen cycle represents one of the most important molecule of hydrogen (H2) and 16 molecules of inorganic
nutrient cycles found in terrestrial and aquatic ecosys- phosphate (Pi) as by-products.
tems. Nitrogen is used by living organisms to produce a
number of complex organic molecules like amino acids, N2 þ 8H þ 8e – þ 16ATP ¼ 2NH3 þ H2 þ 16ADP þ 16Pi
 Ecological Processes | Ammonification 163

This reaction is performed exclusively by bacteria and which NH2 groups are converted into ammonia or its
related organisms using an enzyme complex termed ionic form, ammonium (NHþ 4 ), as an end product.
nitrogenase. The most common nitrogenase consists Bacteria and related microorganisms derive metabolically
of two proteins, one large containing molybdenum, iron, useful energy from the oxidation of organic nitrogen to
and inorganic sulfur (dinitrogenase), the other smaller ammonium. Ammonium is then available to be assimi-
containing iron and inorganic sulfur (dinitrogenase lated and incorporated into amino acids or used for other
reductase). metabolic purposes. If microorganisms produce ammo-
Chemical fixation, through the Haber–Bosch process, nium in excess of their own metabolic requirements, the
is the reaction of nitrogen and hydrogen to produce surplus is excreted into the ambient environment, such as
ammonia. Nitrogen (N2 from the atmosphere) and hydro- soil or water, and is available for use as a nutrient by
gen (H2 from water) gases are reacted over an iron plants, or as a substrate for other microbial processes (e.g.,
catalyst (Fe3þ) and aluminum oxide (Al2O3) and potas- nitrification). Nitrogen transformation of organic nitrogen
sium oxide (K2O) are used as promoters. The reaction is compounds is not limited to microorganisms. Animals
carried out under conditions of 250 atmospheres (atm) excrete urea or uric acid in their nitrogen-containing
and 450–500  C. Delta H (
H) is the heat of reaction or urine, along with diverse organic nitrogen compounds in
enthalpy (92.4 kJ mol1 at 25  C). their feces. The urea, uric acid, and organic nitrogen of
feces are all substrates for ammonification. The general-
N2 þ 3H2 ! 2NH3 þ
H ized reaction for ammonification of soil organic
The Haber–Bosch process produces about 100 tera- compounds is
grams of nitrogen fertilizer per year, mostly in the form of
anhydrous ammonia, ammonium nitrate, and urea. That
fertilizer is responsible for sustaining 40% of the Earth’s
population, as well as causing various deleterious envi-
ronmental consequences. The generalized reaction for ammonification of urea is
urease
COðNH2 Þ2 þ 2HOH ¼ ðNH4 Þ2 CO3
Mineralization
ðNH4 Þ2 CO3 þ HOH ¼ 2NHþ –
4 þ 2OH þ CO2
Once nitrogen is fixed, it is subject to several chemical reac-
tions which can convert it to different organic and inorganic Nitrification
forms. Plants and microorganisms incorporate fixed nitrogen
into their cellular tissue. Animals receive their supply of Nitrification is the final step of mineralization. During the
nitrogen through the food they eat. These living organisms process of nitrification, ammonia or ammonium ions are
then use the nitrogen to manufacture amino acids and con- oxidized to nitrite (NO 
2 ) and then to nitrate (NO3 ).
vert them into proteins. Nitrogen in living and dead organic
matter and organic nitrogen fertilizers, such as urea, occurs
predominantly in the amino form (NH2). Mineralization
Ammonia and Ammonium in the
occurs in soil and sediment as microorganisms convert
Environment
organic nitrogen into inorganic forms. Mineralization is a
three-step process that begins with aminization, followed
Circulation of nitrogen in soil, water, and the atmosphere
by ammonification, and ends with nitrification.
results in numerous consequences as nitrogen undergoes
various transformations within the nitrogen cycle. As with
Aminization all components of the nitrogen cycle, the proper function-
ing of ammonification is essential for healthy, balanced,
Aminization is the first step of mineralization in which ecosystems.
microorganisms break down complex proteins into sim-
pler amino acids, amides, and amines.
Soil
Proteins ¼ RNH2 þ CO2
In crop and livestock production systems nitrogen is
(R designates a carbon chain of indefinite length) converted into cellular tissue. In crop production systems,
crop production (grain, fruit, forage, biomass) is sustained
through photosynthesis and uptake of water, nitrogen,
Ammonification
and other essential plant nutrients. In livestock produc-
Ammonification is the second step of mineralization. tion systems, animals assimilate nitrogen through the
Ammonification refers to any chemical reaction in consumption of amino acids in grains and forages.
164 Ecological Processes | Ammonification

Nitrogen is reintroduced into the soil system in the form high-pH soils or when applied to soil with large amounts
of crop residues and animal manure. In the absence of of crop residue on the soil surface, such as in no-till crop
ammonification, these organic forms of nitrogen would production. Ammonia, urea, and manure banded below
accumulate in large quantities. the soil surface or incorporated by tillage operations
Humans have a major influence on the nitrogen within 3 days can minimize ammonia volatilization and
cycle, especially through the use of manure and indust- promote conversion of available ammonia to ammonium
rially manufactured fertilizers in agricultural systems. In through ammonification.
intensively managed agricultural systems, nitrogen is In saturated soil, under anaerobic conditions, nitrogen
often the most limiting plant nutrient. Under nitrogen- can undergo respiratory denitrification, a microbial pro-
limited conditions, crop producers increase the availabil- cess wherein nitrate is transformed to dinitrogen gas.
ity of soil nitrogen by applying nitrogen fertilizer. Denitrification results in the production of molecular
Conventional cereal crop producers generally supply nitrogen or nitrogen oxides (i.e., nitrous oxide). These
just over half the crop nitrogen needs as industrially nitrogen gases are reintroduced into the atmosphere.
manufactured fertilizer and/or manure, with the other Formation of molecular nitrogen is favored where there
half supplied by recycled nitrogen from crop residue, is an available energy supply (i.e., carbon). The rate of
soil organic matter, atmospheric deposition, and biolo- denitrification is influenced by pH, being much slower in
gical nitrogen fixation. acid than in neutral or alkaline systems. Nitrate may also
The most common nitrogen sources of industrially be removed from saturated soil and sediment by dissim-
manufactured fertilizers contain nitrogen in the nitrate ilatory nitrate reduction. Dissimilatory nitrate reduction
and/or ammonium form or as urea. In some agricultural results in nitrate ammonification (nitrate reduction to
systems, compost or other organic materials (e.g., animal ammonium). The ammonification pathway results in
manure) may be added to soils as a nitrogen fertilizer microbial excretion of ammonium into the environment
source. Whether nitrogen is supplied by industrially man- where it is available for use as a plant nutrient, or as a
ufactured fertilizer or from animal manure, ammonia and substrate for nitrification. Compared to denitrification,
the organic forms of nitrogen must be converted to avail- nitrate ammonification is a less significant process for
able ammonium through ammonification before they are nitrate reduction.
available for plant and/or microbial assimilation.
In soil environments ammonia is rapidly converted to
Water
ammonium and subsequently to nitrate. The majority of
nitrogen assimilated by plants is usually in the nitrate Nitrogen cycling in aquatic ecosystems requires consid-
form; however, under flooded conditions, such as in rice eration of nitrogen inputs and the fate of those inputs. The
production, the soil is devoid of oxygen, biological nitri- major controls on nitrogen supply to a water body include
fication is limited, and most nitrogen stays in the land-use practices, landscape vegetation, atmospheric
ammonium form. Ammonium nitrogen, due to its posi- loading, soil processes, and hydrology, including artificial
tive charge, may be strongly adsorbed by ion-exchange drainage. The nitrogen status of a water body will largely
reactions to negatively charged surfaces of clay minerals depend on nitrogen storage, uptake, release, and exchange
or organic matter. Consequently, ammonium is not lea- by abiotic and biotic processes, within and between sedi-
ched very effectively by water as it percolates downward ments and the water column, and subsequent transport
through the soil. In contrast, nitrate is highly soluble in longitudinally downstream, in the case of flowing water.
soil water and is readily leached which can lead to sur- Biologically available forms of nitrogen (ammonia-,
face and groundwater degradation. In situations where nitrate-, and organic-nitrogen) are subject to an extensive
rates of nitrogen fertilization are greater than crop combination of physical and biogeochemical processes in
demand, the ability of the ecosystem to assimilate the aquatic systems. Once in an aquatic system, nitrogen is
nitrogen input becomes saturated. High-nitrate ground- highly chemically and biologically active, undergoing
water poses risks for human health, while surface waters numerous transformations and partitioning between the
may experience an increased productivity through dissolved and particulate phases, between sediment and
eutrophication. water column, and between the biotic and abiotic
Nitrogen loss in the gaseous ammonia form into the environments.
atmosphere is called ammonia volatilization. Ammonia The ammonification of organic nitrogen to ammonia
emissions occur from livestock housing and manure stor- or ammonium in water is similar to the process that
age systems, manure applied to soil, and ammonia occurs in soil. In aquatic environments, cyanobacteria
containing industrially manufactured fertilizers. (e.g., Anabaena spp.; Nostoc spp.) are important atmospheric
Ammonia losses from soil increase as soil moisture and nitrogen-fixing bacteria. Organic nitrogen in aquatic sys-
pH (acidity) increase. Ammonia emissions can also occur tems may be dissolved in the water column or it may be
when urea fertilizer granules are applied on the surface of associated with organic material deposited in sediments.
 Chemical Ecology | Animal Defense Strategies 165

In either case, ammonification converts organic nitrogen residence times in the atmosphere and are reintroduced
to ammonia and ammonium which, under aerobic condi- into soil and water ecosystems usually within hours to
tions, are rapidly converted to nitrate by nitrification. days. Regional accumulation of ammonia and ammonium
Ammonia is known to be acutely toxic to some freshwater can occur in the lower atmosphere. Atmospheric
vertebrates and invertebrates. Equilibrium exists in water ammonia reacts to form ammonium aerosol which is
between toxic ammonia and nontoxic ammonium. The associated with decreased atmospheric visibility, acid
dynamic equilibrium between ammonia and ammonium rain, soil acidification, eutrophication, and human health
is affected by water temperature and pH. At a pH of 6.0 impacts.
the ratio of ammonia to ammonium is about 1 to 3000 but
decreases to 1 to 30 when the pH rises to 8.0 (becomes less
acidic). Warm water will contain more toxic ammonia See also: Acidification; Atmospheric Deposition;
than cool water. Biological assimilation of ammonium by Biodegradation; Decomposition and Mineralization;
bacteria, biofilms, and aquatic plants is preferred to nitrate Denitrification; Nitrification; Nitrogen Cycle.
assimilation.
Nitrate disappearance in aquatic ecosystems is gener-
ally due to either respiratory denitrification or Further Reading
dissimilatory nitrate reduction to ammonium. Both these
Atlas RM and Bartha R (1987) Microbial Ecology. Menlo Park, CA:
processes occur exclusively in sediments. Regardless of Benjamin/Cummings Publishing.
the amount of nitrogen entering aquatic systems from Brady NC and Weil RR (1999) The Nature and Properties of Soils, 13th
terrestrial sources, any substantial reduction in nitrogen edn. Englewood Cliffs, NJ: Prentice Hall.
Galloway JN, Aber JD, Erisman JW, et al. (2003) The nitrogen cascade.
will decrease the impacts of nitrogen loading. BioScience 53: 341–356.
Galloway JN, Cowling E, Erisman JW, Wisniewski J, and Jordan C (eds.)
(2002) Optimizing Nitrogen Management in Food and Energy
Atmosphere Production and Environmental Protection. Lisses: A. A. Balkema
Publishers.
The atmosphere receives and circulates nitrogen as air Ladd JN and Jackson RB (1982) Biochemistry of ammonification.
emissions of nitrogen oxide (NOx), ammonia and ammo- In: Stevenson FJ (ed.) Nitrogen in Agricultural Soils, pp. 173–228.
Madison, WI: ASA-CSSA-SSSA.
nium (NHx), and nitrous oxide (N2O) from aquatic and Mortvedt JJ, Murphy LS, and Follett RH (1999) Fertilizer Technology and
terrestrial ecosystems. These gases have relatively short Application. Willoughby, OH: Meister Publishing.

Animal Defense Strategies

D Spiteller, Max Planck Institute for Chemical Ecology, Jena, Germany
ª 2008 Elsevier B.V. All rights reserved.

Introduction Reptile Defense

Mechanical Barriers Bird Defense
Hiding, Camouflage, and Mimicry Mammalian Defense
Arthropod Defense Conclusions
Amphibian Defense Further Reading

Introduction introduced into the attacker, for example, with the help
of a sting (bees) or a poison fang (snakes). A form of
In contrast to plants, animals cannot regenerate comple- passive defense is an unpleasant, often bitter taste of a
tely after attack. Therefore, their defense often is to rely prey that will teach the predator to avoid further feeding
on constitutively expressed defensive compounds. on such species.
Especially those animals which are too slow to escape Defensive compounds are either produced by the
their predators have developed very effective repellents organism itself, or taken up from the food and stored
or toxins. It can be distinguished between active and (sequestered), or are obtained from associated symbiotic
passive defense. For active defense, toxins are actively microorganisms.