Nitrification
Nitrification
Nitrification as a bacterial process
Environmental influences on nitrification
Nitrification is an aerobic microbial process by which specialized bacteria oxidize ammonium to nitrite and then to nitrate. Nitrification is a very important part of the nitrogen cycle, because for most plants nitrate is the preferred chemical form of nitrogen up take from soil or water.
Nitrification is a two-step process. The first stage is the oxidation of ammonium (NH4+) to nitrite (NO2–), a function carried out by bacteria in the genus Nitrosomonas. The nitrite formed is rapidly oxidized to nitrate (NO3–) by bacteria in the genus Nitrobacter. Because nitrate and nitrite are much more mobile in soils than ammonium, nitrification can be viewed as a process that mobilizes nitrogen, making it more available for plant uptake but potentially allowing it to leach from the ecosystem. The latter is an undesirable attribute of nitrification because fixed nitrogen is an important component of the nutrient capital of ecosystems. In addition, large concentrations of nitrate or nitrite can pollute ground-water and surface waters.
Nitrification as a bacterial process
Nitrification is an autotrophic process during which bacteria couple energy release from the oxidation of ammonium with the biosynthesis of simple inorganic molecules such as carbon dioxide and water into organic compounds. Because chemical energy is being tapped by the bacteria, nitrification is known as a chemoautotrophic process rather than photoautotrophic, as when green plants utilize sunlight in their photosynthetic productivity.
Only a few types of aerobic bacteria are capable of performing the chemical reactions of nitrification. The first step in nitrification is the oxidation of ammonium to nitrite. This function is mostly carried out by bacteria in the genus Nitrosomonas, with lesser activity by the genera Nitrosospira, Nitrosococcus, and Nitrosolobus. The nitrite formed by these bacteria does not accumulate in soil because it is rapidly oxidized to nitrate. This stage is mostly accomplished by bacteria in the genus Nitrobacter, along with Nitrosospira and Nitrosococcus.
Environmental influences on nitrification
Any chemical reaction requires substrate molecules, which in the case of nitrification is ammonium. The most important natural source of this substrate is ammonium released from decaying organic matter through the microbial process of ammonification, during which this ion is produced as a waste product of the oxidation of various forms of organic nitrogen such as proteins. There are also inputs of ammonium from the atmosphere, both dissolved in precipitation and through the dry deposition of gas. The biological fixation of atmospheric dinitrogen (or nitrogen gas, N2) into ammonia can be another important source of input, especially when legumes are cultivated in agriculture as well as in some natural ecosystems, for example, sites dominated by alders (Alnus spp.). Ammonium may also be added to agricultural soils in large quantities when inorganic fertilizers are used or when manure or sludges are spread on fields.
The genera of bacteria that are responsible for nitrification are highly sensitive to acidity, so this process does not occur at significant rates in acidic soil or water, especially in those with pH less than 5.5. Plants that grow in acidic habitats such as bogs and some forests must be capable of utilizing ammonium as their source of nitrogen nutrition because nitrate is not available in those habitats. Because Nitrobacter is somewhat more sensitive to acidity and some other stresses than Nitrosomonas, nitrite can accumulate under some conditions.
Interestingly, nitrification is a process that actually generates acidity, equivalent to two H+ ions for every ion of NO3– produced by the oxidation of NH4+. However, the ammonification of organic nitrogen to ammonium consumes one H+, as does the uptake of nitrate from soil by plant roots. Therefore, nitrification only acidifies soils if the ammonium substrate is added directly, for example through fertilization or by atmospheric deposition, or if the nitrate is not taken up by plants and leaches from the soil.
The nitrifying bacteria are also very sensitive to high temperatures. Their populations are substantially reduced by exposures to temperatures of 212°F (100°C), and they are virtually eliminated at temperatures hotter than 284°F (140°C). As a result, nitrifying bacteria are often uncommon after a ground fire. The rates of nitrification are correspondingly small, even if there is an abundant substrate of ammonium.
The rate of nitrification is known to decline during some ecological successions. This is probably caused by an increasing acidification of the ecosystem and perhaps also by the presence of organic chemicals that inhibit the nitrifying bacteria. Decreasing nitrification has been observed during the succession of abandoned pastures into old-field conifer forests in eastern North America as well as in conifer forest successions elsewhere. A potential benefit of decreasing nitrification during succession is that this causes the major form of soluble, inorganic nitrogen to become ammonium, an ion that is bound readily by soils and is not easily leached. However, nitrification does not always decrease during succession; it is known to increase when some abandoned farmlands develop into an angiosperm forest which tends not to acidify soils as much as most conifer forests.
Humans and nitrification
The use of nitrogen-containing fertilizers in agriculture has a strong influence on nitrification and on the nitrogen cycle more broadly. Rates of fertilization in intensive agricultural systems often exceed 500 kg of nitrogen per hectare per year. Much of the nitrogen addition occurs as ammonia or ammonium which is the substrate for nitrification, so this process can occur very rapidly, and nitrate may be present in large concentrations.
If soils with large nitrate concentrations become wet and anaerobic conditions develop, the rate of denitrification is greatly increased. Denitrification represents a loss of fixed nitrogen capital, and the emitted nitrous oxide (N2O) may contribute to an enhancement of Earth’s greenhouse effect.
If the availability of nitrate overwhelms the ability of the plant crop and soil microbes to assimilate this nutrient, some of the nitrate will leach from the site into groundwater and surface waters such as streams and rivers. This can contribute to the increased productivity of surface waters through eutrophication. In addition, large concentrations of nitrate in ground-water are of great concern for several reasons. Nitrate can react with amino compounds to form nitrosamines, which are poisonous and carcinogenic. Nitrate itself is not particularly toxic, but it can be chemically reduced in the gut of animals to form toxic nitrite. This reaction occurs especially rapidly in the relatively alkaline gut of infant humans, so
KEY TERMS
Ammonification —The microbial conversion of organic nitrogen to ammonium in soil or water.
Denitrification —The anaerobic, microbial reduction of nitrate to gaseous nitrous oxide (N2O) or nitrogen gas (N2) which are then emitted to the atmosphere.
Dinitrogen fixation (nitrogen fixation) —The conversion of atmospheric dinitrogen (i.e., N2) to ammonia or an oxide of nitrogen. This process can occur inorganically at high temperature and/or pressure and biologically through action of the microbial enzyme, nitrogenase.
Leaching —The process of movement of dissolved substances in soil along with percolating water.
Nitrification —The process by which Nitrosomonas bacteria oxidize ammonium to nitrite which is then oxidized by Nitrobacter to nitrate.
they are especially sensitive to nitrite poisoning if they drink well waters with large concentrations of nitrate. Nitrite combines with hemoglobin in the blood, forming a relatively stable complex that is therefore not available to transport oxygen and carbon dioxide and resulting in a toxic condition known as the “blue baby” syndrome. Cattle and sheep can also be poisoned by excessive exposures to nitrate, because nitrites are also readily formed by bacteria in their rumen.
See also Nitrogen fixation.
Resources
BOOKS
Freedman, B. Environmental Ecology. 2nd ed. San Diego: Academic Press, 1995.
McArthur, J.V. Microbial Ecology: An Evolutionary Approach. New York: Academic Press, 2006.
Sylvia, D.M., et al. Principles and Applications of Soil Microbiology, 2nd ed. Upper Saddle River, NJ: Prentice Hall, 2004.
Bill Freedman
Nitrification
Nitrification
Nitrification is an aerobic microbial process by which specialized bacteria oxidize ammonium to nitrite and then to nitrate. Nitrification is a very important part of the nitrogen cycle , because for most plants nitrate is the preferred chemical form of nitrogen uptake from soil or water .
Nitrification is a two-step process. The first stage is the oxidation of ammonium (NH4+) to nitrite (NO2-), a function carried out by bacteria in the genus Nitrosomonas. The nitrite formed is rapidly oxidized to nitrate (NO3-) by bacteria in the genus Nitrobacter. Because nitrate and nitrite are much more mobile in soils than ammonium, nitrification can be viewed as a process that mobilizes nitrogen, making it more available for plant uptake but potentially allowing it to leach from the ecosystem . The latter is an undesirable attribute of nitrification because fixed nitrogen is an important component of the nutrient capital of ecosystems. In addition, large concentrations of nitrate or nitrite can pollute groundwater and surface waters.
Nitrification as a bacterial process
Nitrification is an autotrophic process during which bacteria couple energy release from the oxidation of ammonium with the biosynthesis of simple inorganic molecules such as carbon dioxide and water into organic compounds. Because chemical energy is being tapped by the bacteria, nitrification is known as a chemoautotrophic process rather than photoautotrophic, as when green plants utilize sunlight in their photosynthetic productivity.
Only a few types of aerobic bacteria are capable of performing the chemical reactions of nitrification. The first step in nitrification is the oxidation of ammonium to nitrite. This function is mostly carried out by bacteria in the genus Nitrosomonas, with lesser activity by the genera Nitrosospira, Nitrosococcus, and Nitrosolobus. The nitrite formed by these bacteria does not accumulate in soil because it is rapidly oxidized to nitrate. This stage is mostly accomplished by bacteria in the genus Nitrobacter, along with Nitrosospira and Nitrosococcus.
Environmental influences on nitrification
Any chemical reaction requires substrate molecules, which in the case of nitrification is ammonium. The most important natural source of this substrate is ammonium released from decaying organic matter through the microbial process of ammonification , during which this ion is produced as a waste product of the oxidation of various forms of organic nitrogen such as proteins . There are also inputs of ammonium from the atmosphere, both dissolved in precipitation and through the dry deposition of gas. The biological fixation of atmospheric dinitrogen (or nitrogen gas, N2) into ammonia can be another important source of input, especially when legumes are cultivated in agriculture as well as in some natural ecosystems, for example, sites dominated by alders (Alnus spp.). Ammonium may also be added to agricultural soils in large quantities when inorganic fertilizers are used or when manure or sludges are spread on fields.
The genera of bacteria that are responsible for nitrification are highly sensitive to acidity, so this process does not occur at significant rates in acidic soil or water, especially in those with pH less than 5.5. Plants that grow in acidic habitats such as bogs and some forests must be capable of utilizing ammonium as their source of nitrogen nutrition because nitrate is not available in those habitats. Because Nitrobacter is somewhat more sensitive to acidity and some other stresses than Nitrosomonas, nitrite can accumulate under some conditions.
Interestingly, nitrification is a process that actually generates acidity, equivalent to two H+ ions for every ion of NO3– produced by the oxidation of NH +4 . However, the ammonification of organic nitrogen to ammonium consumes one H+, as does the uptake of nitrate from soil by plant roots. Therefore, nitrification only acidifies soils if the ammonium substrate is added directly, for example through fertilization or by atmospheric deposition, or if the nitrate is not taken up by plants and leaches from the soil.
The nitrifying bacteria are also very sensitive to high temperatures. Their populations are substantially reduced by exposures to temperatures of 212°F (100°C), and they are virtually eliminated at temperatures hotter than 284°F (140°C). As a result, nitrifying bacteria are often uncommon after a ground fire. The rates of nitrification are correspondingly small, even if there is an abundant substrate of ammonium.
The rate of nitrification is known to decline during some ecological successions. This is probably caused by an increasing acidification of the ecosystem and perhaps also by the presence of organic chemicals that inhibit the nitrifying bacteria. Decreasing nitrification has been observed during the succession of abandoned pastures into old-field conifer forests in eastern North America as well as in conifer forest successions elsewhere. A potential benefit of decreasing nitrification during succession is that this causes the major form of soluble, inorganic nitrogen to become ammonium, an ion that is bound readily by soils and is not easily leached. However, nitrification does not always decrease during succession; it is known to increase when some abandoned farmlands develop into an angiosperm forest which tends not to acidify soils as much as most conifer forests.
Humans and nitrification
The use of nitrogen-containing fertilizers in agriculture has a strong influence on nitrification and on the nitrogen cycle more broadly. Rates of fertilization in intensive agricultural systems often exceed 500 kg of nitrogen per hectare per year. Much of the nitrogen addition occurs as ammonia or ammonium which is the substrate for nitrification, so this process can occur very rapidly, and nitrate may be present in large concentrations.
If soils with large nitrate concentrations become wet and anaerobic conditions develop, the rate of denitrification is greatly increased. Denitrification represents a loss of fixed nitrogen capital, and the emitted nitrous oxide (N2O) may contribute to an enhancement of Earth's greenhouse effect .
If the availability of nitrate overwhelms the ability of the plant crop and soil microbes to assimilate this nutrient, some of the nitrate will leach from the site into groundwater and surface waters such as streams and rivers . This can contribute to the increased productivity of surface waters through eutrophication . In addition, large concentrations of nitrate in groundwater are of great concern for several reasons. Nitrate can react with amino compounds to form nitrosamines, which are poisonous and carcinogenic. Nitrate itself is not particularly toxic, but it can be chemically reduced in the gut of animals to form toxic nitrite. This reaction occurs especially rapidly in the relatively alkaline gut of infant humans, so they are especially sensitive to nitrite poisoning if they drink well waters with large concentrations of nitrate. Nitrite combines with hemoglobin in the blood , forming a relatively stable complex that is therefore not available to transport oxygen and carbon dioxide and resulting in a toxic condition known as the "blue baby" syndrome . Cattle and sheep can also be poisoned by excessive exposures to nitrate, because nitrites are also readily formed by bacteria in their rumen.
See also Nitrogen fixation.
Resources
books
Atlas, R. M., and R. Bartha. Microbial Ecology. Menlo Park, CA: Benjamin/Cummings, 1987.
Freedman, B. Environmental Ecology. 2nd ed. San Diego: Academic Press, 1995.
Bill Freedman
KEY TERMS
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .- Ammonification
—The microbial conversion of organic nitrogen to ammonium in soil or water.
- Denitrification
—The anaerobic, microbial reduction of nitrate to gaseous nitrous oxide (N2O) or nitrogen gas (N2) which are then emitted to the atmosphere.
- Dinitrogen fixation (nitrogen fixation)
—The conversion of atmospheric dinitrogen (i.e., N2) to ammonia or an oxide of nitrogen. This process can occur inorganically at high temperature and/or pressure and biologically through action of the microbial enzyme, nitrogenase.
- Leaching
—The process of movement of dissolved substances in soil along with percolating water.
- Nitrification
—The process by which Nitrosomonas bacteria oxidize ammonium to nitrite which is then oxidized by Nitrobacter to nitrate.
Nitrification
Nitrification
A biological process involving the conversion of nitrogen-containing organic compounds into nitrates and nitrites . It is accomplished by two groups of chemo-synthetic bacteria that utilize the energy produced. The first step involves the oxidation of ammonia to nitrite, and is accomplished by Nitrosomas in the soil and Nitrosoccus in the marine environment . The second step involves the oxidation of nitrites into nitrates , releasing 18 kcal of energy. It is accomplished by Nitrobacter in the soil and Nitrococcus in salt water. Nitrification is an integral part of the nitrogen cycle , and is usually considered a beneficial process, since it converts organic nitrogen compounds into nitrates which can be absorbed by green plants. The reverse process of nitrification, occurring in oxygen-deprived environments, is called denitrification and is accomplished by other species of bacteria.