Soil, ammonification

Besides nitrogen fixation, the only other major source of reduced nitrogen is the decomposition of soil or aquatic organic matter. This process is called ammonification. Heterotrophic bacteria are principally responsible for this. These organisms utilize organic compounds from dead plant or animal matter as a carbon source, and leave behind NH3 and NHJ, which can then be recycled by the biosphere. In some instances heterotrophic bacteria may incorporate a complete organic molecule into their own biomass. The majority of the NH3 produced in this way stays within the biosphere however, a small portion of it will be volatilized. In addition to this source, the breakdown of animal excreta also contributes to atmospheric... 

The low temperatures and low soil pH that usually prevail at higher altitudes and latitudes (e.g., heathlands) restrain nitrification and (to a lesser extent) ammonification (92). Studies of N relations in temperate and boreal ecosystems have dem-... 

Measurements other than respiration rate can also be used as indicators of soil microbial activity. These include measurements of the rate of multienzyme processes such as arginine ammonification rate (Alef and Kleiner 1995) fluorescein diacetate (FDA) hydrolysis rate (Alef 1995) and measurement of key endocellular enzymes such as dehydrogenase (Tabatabai 1994). 

Alef K, Kleiner D (1995) Arginine ammonification. In Alef K, Nannipieri P (eds) Methods in applied soil microbiology and biochemistry. Academic Press, London, pp 238-240... 

Lipman CB, Burgess PS (1914) The effects of copper, zinc, iron and lead salts on ammonification and nitrification in soils. University of California Publications in Agricultural Science 1 127-139... 

Burger M, Jackson LE (2003) Microbial immobilization of ammonium and nitrate in relation to ammonification and nitrification rates in organic and conventional cropping systems. Soil Biol Biochem 35 29-36... 

Measured ammonification, nitrification, and denitrification of the soil in GEM, and its nonrecombinant parent. 

In 1888, Beijerinck published a series of reports entitled Die bakterien der Paplionacen-Knollchen which he called Bacillus radicicola. At about the same time (1885-1891) Bertholet, Warington and Winogradsky had isolated the main microorganisms from soil and water responsible for ammonification, nitrification and denitrification. 

The nitrogen supplies on land consist of the assimilable nitrogen in the soil VS2 0.19-104tkm-2, in plants (12 1091), and living organisms (0.2 1091). A diversity of nitrogen fluxes is formed here of the processes of nitrification, denitrification, ammonification, fixation, and river run-off. The intensities of these fluxes depend on climatic conditions, temperature regime, moisture, as well as the chemical and physical properties of soil. Many qualitative and quantitative characteristics of these dependences have been described in the literature (Hellebrandt et al., 2003). Let us consider some of them. 

Lin, Q. and Brookes, P. C. (1999b). Arginine ammonification as a method to estimate soil microbial biomass and microbial community structure. Soil Biol. Biochem. 31,1985-1997. 

Mineralization is usually defined as the production of ammonium from soil organic matter. This is sometimes called ammonification, which is a less confusing term. Mineralization usually causes only a small fractionation ( l%o) between soil organic matter and soil ammonium. In general, the 6 N of soil ammonium is usually within a few per mil of the composition of total organic nitrogen in the soil. 

Nitrogen is transferred to the atmosphere by low- and high-temperature processes. The high-temperature processes are biomass combustion and fossil-fuel combustion the low-temperature processes are volatilization of gases from soils and waters and turbulent injection of particulate matter into the atmosphere. The gases are generated primarily as a result of microbial activity (e.g., nitrification, denitrihcation, and ammonification). 

For the most part, nitrogen cycles within the ocean have the same microbial processes as in the soil (Figure 1). BNF is the dominant source of new nitrogen to the ocean, with other smaller contributions coming from atmospheric deposition and riverine runoff. Ammonification, nitrification, uptake, and decomposition are all critical components. There are two primary removal mechanisms—denitrification and burial in marine... 

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. 

Ammonification—The microbial conversion of organic nitrogen to ammonium in soil or water. 

Ammonification is the process by which the organically bound nitrogen of microbial, plant, and animal biomass is recycled after their death. Ammonification is carried out by a diverse array of microorganisms that perform ecological decay services, and its product is ammonia or ammonium ion. Ammonium is a suitable source of nutrition for many species of plants, especially those living in acidic soils. However, most plants cannot utilize ammonium effectively, and they require nitrate as their essential source of nitrogen nutrition. 

Ammonia is the primary basic gas in the atmosphere and, after N2 and N20, is the most abundant nitrogen-containing compound in the atmosphere. The significant sources of NH3 are animal waste, ammonification of humus followed by emission from soils, losses of NH3-based fertilizers from soils, and industrial emissions (Table 2.8). The ammonium (NH ) ion is an important component of the continental tropospheric aerosol. Because NH3 is readily absorbed by surfaces such as water and soil, its residence time in the lower atmosphere is estimated to be quite short, about 10 days. Wet and dry deposition of NH3 are the main atmospheric removal mechanisms for NH3. In fact, deposition of atmospheric NH3 and NH4" may represent an important nutrient to the biosphere in some areas. Atmospheric concentrations of NH3 are quite variable, depending on proximity to a source-rich region. NH3 mixing ratios over continents range typically between 0.1 and lOppb. 

Phosphorus is necessary for all organisms as a constituent of nucleic acids, phospholipids and other organic phosphate compounds. Its frequent deficiency in soils must be supplemented with phosphate fertilizers. Phosphorus is liberated from organic matter during ammonification. Phosphate is also made available to plants as a result of the formation by microorganisms of organic acids which dissolve insoluble inorganic phosphate compounds in the soil. 

Mineralization is basically a sequence of enzymatic reactions. Ammonia is stable under anaerobic conditions therefore, it is the primary form of nitrogen in wetland soils. Globally, ammonia represents only about 15% of the nitrogen released into the atmosphere. Although ammonification can occur in both aerobic and anaerobic environments, a higher concentration of ammonia is seen in anaerobic conditions due to the lower demand for nitrogen by anaerobic organisms. 

Temperature. The rate of ammonification increases with an increase in soil temperature. In contrast to most microbial processes, optimum temperature for conversion of organic nitrogen to ammonium nitrogen is between 40 and 60°C. These temperatures are seldom encountered under field conditions. In general, several studies reported that the rate of ammonification doubles with a temperature increase of 10°C, especially in the temperature range of 15-40°C (Kadlec and Reddy, 2001). 

Soil pH In most wetlands, pH is buffered around neutrality, whereas under drained soil conditions, pH of the soil decreases as a result of nitrate accumulation during mineralization. The optimum pH range for ammonification is between 6.5 and 8.5. 

The fate of ammonium nitrogen in wetland soils is summarized in Figure 8.25. Ammonification of organic nitrogen results in the release of ammonium into the soil solution, which is readily partitioned into dissolved phase and an adsorbed phase, maintaining a certain level of equilibrium between these two pools. Depending on the conditions found in wetlands, the fate of ammonium in soil solution includes (1) loss via volatilization as ammonia, (2) oxidation of ammonia by nitrifiers,... 

In the process of ammonification, hydroxylamine (NH2OH) is an important intermediate in two directions, denitrification direct to ammonium as well as the oxidation of ammonium to nitrate (nitrification). As long as nitrogen remains in its reduced form (NH4), it remains in the local environment because of its affinity for soil absorption and its rapid uptake by biota. NH4 is in equilibrium with NH3, which can escape to the atmosphere, depending on pH, temperature, soil moisture, soil type and atmospheric NH3 partial pressure. The equilibrium between emission and deposition (gas uptake) is called the compensation point, similar factors control the emission/dry deposition of NO. 

In summary, ammonia oxidation is negligible (4%) compared with the main fate of NH3, deposition (40 %) and particle formation (55 %) the numbers in parenthesis provide the percentage of emitted NH3 (Moller 2003). Thus, ammonia remains in its oxidation state -3, is mainly seen as ammonium (NH4) in air and returns to soils and waters as ammonium, where it moves between the amino group (—NH2) in the biomass and nitrate through nitrification and ammonification. 

Ammonium may be discharged directly into the sub-surface, or can be generated within the soil by ammonification. Its transport and fate involves a combination of the processes of adsorption, cation exchange, incorporation into biomass and release to the atmosphere in a gaseous form (Canter et al, 1987). Adsorption is possibly the main method of ammonium removal, and is particularly important under anaerobic conditions. With increasing pH, ammonium reacts to produce ammonia gas and can therefore be more easily released from the soil. 

I. AMMONIFICATION IN THE SOIL The dead bodies and excreta of living beings are attacked in the ground by the exoenzymes of many bacteria. For example, the exoenz3rmes of many Clostridia attack this dead matter and the proteins are converted to amino acids. Many bacteria release ammonia from these amino acids. The most active ammonifying oi anisms are Bacillus mycoidesy Proteus vulgaris and various actinomycetes. Quantitatively the most important process is oxidative deamination (p. 210). 

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