Forms of Nitrogen in the Soil

In addition to nitrogen occurring as atmospheric dinitrogen gas in soil pore spaces, nitrogen occurs in both organic and inorganic forms in the soil.

Organic Nitrogen

Several organic compounds (compounds containing carbon) compose the organic fraction of nitrogen in soil. Soil organic matter exists as decomposing plant and animal residues, relatively stable products of decomposition-resistant compounds and humus. Nitrogen has accumulated in these various organic fractions during soil development.

Organic matter formation and stability is largely related to long-term moisture and temperature trends. With higher average temperatures, soil organic matter decreases. As moisture increases, soil organic matter increases. Higher temperatures lead to more rapid and complete organic matter decomposition to soluble products which can leach from soil. Increasing moisture causes more plant growth, resulting in more organic residue as you move south and east in the Great Plains (Figure 1.3).

Figure 1.3. Soil organic matter increases as you move south and east in the Great Plains (adapted from the Nature and Properties of Soils, Nyle C. Brady, 1974, MacMillan Publishers)

Through thousands of years of development, soils in the Midwest have accumulated significant quantities of organic matter. Yet, organic matter levels have declined due to the cultivation of virgin soils. This has increased organic matter oxidation and decreased soil organic matter nitrogen for crop uptake (Figure 5.1). Soils that once contained 4 to 5 percent organic matter may contain only 1 to 2 percent after 50 years of cultivation. However, soils under cultivation in the Midwest have, for the most part, reached a new equilibrium of organic matter levels with widespread commercial fertilizer use. Reduced tillage techniques in combination with legume rotations and judicious fertilizer use may help maintain or slightly increase organic matter levels with time.

Figure 5.1. The influence of tillage on organic nitrogen in soils in the Midwest. [Adapted from Hase, et al. (1957)]

The Nitrogen Cycle

Ammonium (NH4+) and nitrate (NO3) are the predominate inorganic forms of nitrogen in soils. Ammonium exists in exchangeable and nonexchangeable forms. Nitrite (NO2) and nitrous oxide (N2O) are present in soil in lesser quantities. Plants normally use nitrogen in only the ammonium and nitrate forms. Nitrite is actually toxic to plants. The nitrogen cycle (Figure 5.2) shows reactions that various inorganic nitrogen compounds undergo in soil. The nitrogen cycle, as typically described, begins with nitrogen in its simplest stable form, dinitrogen (N2), and follows it through the processes of fixation, mineralization, nitrification, leaching, plant assimilation, ammonia volatilizationdenitrification, and immobilization.

Figure 5.2.  The nitrogen cycle

Nitrogen Fixation

As described earlier, fixation is the process of converting dinitrogen gas to chemically reactive forms — where nitrogen combines with other elements such as oxygen, hydrogen, and carbon. These forms are dependent on fixation. Lightning fixes nitrogen into various oxides that rain and snow deposit. Typically, this is less than 10 pounds of total nitrogen per acre per year. Bacteria can convert nitrogen to organic forms through fixation. Fixation can occur either in free-living organisms or symbiotically in association with legumes. Nitrogen is also fixed industrially through several processes.

Nitrogen Mineralization

Once nitrogen is fixed, it is subject to several chemical reactions which can convert it to different organic or inorganic forms. Mineralization occurs in soil as microorganisms convert organic nitrogen to inorganic forms. The first step of mineralization is called aminization, in which microorganisms (primarily heterotrophs) break down complex proteins to simpler amino acids, amides, and amines. (Heterotrophic microorganisms require preformed organic compounds as sources of carbon and energy. Autotrophic microorganisms can derive energy from the oxidation of inorganic elements or compounds such as iron (Fe), sulfur (S), ammonium, nitrite, or from radiant energy.) They derive their carbon from carbon dioxide (CO2). For example, urea is an amide added directly to soil either in animal urine or as commercial fertilizer.

Aminization: Proteins ——> R+ -NH2 + R-OH

Ammonification is the second step of mineralization in which amino (NH2) groups are converted to ammonium. Again, microorganisms (primarily autotrophic) accomplish this action.

Ammonification: R-NH2 + H2O —> NH3 + R-OH


Microbial activity is also responsible for the two steps of nitrification. Nitrosomonas (obligate autotrophic bacteria) convert ammonium to nitrite. Nitrification inhibitors, such as nitrapyrin (N-ServeR) or dicyandiamide (DCD), interfere with the function of these bacteria, blocking ammonium conversion to leachable nitrate. The second step of nitrification occurs through Nitrobacter species, which convert nitrite to nitrate. This step rapidly follows ammonium conversion to nitrite, and consequently nitrite concentrations are normally low in soils.

                                                  Nitrosomonas              Nitrobacter                      

                      Organic Nitrogen ——————> Nitrite ——————> Nitrate

                      2NH4+ + 302 —> 2NO2 + 2H2O + 4H+ + 2NO2- + O2 —>2NO3

Mineralization and nitrification are influenced by environmental factors that affect biological activity such as temperature, moisture, aeration, pH, and so forth. Nitrification, for example, occurs very slowly at cold temperatures and ceases once the temperature declines below freezing (Figure 5.3). The rate increases with increasing temperature until bacterial viability is reduced (around 95oF to 100oF), and then nitrification begins to decline as the temperature increases. Moisture and oxygen are necessary for microbial function in both the mineralization and nitrification processes. Excessive moisture limits oxygen availability, reducing mineralization and nitrification rates, which, perhaps, leads to anaerobic soil conditions. Rates of mineralization and nitrification proceed most rapidly at pH levels near 7, and decline as soils become excessively acid or alkaline.

Figure 5.3.  Reductions in nitrification based on temperatures.  (Adapted from Western Fertilizer Handbook, 1995)


Saturating soils with a ready supply of nitrate can cause denitrification — the conversion of nitrate to various gaseous forms of nitrogen which can be lost to the atmosphere (nitric oxide, nitrous oxide, dinitrogen). Denitrification occurs under oxygen-limiting conditions when anaerobic bacteria use nitrate in respiration in the presence of carbon sources such as organic matter.

Low field areas which are subject to ponded water for sustained periods during the irrigation season often exhibit nitrogen deficiencies related to denitrification losses.

NO3 ——> NO2——>NO ——> N2O ——> N2

Denitrification losses from saturated soil will vary with temperature and the amount of carbon (organic matter) available. Table 5.1 illustrates the effect that time and temperature can have on potential nitrogen losses from denitrification.

Time (days) Temperature (degrees F) Nitrogen loss (percent)
3 75 - 80 6
5 55 - 60 10
10 55 - 60 25

Table 5.1.  Denitrification rates from saturated soil

Ammonia Volatilization

Ammonia (NH3) loss to the atmosphere is called ammonia volatilization. Technically, ammonia volatilization is different from gaseous loss of applied anhydrous ammonia, which is not retained in the soil. Instead, ammonia volatilization occurs when ammonium in the soil, because of pH, is converted to ammonia, which is lost as a gas. In Nebraska ammonia volatilization is normally only a problem with fertilizers containing urea, such as urea or urea-ammonium nitrate (UAN) solution. Urea is decomposed, or hydrolyzed, enzymatically in soil to ammonium.

CO(NH2)2 + H+ 2H20 —> 2NH4+ HCO3

Urea + Hydrogen + Water ——> Ammonia + Carbonate

NH4+ + OH- —> NH4OH + NH3_ + H2O

Ammonia loss can be significant where the producer surface-applies fertilizers containing urea and does not incorporate them. This is particularly true if significant amounts of residue are present and conditions are warm and moist. The amount of total nitrogen loss from fertilizers containing urea due to ammonia volatilization can vary considerably, from no loss to 50 percent or more of the applied nitrogen. Typical losses from urea broadcast to a silt loam soil in the spring, without rain for at least a week after application, may range from 10 to 20 percent of the applied nitrogen. The potential for ammonia volatilization is influenced by soil moisture, temperature, soil pH, soil buffering capacity, urease activity, residue cover, precipitation, wind and other factors. Warm, moist soil with heavy residue and urea broadcast on the surface are ideal conditions for ammonia loss. Precipitation or irrigation of 1/2 inch or more is adequate to move urea far enough into the soil to minimize volatilization loss. Tillage also will move urea into the soil to minimize or prevent volatilization of the nitrogen.

Nitrogen Leaching

For leaching to occur, nitrogen must be in a water soluble, mobile form and abundant enough to transport nitrogen through the soil. Although urea and nitrite are mobile, neither exists in significant concentrations in soil.  Nitrate is the nitrogen form most susceptible to leaching.  Nitrate leached below the root zone (four to six feet) for most agronomic crops will eventually leach downward until it reaches a saturated zone. Nitrate leached below four to six feet is generally unrecoverable by most crops except deep rooted species such as alfalfa. The rate of nitrate movement downward depends on a variety of factors, including soil texture, precipitation and irrigation amounts, and crop uptake of water and nitrate. Nitrate leaching from relatively sandy soils overlying coarse-textured vadose zones (zone of material between the surface and the water table) and shallow aquifers (such as in the Central Platte Valley) can leave the root zone and enter the aquifer in a matter of months, while nitrate leaching from upland, silt loam soils overlying aquifers 100 feet or more below the surface can take 25 to 30 years to reach the aquifer. 

Figure 5.4 shows the nitrate levels in the vadose zone of a 35-year irrigated continuous corn field and a native grass pasture. In this example from Seward County, the native grass pasture contains 307 pounds of nitrogen per acre to a depth of 80 feet, while the continuous corn field contains 1,224 pounds of nitrogen per acre to a depth of 100 feet.

Figure 5.4.  The effect of nitrate levels in the vadose zone of irrigated continous corn and pasture.  (Upper Big Blue Natural Resource District -- Mid-Nebraska Water Quality Demonstration Project)


Immobilization, or the temporary tying up of inorganic nitrogen by soil microorganisms decomposing plant residues, is not strictly a loss process. Immobilized nitrogen will be unavailable to plants for a time, but will eventually become available as residue decomposition proceeds and populations of microorganisms decline (Figure 5.5). Fertilizer nitrogen immobilization can be reduced by placing fertilizers below crop residues instead of incorporating fertilizer into the soil with residue. The producer can accomplish this most directly by knifing in anhydrous ammonia or solutions.

Figure 5.5.  Levels of nitrogen available to plants based on microbial decomposition.

The duration of the nitrate depression period during immobilization depends on environmental factors such as moisture and temperature and the carbon-to-nitrogen (C:N) ratio of the residue. Soil organic matter contains an average of about 50 percent carbon and 5 percent nitrogen. This ratio (10:1) is relatively constant for organic matter. The C:N ratio of plant residue ranges from 10:1 for young leguminous plant tissue to as high as 200:1 for straw of some grains. Plant tissues low in nitrogen generally are more resistant to decomposition and require a longer time before the nitrogen is available to plants.

When a plant residue with a wide C:N ratio is incorporated into the soil, microbial decomposition starts. Microorganism populations increase greatly, evidenced by increased release of CO2 leaving the soil through respiration. The microorganisms take nitrogen from the soil for proteins. Consequently, for a time the concentration of inorganic nitrogen in the soil declines, and may be deficient for plant growth. As residue decomposes, the C:N ratio narrows. At a ratio of approximately 17:1, nitrogen becomes available for plant use. Decomposition continues until the ratio is approximately 11:1 or 10:1.

Source C:N Ratio
undisturbed top soil 10:1
alfalfa 13:1
cattle manure 20:1
corn stalks 60:1
wheat straw 80:1
coal and shale oil 124:1
oak 200:1

Table 5.2.  Typical carbon-to-nitrogen ratios for elected organic materials

Plant Assimilation

Plants use nitrogen in primarily the nitrate or ammonium forms. If any preference exists, it is usually for ammonium early and nitrate late in the growing season. Research has shown that growth is optimized with a mixture of both ammonia and nitrate, with ammonium used preferentially for synthesis of amino acids and proteins. Some plants also can directly use urea (Harper, 1984), although in most cases urea-nitrogen will hydrolyze to ammonium-nitrogen prior to uptake. For plants to take up nitrogen, it must move with water toward the root — a process called mass flow. Consequently, nitrate-nitrogen that has moved below the root zone has potential to move up into the root zone as surface horizons of soil dry out and crops use water deeper in the profile. Conversely, plants may exhibit symptoms of nitrogen deficiency even though the soil contains adequate amounts of nitrogen, if moisture and consequently mass flow of nitrogen is limited.