© 2007 Donald G. McGahan (aka soilman) All Rights Reserved

Nitrogen is a primary and macro nutrient delivered to higher plans and, most, organisms in the soil as soluble ions.

The control of nitrogen (N) availability is dependent upon organic matter breakdown, reductions and oxidations in the soil. The reductions and oxidations (redox) are tied to organisms energy dynamics.

Nitrogen has volatile components that can be lost from the soil to the atmosphere.

Nitrogen is a major component of:

  • All proteins
  • Enzymes (enzymes are actually special proteins)1
  • Chlorophyll molecule

Nitrogen Deficiency (plant visual symptoms)

  • Chlorosis
    • Chlorosis is a yellowish or pale green leaf color
  • Stunted appearance
  • Thin spindly stems
  • Low shoot to root ratio
  • Mature quickly

Nitrogen is very mobile within the plant. The plant scavenges the N from compounds in the older leaves and translocations it to the newest vegetative structures. This is seen as chlorosis in the older leaves, senescent leaves, and loss of the older leaves.

Nitrogen Oversupply

  • Excessive vegetative growth
  • Enlarged–but weak–stems
  • Leads to lodging (falling over)
  • Delays plant maturity
  • Plants especially susceptible to disease
  • Plants especially susceptible to insect pests

Generally excess N can negatively impact color (fruit), flavor (fruit), vitamin levels (vegetables and roots), and cause low sugar levels (vegetables and roots) in plants. Vegetative parts of the plants can develop high levels of nitrate nitrogen harmful to livestock and human children when consumed.

Leaching of excess nitrogen is a major water pollution problem. In aquifers with excess nitrogen the nitrite (NO₂¯) content in the can cause methemoglobinemia "blue baby syndrome" which when consumed impacts young infants most strongly.

Plant uptake

Plants uptake N as:

  • Nitrate (NO₃¯)
  • Ammonium (NH₄⁺)
  • Dissolved Organic Nitrogen (DON)

In most systems the primary forms of plant uptake are the mineral forms NO₃¯ and NH₄⁺ and the proportional mix between the NO₃¯ and NH₄⁺ is dependent upon the soil chemophysical conditions. The fraction of DON that is absorbed by plants is also dependent upon the soil chemophysical conditions.

Nitrogen Sources

  • Considerable N exists in crustal rocks 2,000 Eg (An exagram is 10¹⁷)
  • Even more N exists in the atmosphere 4,000 Eg

The N locked away in the crustal rocks largely does not interface with soil processes.

The dominate form of atmospheric N, N₂, does interface with soil processes as it is quite inert. The air overlying the earths soils contains 78% gaseous nitrogen, but it is in a very stable di-nitrogen form (N₂) with a triple bond. The oxidation state of these N's is zero (0) or N⁰.

Atmospheric N₂ with its triple bond can be made more reactive by lighting breaking the triple bond or by biologically mediated means. This process is termed nitrogen fixation and should not be confused with ammonium fixation by minerals.

Reactive nitrogen compounds have N–usually–bonded to H, O, or C.
Examples are NH₄⁺, NO₃¯, N₂O, and amino acids R-C-NH₂.

Forms and Fates of Reactive Soil Nitrogen

Erosion and Runoff are losses of any nutrient element. Additionally there are six fates of specific interest:

  1. Immobilization by microorganisms
  2. Plant uptake
  3. Anammox
    • The anaerobic oxidation of NH₄⁺ in conjunction with nitrite (NO₂¯) to produce N₂O gas
  4. Volatilization
    • After being transformed into ammonia gas
  5. Nitrification
    • The microbial oxidation of ammonium (NH₄⁺) to nitrite (NO₂¯) and subsequently to nitrate (NO₃¯)
  6. Fixation or strong sorption
    • In the interlayers of certain 2:1 clay minerals

N Mineralization

The oxidative decomposition of the chemical compounds in organic matter making the nutrients in those compounds available to plants in soluble inorganic forms.

Nitrogen mineralization is a two step process

  1. Aminization
    • Degradation of organic N molecules
    • Proteins, chitin ⇨ amino acids, amino sugars, amines, urea
    • The substituent R–NH₂ is an amino group
  2. Ammonification
    • Amino group is split from the organic molecule
    • Amino acid + H₂O ⇨ NH₃ + organic rest + energy
    • NH₃ + H₂O ⇨ NH₄⁺ + OH¯


Microbial reduction of nitrate to form gaseous N2 or N20.

The bacteria Nitrosomonas converts ammonium to nitrite for energy.

NH₄⁺ + 1½ O₂ ⟶ NO₂¯ + H₂O + 2 H⁺ + 275 kJ energy

The bacteria Nitrobacter converts nitrite to nitrate for energy.

NO₂¯ + ½ O₂ ⟶ NO₃¯ + 76 kJ energy

Formation of nitrite (NO₂¯) is the slower reaction and conversion to nitrate (NO₃¯) is the faster reaction. Nitrite (NO₂¯) is quite toxic to most plants making the conversion and accumulation of nitrate more pronounced.

Organisms other than Nitrosomonas and Nitrobacter perform each of the two steps, but no organism is know to perform both steps. Nitrification is an heterotrophic aerobic process (requires oxygen and CO₂) and is therefor sensitive to water content levels. Temperature is also important where the most rapid conversion is between 20 and 30 ℃ and the conversion is quite slow below 5 ℃.

Ammonia volatilization

Ammonia volatilization
The transformation to ammonia and subsequent loss by evaporation or dispersing in vapor.

One fate of ammonium (NH₄⁺) is ammonia volatilization.

NH₄⁺ + OH¯ ⇄ H₂O + NH₃↑

  • Ammonia volatilization is more pronounced at high pH levels (i.e., OH-ions drive the reaction to the right)
  • Ammonia gas–producing amendments, or the addition of water, drives the reaction to the left, raising the pH of the solution in which they are dissolved


The incorporation N into the construction of microbiological organisms (μ–biol or μ–biols).

Plant uptake

Plant uptake
Plants will uptake ammonium (NH₄⁺) and nitrate (NO₃¯) from the soil solution.
This is distinct from immobilization.
The μ–bio will typically outcompete plants for these ammonium (NH₄⁺) and nitrate (NO₃¯) N sources if they are scarce in the soil solution.

Gaseous N Losses

The conversion of nitrate (NO₃¯) to gaseous forms.
These are reduction reactions.
These reductions are a result of the reactant being an electron acceptor.

2 NO₃¯ ⟶ 2 NO₂¯ ⟶ 2 NO(g) ⟶ N₂O(g) ⟶ N₂(g)

  • Nitrate (NO₃¯) N⁵⁺
  • Nitrite (NO₂¯) N⁴⁺
  • Nitric oxide gas (NO(g)) N²⁺
  • Nitrous oxide gas (N₂O(g)) N¹⁺
  • Dinitrogen gas (N₂(g)) N⁰
The conversion of ammonium (NH₄⁺) to dinitrogen (N₂) gaseous form.
Nitrite is used as the electron acceptor.
The nitrate is thought to come from the anaerobic nitrification reaction, but the anammox reduction is anaerobic.

NH₄⁺+ 1½ O₂ ⟶ NO₂¯ + 2 H⁺ + H₂O

NH₄⁺+ NO₂¯ ⟶ N₂ + 2 H₂O

Net Reaction: NH₄⁺+ 1½ O₂ ⟶ N₂ + 2 H⁺ +3 H₂O

Biological Nitrogen Fixation

Biological Nitrogen Fixation
Reduction and assimilation of N2, a capability of certain free-living and symbiotic bacteria.

Biological N fixation utilizes the enzyme nitrogenase. A few species of bacteria, actinomycetes, and cynobacteria convert atmospheric N₂ gas to organically combined aside groups.

The energy required for the fixations is high and this is why most N fixation is carried out by a symbiotic relationship between microbes and photosynthesizing plants. Symbiosis between Rhizobium or Bradyrhizobium and the legume family of plants in nodules on the plant roots. Frankia actionmycetes also perform N fixation in root nodules.

Lighting discharges, fires, automotive exhaust, and ammonia from volatilizations can be (re)deposited into the soil concomitant with precipitation events.

Nitrogen Losses

Nitrogen Losses
  • Leaching below the plant rooting zone
  • Runoff and erosion

Water containing > 45 ppm nitrate is considered unfit as drinking water (methemoglobinemia (Blue Baby Syndrome).

  1. Bailey, Regina. “The Function and Structure of Proteins.” ThoughtCo. (accessed July 8, 2019).