TD No.
04 - Part 1 Pedology
Chapter III: The Chemical and Biological Properties of Soil
6- Microbial Transformations
In all terrestrial ecosystems, essential life elements, known as biogenic elements, are
integrated into various living entities such as plants, animals, and microorganisms, and are
later released.
This process is often described as an element renewal, where these cyclic transformations of
the elements form what is called the material cycle.
Just as the continuous supply of solar energy captured by photosynthetic organisms, mainly
plants, these cyclic transformations, also known as biogeochemical cycles, are essential for
maintaining life on Earth.
The impact of microorganisms on these cycles varies depending on the element in question.
For carbon (C), nitrogen (N), and phosphorus (P), the intervention of microorganisms is
crucial.
In their absence or inactivity, the natural nitrogen supply in soils would be interrupted, and
the renewal of carbon, nitrogen, and phosphorus would be blocked, leading to the
accumulation of these elements in an organic form that is unusable by plants.
However, for other elements such as phosphorus (P), the action of microorganisms is less
pronounced.
1- Nitrogen Cycle
A- Definition
A natural cyclic process during which atmospheric nitrogen enters the soil, becomes part of
living organisms, and then returns to the atmosphere. Nitrogen in the soil is present in plant
residues, animal excrement, decomposing organic matter, humus, microbial biomass, and the
soil solution. It exists in three different forms:
● N2 in the air of the soil;
● Mineral:
● Nitrates NO3- directly assimilable by plants but can be leached into deeper horizons
or, to a lesser extent, volatilized into the atmosphere as ammonia (NH3) or N2
● Nitrites (NO2-) in the soil solution and NH4+
● Organic (98-99% of the total nitrogen in the soil) in organic molecules.
B- Nitrogen in the Soil
● Organic nitrogen is transformed into mineral nitrogen through the action of soil
bacteria (ammonification NH4+ followed by nitrification NO3-).
● The rate and intensity of these transformations depend on:
• The type of soil,
• The climatic conditions: rapid in sandy/clay soils and favored by heat and humidity.
C- Proportions of Different Forms of Nitrogen According to the Intensity of
Mineralization
● Significant mineralization: slightly alkaline pH, mainly NO3- (NH4+ is rare).
● Limited mineralization: slightly acidic pH, mainly NO3- (a little NH4+).
● Moderate and irregular mineralization: poor drainage, equal amounts of NH4+ and
NO3-.
● Low mineralization:
In heavy or acidic soils, NH4+ > NO3-.
In calcareous soils, NO3- > NH4+.
Most living organisms cannot use the molecule (N2); they need fixed nitrogen in which
nitrogen atoms are bound to other types of atoms: hydrogen in ammonia (NH3) or oxygen in
nitrate ions (NO3).
Processes are necessary to transform atmospheric nitrogen (N2) into a form that can be
assimilated by organisms: Nitrogen fixation, nitrification, and denitrification.
● Fixation: This refers to the conversion of atmospheric nitrogen into nitrogen that can
be used by plants and animals.
It is carried out by certain bacteria living in the soil or water, which are capable of
assimilating diatomic nitrogen (N2). Specifically, cyanobacteria and certain bacteria
that live symbiotically with plants (e.g., legumes) have the ability to produce
ammonia (NH3) from nitrogen and atmospheric hydrogen through an enzyme called
Nitrogenase. Ammonia can also come from the decomposition of dead organisms
(action of saprophytic bacteria) in the form of ammonium ions (NH4+). In soils with
high pH, ammonium is converted into gaseous ammonia.
● Nitrification: This process transforms the products of fixation (NH4+, nitrate ions
NH3) into (NOx) (either NO2- and NO3-), nitrites and nitrates.
● Plants absorb (NO3-) and, to a lesser extent, ammonia present in the soil through their
roots, incorporating them into amino acids and proteins.
● Plants thus constitute the primary source of nitrogen that can be assimilated by
animals.
● Denitrification: Through the action of denitrifying bacteria (which transform organic
matter), nitrogen returns to the atmosphere in its molecular form (N2), with secondary
products of CO2 and nitrous oxide (N2O) (a greenhouse gas).
● Human activity contributes to increased denitrification, especially through the use of
fertilizers that add ammonia compounds (NH4+, NH3) and nitrates (NO3-) to the soil.
The use of fossil fuels in engines or thermal power plants transforms nitrogen into
nitrogen oxides (NO2-).
