Chapter 7

SOIL BIOLOGICAL PROPERTIES AND

SOIL ORGANIC MATTER

Most Essential Learning Outcomes

After reading this section, you must have:

1. Discussed the biological properties of soils

2. Knew how to evaluate soil biological properties
3. Discussed the nature and significance of soil organic matter
4. Explained how soil biological properties affect land use and soil management

Indicative Content (Week 11-12)

 Soil fauna and flora

 Soil microorganisms
 Biological nitrogen fixation
 Mycorrhiza
 Soil organic matter

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Soil Fauna and Flora

Soil is the habitat of a multitude of organisms. Because of this, there is constant interaction
between soil organisms and the soil itself. Soil organisms constantly change the soil, which in
turn affects the organisms themselves.

The species diversity of soil animals even within a small area, is very high. All major animal
phyla except Coelenterata and Eichinodermata, are represented in the soils of the world. The
higher taxa (orders,classes) of the smallest soil animals are the most widespread in terrestrial
ecosystems.

All small and large soil organisms play important roles in the intricate biological processes
operative in soils. They accomplish a lit of biochemical reactions necessary for nutrient cycling
and other vital soil processes. They mix the soil (bioturbation), help stabilize soil structure and
decompose plant and animal residue. They also participate in soil formation.

Soil organisms include both flora (plants) and fauna (animals).

Soil fauna
● soils animals vary from the microscopic like protozoa to the small mammals.

Effects of soil animals on the soil:

● mounding
● mixing
● formation of voids
● back-filling of voids
● formation and destruction of peds
● regulation of soil erosion
● regulation of plant litter and nutrient cycling
● production of special compounds

Soil flora
 except for the roots of higher plants, soil flora consists mostly of microscopic organisms
which play vital roles in biochemical processes in the soil.

Soil microorganisms
● are very small soil fauna and flora. Their most important functions in the soil are organic
material decomposition and elemental transformations.

Two broad classes:

● heterotrophic or chemoorganotrophic
● autotrophic or lithotrophic

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Five major groups of soil microorganisms:

● Bacteria – the most prominent and numerous soil microorganisms. Examples are
nitrosomonas, nitrobacter and thiobacillus.
● Actinomycetes – heterotrophic microorganisms than generally produce slender, branched
filaments that developed into a mycelium. They are second to bacteria in abundance.
● Fungi – heterotrophic microorganisms which possess a filamentous mycelium network of
individual hyphal strands. They account for a great part of microbial biomass in well-
aerated soils and are dominant in acid soil environments.
● Algae – autotrophic microorganisms that occur in lesser number than bacteria,
actinomycetes, and fungi. They are abundant in moist environments and their major
function in terrestrial ecosystems is the generation of organic matter from inorganic
substances.
● Protozoa – simplest form of animal life. They are microscopic terrestrial animals which are
typically devoid of chlorophyll. They are found in moist soils but their role is still poorly
understood.

Biological activity in the soil

The activities of specific groups of soil organisms are commonly identified by:
● their numbers per unit volume of soil
● their weight per unit volume or area of soil (biomass)
● their metabolic activity in terms of:
soil enzyme activity
● are proteins produced by living cells in the soil such as microorganisms, soil animals,
roots or plant remains.

rate of soil respiration

● generally indicated by CO2 production

Biological Nitrogen Fixation (BNF)

The capability of biological fixation of atmospheric nitrogen (N2) is restricted to organisms

with prokaryotic cell structure namely: bacteria and blue-green algae (Cyanobacteria)

The conversion of the inert N2 molecule into combined nitrogen ( NH 3, NO3-, etc.) which
can be utilized as a mineral nutrient is brought about either by reduction to ammonia ( NH 3) or
oxidation to nitrate ( NO3-). The conversion, called fixation, is highly energy consuming. In both
industrial and biological fixation the reaction N 2---> 2NH3 dominates. In industrial fixation, N2 is
catalytically reduced to NH3 by reaction with hydrogen ( from natural gas) in the Haber- Bosch
process ( N2 + 3H2---> 2NH3) under conditions of high temperature and pressure. In contrast,
biological nitrogen fixation occurs at low temperature and atmospheric pressure.

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Three strategies of biological N 2 fixation in terrestrial ecosystems:
1. symbiotic
2. associative
3. free-living

Mycorrhizas

Mycorrhizas (fungus-root association) are the most widespread associations between

microorganisms and higher plants. On a global basis, the association occurs in 83% of
dicotyledonous and 79% of monocotyledonous plants and in all Gymnosperms. Non-mycorrhizal
plants occur in habitats where the soils are either very dry or saline, or waterlogged, severely
disturbed as in mining areas, or where soil fertility is extremely high or extremely low.

As a rule, the fungus is strongly or wholly dependent on the higher plant, whereas the
plant may or may not benefit from the association. Only in some instances (orchids) are the
mycorrhizas essential. Mycorrhizal associations are therefore either mutualistic, neutral, or
parasitic depending on the circumstances although mutualism is the dominant type.

Groups of mycorrhiza:
➢ endomycorrhiza
➢ ectomycorrhiza

Formation of soil organic matter

First Phase. This is also called the biochemical phase. This involves enzymatic reactions in the
cells upon the death of the plant or an animal resulting in the breaking down of the compound into
individual components. However, there is no observable change in the structure of the organic
material. Much of the mineral nutrients such as Fe, K, Mg, Ca, are released and washed out by
the rain.

Second Phase. This is the mechanical disintegration phase. This involves the mechanical
disintegration of the organic material through the activities of the meso and macro fauna. In the
soil profile, the organic material is mixed with the soil in process called bioturbation.

Third Phase. This is the microbial decomposition phase. The disintegrated plant and animal
residues including the excrements of soil animals are acted upon by microorganisms resulting in
complete change of the molecular structure of the organic materials and the synthesis of stable
products called humic substances or humus. The process of humic substances formation is called
humification.

During the decomposition process, several intermediate products are produced during the
transformation of C, O and H in the organic material into CO 2 and H2O with the release of energy
for the microorganisms (approx. 5 kilocalories per gram of air-dry substance). In addition,

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organically bound elements are released as inorganic forms such as CO 2, CH4, NH4+, NO3-, SO42-
, HPO42-, K+, Ca2+, and Mg2+ in a process known as mineralization.

Factors affecting decomposition process

Kinds of organic material - this controls the composition of the decomposer community and their
activity and distribution. Materials containing high lignin and cellulose are slow to decompose. On
the other hand, young plant materials then are easier to decompose. Materials like rice straw
having a C:N ratio greater than 25:1 slows down the decomposition process. Also, the presence
of inhibitory substances like phenols often inhibit the decomposition process.

Climate - warm and humid climate favors rapid decomposition. Thus, the decomposition process
in the tropics is four times faster than the temperate regions.

Soil characteristics - aside from drainage, the most dominant soil characteristics affecting the
decomposition process are soil pH, soil texture and soil structure.

Soil pH- basic soil environment enhances litter decomposition while in acidic soil, the initial
decomposition is generally slow. Ca which is high in basic soils enhances the formation of stable
humus compounds.

Soil texture- heavy soils generally show lower decomposition rates than sandy soils. This is due
to the adsorption of organic matter on clay surfaces and the restricted movement of
microorganisms in the soil.

Soil structure- organic matter is protected from decomposition inside aggregates. A significant
proportion of this protected organic matter is found inside stable aggregates.

Major components of soil organic matter

The soil organic matter is comprised of a mixture of undecomposed, slightly and

completely decomposed plant and animal residues in the soil. They could be divided into:

Plant and animal residues- these are undecomposed or slightly decomposed plant and animal
materials composed essentially of carbohydrates, lignins and lipids.

Humic substances- these are the result of complete decomposition (microbial, enzymatic and
chemical transportation). Humic substances are amorphous, polymeric, brown-colored
components of soil organic matter having no morphological resemblance to the plant tissue from
which they are derived. They are the most abundant of the naturally occuring organic
macromolecules of nature and the major component of the soil organic matter in well humified
soils. They contain functional groups such as the phenolic (OH), alcoholic (OH), carboxylic (-
COOH), carboxyl (>C=O) and amino (-NH2).

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General classes of humic substances:

Humic substances are divided into three classes based on their solubility in aqueous acid and
base:
● fulvic acids – are humic substances soluble in acid and base. They are dominant in acidic
infertile soils.
● humic acids – are humic substances that are precipitated when the alkali soluble
components are acidified to pH 1.0. They are the most abundant humic substances
occurring in acidic fertile soils.
● Humins – are humic substances that are insoluble in both acid and base. They are mostly
present in fallowed soils.

Role of organic matter in the soil

● Soil organic matter serves as an exchanger or sorption agent.
● Soil organic matter acts as a buffer system for the pH-value and ion concentration.
● Soil organic matter is a source of nutrients particularly N, P, K, Ca, Mg and S and some
trace elements.
● Soil organic matter form stable complexes with toxic metals (Al, Cd, Pb, etc.) thereby
detoxifying them.
● Soil organic matter increases the water-holding capacity of the soil.
● Soil organic matter is the major cementing agent of soil particles and thus is vital in soil
aggregation and in improving soil structure. This also reduces soil erosion.
● Soil organic matter is a habitat and source of nutrients for microorganisms and soil
animals.
● Soil organic matter may protect a plant against diseases.

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