THE SOIL ENVIRONMENT

Soil environment is the outer, loose region of the earth’s surface that supports the life of plants
and other organisms. Soil is one of the most dynamic sites of biological interactions in nature.
The soil environment consists of a variety of physical, biological and chemical factors that
affect the abundance and diversity of microbes found in the soil. It consists of a solid and
porous fraction within which various physical and chemical factors affect the microorganism
present, that includes texture, temperature, pH, oxygen, cation exchange capacity and redox
reactions. Soil is the region where most of the physical, biological and biochemical reactions
related to decomposition of organic matter, degradation, cycling of nutrients, mineral and metal
transformation occur.

Components of Soil:

Soil is a mixture of five major components which include:

• organic matter
• mineral matter
• soil air
• soil water
• soil microorganisms/living organisms
The amount/ proportion of these components varies with soil type and climatic condition
prevalent in the environment. The first four components of the soil can be categorized into two
major groups:

solid fraction (soil mineral and organic matter)

soil pores (soil air and soil water)

1. Inorganic Matter: This is formed as a result of decomposition, disintegration and

weathering process of parent rocks and bedrocks. Different types of inorganic
compounds containing various minerals are present in soil. Amongst them the dominant
minerals are Silicon, Aluminum and iron and others like Carbon, Calcium Potassium,
Manganese, Sodium, Sulphur, Phosphorus etc. are in trace amount. The proportion of
 mineral matter in soil is slightly less than half of the total volume of the soil (about
45%).

2. Organic matter/components: This is obtained from the organic residues of plants and
animals deposited in the soil. This component of soil not only serve as an essential food
source for microorganisms but also supplies energy for the vital metabolic processes
which are characteristics of all living organisms. Organic matter in the soil is the
potential source of N, P and S for plant growth. Microbial decomposition of organic
matter releases the unavailable nutrients in available from. The proportion of organic
matter in the soil ranges from 3-6% of the total volume of soil.

3. Soil is an excellent culture media for the growth and development of various
microorganisms. Soil contains several distinct groups of microorganisms and amongst
them bacteria, fungi, actinomycetes, protozoa and viruses are the most important. But
bacteria are more numerous than any other kinds of microorganisms. In the upper layer
of soil (top soil up to 10-30 cm depth i.e. Horizon A), the microbial population is very
high which decreases with depth of soil. Each organisms or a group of organisms are
responsible for a specific change / transformation in the soil. The final effect of various
activities of microorganisms in the soil is to make the soil fit for the growth and
development of higher plants.
Physico-chemical Factors that Control Biological Activity in the Soil
pH
pH change in soil is due to both biotic and abiotic processes. Microbes consume and release
H+ through redox reactions and fermentation. Abiotic processes such as rainfall can also affect
the pH of the soil. In areas of high rainfall, acidic soils can be created through leaching of bases
from the soil, while more basic soils are typically located in arid environments. pH affects
microbial diversity because many microbial species cannot tolerate extreme levels of pH (high
or low). Alterations in pH can render essential microbe enzymes inactive and/or denature
proteins within the cells and prevent microbial activity from occurring. However, there are
microbes that can withstand extreme pH environments. At pH below 5, fungi and acidophilic
bacteria have a competitive advantage over other bacteria that thrive at a more neutral pH.
Oxygen
Oxygen (O2) is a very important component of the productivity of both microbes and plant
roots. Oxygen has a very high electrical potential (Eh), meaning that it has a lot of potential to
produce energy when used as an electron acceptor in an oxidation-reduction reaction.
In areas where oxygen is not present, soil microbes may use alternative electron acceptors such
as nitrate, manganese, iron, sulfate, and carbon dioxide.

Redox Reactions
Reduction-oxidation (redox) reactions are chemical reaction in which reactants experience a
change in oxidation number (which means these reactants either gain or lose electrons) . Many
reactions in the soil involve the gain or loss of electrons, obtaining or releasing energy. Redox
reactions are important in the soil, because microbes obtain energy through redox reactions for
their metabolism, and the redox state can also determine the microbial processes that will occur.

For example, the photosynthesis and respiration processes are the coupled reactions in the soil,
where plants required energy from light and reduce carbon dioxide to glucose, which then be
used by microbes in the soil as the energy for their metabolism.

The tendency of compounds to accept or donate electrons is expressed as “redox potential”

(Eh). Redox potential measurements allow for rapid characterization of the degree of reduction
and for predicting stability of various compounds that regulate nutrients and metal availability
in soil and sediment. The inorganic oxidants include oxygen, nitrate, nitrite, manganese,
sulfate, and CO 2, while the reductants include various organic substrates and reduced inorganic
compounds (NH4+, Fe2+, Mn2+, CH4, and H2).

Anaerobic environments such as wetland soils and flooded soils are usually limited by electron
acceptors and have an abundant supply of electron donors. In this case, most microbes’ activity
is limited, and facultative and obligate microbes reduce the minerals following the electron
tower. Aerated soils are usually limited by electron donors and have an abundant supply of
electron acceptors (primarily O2).

Cation Exchange Capacity

Cation exchange capacity (CEC) is the ability of a soil to hold and exchange cations. The
amount of CEC in soil is highly dependent on the texture and organic matter of the soil. The
high surface area and negative charge of clay allows it to bind and exchange with soil solution,
which contains cations that are important for plant and microbial health.

At typical soil pH values (5-8), microbes and clay particles are both negatively charged, but
microbes still bind to clay. This binding could be due to van der waals, hydrogen bonding,
sharing electrons and ion exchange.

Salinity
Soil salinity refers to the salt content in the soil. The concentrations and types of ion in solution
in the soil can cause modifications in the dispersion of the clay fraction, degrading the original
soil fraction. The sodium ion, being monovalent, increases the width of the diffuse double layer
on the surface of the clays, reducing the attractive forces between them with a consequent
increase in particle dispersion. The consequence of this dispersion of the clay is also shown by
a reduction in stability of the soil aggregates, which are thus easily transported by rain or
irrigation.

Soil salinization is a big problem for soils in arid or semi-arid regions and agricultural soils
throughout the world. Salts can adversely affect plant and microbial growth, due to destruction
of the soil structure and its consequent compacting. The stress of high salt concentration can
be detrimental for sensitive microorganisms and decrease the activity of surviving cells, due to
the metabolic load imposed by the need for stress tolerance mechanisms.

Texture
Soil texture is defined as the distribution of sand (0.05-2.0 mm), silt (0.002-0.05mm), and clay
(< 0.002mm) in soil. Soil texture indirectly influences properties such as: water holding
capacity, porosity, aeration and nutrient availability.
Clay particles have a very high surface to volume ratio, which makes them very chemically
active and have high nutrient availability. Due to the adhesion of water, soils high in clay will
also have a highwater holding capacity. Soils with a high clay content will often have a very
active microbial community, especially in areas of the rhizosphere.

SOIL TEXTURAL TRIANGLE

Soil Texture Triangle Activity

Using the soil texture triangle, scientists have created classes which break the distribution of
particle sizes (soil textures) into 12 categories: clay, sandy clay, silty clay, sandy clay loam,
clay loam, silty clay loam, sand, loamy sand, sandy loam, loam, silt loam, silt.
The soil texture triangle is one of the tools that soil scientists use to visualize and understand
the meaning of soil texture names. The textural triangle is a diagram which shows how each of
these 12 textures is classified based on the percent of sand, silt, and clay in each.
Note that these percentages are based on the USDA definition of sand and silt only.

How to use the Soil Texture Triangle

Soil classification is typically made based on the relative proportions of silt, sand and clay.
Follow any two component percentages to find the nominal name for the soil type. For
example, 30% sand, 30% clay and 40% silt:

Find 30% along the bottom (sand) line, and follow the slanted line up and to the left. Stop at
the horizontal line for 30% clay, and find the soil type: clay loam.
 USDA textural classes of soils1
Common names of soils (General
Sand Silt Clay
texture)
86-100 0-14 0-10
Sandy soils (Coarse texture)
70-86 0-30 0-15
Loamy soils (Moderately coarse
50-70 0-50 0-20
texture)
23-52 28-50 7-27
Loamy soils (Medium texture) 20-50 74-88 0-27
0-20 88-100 0-12
20-45 15-52 27-40

Loamy soils (Moderately fine texture) 45-80 0-28 20-35

0-20 40-73 27-40

45-65 0-20 35-55
Clayey soils (Fine texture) 0-20 40-60 40-60
0-45 0-40 40-100
Soil organisms are responsible for a range of ecological functions and ecosystem services
including:
· nutrient cycling and nitrogen fixation,
· control of pest and diseases,
· organic matter decomposition and carbon sequestration,
· maintenance of a good soil structure for plant growth and rainwater infiltration,
· detoxification of contaminants.

Microbial flora
The microflora of a soil is an intimate part of soil organic matter; in fact, much of the colloidal
portion of humus consists of living and dead microbial cells or their disintegrating residues.
The quantity and characteristics of organic matter in any given soil are therefore dependent on
the nature of the microflora and their biochemical transformations that no discussion of the role
of soil organic matter in plant growth would be complete without a consideration of this
microflora population. Four groups of organisms, other than viruses, constitute the microflora
population of soil. These are bacteria, actinomycetes, fungi. Each of these groups is made up
of many genera and hundreds of species. Bacteria constitute the most abundant group of
microorganisms in soil, and they are also the smallest living organisms, apart from viruses that
live in the cells of other organisms. Actinomycetes occur in soil in numbers ranging up to a
high of about 200 million per gram, which makes them second only to the true bacteria. The
fungal population of soils constitutes a very heterogeneous group of organisms.

Bacteria
Bacteria are the most numerous in of the microorganisms in soil. Indeed they are the most
common of all the living organisms on the face of the earth.
They lack nuclear membranes therefore they are termed prokaryotic cells. Their cell walls are
composed principally of peptidoglycans and reproduction is by binary fission. Genetic transfer
is accomplished by conjugation and transduction.
Energy source and carbon source are useful for describing physiological differences among
bacteria and other organisms.
The majority of known bacterial species is chemoorganotrophic and is commonly referred to
as heterotroph and a few species are chemolithotrophs.
The obligate chemolithotrophs used the same physiological pathway i.e Calvin cycle. Their
inability use any known external source of organic carbon is linked to lack of permeases to
move organic molecules across cell membranes. Therefore organic molecules must be
manufactured within the cell.
The following are some bacteria which are prominently encountered in the soil taking part in
soil processes.

Arthrobacter:
Numbers of the genus are numerically prominent in soil constituting up to 40 % of the total
plate count population. They are reported to utilize 85-180 compounds. They are slow growing
and poor competitors in the early stages of decomposition when easily decomposable materials
are rapidly attacked by other genera.

Pseudomonads:
They are aerobic except for denitrifying species that use nitrate as an alternative electron
acceptor. Mo st species are organotrophs, a few are facultative litothrophs using H2 or CO as
an
energy source. They also occur in marine waters, some species cause plant disease, and many
nonpathogens are closely associated with plants. They attack a wide variety of organic
substrate including sugars, amino acids, alcohol and aldose sugars, hydrocarbons, oils, humic
acids and many of the synthetic pesticides.

Xanthomonas:
This is closely related to Pseudomonas, it embraces similar properties ecept that molecular
oxygen is the only electron acceptor and nitrates are not reduced. They are pathogenic to many
plants.

Sporulating Bacilli:
These members of the genus Bacillus produce heat resistant endospores and sporulation is not
repressed by exposure to air. They are mostly vigorous organotrophs and their metabolism is
strictly respiratory, strictly fermentative or both. There is great diversity within the genus as
shown by the array of products formed by different species during the course of glucose
fermentation, products include; glycerol, 2,3-butanediol, ethanol, hydrogen, acetone and
formic, acetic, lactic and succinic acids. Some species are facultative litotrophs that use H2 as
an
energy source in the absence of organic carbon. Bacillus polymyxa is able to fix nitrogen.
Several species produce lytic enzymes and antibiotic that are destructive to other bacteria eg
Bacillus thuringiensis produce toxin which is pathogenic to insect lavae. Bacillus mercerans is
used for retting flax, Bacillus anthracis is a highly animal pathogen.

Clostridium:
This is a sporogenic genus, most are strict anaerobes. The genus is of economic importance
used commercially for the production of alcohols and commercial solvents. Several species
such
as C butyrichum and C pasterianum fix nitrogen. They are widely distributed in soils, marine
and
freshwater sediments, manures and animal intestinal tract. Some species are pathogenic to
animals, eg C tetani and C butilinum.

Azotobacter:
This is an aerobic organotrophic bacterium capable of fixing nitrogen asymbiotically. Other
genera fixing nitrogen asymbiotically are Azomonas, Beijerinkia, Dexia and Azospirillum.
And
Rhizobium are known to fix nitrogen symbiotically. A related genus Agrobacterium induces
galls on hairy root but does not fix nitrogen. Nitrosomonas and Nitrobacter are
chemolithotrophic genera. Nitrosomonas convert NH4+ to NO2 - and Nitrobacter convert NO2
- to NO3-.
Lactobacillus:
This is a fermentative organotrophic bacterium; it is commonly associated with plant herbage.
Its lactic acid production is exploited in silages, butter, milk and local dairy products.
Enterobacter is also fermentative found in animal feces and sewage; some species are widely
distributed in soil.

ACTINOMYCETES
About 90 % of the actinomycetes isolated from soil belong to the genus Streptomyces. Its
members produce a well-developed, compact branched mycelium and compact colonies on
agar plates. Reproduction is by production of aerial spores and by mycelial fragmentation. They
are intolerant of waterlogged soil, less tolerant of dessication than fungi and generally
intolerant of acidity. Thus causal organism of potato scab S scabis is controlled in poorly
buffered soils such as sand by sulphur and ammonium amendment which result in lowered soil
pH. Many Streptomyces produce antibiotics, antibacterial, antifungi, antialgal, antiviral,
antiprotozoal, or antitumor. Streptomyces also produce geosmin which is responsible for the
musty smell of freshly plowed soil and partly responsible for the musty smell of earthen
cellersand old straw piles. It appears that Streptomyces is mainly responsible for the
maintenance of soil biological balance.

FUNGI
These are the eukaryotic organisms variously referred to as mold, mildews, rusts, smuts, yeasts,
mushrooms and puffballs. Fungi are the organotrophs primarily responsible for decomposition
of organic residues even though they are always outnumbered by bacteria. Important classes
encountered in soil include;

Aerasiomycetes:
These are unicellular; the unit of structure is the uninucleate amoeba that feeds by engulfing
bacteria. Single cells characteristically aggregate into pseudoplasmodium in which the cell
does not fuse but behave as a mobile communal unit, this later change into a fruiting structure
called sporocarp which bears the asexual spores.

Myxomycetes:
These are true slime forming asexual creeping plasmodium, they are animal like in their feeding
but fungus like in their reproductive structure and spore formation. They are widely distributed
especially in association with decaying vegetation in cool moist locations.

Oomycetes:
They are found in water and soil, they are highly destructive to plant, and they produce
biflagellate asexual motile spores called zoospores. Pythium and Phythophthora are commonly
encountered in soil.

Chytridiomycetes:
They are prevalent in aquatic habitat, but also commonly encountered in soil, some members
are parasitic on algae, higher plants or insect lavae.

Zygomycetes:
They ferment different carbohydrate substrates. They are mostly saprobic, but some are
phytopathogenic, some parasite on other fungi, some produce animal trapping mechanisms.
The mucorales which are the largest order are important economically as they are used for
commercial production of alcohol and organic acids.

Ascomycetes:
Ascomycetes and Basidiomycetes are called the higher fungi. The ascomycetes are
distinguished by the formations of ascus within which are ascospores following sexual
reproduction. Many of them are saprophytic having a range of impacts e.g., plant pathogenicity,
some are destructive on materials. Others are beneficial eg the fermenting activities of yeast
which has long been exploited in beer, wine and bakeries.

Basidiomycetes:
This include a wide selection of fungi, they differ from other fungi by the production of
specialized structure called basidium. Many of them are plant parasite thus causing heavy
losses of crop and tree plants. Some are beneficial eg mycorrhizal-forming relationship with
plants; mushroom has commercial importance as edible food. They are vigorous decomposers
of woody materials.

Deuteromycetes:
This embraces fungi with septate hyphae but reproduce only by means of conidia, they do not
have a sexual reproductive phase, and they are called fungi imperfecti. They are mostly
saprobic in soil, some may be parasiticon other fungi, higher plants, humans and other animals
eg species of Aspergillus, Penicillium, Trichoderma, Fusarium.