Soil Microbiology

Soil Environment & Soil Organisms

• WHAT IS SOIL?

• The outer loose material of the earth’s surface is soil. Under the
soil lies the bedrock.

• Soil is a mixture of different things like rocks, minerals and dead

decaying plants and animals.

• Soil is composed of 5 major components

– Mineral matter
– Water
– Air
– Organic matter
– Living organisms

• Types of soil:
– Sand
– Silt
– Clay
 Reactions that occur in soil
• Destruction of organic matter

• Weathering of rocks

• Nutrition of agricultural crops

• O Horizon

• At the top of the profile is the O horizon. The O

horizon is primarily composed of organic matter.
Fresh litter is found at the surface, while at depth
all signs of vegetation structure has been destroyed
by decomposition.

• The decomposed organic matter, or humus,

enriches the soil with
– nutrients (nitrogen, potassium, etc.),
– aids soil structure (acts to bind particles), and
– enhances soil moisture retention.
• A Horizon

• Beneath the O horizon is the A horizon. The A

horizon marks the beginning of the true mineral
soil. In this horizon organic material mixes with
inorganic products of weathering. The A horizon
typically is dark colored horizon due to the
presence organic matter.
• Eluviation, the removal of inorganic and organic
substances from a horizon by leaching occurs in the
A horizon. Eluviation is driven by the downward
movement of soil water.
• E Horizon

• The E horizon generally is a light-colored horizon

with eluviation being the dominant process.
Leaching, or the removal of clay particles, organic
matter, and/or oxides of iron and aluminum is
active in this horizon. 

• Under coniferous forests, the E horizon often has a

high concentration of quartz giving the horizon an
ashy-gray appearance
• B Horizon

• Beneath the E horizon lies the B horizon. The B horizon is a zone of

illuviation where downward moving, especially fine material, is
accumulated.  The accumulation of fine material leads to the
creation of a dense layer in the soil. In some soils the B horizon is
enriched with calcium carbonate in the form of nodules or as a layer.
This occurs when the carbonate precipitates out of downward
moving soil water or from capillary action.

• Eluviation is significant in humid climates where ample precipitation

exists and a surplus in the water balance occurs. Illuvial layers are
found low in the soil profile.

• Illuvial zones are found closer to the surface in semiarid and arid
climates where precipitation is scarce. Capillary action brings cations
like calcium and sodium dissolved in soil water upwards where they
precipitate from the water.
• C Horizon

• The C horizon represents the soil parent

material, either created in situ or transported
into its present location.

• Beneath the C horizon lies bedrock.

• There are 5 major groups of microorganisms
in soil:

– Algae
– Protozoa
– Fungi
– Actinomycetes
– Bacteria
 Known functions of microorganisms in soil:

• Algae:
– Contribute organic matter that improves soil structure
– Contribute sugars that supply food for other soil organisms

• Protozoa
– Feed on soil bacteria; aiding in release of nutrients for plant and
also increases growth rate of other bacteria.

• Fungi
– Break organic matter and improve soil’s physical structure
– Mycorrhizal fungi is a key to form soil agregates which build good
soil structure.
• Actinomycetes
– Decompose organic matter to release nutrients
for other microbes
– Produce antibiotics which work as disease control

• Bacteria
– Work as food source for protozoa and nematodes
– Breakdown toxic chemicals and organic molecules
 Bacteria
• Bacteria is the most numerous/abundant group than the
others.

• A teaspoon of productive soil generally contains between

100 million and 1 billion bacteria.

• They are capable of rapid growth.

• They are also capable of vigorous decomposition of dead

organic matter
• There are an estimated 60,000 different
bacterial species, most which have yet to be
even named, and each has its own particular
roles and capabilities. Most live in the top
10cm of soil where organic matter is present.
 A FEW IMPORTANT BACTERIA

• Nitrogen-fixing bacteria form symbiotic associations

with the roots of legumes like clover and lupine, and
trees such as alder and locust. Visible nodules are
created where bacteria infect a growing root hair.
The plant supplies simple carbon compounds to the
bacteria, and the bacteria convert nitrogen (N2) from
air into a form the plant host can use. When leaves
or roots from the host plant decompose, soil
nitrogen increases in the surrounding area.
• Nitrifying bacteria change ammonium (NH4+)
to nitrite (NO2-) then to nitrate (NO3-) – a
preferred form of nitrogen for grasses and
most row crops. Nitrate is leached more easily
from the soil, so some farmers use nitrification
inhibitors to reduce the activity of one type of
nitrifying bacteria. Nitrifying bacteria are
suppressed in forest soils, so that most of the
nitrogen remains as ammonium.
• Denitrifying bacteria convert nitrate to
nitrogen (N2) or nitrous oxide (N2O) gas.
Denitrifiers are anaerobic, meaning they are
active where oxygen is absent, such as in
saturated soils or inside soil aggregates.
• Disease suppressors
Bacillus megaterium is an example of a bacterium
that has been used on some crops to suppress the
disease-causing fungus Rhizoctonia solani.
Pseudomonas fluorescens may also be useful against
this disease.

Bacillus subtilis has been used to suppress seedling blight of

sunflowers, caused by Alternaria helianthi.

A number of bacteria have been commercialised

worldwide for disease suppression. However,
suppression is often specific to particular diseases of
particular crops and may only be effective in certain
circumstances.
Soil bacteria are divided into 2 major divisions.

Soil bacteria

Indigenous Invaders
(autochthonous) (allochthonous)
• Authochthonous bacteria:
– True residents of soil
– Take part in the biochemical function of the soil community
– Some grow rapidly, some grow slowly in soil

• Allochthonous bacteria
– Transient resident of soil
– Do not play any significant role in biochemical activities of soil
community
– Normally stays inert in soil; Sometimes grow a little
• Allochthonous bacteria enter soil through

– Precipitation
– Diseased tissue
– Animal manure
– Sewage sludge
 Bacteria fall into four functional groups.

• Most are decomposers that consume simple carbon

compounds, such as root exudates and fresh plant litter.
– By this process, bacteria convert energy in soil organic matter into
forms useful to the rest of the organisms in the soil food web.
– A number of decomposers can break down pesticides and
pollutants in soil.
– Decomposers are especially important in immobilizing, or
retaining, nutrients in their cells, thus preventing the loss of
nutrients, such as nitrogen, from the rooting zone.
• A second group of bacteria are the mutualists that form
partnerships with plants. The most well-known of these are
the nitrogen-fixing bacteria.

• The third group of bacteria is the pathogens. Bacterial

pathogens include Xymomonas and Erwinia species, and
species of Agrobacterium that cause gall formation in
plants.

• A fourth group, called lithotrophs or chemoautotrophs,

obtains its energy from compounds of nitrogen, sulfur, iron
or hydrogen instead of from carbon compounds. Some of
these species are important to nitrogen cycling and
degradation of pollutants.  
 WHAT DO BACTERIA DO?
Bacteria from all four groups perform important services
related to:

• Water dynamics. Some bacteria affect water movement by

producing substances that help bind soil particles into small
aggregates (those with diameters of 1/10,000-1/100 of an
inch or 2-200µm). Stable aggregates improve water
infiltration and the soil’s water-holding ability.

• Nutrient cycling, and

• Disease suppression. In a diverse bacterial community,

many organisms will compete with disease-causing
organisms in roots and on aboveground surfaces of plants.