Soil

Microbiology
It is branch of science dealing with study of soil
microorganisms and their activities in the soil, their
functions, and how they affect soil properties
OR
A study of the microorganisms in soil, their
functions, and the effect of their activities on the
character of the soil and the growth and health of
plant life.
Microorganisms in soil are important because they
affect the structure and fertility of different soils by
showing phenomenon of mutualism and symbiosis
Components of Soil:

• Organic matter.
• Mineral matter.
• Soil air.
• Soil water.
• Soil microorganisms.
factors affecting microbial
distribution
• Amount and type of nutrients available
• pH (neutral conditions favour bacteria, while fungi
flourish in mildly acidic conditions)
• temperature
• moisture
 Classification of Soil Microorganism

Microorganisms may be present in soils in huge numbers, mostly

attached to soil particles.
Their numbers vary according to the availability of suitable nutrients.
Types of microorganisms
• Bacteria
• Actinomycetes
• Fungi
• Algae
• protozoa
Bacteri
asmallest organisms in the soil
Prokaryotic(simple cell structure with no internal
organelles)
most abundant microorganisms in the soil
Serve many important purposes, one of those being
nitrogen fixation among other biochemical processes.
Important Bacteria in Soil:
 Bacteria are the most numerous of the culturable soil
microorganisms.
 Their numbers are often as high as 1 x 108 per gram of soil.
1. Nitrogen-Fixing Bacteria:
 Two kinds of nitrogen-fixing bacteria are recognized.
The first kind, the free-living (nonsymbiotic) bacteria, includes
the cyanobacteria (or blue-green algae) Anabaena and Nostoc
and genera such as Azotobacter (six species of Azotobacter –
Gram-ve e.g. examples include Rhizobium, associated with
leguminous plants), Beijerinckia, and Clostridium
 Second 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.
2. Nitrifying bacteria:

 Change ammonium (NH4+) to nitrite (NO2-) then to nitrate (NO3-) – a

preferred form of nitrogen for grasses and most raw crops.
 Nitrifying bacteria are chemolithotrophic organisms that include species of
the genera Nitrosomonas (Gram –ve chemoautotrophic bacteria),
Nitrosococcus, Nitrobacter and Nitrococcus (Gram –ve chemoautotrophic
bacteria).
 These bacteria get their energy by the oxidation of inorganic nitrogen
compounds. Types include ammonia-oxidizing bacteria (AOB) and nitrite-
oxidizing bacteria (NOB).
 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.
3. Denitrifying bacteria:

 Convert nitrate to nitrogen (N2) or nitrous oxide (N2O) gas.

 depleting soil fertility and reducing agricultural productivity
 Denitrifiers are anaerobic, meaning they are active where
oxygen is absent, such as in saturated soils or inside soil
aggregates.
 Thiobacillus denitrificans, Micrococcus denitrificans, and some
species of Serratia, Pseudomonas, and Achromobacter are
implicated as denitrifiers.
 Pseudomonas aeruginosa can, under anaerobic conditions (as in swampy
or water-logged soils), reduce the amount of fixed nitrogen (as fertilizer) by
up to 50 percent.
4. Actinomycetes:

 Are a large group of bacteria that grow as hyphae like fungi.

 They are responsible for the characteristically “earthy” smell
of freshly turned, healthy soil.
 Actinomycetes decompose a wide array of substrates, but are
especially important in degrading recalcitrant (hard-to-
decompose) compounds, such as chitin and cellulose, and are
active at high pH levels.
 A number of antibiotics are produced by actinomycetes such
as Streptomyces.
Soil-related bacterial infections:
•Tetanus (caused by the toxin-producing, anaerobic, spore-bearing,
Gram-positive bacteria Clostridium tetani).

• Botulism (caused by the toxin-producing, anaerobic, spore-bearing,

Gram-positive bacteria Clostridium botulinum).

• Wound infections

• Gastroenteritis (Clostridium perfringens is present in soil, from

which it is ingested into GIT. It is associated with a variety of human
diseases including classic food poisoning. Evidence suggests that most
cases of gastrointestinal disease caused by C. perfringens have their
source from food contaminated by other humans or by animal feces
rather than directly from the soil).
•Other Organisms involved in Gastoentritis include:
Bacillus cereus, Campylobacter jejuni, E. coli & Listeria
monocytogenes

• Anthrax (caused by the Gram-positive, spore-forming rod

Bacillus anthracis)
 Fung
i population compared to other microorganisms.
• Next to bacteria, fungi are abundant in soil

Fungi are important in the soil as:

• Food sources for other, larger organisms.
• Pathogens.
• Beneficial symbiotic relationships with plants or
other organisms.
• Help to reduce crop residues.
• Biochemically process nutrients to improve the soil
they inhabit.
Factors effecting growth of
fungi
Quality as well as quantity of organic mater (OM) in
the soil has a direct correlation to the growth of
fungi.

Fungi abundant in acidic areas compared to bacteria.

Fungi also grows well in dry, arid soils (aerobic, or

dependent on oxygen).
Examples
1.Saprophytic fungi (decomposers)
Decomposers or saprophytic fungi convert dead organic matter into fungal
biomass (ie their own bodies), carbon dioxide and organic acids.
 Pleurotus ostreatus (oyster mushroom)
 Lentinula edodes (shiitake)
 Stropharia rugosoannulata (king Stropharia).

2.Mutualists Fungi
the mycorrhizal fungi – colonize plant roots. In exchange
for carbon from the plant, mycorrhizal fungi help solubolize
phosphorus and bring soil nutrients (phosphorus, nitrogen,
micronutrients, and perhaps water) to the plant.
 Ectomycorrhizae
 endomycorrhizae
3.Pathogenic fungi
Pythium,
Rhizoctonia,
Phytophthora
Verticillium
These organisms penetrate the plant and decompose
the living tissue, creating a weakened, nutrient
deficient plant, or death and cause major economic
losses in agriculture each year.
Alga
eAlgae can make its own nutrients through a process
known as photosynthesis
distributed evenly wherever sunlight and moderate
moisture is available
do not have to be on the soil surface or directly
exposed to sun rays
can live below the soil surface as long as the algae has
uniform temperature and moisture conditions.
Algae in
soil
Possess the character of symbiotic nitrogen fixation in
association with other organisms like fungi, mosses, and
liverworts
association fix nitrogen symbiotically in rice fields.
Plays important role in the maintenance of soil
fertility
especially in tropical soils
Add organic matter to soil when die and thus increase the
amount of organic carbon in soil
Most of soil algae (especially Blue Green Algae) act as
cementing agent in binding soil particles and thereby
reduce/prevent soil erosion
Protozoa
• eukaryotic organisms
• Sexual reproduction
• Biological control agent: Maintain equilibrium in soil
microbes, regulate bacterial population in soil
• They can withstand adverse soil conditions as they are
characterized by "cyst stage" in their life cycle.
• Protozoa are abundant in the upper layer (15 cm) of soil.
Soil moisture, aeration, temperature and PH are the
important factors affecting soil protozoa.
• Protozoa can be split up into three
flagellates, amoebae, and ciliates
Scope and Importance of Soil
Microbiology
• Living organisms both plant and animal types constitute
an important component of soil.

• Though these organisms form only a fraction (less than

one percent) of the total soil mass, but they play
important role in supporting plant communities on the
earth surface.

• While studying the scope and importance of soil

microbiology, soil-plant-animal ecosystem as such must
be taken into account.
Soil microbes and plant
growth
best medium for plant growth.
convert complex organic nutrients into simpler
inorganic forms which are readily absorbed by the
plant for growth.
produce variety of substances like IAA (Indole acetic
acid), gibberellins, antibiotics etc. which directly or
indirectly promote the plant growth.
Threats to microbes in
soil
Soil degradation (erosion, Invasive specie, Global
warming, Land use change, chemical pollution) which
is accelerated by anthropogenic activities
Climate driven factors such as temperature,
precipitation, wind or rain intensity can contribute in
the distribution of soil organic matter
soil compaction and reduction of soil porosity reduces
of available habitats for soil organisms
Alteration of soil aeration and humidity status due to
soil compaction can seriously impact the activity of
soil organisms.
Oxygen limitation can modify microbial
(favouring microbes activity that can
conditions. This alters withstand
the types andanaerobic
distribution of
all organisms found in the rest of the soil food web
 Possible impacts of chemical
pollution on soil biodiversity and its
impacts on soil organisms

Chemica Affected Affected Affected

l soil soil soil
pollutan organisms function service
t
Pesticides Biological OM decomposition, Nutrient cycling,
regulators, mineralisation soil fertility, water
chemical regulation
engineers
GM plants Chemical engineers Mineralization, OM Nutrient cycling,
decomposition soil fertility

Industrial chemicals Chemical engineers Nutrient cycling,

soil fertility
Reference
• Essential Microbiology by Stuart Hogg The University
of Glamorgan, UK
• Prescott's Microbiology