Soil Microbiology

Soil

Soils correspond to the surface layer of the

Earth's crust (lithosphere: litho = rock).

They develop as a result of the weathering of

geological rock formations.

Soil
Soil consist of
mineral particles (from the eroded rocks) and

organic matters (from the remains of plants,

animals, and microorganisms).

Mineral and organic particles are intimately

mixed in soil, forming various types of soil
aggregates.
Soil microbiology
They are found in association with air (i.e. the soil
atmosphere) and an aqueous phase (i.e. the soil
solution) in the pores existing between particles
and/or aggregates.
Air and water = limiting factor
Limit number and type of microorganisms
 Oxygen level in
O2 sandy soil particle.
Microorganisms:
The soil represents a favorable habitat for
microorganisms and is inhabited by a wide range
of microorganisms, including bacteria, fungi,
algae, viruses and protozoa.
Microorganisms are found in large numbers in soil
- usually between one and ten million
microorganisms are present per gram of soil.
Microorganisms:

Bacteria and fungi being the most prevalent.

However, the availability of nutrients is often

limiting for microbial growth in soil and most soil
microorganisms may not be physiologically active
in the soil at a given time.
Microorganisms and their significance:
Almost every chemical transformation taking
place in soil involves active contributions from soil
microorganisms.

Active role in soil fertility as a result of their

involvement in the cycle of nutrients like carbon
and nitrogen, which are required for plant growth.
Microorganisms and their significance:
Soil microorganisms are responsible for the
decomposition of the organic matter entering the soil
and therefore in the recycling of nutrients in soil.

Certain soil microorganisms such as mycorrhizal fungi

can also increase the availability of mineral nutrients
(e.g. phosphorus) to plants.
1. CO2 fixation by photoautotrophs and chemoautotrophs.

2. Methanogenesis from inorganic (CO2+H2) or organic matter, involves

various archaea methanogens (Methanobacterium, others). Global CH4
production ~1011 kg / yr (~85% biogenic)
Microorganisms in C cycle:
Carbon fixer
Photoautotrophs
Anaerobic – Chromatium (purple, sulfur bacteria)
Aerobic – cyanobacteria

Chemoautotrophs - anaerobic
Methanotrophs: Methylomonas
Sulfur oxidizer: Thiobacillus
Microorganisms in C cycle:
Methanogenesis – anaerobic degradation of
carbon: strictly by microbes.
Anaerobic respiration involves the complete oxidation of
organic substances
(CH2O)n + Xox -----> CO2 + Xred
X = electron acceptor
(NO3-, SO42-, S0, Fe3+)

Methanobacterium
Microorganisms in C cycle:
Anaerobic decomposition of organic substances to CO2
and CH4 involving many different reactions and species of
microorganisms. This is also called interspecies hydrogen
transfer [the gut,sediments, soils, and the rumen].
a. Complex polymers →monomers
b. The monomeric subunits → organic acids
c. Fermentations → acetate, CO2, and H2
d. Methanogens produce methane (i.e. CH4)
1. Nitrogen fixation
2. NH3 assimilation
3. Ammonification
4. Nitrosification
5. Nitrification
6. Nitrate assimilation
7. Dissimilatory nitrate
reduction
8. Denitrification
• Nitrogen fixation N2 → NH3 (aerobic)

• free-living: Azotobacter, cyanobacteria;

• symbiotic: Rhizobium, Frankia

• (anaerobic): Clostridium perfringens, purple &

green sulfur phototrophs.

2. NH3 assimilation (aerobic & anaerobic)

3. Ammonification (organic N→ NH3)

4. Nitrosification (aerobic), Nitrosomonas

5. Nitrification (aerobic), Nitrobacter

6. Nitrate assimilation (NO3-→ NH3 → amino acids)

7. Dissimilatory nitrate reduction (NO3 -→ NO2-)

8. Denitrification (NO3- → N2) Bacillus, Pseudomonas,

Biogeochemical Sulfur Cycle:
1. Sulfur oxidation (S°→ SO3-2→ SO4-2): (aerobic) many
chemolithotrophs; (anaerobic) purple & green
photoautotrophs
2. Assimilatory sulfate reduction (SO4-2→ organic S)
3. Desulfurylation (organic S decomposition → H2S)
4. H2S oxidation (H2S → S°)
Aerobic: Thiobacillus, Beggiotoa (chemolithotrophs).
Anaerobic: Chlorobium, Chromatium
Biogeochemical Sulfur Cycle:
5. Dissimilatory sulfate and sulfite reduction (solid purple
arrows)
SO4-2 or SO3-2 → H2S:
Desulfovibrio and related organisms
6. Elemental sulfur reduction (S°→ H2S) Desulfuromonas,
thermophilic archaea, cyanobacteria in hypersaline
sediments.
Microorganisms and their significance:

Other soil microorganisms can increase the

amount of nutrients present in the soil.

The microorganisms, which improve the fertility

status of the soil and contribute to plant growth,

have been termed 'biofertilizers‘.

Microorganisms and their significance:
Similarly, other soil microorganisms have been
found to produce compounds (such as vitamins
and plant hormones) that can improve plant
health and contribute to higher crop yield.

These microorganisms (called 'phytostimulators')

are currently studied for possible use as microbial
inoculants to improve crop yield.
Microorganisms and their significance:
Some soil microorganisms are pathogenic to
plants. Large numbers are routinely found in the
soil and many of them can infect the plant through
the roots.
Microorganisms and their significance:
Some native microorganisms present in the soil are

antagonistic to the pathogens and can prevent the

infection of crop plants.

Competition for nutrients and/or production of inhibitory

compounds such as secondary metabolites (antimicrobial

metabolites and antibiotics) and extracellular enzymes.

Microorganisms and their significance:
Other soil microorganisms produce compounds
that stimulate the natural defense mechanisms of
the plant and improve its resistance to pathogens.
The last two groups have been termed
'biopesticides' (= biological control).
Major groups of soil microorganisms :
Bacteria:

Numerically abundant (109 cells/g soil) but most

non-culturable

Along with fungi, most important decomposers of

organic matter
Major groups of soil microorganisms :
Bacteria:
Specialized groups participate in all biogeochemical
cycles
Their extracellular polymers help bind soil particles
into aggregates
Some form beneficial or pathogenic interactions
with plants
Important group of bacteria

Actinomycetes sp. Rhizobium sp.

Pseudomonas aeroginosa Bacillus sp.

Major groups of soil microorganisms :
Nitrogen fixing organisms: bacteria

Examples of nitrogen-fixing bacteria

(* denotes a photosynthetic bacterium)
Free living Symbiotic with plants
Aerobic Anaerobic Legumes Other plants
Azotobacter Clostridium (some) Rhizobium Frankia
Beijerinckia Desulfovibrio Azospirillum
Purple sulphur bacteria*
Klebsiella (some)
Purple non-sulphur bacteria*
Cyanobacteria Green sulphur bacteria*
(some)*
Major groups of soil microorganisms :
Actinomycetes:
specialized filamentous prokaryotes
participate in decomposition of complex
organic compounds
produce many 2nd metabolites, e.g.,
antibiotics, geosmins (earth odor) that give
soil its characteristic distinctive aroma
Major groups of soil microorganisms :
Fungi:
the major component of microbial biomass in soils
major participants in decomposition of organic
matter
hyphal growth helps bind soil particles into stable
aggregates
Ectomycorrhizae - sheath
Major groups of soil microorganisms :
Fungi:
Some associate with plant roots: major plant
pathogens,
Beneficial symbionts
increase nutrient uptake
and decrease disease incidence
Major groups of soil microorganisms :
Protozoa:
major predators of soil bacteria,
grazing activities accelerate decomposition of organic
matter in soil
Very abundant in well drained surface soils.
There are some 250 different species in soils
Major groups of soil microorganisms :
Cyanobacteria and algae (green algae, diatoms):
Photoautotrophs, form surface algal crusts important in
H2O retention

Some cyanobacteria carry out free-living and symbiotic

N2-fixation
Major groups of soil microorganisms :
Viruses:
Numerically abundant, ecology not well defined
Both lytic and lysogenic bacteriophage (latter very
common)
Persistance and migration of human enteroviruses
pose serious health issues with land disposal of
sewage and fecal wastes
Winogradsky column
Metagenomics method

Using 5S and 16S rRNA gene sequence analysis.

Can use to study uncultivated microbial majority
Main reason –
cannot culture – nutrition and physiological

Nature of culture does not reflect natural behavior