Lecture 1

Soil Microbiology
Prof. Dr. Mohsen A. Sayed

mohsenab2005@yahoo.com

01005191713
 Soil Microbiology
• Microbial Ecology:
• The soil environment:
• Term soil in agriculture: is the region support
plant life.
• Term soil in microbiology: is the region of many
biochemical reactions.
• General description of soil:
• Minerals (clay: texture), water, air, living
organisms (1%) and organic matter (3-6%).
• Vertical section in soil:
• Horizone A: inorganic constituents, organic
matter, few plant roots and microflora.
• Horizone B: deposits of upper layer.
• Horizone C: rocks
• Differences among soils:
• Spodosols: north hemisphere in temperate humid
poor in organic matter, acidic, formed by
decomposition of organic matter.
• Mollisols: in temperate, tropical with thick A
horizone, rich in organic matter.
• Oxisols: in tropical and semitropical.
• Ultisols: in tropical and semitropical.
• Aridisols: in desert regions. Little in organic matter.
Spodosols
Mollisols
Oxisols
Ultisols
Aridisols
 Subdivisions of the soil

Mineral soils Organic soils

(Histosols)

Matter Inorganic matter 60-95 % organic

matter
Include Mucks and
peats due to
decomposition of
organic matter by
microorganisms.
 Local differences among soils
• Depth, color, pH, chemical composition,
physical and biological variation.
 Some physical consideration
• Soil minerals: 50 %
• Air & water: 50 %
• Pore space: large in sandy soil, small in clay
soil, affect movement and retention of water.
• Free (gravitational water): water moves under
the effect of gravity.
• Soil solution: contain inorganic salts, nutrients
N, K, Mg, S, Ca, little P, little organic matter.
• Gas in soil: air, CO2 (10-100 folds that of air),
O2 is less, N2 & CH4 more than in air.
 Some chemical consideration
• Organic matter (0.5-10%).
• Surface silicon dioxide > subsoil.
• Ability of soil to retain ions: NH4+, K+, Ca++, Mg++
attach to clay (-ve).
• Cation exchange capacity of soil: is a measure
of the capacity of the clay and colloids to
remove positive ions from solution.
 The organic fraction (Humus)
• Due to decomposition activity of microflora.
• Food reservoir.
• Plant or animal remains fall, decompose,
organic complexes in dynamic state (change
from time to time).
• Cations: C, H, O2, N2, P, S,…
• Polysaccharides, amino acids, polymers
(heterogenous group of substances).
 Bacteria
• (bacteria, actinomycetes, fungi, algae, protozoa).
• Most abundant, rapid growth, vigorous
decomposition, aerobic & anaerobic.
• Two groups:
1. Indiginous (autochthonous): have resistant
stages.
2. Invaders (allochthonous) do not participate in
activity, enter with rain, tissue, manure, sewage.
• Classified according to Bergy’s manual:
• According to O2:
1. Aerobic
2. Anaerobic
3. Facultative anaerobic
• Shape:
1. Bacilli (endospores)
2. Cocci
3. Spiral
• Distribution & abundance:
• Every where
• Examination:
1. Direct examination
2. Plate count
• Factors affecting count:
1. Soil type
2. Cultivation practice
3. Temp.
 Environmental influences
• Moisture, aeration, temp, organic matter, pH,
inorganic supply, cultivation practice, season,
depth.
• Morphology and generic groups:
1. Stain
2. Biochemical
3. genetics
 Nutrition
• Utilize N2, pectin, cellulose, vitamin B, amino acids, growth factors.
• Chemoautotrophic bacteria:
1. Heterotrophic (chemoorganotrophic): require organic nutrients as
source of carbon and energy.
2. Autotrophic (lithotrophic): take energy from light by oxidation of
inorganic comp.
a) Photoautotrophs (photolithotrophs): take energy from
sun light.
b) Chemoautotrophs (chemolithotrophs): obtain energy
from oxidation reaction.
i)Obligate (inorganic).
ii)Facultative (organic or inorganic).
 Chemoautotrophic
• According to element oxidation:
• Nitogen compound oxidized:
• 1) ammonium oxidized to nitrite
(Nitrosomonas)
• NH4+ + O2 ----NO2- + 2H + H2O
• 2) nitrite oxidized to nitrate (Nitrobacter).
• NO2- + O2 -----NO3
• Inorganic sulfur compounds converted to
sulfate (Thiobacilus).
• S+ O2 + H2O-------H2SO4
• Ferrous iron to ferric (Thiobacillus
ferroxidans).
• H2 oxidized by several genera.
• 2H2 + O2------2H2O
• Importance of chemoautotrophs: form nitrate
for plants. Form sulfur for control of diseases.