Soil Microbiology 4

Lecture 4
Organic matter decomposition

• Source of organic matter (plants – animals -
microorganisms).
• Components of plant organic matter (cellulose
(10-60)% - Hemicelluloses (10-30) %- Lignin (5-
30)%
• water soluble fraction (5-30)%
• Ether and alcohol soluble fraction-protein -
minerals (1-13)%
• As plant age, the water insoluble increase,
water soluble decrease.
Carbon assimilation
• Definition (substrate C converted to protoplasmic C).
• Carbon fixation or сarbon assimilation is the process
by which inorganic carbon (particularly in the form
of carbon dioxide) is converted to organic compounds
by living organisms. The compounds are then used to
store energy and as structure for other biomolecules.
• Fungi……anaerobic bacteria.
• Carbon is taken with (N, P, K, S)
• Efficiency (20-40)% ,the rest CO2
• importance of assimilation in immobilization.
• Immobilization reduction in quantity of
nutrients of plants by microorganisms.
• Factors (amount of microbes , C, N, C:P , C:S,
C:K; environment ).
Decomposition and CO2 evaluation
• Organic matter + microbial flora form CO2.
• by heterotrophic microorganisms
• indicate level of microbial activity
• Rate of decomposition is measured by (CO2
released, organic matter decrease or
disappearance of substance).
• 3 simultaneous processes take place during
transformation:
• Plant, animal tissues disappear.
• New microbial cells are formed.
• End products are formed.
Mineralization
• Organic C is converted to inorganic C.
• Two decomposition processes:
1. Humus: measure biological availability in soil carbon.
2. Added substrate: measure biodegradation of the test
compound.
• Complex compound converted to simple compounds.
• Insoluble polysaccharide converted to soluble sugars
and acids.
Decomposition of Soil Organic Matter
• (Humus release of CO2)

• Factors:
• Soil type, Temp, Water, Time of day, Season of
Year, Soil CO2 released by microorganisms , pH,
Organic Matter , Depth, Aeration , Fresh
Substrate may accelerate or reduce humus
composition, the enhancement is known as
Priming: ex. Glucose.
Subsidence
• Soil shrink through biological decomposition-
cultivation enhance - liming enhance).
• Breakdown of added
Carbonaceous materials
• Factors (The same factors), tissues of young
plant> old plant .... Lignin content small> large.
• Changes during organic matter decomposition (easy
then hard) water soluble then cellulose, hemicelluloses
and finally Lignin.
• anaerobic carbon mineralization as O2 decrease,
decomposition increase.
• Organic matter gives intermediates as H2, acids and CH4)
• Primary Flora ( all types of microorganisms).
• Flora
• amount, type of Organic Matter determine community
• Certan group pre- dominate for few days ( primary
flora), other maintain high population for long
period.
• The population responding to organic amendments
feed on:
1. Organic substrata added
2. Intermediates formed during decomposition
3. Protoplasm of microbes
• When succulent plant tissue is added, bacteria
increase then by 7th day bacteria decrease.
• Fungi pre-dominate after addition of mature
crop residue.
• Sugars: bacteria increase then Fungi decrease.
Microbiology of Cellulose
• Structure ( 2000-10000 glucose units ) by B 1.4
glucosidic linkage.
• Molecular weight (200000 to 2400000).
• Factors (inorganic nitrogen increase -organic
phosphorus increase-meso, thermo
• Temp – O2 - neutral pH –Lignin decrease).
• Form large part of humus & form cell wall ( cellulose
micells give micro fibril which form cell wall.
• Micro flora ( all types of microorganisms).
• Thermophilis streptomyces increase, Fungi
increase, bacteria increase to form ethanol,
acids.
• Biochemistry (product of break down by
different microorganisms).
Microbiology of hemicellulose
• Structure:
• Homoglycan: contains Single monosaccharide
type. ex. Xylan, mannan.
• Heteroglycan: contain more than one kind of

monosaccharidc or uronic acid ex.
Glucomannans, Arabinomannan.
•
• Factors: Same as glucose.
• Microorganisms:
• Aerobic, Anaerobic microorganisms, Fungi, Bacteria,
Actinomycetes. hemicellulose can not pass to inside
the cell.
• Enzyme
1. Endoenzymes randomly cleave the polymer
2. Exoenzymes cleave single dimer or monomer
3. Glycosidases : cleave disaccharide to simple sugars.
Lignin Decomposition
• Structure (Phenyl - Propane)
• Factors
• Micro flora (Bacteria- Basidomycetes - some
Ascomycetes)
• Biochemistry
• Lignin in plants.
• Lignin, age of plant.
• It is also found in Fungi and Algae.
• Structure:
• C,H,O , aromatic rather than carbohyarate.
• Basic unit is Phenyl - Propane linked by ether
bonds.
• Resistant to enzymatic degradation.
• Factors affecting the rate of decomposition are
• Temp, Nitrogen and Plant age.
• Anaerobic conversion occurs but slower.
• Thermophilic bacteria can attack lignin.
• Microbiology:
• Basidiomycetes: Agaricus
• Activity: disappearance of lignin in soil to form
Vanillin, Vanillic acid, Aromatic compounds.
• disappearance of purified lignin in culture
• To adapt microbe to grow on lignin start with
glucose-lignin and decrease glucose gradually.
• Other filaments fungi
• Bacteria
Microbiology of other polysaccharides
• Starch ( Structure( amylose - amylopectin) ,
enzyme (induced alpha, beta amylase),
microorganisms(all)).
• Pectic substance ( Structure( middle -
galactouric acid ) , enzyme inducible
extracellular pectin estrase, all
microorganisms.
• Have 4 types:
• Protopectin (soluble)
• Pectin (soluble)
• Pectinic acid (colloidal)
• Pectic acid (soluble).
• Inulin (structure (fructose units 25-28) enzyme
(inulinase, fructosanase) microorganisms all.
• Chitin
• Structure: amino sugar units
• (C6H9O4NHCOCH3)n
• N- acetyl glucosamine
• Found in fungi, insects crustacean.
• Chitosan: similar to chitin but lost acetyl group
(COCH3).
• Microorganisms: all
• Factors.
Nitrogen cycle
• Nitrogen mineralization (mean, organisms,
factors).
• Ammonification, nitrification, nitrogen
immobilization (mean, flora, factors).
• Denitrification: gasous loss
• Nucleic acid metabolism (flora, factors).
Decomposition of urea
• By urease or by
• Urea + CO2…..> allophamic acid….> NH3+ CO2
• 3 microbiological reactions of nitrification:
• Complete reduction to NH3
• Incomplete reduction to nitrite
• Formation of nitrite, N2, NO2, gases.
Nitrogen fixation
• Symbiotic:
• Rhizobium on leguminous
• Non leguminous
• Factors: N2, P, K, pH, cobalt
• Non-symbiotic:
• By free living bacteria (aerobic & anaerobic),
blue green algae (Nostoc & Anabaena).
• Factors:
• Chemical (inorganic nutrients).
• Physical.
• Conditions: large population, rapid division,
grow on N2.
Microbial transformation of phosphorus &
sulphur
• ‫ التعليق بنفس مبادىء النيتروجين‬+ ‫الرسم‬
Pesticides
• Definition: organic chemicals designed to
control pest population.
• Types: insecticides, herbicides, fungicides,
nematicides.
• Route: on surface of plant or soil.
• Role: inhibit or kill certain species.
• Modification or destruction: suppress
population or microbe metabolize.
• Effect: toxic, persistent, long duration, adsorbed on
soil particles.
• Its impact on soil processes:
1. Nitrification
2. Nodule formation
• Persistence: rate of disappearance depend on
microbial activity. It is enhanced by temp, increase in
organic matter.
• Recalcitrant: molecules that endure (can not
metabolized).
• Metabolism: two types:
1. Support growth
2. Does not support growth (co-metabolism) not
energy source cannot multiply at its expense.
• Detoxification.
• Degradation.
• Conjugation.
• Condensation.
• Activation.
• Defusing: non toxic molecule ….> non toxic
product can not be attacked.
• Changing of toxicity spectrum
• Reaction for initial steps in pesticide
metabolism:
• Addition of OH.
• Oxidation of NH2.
• Oxidation of sulfur.
• Addition of O2.
• Addition of methyl group.
• Removal of methyl group.
• Removal of chlorine.
• Reduction of nitro group.
• Replacement of Sulphur.
• Chlorine migration.
• Cleavage of ether bond.
• Metabolism of side chain.
• Hydrolysis.
• Ring cleavage.

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Lecture 4

Organic matter decomposition

• (Humus release of CO2)

• Heteroglycan: contain more than one kind of

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