SST 5501

SOIL-PLANT-MICROBE
INTERACTIONS
LECTURER
PROF. DR. ZULKIFLI HJ. SHAMSUDDIN

LECTURE 1.
MICROBES IN AGRICULTURE
INTRODUCTION
1. Soil ecosystem
2. Soil microorganisms and their
functions
3. Factors affecting soil
microorganisms

Soil-plant-microbe interactions
Plant

Soil

Microbes

Soil Ecosystem
Each ecosystem consists of a community of
plants and animals in an environment that
supplies them with raw materials for life, i.e.,
chemical elements and water.
is delimited by the climate, altitude, water
and soil characteristics, and other physical
conditions of the environment.
eg. an ocean or a forest.

Principles of Ecology
or ecological science
A scientific study of the distribution
and abundance of living organisms and
how these properties are affected by
interactions between the organisms
and their environment.

PLANTATION
S

MANGROVE

FLOODED
SOIL

BACTERIA

The smallest and most numerous in

soil
most important microbial group in
soil
> 400 genera
> 104 species
a lot more species unknown

Classification of bacteria

4 groups based on cell wall

1. Gram Negative
2. Gram positive
3. Mycoplasma (no cell wall)
4. Archaebacteria (cell wall without
peptidoglycan)

Major groups of bacteria in soil:

Gram-Negative Aerobic Rods and Cocci
Facultative Anaerobic Gram-negative rods
Dissimilatory Sulfate- or sulfur Reducing Bacteria
Endospore-Forming Gram-positive Rods and Cocci
Irregular, Nonsporing, Gram-Positive Rods
Anoxygenic Phototrophic Bacteria
Oxygenic Photosynthethic Bacteria
Aerobic Chemolithotropic Bacteria and Associated
Organisms
& others ?????

Eukaryotes

Fungi
Algae
Protozoa
Microfauna
nematodes

Functions of soil microorganisms

Beneficial and Negative Interactions
Beneficial activities:1. Decomposition of plant residue &
organic material
Humus synthesis, mineralization of organic
N, S, and P

2. Increase plant nutrient availability- P,

Mn, Fe, Zn, Cu
Mycorrhizal association
Organic chelating agents
Oxidation-reduction reaction
P-solubilization

3. Nitrogen fixation
N2 fixed biologically ; nitrogenase
enzyme
Symbiotic and non-symbiotic
Symbiotic legume and non-legume
Rhizobium, Frankia (actinomycetes),
cyanobacteria (Azolla-Anabaena)

Associative microbes (Azospirillum,

Bacillus) and free-living
cyanobacteria
Free-living microbes (Azotobacter,
Beijerinckia)

4. Promoting plant growth

Plant growth-promoting bacteria
Production of growth hormones
(Auxin, Gibberellin, Cytokinins),
Protection against root pathogens
and pseudopathogens
Enhance nutrient use efficiency

5. Controlling deleterious microbes and

plants (Biocontrol agent)
Plant diseases
Soil nematodes and insects
Weeds

6. Biodegrading synthetic pesticides or

contaminants (bioremediations)
Degradation of organic wastes and
pollutants to CO2 and H2O
- Xenobiotic compounds
- Recalcitrants

7. Enhancing drought tolerance of plants

Mycorrhizal symbiosis
PGPR

8. Improving soil aggregates

9. Mineral transformation
Oxidation and reduction of elements
(sulfur, nitrate)

 Harmful Interactions
a. Plant disease
b. Phytotoxicity

 Neutral or variable effects

Attachment
Free enzyme release
Nutrient flux
Competition
Allelopathy

Factors affecting soil

microorganisms
Biotic factors
Soil organisms; macro and micro, plant
roots

Non-biotic (Abiotic) factors

Soil physical and chemical properties

Biotic: Organisms in soil

Microflora:- bacteria, actinomycetes,
fungi, algae, virus
Microfauna:- microscopic size soil animals;
protozoa, nematodes,
Macrofauna:- earthworm & small mammals

Abiotic factors
Physical properties: Soil texture,
structure, moisture, temperature,
redox potential, solar irradiation,
Chemical properties: Soil pH, cation
exchange capacity (CEC), AEC, EC,
minerals, organic compounds

Abiotic components (physical

and chemical properties)
a) Soil physical properties
texture, structure, soil density, pore
space, moisture, water potential
(osmotic, matric, gravitational),
aeration, radiation (solar, uv),
adsorption

Soil texture
Distribution (%) of sand, silt and
clay particles in soil
Sand (0.5 to 2.0 mm)
Silt (0.002 to 0.05mm)
Clay ( < 0.002mm)

12 major textural classes

not changed with management

Influence of soil texture: Soil type: sandy, clayey, loamy;

coarse- or fine- textured (do not
apply to organic soil)
Amount and type of clay (Kaolinite,
montmorilonite)
Cation exchange capacity (CEC)
Soil buffering capacity (pH)
Aeration and drainage

Soil clay
1. Effect on microbial population
Clay such as montmorilonite has higher
biological activity than that of kaolinite
Clay with high CEC, retain moisture and
organic substrates
Provide microhabitats (3 to 6 um)
sufficient for the entry of bacteria but
not protozoa

2. Effect on pathogen infectivity

Diseases are rare in clay soils
Due to bacterial pathogen get
trapped between expanding clay
layers

3. Effect on vertical descent

Rainfall and irrigation would move
microbes deeper into soil
Less movement in clay soil due to
adherence of cells to clay particles
and reduced pore size

Soil structure
Arrangements of soil fractions/particles in
soil Soil aggregates
Various shapes and sizes
Aggregation; stability is affected by soil
organisms through production of
extracellular polysaccharides, glomalin
(glucoprotein) and hyphae

Influence of soil structure:1. Soil pores (variable sizes):> 75 um

Macropores
30 to 75 um
Mesopores
5 to 30 um
Micropores
Ultramicropores 0.1 to 5 um
< 0.1 um
Cryptopores

2. Aeration and drainage

3. Water holding capacity

Aeration
O2, CO2, N2 in pores or dissolved in
water
Important for: Root growth
Biological decomposition
Respiration by roots, microbes & fauna

Can be influenced by:Soil structure, texture, moisture, pores

Can affect: Redox potential ( oxidation and reduction);
the tendency of a compound to accept or
donate electrons)
soil color (red, yellow, reddish brown, blue,
gray, mottle)

Table : Gaseous content in atmosphere

and in soil
Gas
N2

Atm (%)
79.0

Soil (%)
79.0

O2

20.9

20.6

CO2

0.03

0.25

CO2 in soil 10 - 100 X higher than

in atmosphere due to:
Activities/respiration of soil
organisms and roots
Physical barriers that inhibit gas
diffusion

Consumption of O2 by organisms:Aerobic ( + O2 ), Anaerobic ( - O2 );

obligate / facultative
Microaerophilic

Soil atmosphere (gasses)

1. Oxygen
Important in microbial processes;
aerobes
Constant diffusion into soil
Affected by soil porosity
Affect redox potential

2. Carbon dioxide

0.3 to 5% in soil but can reach 20% when

biological activity intense eg. near
rhizosphere or organic matter
Variable effect on microbes
Nitrifying bacteria prefer 0.15%
Most microbial activities are inhibited at
high CO2 concentration (0.03 to 5%)
Fusarium oxysporum occur at 20%

3. Ammonia
Source of NH3 from hydrolysis of urea,
proteins and nucleic acids of organic matter
Soils applied with nitrogenous organic
fertilizer has high NH3
Some bacteria sensitive to NH3 eg.
Nitrifying bacteria Nitrobacter
Reduce fungal germination
Control pathogens

4. effect of volatile compounds released by

roots
Roots release CO2, acetaldehyde, ethanol,
formic acids gases, flavanoids
Signal molecules to endosymbiotic fungi
Stimulate spore germination,
Interaction between plants and
ectomycorrhizal fungi produce volatile
signals (terpenes).

5. effect of volatile compounds release by

germinating seeds
Seeds produce exudates including volatile
compounds; aldehydes, alcohols, ketones
Stimulate soil microflora or may inhibit
certain groups
Important in attracting pathogens; eg.
Pythium stimulated by volatile exudate of
pea

6. Effect of volatile compounds emitted by plant

debris
Decomposing plant residues my produce large

quantities of alcohols (methanol and ethanol),

aldehydes
Stimulate microflora, rapid increase in

respiration, bacterial population

May produce toxic compounds (methyl sulphide,

isothiocyanates, which inhibit fungal parasite

such as Aphanomyces sp.

Moisture
Soil water
Required by all organisms for
existence, mobility and activities
Solvent for inorganic/organic
materials

Water
Universal solvent; indispensable for
metabolic processes, mechanical and
physical effects
Provides mobility to microbes
Affect gaseous exchange
Buffer the rise in temperature

Microbes in Dry condition

Reduction in populations and activities
Bacteria more sensitive to dry condition compared
to fungi
Low activity at wilting point (-1.5 MPa) and arrested
at -6 to -8 MPa
Gram-positive with thick cell wall survive better
than Gram-negative
But Gramnegative have polysaccharide capsule
Fungi survive at (-20 to -30 MPa), form spores,
some at -65 to -69 MPa.

Microbes in flooded condition

1. Prolonged submersion eg. in rice field
disturb the biological equilibria; fungal population
can be reduced by bacteria
Aerobic slowly change to anaerobic condition;
redox potential change to negative
2. Temporary flooding

Temperature
Depend on intensity of absorbed sun
radiation, humidity, nature of plant
cover, soil depth

Direct effect of temperature on

microorganisms
Distribution of microbes differ with
location; tropical and temperate
regions
Psychrophiles, mesophiles,
thermophiles
Tolerance to temperature associate
with protein synthesis

Effect temperature on
interactions between microbes and
plants
Temperature affects the infectivity of pathogen
or symbionts
Eg. Verticillium dahliae has optimum temperature
of 28oC and cotton plant 32oC, plant are
susceptible at 22oC; as production of phytoalexins
by plants is weak at 22oC
Genes for hypersensitivity may lose activity at
higher temperature

B. Soil Chemical properties

pH, quantity and quality of organic
matter, inorganic nutrients, growth
regulators, growth inhibitors, toxic
compounds or pollutants, hormones,
redox potential (Eh)

Soil pH
Soil acidity
Concentration of H+
(active/exchangeable, residual
acidity); pH = log10 1/[H+]
optimum pH for most organisms
[pH 6 7]
availability of nutrients

Strongly Acid Medium Acid Slightly Acid Very Slightly Acid Very Slightly Alkaline Slightly AlkalineMedium Alkaline Strongly
Alkaline

Causes of Soil acidity

Heavy fertilization
Acid rain
Leaching of bases
S-oxidizing bacteria
Nitrification

Acidity influences;
- Types and quantity of organisms
- Enzymes activities
Types of organisms:
Acidophiles acidic condition; pH 1 6
Alkalophiles alkaline condition; pH 7 13

Soil pH
1. Effect on microbial equilibria
Fungi dominant in acidic soil;
bacteria including actinomycetes in
neutral/slightly alkaline soils

2. Effects on microbial growth and

activity

Optimal pH for fungal and bacterial

activity differ between species
Acidity affects growth, sporulation,
metabolite production, parasitic activity,
Affects diseases; eg. Potato scab
(Streptomyces scabies) occur at alkaline
condition;
Antibiotic production by G. graminis is
higher at pH 7.2 then pH 5.2

3. Effect on superficial charges of

microbial walls
Microbial wall containing glycoproteins has
electric charges which depend on ambient
pH; most often exhibit negative charges
similar to clay particles.
Eg. Amino acids at high pH; dissociation;
negative charges
R-COOH

R-COO- + H +

Amine at low pH; positive charges

R-NH2 + H2O

R-NH3+ + OH-

Redox potential (Eh)

Oxidation and reduction potential of
material for losing or gaining
electrons (potential difference
measured in millivolts; mv)= Eh
Microorganisms gain energy from
oxidation of reduced compounds; loss
of electrons

i) Aerobic/oxic condition microbes use O2

as electron acceptor
Eg. Fe2+
Fe3+ ( loses electron, oxidized,
positive)
ii) Anaerobic/anoxic microbes use NO3-,
Fe3+, Mn 4+, SO42- , CO2 and organic
material as electron acceptor
Eg. Fe3+
Fe2+ (gains electron, reduced,
negative)

Nutrients
Organisms require nutrients (macro
and micro) like the plants
Essential nutrients:- C, H, O, N, P, K,
Ca, Mg, S, Mn, Zn, Cu, Mo, B
Availability depends on soil pH

Xenobiotic compounds
Synthetic compounds produced by
industries (pesticides, complex toxic
wastes) that can pollute soil
Remain in soil for a long time

Effect of pesticides
Herbicides, nematicides, insecticides, fungicides
are applied in soil or spread on soil surface, or
sprayed on leaves will finally fall onto soil
May disturb or change soil community
Toxic to mycorrhiza and rhizobia
May increase pathogen as population of antagonist
decreases
Inhibition of plant defense mechanisms