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    Soil-Plant-Microbe Interactions: Lecturer Prof. Dr. Zulkifli Hj. Shamsuddin

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    Nur Farhana Che Hassan
    This document provides an overview of microbes in agriculture and their interactions with soil and plants. It discusses the key components of the soil ecosystem and principles of ecology. It describes the major types of microbes found in soil such as bacteria, fungi, algae and protozoa. It outlines the many beneficial functions of soil microbes such as nutrient cycling, nitrogen fixation, and promoting plant growth. It also examines factors that affect soil microbe populations like moisture, temperature, soil texture and pH. The document provides a comprehensive introduction to the complex relationships between microbes, plants and soil.

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    Soil-Plant-Microbe Interactions: Lecturer Prof. Dr. Zulkifli Hj. Shamsuddin

    Uploaded by

    Nur Farhana Che Hassan
    114 views67 pages
    This document provides an overview of microbes in agriculture and their interactions with soil and plants. It discusses the key components of the soil ecosystem and principles of ecology. It describes the major types of microbes found in soil such as bacteria, fungi, algae and protozoa. It outlines the many beneficial functions of soil microbes such as nutrient cycling, nitrogen fixation, and promoting plant growth. It also examines factors that affect soil microbe populations like moisture, temperature, soil texture and pH. The document provides a comprehensive introduction to the complex relationships between microbes, plants and soil.

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    soil microbiology

    Original Title

    Sst5501 Lecture 1. Microbe in Agriculture.modified

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    This document provides an overview of microbes in agriculture and their interactions with soil and plants. It discusses the key components of the soil ecosystem and principles of ecology. It describes the major types of microbes found in soil such as bacteria, fungi, algae and protozoa. It outlines the many beneficial functions of soil microbes such as nutrient cycling, nitrogen fixation, and promoting plant growth. It also examines factors that affect soil microbe populations like moisture, temperature, soil texture and pH. The document provides a comprehensive introduction to the complex relationships between microbes, plants and soil.

    Copyright:

    © All Rights Reserved
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    114 views67 pages

    Soil-Plant-Microbe Interactions: Lecturer Prof. Dr. Zulkifli Hj. Shamsuddin

    Uploaded by

    Nur Farhana Che Hassan
    This document provides an overview of microbes in agriculture and their interactions with soil and plants. It discusses the key components of the soil ecosystem and principles of ecology. It describes the major types of microbes found in soil such as bacteria, fungi, algae and protozoa. It outlines the many beneficial functions of soil microbes such as nutrient cycling, nitrogen fixation, and promoting plant growth. It also examines factors that affect soil microbe populations like moisture, temperature, soil texture and pH. The document provides a comprehensive introduction to the complex relationships between microbes, plants and soil.

    Copyright:

    © All Rights Reserved
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    of 67

    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

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