Agricultural Microbiology Notes

Agricultural Microbiology Notes For IBPS AFO NABARD

Topic	Details
Introduction
Definition of Microbiology	Microbiology is the science of small living organisms that are found in soil, water, and air. These organisms are too small to be seen with unaided eyes and are termed microorganisms.
Types of Microorganisms	Microorganisms include viruses, bacteria, fungi, protozoa, and some algae.
Importance of Microorganisms	Microorganisms are integral and functionally important components of diverse habitats, including soil and human surroundings. They are omnipresent and impact all aspects of life, making microbiology a central and significant field in biological science.
Conventional View	Traditionally, microorganisms were seen only as decomposers, while green plants were producers and animals were consumers.
Interdependence	Plants, animals, and microorganisms are interdependent.
Sizes of Microorganisms	Viruses are the smallest, while algae are considered the largest microorganisms. Some fungi and algae are visible to the naked eye.
Viruses	Viruses are not considered independent living cells due to their inability to exist outside living bodies. They are genetic material surrounded by a protein coat.
Cellular Organization	Bacteria, fungi, protozoa, and algae are simple organisms, mostly single-celled with no complex cellular organization. Multicellular microorganisms do not have a diverse range of cell types.
Study of Microorganisms	The study of microorganisms is called microbiology.
Significance of Microbiology	Microbiology is significant for understanding natural processes such as organic matter decomposition, atmospheric nitrogen fixation, and nutrient release. It provides insight into cellular functions.
Applied Science	Microbiology has industrial applications and is important for understanding pathogenic properties. It is also crucial in molecular and biotechnological research due to the biotransformation potential of microorganisms.

Types of Microorganisms

Table 1.1: Types of Microorganisms	Approximate Range of Sizes	Cellular Class
Viruses	0.01 to 0.25 µm	Acellular
Bacteria	0.1 to 10 µm	Prokaryotic
Fungi	2 µm to 1m	Eukaryotic
Algae	1 µm to few meters	Eukaryotic
Protozoa	2 µm to 1000 µm	Eukaryotic

 

Topic	Details
Introduction
Definition of Microbiology	Study of living organisms of microscopic size, including bacteria, fungi, algae, protozoa, and viruses.
Scope of Microbiology	Concerned with the form, structure, reproduction, physiology, metabolism, and classification of microorganisms. Studies their distribution in nature, relationships with other organisms, effects on humans, and reactions to physical and chemical agents.
Protoplasm in Cells	All living cells contain protoplasm, a colloidal organic complex consisting largely of proteins, lipids, and nucleic acids.

 

Different Microbial Groups	Details
Procaryotic Protists
Bacteria	Unicellular, procaryotic, multiply by binary fission. Cyanobacteria (Blue Green Algae) included.
Practical Significance of Bacteria	Cause diseases, contribute to natural cycling and soil fertility, spoil food, make food.
Eucaryotic Protists
Algae	Simple organisms, can be unicellular or form aggregations of similar cells. Some large brown algae have complex structures. Contain chlorophyll and perform photosynthesis. Found in aquatic environments or damp soil.
Fungi	Eucaryotic, devoid of chlorophyll, usually multicellular. Not differentiated into roots, stems, and leaves. Range from single-celled yeasts to multicellular mushrooms. Composed of mycelium. Reproduce by fission, budding, or spores.
Protozoa	Unicellular, eucaryotic, differentiated based on morphological, nutritional, and physiological characteristics. Some cause diseases in humans and animals.
Viruses
Characteristics of Viruses	Not protists or cellular organisms. Studied using microbiological techniques. Cause diseases. Visualized with electron microscope. Cultivated only in living cells.

Importance of Microorganisms

Importance of Microorganisms	Details
Ubiquity of Microorganisms	Found everywhere in nature: air, oceans, mountain tops, on and inside human bodies.
Beneficial Roles	Involved in making cheese and wine, producing penicillin, interferon, and alcohol, processing domestic and industrial wastes.
Detrimental Roles	Cause diseases, spoil food, deteriorate materials like iron pipes, glass lenses, and wood pilings.
Selman A. Waksman’s Observation	Microbes play important roles in industry, agriculture, food preparation, shelter, clothing, health, and disease. Discovered antibiotic Streptomycin, Nobel Prize in 1952.

 

Importance of Microorganisms	Details
Ideal Specimens for Study
1. Attractive Models	Microorganisms are ideal for studying fundamental processes.
2. Space and Growth Efficiency	Can be grown in test tubes or flasks, require less space, grow rapidly, and reproduce at a high rate. Some species can undergo 100 generations in 24 hours.
3. Detailed Study	Can observe life processes actively: metabolizing, growing, reproducing, aging, and dying.
4. Physiological and Biochemical Potentialities	Some bacteria can fix atmospheric nitrogen, while others require inorganic or organic nitrogenous compounds for metabolic activity.

Germ Theory of Diseases

Topic	Details
Germ Theory of Diseases
Von Plenciz (1762)	Described that living agents cause disease. Different germs are responsible for different diseases.
A. Bassi (1836)	Recognized that a fungus was the causative organism for disease in silkworms.
M.J. Berkeley (1845)	Proved that Potato Blight of Ireland was caused by a fungus.
J.L. Schönlein	Showed that certain skin diseases of humans are caused by fungal infections.
Louis Pasteur	Worked on silkworm disease, isolating the protozoan parasite causing Pebrine. Demonstrated disease elimination by using healthy caterpillars for breeding. Worked on anthrax, isolating microbes from diseased cattle and sheep.
Robert Koch (1876)	Concluded the germ theory of disease by working on anthrax in animals. Established Koch’s postulates to identify causative agents of infectious diseases.
Koch’s Postulates	a) The microorganism must be present in every case of the disease. b) The microorganism must be isolated from the diseased host and grown in pure culture.  c) The disease must be reproduced when a pure culture is inoculated into a healthy host.  d) The microorganism must be recoverable from the experimentally infected host.

 

Pure Culture Methods	Details
O. Brefeld	Introduced isolating single cells of fungi and cultivating them on solid media by adding gelatin to liquid medium.
Joseph Lister	Obtained pure cultures of bacteria by serial dilution in liquid media. Isolated Bacterium lactis. Developed antiseptic surgery in 1864.
Robert Koch	Developed pure culture techniques for bacteria, including streak plate and pour plate methods. Initially used sterile potato surfaces, later replaced gelatin with agar as a solidifying agent.
Advantages of Agar	Agar is not easily degraded by most bacteria and melts at 98°C and solidifies at 44°C, making it a superior solidifying agent compared to gelatin.
Nutrient Media	Koch developed nutrient broth and nutrient agar for bacterial growth.

 

Enrichment Culture Technique	Details
Beijerinck and Winogradsky	Developed the technique of enrichment culture by modifying the composition of the medium or incubation conditions to isolate specific organisms from a mixed population.

 

Food Preservation	Details
François Appert	Developed a method to preserve highly perishable food by enclosing it in airtight containers and heating. This process is known as Appertization, the principle of food canning.

 

Air Filtration and Sterilization	Details
Schroder and von Dusch	Passed air through cotton into flasks containing heated broth to filter out microbes and prevent growth, initiating the basic technique of plugging bacterial culture tubes.
John Tyndall	Concluded that microorganisms exist in two forms: heat labile (vegetative) and heat resistant (endospores). Developed a sterilization method called Tyndallization by discontinuous heating to kill all bacteria in infusions.

Bacterial Cell Structure

Topic	Details
Typical Bacterial Cell Structure	Functions of Different Parts of Bacterial Cells
External Structures
Flagella (flagellum) and motility
Structure	Hair-like helical appendages that protrude through the cell wall and are responsible for swimming motility. Composed of three parts: basal body, short hook, and helical filament.
Components	Basal body: associated with cytoplasmic membrane and cell wall. Hook and filament: made up of protein (flagellin).
Growth	Grows at the tip.
Flagellar Arrangement	Monotrichous: single polar flagellum. Lophotrichous: cluster of polar flagella. Amphitrichous: flagella at both poles. Peritrichous: surrounded by lateral flagella.
Endoflagella	Present in spirochetes, providing swimming motility.
Gliding Motility	Exhibited by some bacteria (e.g., myxobacteria) when in contact with solid surfaces.
Tactic Movements	Movement in response to environmental stimuli. Chemotaxis: movement toward (positive) or away (negative) from chemicals. Phototaxis: movement toward increasing light intensities.

 

Pili (Fimbriae)	Details
Structure	Hollow, non-helical, filamentous appendages. Thinner, shorter, and more numerous than flagella.
Functions	F-pilus (Sex pilus): port of entry for genetic material during bacterial mating. Some pili play roles in human infection.

 

Capsule	Details
Structure	Organic exopolymers forming an envelope outside the cell wall. Visible by light microscopy if thick (capsule) or too thin (microcapsule). Called “slime” if the layer is abundant.
Functions	Block attachment of bacteriophages. Antiphagocytic properties. Protection against drying by binding water molecules. Promote attachment to surfaces.

 

Sheaths	Details
Structure	Hollow tube enclosing chains or trichomes of bacterial cells.
Common Locations	Found in species from freshwater and marine environments.

 

Cell Wall Composition	Details
Structure	Very rigid, giving shape to the cell. Accounts for 10-40% of dry weight of the cell.
Breaking Methods	Broken by sonic or ultrasonic treatment or by high pressure and sudden release.
Eubacteria vs. Archaebacteria	Eubacteria: cell wall made of peptidoglycan. Archaebacteria: cell wall made of proteins, glycoproteins, or polysaccharides.
Peptidoglycan Composition	Polymer of N-acetylglucosamine, N-acetylmuramic acid, L-alanine, D-alanine, D-glutamate, and a diamino acid. Present only in prokaryotes.

 

Gram Staining	Details
Method	Introduced by Christian Gram in 1884. Differentiates bacteria into Gram positive (deep violet) and Gram negative (red).
Gram Positive vs. Gram Negative	Character: 1. Thickness; 2. Layers; 3. Peptidoglycan; 4. Other Constituents; 5. Susceptibility to Penicillin; 6. Susceptibility to Mechanical Disintegration Gram Positive: 1. Thicker wall (20-25 nm); 2. Single thick layer; 3. Accounts for 50% dry weight of cell wall; 4. Polysaccharides and Teichoic acids; 5. More susceptible; 6. Less susceptible Gram Negative: 1. Thinner wall (10-15 nm); 2. Two layers (Peptidoglycan layer and outer membrane); 3. Accounts for only about 10% of cell wall; 4. Outer membrane rich in phospholipids, proteins, or lipopolysaccharides; peptidoglycan layer linked to outer membrane by Braun’s lipoprotein; 5. Less susceptible; 6. More susceptible

Bacterial Size

Characteristic	Details
Size	Typically 0.5–5.0 microns in length (0.2–1.5 µm in diameter).
Micron Definition	1 micron = 0.001 mm = 10^-6 m.
Visibility	Can be visualized with light microscopes; limit of resolution ~200 microns.

Bacterial Morphology

Shape	Description	Examples
Cocci	Spherical or oval cells. Occur singly or in clusters.	Micrococcus sp., Neisseria gonorrhoeae
Bacilli	Cylinder-shaped; may have different ends.	Bacillus spp., Lactobacillus spp.
Spirilli	Curved forms; slender or spiral.	Vibrio cholerae, Treponema pallidum
Actinomycetes	Branched filamentous hyphae resembling fungi.	Actinomyces spp.
Mycoplasma	Cell wall-deficient; variable shapes.	Mycoplasma spp.

Bacterial Structure

Outside Cell Wall	Inside Cell Wall
Capsule	Cytoplasmic membrane
Flagella	Cytoplasm
Pili	Ribosome
Slime	Mesosome
	Cytoplasmic inclusions
	Nucleoid
	Spore

Cell Wall Functions

Function	Details
Protection from osmotic lysis	Prevents cell from bursting due to water uptake.
Virulence factor	Can contribute to disease-causing ability.
Defence against immune response	Helps evade host defenses.
Protection from toxic substances	Offers resistance to harmful compounds.

Chemical Composition of Cell Walls

Component	Description
Peptidoglycan	Made of N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM).
Teichoic acid	Links peptidoglycan to cytoplasmic membrane.

Major Differences Between Gram-positive and Gram-negative Bacteria

Characteristic	Gram Positive	Gram Negative
Cell Wall Structure	Smooth, single-layered	Wavy, double-layered
Cell Wall Thickness	20 to 80 nanometers	8 to 10 nanometers
Peptidoglycan Layer	Thick	Thin
Teichoic Acids	Present	Absent
Outer Membrane	Absent	Present
Porins	Absent	Present in outer membrane
Morphology	Cocci or spore-forming rods	Non-spore forming rods
Flagella Structure	2 rings in basal body	4 rings in basal body
Lipid Content	Very low	20 to 30%
Lipopolysaccharide	Absent	Present
Toxins Produced	Exotoxins	Endotoxins or Exotoxins
Antibiotic Resistance	More susceptible	More resistant
Examples	Staphylococcus, Streptococcus	Escherichia, Salmonella
Gram Staining Characteristics	Retain crystal violet (purple)	Do not retain stain (pink)

Introduction to Genetics

Concept	Details
Genetic Variation	Key to species survival, allowing adaptation via natural selection.
Bacterial Reproduction	Bacteria reproduce by binary fission, producing clones.
Genetic Diversity	Limited by binary fission, mainly through mutations and recombination.

Genetic Recombination Mechanisms

Mechanism	Description
Transformation	Uptake of free DNA from the environment.
Conjugation	Transfer of DNA through direct contact via a conjugation tube.
Transduction	DNA transfer mediated by bacteriophages (viruses that infect bacteria).

Transformation

Key Points	Details
First Demonstration	Conducted by Griffith in 1928 with Streptococcus pneumoniae.
Experiment Findings	Heat-killed virulent bacteria can transform non-virulent strains.
DNA’s Role	Confirmed by Avery et al. in 1944 that DNA is the transforming agent.

Conjugation

Key Points	Details
Discovery	Found by Lederberg and Tatum in 1946.
Process	Involves a conjugation tube facilitating plasmid transfer.
F Factors	Plasmids that facilitate conjugation; F+ (donor) and F- (recipient) cells.

Transduction

Type	Details
Generalized	Involves bacteriophages transferring random DNA fragments.
Specialized	Bacteriophage DNA integrates into the host genome, sometimes carrying host genes.

 Transposable Elements (Transposons)

Definition	Details
Jumping Genes	DNA sequences that can move within a genome, contributing to mutations.
Discovery	First identified by McClintock in maize genetics (1940).

Plasmids

Definition	Details
Extra-chromosomal DNA	Circular, non-essential DNA providing advantages like antibiotic resistance.
Significance	Confer antibiotic resistance, produce toxins, and carry virulence genes.

Applications of Plasmids

Application	Details
Cloning	Used as vectors for DNA cloning in genetic engineering.
Protein Production	Facilitate large-scale production of proteins like insulin.
Gene Therapy	Used for gene transfer in therapeutic applications.

Genetic Engineering

Concept	Details
Gene Transfer	Deliberate transfer of beneficial genes across organisms.
Applications	Producing useful proteins and generating organisms with desired traits.

Genetically Modified Organisms (GMOs)

Definition	Details
Modified Genes	Organisms with altered genetic material through genetic engineering.
Purpose	Create crops resistant to pests/herbicides, enhance yield.

Agricultural Microbiology

Section	Key Points
4.1 Introduction	– Study of microorganisms and their processes in soil. – Soil is a habitat for a variety of life-forms, including microorganisms. – Interactions alter soil conditions.
4.2 Microbial Groups in Soil	– Soil contains bacteria, actinomycetes, fungi, cyanobacteria, algae, viruses, and protozoa. – 1-10 million microorganisms per gram of soil; bacteria and fungi are most prevalent.
Bacteria	– Dominant group, equal to half of soil microbial biomass. – Present in all soil types, population decreases with depth. – Common genera: Pseudomonas, Bacillus, etc.
Actinomycetes	– Share characteristics with bacteria and fungi. – Increase with decomposing organic matter. – Optimal pH: 6.5-8.0; waterlogging is unfavorable.
Fungi	– Possess filamentous mycelium, dominant in acid soils. – Common genera: Aspergillus, Penicillium, etc. – Degrade organic matter and aid in soil aggregation.
Cyanobacteria	– Capable of fixing atmospheric nitrogen. – Can resist drought; re-emerge rapidly after moisture.
Algae	– Photosynthetic pigments distinguish them from other microbes. – Most common: Green microalgae (Chlorophyceae).
Viruses	– Smallest soil inhabitants; attack bacteria and actinomycetes.
Protozoa	– Unicellular, lack chlorophyll. – Important genera: Cercomonas, Entosiphon, etc. – Increase with organic manure application.
4.3 Role of Microbes in Soil Fertility	– Contribute to soil formation, nutrient cycling, and waste detoxification. – Support plant growth and regulate greenhouse gas emissions.
4.4 Biogeochemical Cycling of Nutrients	– Microorganisms affect carbon, nitrogen, phosphorus, and sulfur cycles.
Carbon Cycle	– Involves photosynthesis and respiration. – Long-term storage through sedimentation and fossil fuel formation.
Phosphorus Cycle	– Phosphorus moves through lithosphere, hydrosphere, and biosphere. – Key steps: weathering, absorption, decomposition, and uplift.
Nitrogen Cycle	– Involves fixation, nitrification, assimilation, ammonification, and denitrification. – Key for plant nutrient availability.
Sulfur Cycle	– Involves weathering, decomposition, and atmospheric interactions. – Acid rain results from sulfur compounds.
4.5 Microflora in Rhizosphere	– Regions around plant roots host distinct microflora.

 

Section	Key Points
Introduction	– Modern agriculture relies on mineral fertilizers, pesticides, and herbicides. – Concerns about health and environmental impacts of these practices are increasing. – Excessive nitrogen fertilizers can contaminate groundwater and contribute to greenhouse gas emissions.
Microorganisms in Agriculture	– Microorganisms play a crucial role in supporting plant and animal life, despite making up less than 1% of soil mass. – Increased awareness of chemical hazards has led to interest in environmentally friendly agricultural practices. – Soil microbes are essential for processes like nitrogen fixation, decomposition, and nutrient cycling.
Major Applications of Soil Microorganisms	(i) Microbes decompose complex organic matter. (ii) Microbes recycle nutrients. (iii) Microbes maintain soil moisture. (iv) Microbes create soil structure. (v) Microbes fix nitrogen. (vi) Microbes promote plant growth. (vii) Microbes control pests and diseases.
Biofertilizers	– Beneficial microorganisms are used as biofertilizers to enhance nutrient availability and plant growth.
Classes of Biofertilizers	(i) N2-fixing bacteria: Examples include Azotobacter, Rhizobium, and Frankia. (ii) Phosphorus solubilizing microorganisms (PSM): Include Bacillus and Penicillium. (iii) Phosphorus mobilizers: Arbuscular mycorrhizal fungi (AMF) enhance phosphate uptake. (iv) Zinc and Silicate solubilizers: Convert zinc and silicates to available forms. (v) Plant growth promoting rhizobacteria (PGPR): Enhance plant health and yield. (vi) Fungi as biofertilizers: Mycorrhizal fungi improve nutrient absorption.
Mycorrhizal Fungi	– Mutualistic associations between fungi and plants, facilitating nutrient transfer. – Types include AM fungi, ectomycorrhizal fungi, and endomycorrhizal fungi, each with distinct roles in nutrient uptake and plant health.

Importance of Biofertilizers

Section	Key Points
Importance of Biofertilizers	(i) Supplement fertilizer supplies economically and environmentally. (ii) Can fix 20-200 kg N/ha and mobilize 30-50 kg P2O5/ha. (iii) Enhance plant growth and photosynthesis. (iv) Provide growth-promoting substances and vitamins. (v) Protect plants from pests and diseases. (vi) Can increase crop yield by 10-50%. (vii) Improve soil health and physical properties.
Biopesticides	– Derived from natural sources like plants, animals, and microorganisms. – Examples include neem extracts, Bacillus sp., and certain fungi. – Non-toxic and eco-friendly alternatives for pest control.
Types of Biopesticides	(i) Biochemical pesticides: Natural substances controlling pests non-toxically. (ii) Microbial pesticides: Microorganisms like Bacillus thuringiensis target specific pests. (iii) Plant-Incorporated Protectants (PIPs): Pesticidal proteins produced by genetically modified plants. (iv) Botanical pesticides: Plant extracts like neem and pyrethrum used for pest management. (v) Biotic agents: Natural predators and parasitoids used in biological control.
Advantages of Biopesticides	(i) Less toxic than conventional pesticides. (ii) Target-specific, affecting only pests. (iii) Effective in trace amounts; decompose quickly. (iv) Enhance Integrated Pest Management (IPM) by reducing reliance on conventional pesticides while maintaining crop yields.

 

Section	Key Points
Silage Production	– High-moisture fodder produced through controlled fermentation. – Commonly made from grasses, maize, sorghum, and other crops. – Ensilage involves natural fermentation, preserving the forage through lactic acid production. – Quality depends on storage methods, compression, and moisture loss.
Procedure for Silage Production	(i) Construct a silo (500-600 kg capacity). (ii) Harvest at 30-35% dry matter. (iii) Chop fodder into 2-3 cm pieces. (iv) Fill and press in layers (30-45 cm). (v) Complete filling quickly. (vi) Use additives (e.g., molasses) to speed fermentation. (vii) Seal silo with thick plastic. (viii) Weigh down to prevent air flow. (ix) Open after 45 days; feed 5 kg/animal initially.
Advantages of Silage Making	(i) Provides high-quality forage year-round at low cost. (ii) Addresses summer feed shortages. (iii) Preserves 85%+ feed value compared to hay. (iv) Economical use of whole maize/sorghum plants. (v) Avoids hay-making challenges during monsoon. (vi) Weed species can also be ensiled, preventing seed dispersal. (vii) Palatable and moderately laxative feed. (viii) Good source of protein and vitamins. (ix) Less waste as whole plants are utilized. (x) Requires less storage space than dry fodder. (xi) Helps manage weeds effectively.

 

Category	Details
Biofuel Overview	Definition: Solid biomass, liquid fuels, and biogases from plants, microorganisms, or animal waste.
	Environmental Impact: Cost-effective and eco-friendly alternative to fossil fuels.
Types of Biofuels	Primary Biofuels: Unprocessed (e.g., firewood, crop residues).
	Secondary Biofuels: Derived from biomass conversion (e.g., bioethanol, biodiesel, biogas).
	Generations: Classified into first, second, and third generations based on feedstock.
Sources of Biofuel	Algae: High oil yield, no CO2 emissions, potential for green jet fuel.
	Carbohydrate-rich Biomaterials: Fermented from crops (e.g., corn, sugarcane), sustainability concerns.
	Oil-rich Biomaterials: From food crops (e.g., corn, canola) and non-food crops (e.g., jatropha).
	Agricultural Wastes: Controversial as they may be better used as compost.
Biofuel Production	Direct Fermentation: Converts plant materials to sugars and then ferments to alcohol.
	Indirect Fermentation: Uses pyrolysis followed by gas conversion to ethanol.
Utilization of Biofuels	Used directly in adapted engines or blended with fossil fuels for improved properties.
	Limitations: Potential for corrosion and undesirable characteristics.
Agro-Wastes	Definition: Residues from agricultural products (crops, livestock, food processing).
	Types: Crop residues, agro-industry wastes, livestock wastes, food waste.
Utilization of Agro-Wastes	Fertilizer Application: Enhances soil fertility.
	Anaerobic Digestion: Produces methane from agricultural wastes.
	Heavy Metal Adsorption: Agricultural wastes can adsorb heavy metals from wastewater.
	Pyrolysis: Produces oil, char, and gas from agricultural waste.
	Animal Feed: Crop residues can be used as low-cost animal feed.
Waste Management	View wastes as resources to avoid environmental contamination.
	‘3R’ Approach: Reduce, Reuse, and Recycle agricultural wastes for efficient management.

Agricultural microbiology is an important subject in the IBPS AFO (Agriculture Field Officer) and NABARD (National Bank for Agriculture and Rural Development) exams. It encompasses the study of microorganisms and their roles in soil fertility, plant growth, and agricultural productivity.