Unit Two Microorganisms

Unit Two: Microorganisms

Introduction to Microorganisms

• Definition: Microorganisms are life forms that are too small to be seen clearly by unaided eyes and require magnification for observation.

• Characteristics:

  • Micro- means very small, thus they are observed using microscopes.

• Included Organisms:

  • Bacteria

  • Some fungi

  • Some algae

  • Protozoa

  • Viruses

Evolutionary Line of Microorganisms

• Last Universal Common Ancestor (LUCA): The common starting point for all life forms leading to diverse evolutionary paths.

• 3 Domains of Life: Organisms are grouped into Archaea, Bacteria, and Eukarya based on evolutionary relationships.

Universal Phylogenetic Tree

• Purpose: Illustrates evolutionary relationships among all organisms back to LUCA.

• rRNA (SSU): A conserved genetic marker that is used to construct phylogenetic trees and estimate divergence times, showcasing evolutionary relationships.

2.1 Eubacteria

• Definition: Eubacteria literally means "true bacteria."

• General Characteristics:

  • Omnipresent: Found in various environments such as soil, air, and water.

  • Unicellular: Composed of one cell.

  • Prokaryotic: Lack a true nucleus and do not have membrane-bound organelles (like mitochondria, Golgi bodies).

  • Composition: Have thick, rigid cell walls made of peptidoglycan.

  • Nutritional Modes:

  • Autotrophic

  • Heterotrophic (includes parasitic, saprophytic, and symbiotic modes).

  • Chlorophyll: Lack true chlorophyll; some photosynthetic bacteria contain bacteriochlorophyll.

  • Genetic Material: Both DNA and RNA are present in bacterial cells.

  • Reproduction: Can reproduce asexually through binary fission and sexually via conjugation.

Structure of Bacterial Cells

• Electron Microscope Observation:

  • Major features of prokaryotic cells are observable.

2.1.1 Bacterial Shapes

• 3 Main Shapes of Bacteria:

  • Cocci (spherical): Round or oval and mostly non-motile. Examples include Streptococcus pneumoniae and Staphylococcus aureus.

  • Bacilli (rod-shaped): Rod-like or cylindrical; can be motile if they have flagella. Examples include Escherichia coli and Bacillus anthracis.

  • Spirochaetes (spiral or corkscrew): Typically exist as individual cells; can be motile with axial filaments for corkscrew-like motion. Examples include Treponema pallidum (causes syphilis) and Borrelia burgdorferi (causes Lyme disease).

2.1.2 Bacterial Cell Wall and Gram's Staining

• Gram's Staining: Named after Hans Christian Gram, this test distinguishes bacteria based on their staining properties.

  • Differential Staining: Distinguishes organisms based on staining responses.

• Peptidoglycan: A rigid layer in bacterial cell walls made of N-acetyl glucosamine, N-acetylmuramic acid, and amino acids.

• Endotoxin: A component of the cell envelope of certain gram-negative bacteria is a lipopolysaccharide.

Classification Based on Cell Wall Composition and Staining

• Gram-Positive Bacteria:

  • Retain purple stain (crystal violet).

  • Thick cell wall of 20-80 nm.

  • Abundant peptidoglycan which retains the stain.

  • Absent outer membrane.

• Gram-Negative Bacteria:

  • Lose crystal violet, appearing red due to safranin.

  • Thin cell wall of 8-11 nm.

  • Less abundant peptidoglycan.

  • Present outer membrane.

Table 2.3: Differences between Gram-Positive and Gram-Negative Bacteria

Gram Staining Steps

1. Heat Fix: Pass slide through a flame to kill bacteria and adhere to slide.

2. Apply Primary Stain (Crystal Violet): Stains all bacteria purple.

3. Add Mordant (Gram’s Iodine): Binds dye to cell walls; enhances crystal violet retention.

4. Rapid Decolorization (Ethanol, Acetone): Removes crystal violet from Gram-negative cells; leaves it in Gram-positive cells.

5. Counterstaining with Safranin: Stains now colorless Gram-negative bacteria pink, allowing differentiation.

2.1.3 Nutritional Types of Bacteria

• Autotrophs:

  • Obtain carbon from inorganic CO₂.

  • Photoautotrophs: Use sunlight for energy.

  • Chemoautotrophs: Harvest energy from inorganic chemicals.

• Heterotrophs:

  • Obtain carbon from organic molecules.

  • Photoheterotrophs: Use sunlight for energy.

  • Chemoheterotrophs: Retrieve energy from organic compounds (e.g., glucose).

• Energy Sources:

  • Light energy.

  • Energy from oxidizing organic or inorganic molecules.

• Phototrophs: Use light.

• Chemotrophs: Use oxidation of chemical compounds.

• Electron Sources:

  • Lithotrophs: Use inorganic substances.

  • Organotrophs: Extract from organic compounds.

• Primary Classes: Most bacteria are photolithoautotrophic or chemoorganoheterotrophic.

Specific Types of Nutritional Types

• Photolithoautotrophs: Use light energy and CO₂ as carbon (e.g., cyanobacteria).

• Chemoorganoheterotrophs: Use organic compounds for energy and carbon (e.g., pathogenic microbes).

• Photoorganoheterotrophs: Use organic matter as electron donor; found in polluted environments.

• Chemolithoautotrophs: Oxidize inorganic compounds for energy; CO₂ as carbon source.

• Chemolithoheterotrophs: Use inorganic molecules for energy; organic sources for carbon.

2.2 Reproduction of Bacteria

Asexual Reproduction

• Binary Fission: The main method of reproduction in bacteria.

• Process:

  1. Cell grows and doubles in mass.

  2. DNA replicates, resulting in two separate DNA molecules.

  3. Chromosome segregation involves chromosomal proteins, not fully understood.

  4. Septum forms, leading to two genetically identical daughter cells.

Sexual Reproduction

• Conjugation: Transfer of genetic material between two cells of different mating types.

• Process:

  1. Contact occurs between donor (F cells) and recipient (F− cells).

  2. Donor cell has the F factor (fertility factor), essential for DNA transfer.

  3. F factor may be a plasmid or a part of the chromosome.

  4. Sex Pili: Hairlike structures establish a conjugation bridge for DNA transfer.

  5. F plasmid replicates, allowing genetic material transfer which may include antibiotic resistance genes.

2.2 Common Bacterial Diseases

2.3 Archaea

• Definition: Unicellular, microscopic organisms often acting as producers or decomposers, known as Archaeans.

• Characteristics:

  • Prokaryotic: Lacks a membrane-bound nucleus.

  • Single-celled and lacking membrane-bound organelles.

  • Cell walls lack true peptidoglycan.

  • Lipids in cell membranes have branched hydrocarbon chains.

  • Many thrive in extreme environments.

Major Groups of Archaea

1. Methanogens: Strictly anaerobic; generate methane; found in waterlogged soils, gastrointestinal tracts, etc.

2. Extreme Halophiles: Thrive in highly saline environments like the Great Salt Lake.

3. Extreme Thermophiles: Found near volcanic vents; optimum temperatures exceed 80°C.

4. Thermophilic Extreme Acidophiles: Thrive in very acidic and hot environments.

Unique Features of Archaea

• Distinguished from bacteria by unique rRNA sequences, lack of true peptidoglycan, branched lipids, and the start codon code.

• Reproduce through binary fission, budding, and fragmentation.

• Nutritional categories include aerobic, facultative anaerobic, strictly anaerobic, and chemolithoautotrophic to organotrophic.

2.4 Fungi

• Definition: Eukaryotic organisms that are spore-bearing, nutrient-absorptive, lack chlorophyll, and reproduce sexually and asexually.

• Mycology: Study of fungi and fungal toxins; Mycotoxicology focuses on fungus toxicity.

• Mycoses: Fungal diseases in animals.

General Characteristics of True Fungi

1. Eukaryotic.

2. Filamentous Structures: Composed of microscopic filaments (hyphae); can form networks (mycelium).

3. Unicellularity: Some fungi, e.g., yeasts, are unicellular.

4. Cell Wall Composition: Walls primarily made of chitin and glucans, some cellulose.

5. Nuclear Composition: Mostly haploid nuclei; some multinucleate compartments.

6. Achlorophyllous: Incapable of photosynthesis.

7. Nutritional Mode: Chemoheterotrophic; utilize organic carbon sources.

8. Storage Compounds: Include trehalose, glycogen, sugar alcohols, and lipids.

9. Nutritional Variation: Include saprophytic, parasitic, and symbiotic types.

Ecology of Fungi

• Fungi colonize cool, dark, moist places and act as saprobes.

• Form mutualistic relationships (e.g., mycorrhizae).

• Lichens represent a symbiotic relationship between fungi and algae or cyanobacteria.

2.4.1 Classification of Fungi

1. Chytridomycota (Chytrids): Zoospore-producing fungi with motile spores; play a role in nutrient cycling.

2. Glomeromycota: Mycorrhizal fungi that enhance plant health.

3. Zygomycota: Known for rapid growth; some used in food fermentation.

4. Ascomycota: Includes multicellular molds and unicellular yeasts; significant in biotechnology.

5. Basidiomycota: Known for fruiting bodies (mushrooms) that produce spores; also some plant pathogens.

Reproduction in Fungi

• Sporulation: Process of spore formation in fruiting bodies, with asexual and sexual structures.

• Asexual Reproduction: Involves thousands of genetically identical spores produced mitotically or through dust-like spores on conidiophores.

• Sexual Reproduction: Involves mating types fusion and formation of visible fruiting bodies where haploid spores are formed.

Economic Importance of Fungi

Beneficial Aspects

• Play a major role in nutrient recycling, food processing, production of antibiotics, and edible mushrooms.

Harmful Aspects

• Cause plant diseases, spoil materials, and human diseases.

• Mycotoxicosis: Caused by ingestion of fungal toxins; Mycetism refers to mushroom poisoning.

2.5 Protozoa

• Definition: Protozoa are unicellular eukaryotic organisms classified as chemoorganotrophic protists.

• Study Field: Protozoology.

Characteristics of Protozoa

• Unicellular and lack cell walls; some can be free-living or parasitic.

• Oxygen Requirements: Mostly aerobic.

• Locomotion: Move via pseudopodia, flagella, or cilia.

Reproductive Processes

• Asexual Reproduction: Via fission, budding, cyst formation, or multiple fission.

• Sexual Reproduction: Involves conjugation where micronuclei exchange but no new individuals produced.

2.6 Viruses

• Definition: Viruses are obligate intracellular parasites visible only with an electron microscope.

• Virology: Study of viruses.

Characteristics of Viruses

• Cannot grow on artificial media; rely on host cells for replication.

• Lack cellular structures and enzymes for nucleic acid synthesis.

• Considered nonliving; exist between living and non-living states.

Structure of Viruses

• Central Core (genome): DNA or RNA, but not both; one of the smallest sizes ranging from 20 to 450 nm.

• Protein Coat (Capsid): Surrounds the core, made of capsomeres.

• Nucleocapsid: Structure formed by the combination of the core and capsid.

• Envelope: Some viruses, e.g., HIV, have an additional lipoprotein layer derived from the host cell.

Classification of Viruses

1. Viral Symmetry:

   • Helical Symmetry: RNA viruses with a spiral structure.

   • Icosahedral Symmetry: Has 20 triangular faces; led to compact genome structure.

   • Complex Symmetry: Incorporates various shapes and structures.

2. Genome Type: Classified as DNA viruses, RNA viruses, or retroviruses.

3. Host Type:

   • Animal Viruses: Infects animals.

   • Plant Viruses: Infects plants.

   • Bacterial Viruses (Bacteriophages): Infects bacteria.

Phage Life Cycles

• Lytic Cycle: Virulent phages multiply inside bacteria, leading to host lysis.

• Lysogenic Cycle: Temperate phages integrate their DNA into the host cell's DNA and can switch to the lytic cycle under certain conditions.

2.7 Normal Microbiota (Flora)

• Definition: Populations of microorganisms living on another organism without causing disease, typically found in healthy individuals.

• Types:

  • Resident Microbiota: Long-term inhabitants.

  • Transient Microbiota: Temporary inhabitants.

Importance of Studying Normal Microbiota

1. Infection Insight: Understanding normal microorganisms can reveal potential infections.

2. Colonization Understanding: Helps understand effects of non-native microorganisms.

3. Immune Response: Awareness of microbiota’s role in immune protection.

Protective Role

• Normal microbiota protect against pathogens and contribute to health.

• Antibiotics can disrupt normal microbiota, leading to harmful microorganisms overgrowth.

2.8 Germ Theory of Disease and Koch’s Postulates

• Germ Theory: Establishes microorganisms can cause disease.

• Koch’s Postulates: Criteria for linking specific microorganisms to diseases:

  1. Microorganism must be present in diseased animals.

  2. Must be cultivated in pure culture.

  3. Must cause disease when inoculated into healthy animals.

  4. Must be isolated and identified as the same organism.

2.9 Modes of Disease Transmission

• Contact Transmission: Direct or indirect contact.

• Droplet Transmission: From coughing or sneezing.

• Airborne Transmission: Pathogens spread through the air.

• Common Vehicle Transmission: Contaminated substances.

2.10 Uses of Microorganisms

General Contributions

• Microorganisms advance the understanding and applications in human health, agriculture, and the environment.

Agriculture Roles:

• Organic Matter Decomposition: Converts waste into nutrient-rich humus.

• Nitrogen Fixation: Converts atmospheric N₂ to usable forms for plants.

• Recycling: Essential chemical elements transformed into plant-usable forms.

• Sewage Treatment: Reduces sludge volume and removes harmful chemicals.

Bioremediation

• Utilizes microorganisms to degrade environmental pollutants; enhances the ability to detoxify a wide array of pollutants.

Food Production

• Microorganisms are essential for flavor and acidity in foods through fermentation processes.

Medicine Usage

• Microorganisms are crucial in drug development and delivery systems, including insulin production.

Recycling of Minerals in Ecosystems

• Carbon Cycle: Involves carbon fixation and respiration.

• Nitrogen Cycle: Includes nitrogen fixation, nitrification, and denitrification processes.

• Sulfur Cycle: Involves oxidation and reduction processes facilitated by various bacteria.

• Phosphorus Cycle: Involves both organic and inorganic phosphorus cycling in ecosystems.

2.11 Methods of Controlling Microorganisms

1. Sterilization: Kills all microorganisms; methods include heat and chemical agents.

2. Disinfection: Chemical agents destroy or remove pathogens without targeting spores.

3. Antiseptics: Applied to body surfaces to inhibit or destroy pathogens.

4. Sanitization: Cleansing techniques that mechanically remove microorganisms.

5. Preservation: Measures to prevent spoilage of products caused by microorganisms.

6. Decontamination: Removal of contaminants from surfaces or objects.

Conclusion

Microorganisms play a pivotal role in ecosystems, agriculture, human health, and disease dynamics; understanding these aspects allows for better control and utilization of these life forms for various beneficial purposes.