Classification of Microorganisms

Binomial Nomenclature and Taxonomy

• Binomial nomenclature is a two-name system (Genus species) introduced by Linnaeus in the 18th century for naming organisms.

• Originally, organisms were classified into two kingdoms: plants and animals. Modern taxonomy recognizes six kingdoms: Archaea, Monera, Protista, Fungi, Plantae, and Animalia.

• Woese proposed the domain system, a broader classification above kingdom, based on differences in DNA reading mechanisms, especially in Archaea. Domains: Bacteria, Archaea, Eukarya.

• Bergey’s Manual is a key reference for bacterial taxonomy, widely used in medical microbiology for identifying pathogens.

Major Categories of Microorganisms

Archaea

• Primitive prokaryotes with unique DNA transcription and translation mechanisms.

• Commonly found in extreme environments:

  • Extreme halophiles (high salt)

  • Methanogens (produce methane)

  • Thermoacidophiles (high temperature and acidity)

Eubacteria

• Includes typical bacteria and cyanobacteria (blue-green algae).

• Other groups: Rickettsia, Chlamydia, Mycoplasma, and viruses (though viruses are not cellular life forms).

Classification of Bacteria by Shape and Arrangement

Cocci (Spherical)

• Diplococci: pairs (e.g., Neisseria gonorrhoeae)

• Streptococci: chains (e.g., Streptococcus pneumoniae, strep throat)

• Staphylococci: irregular clusters (e.g., staph infections)

• Tetrads: packets of four

• Sarcinae: packets of eight

Bacilli (Rod-shaped)

• Diplobacilli: pairs

• Streptobacilli: chains

• Palisade: side-by-side arrangement (e.g., Corynebacterium diphtheriae)

• Tubercles: Y-shaped clusters (e.g., Mycobacterium tuberculosis)

Variations of Shape

• Coccobacillus: short rods (e.g., Escherichia coli)

• Fusiform: tapered ends (e.g., Mycobacterium)

• Vibrio: comma-shaped (e.g., Vibrio cholerae)

Spirilla (Spiral-shaped)

• Spirillum: short, rigid spirals, motile by flagella

• Spirochete: long, flexible spirals, motile by flexing

Structural Components of Prokaryotic Cells

Glycocalyx and Capsule

• Glycocalyx: Mucopolysaccharide layer outside the cell wall.

• Functions: protection from dehydration, immune evasion (camouflage), resistance to abrasion, attachment to surfaces, food storage, and waste disposal.

• Capsule: Well-organized, tightly bound layer composed of protein, polysaccharide, or both. Protects against dehydration, immune attack, and ingestion by phagocytes.

Cell Wall

• Provides shape, rigidity, and protection against osmotic pressure.

• Gram-positive: Thick peptidoglycan layer (~90%), contains teichoic acids (acidic polysaccharides).

• Gram-negative: Two layers—outer membrane (phospholipid bilayer with proteins and lipopolysaccharide) and thin peptidoglycan layer (5–20%).

• LPS Structure (Gram-negative):

  • O-side chain (O-antigen): variable sugars, antigenic properties

  • Core polysaccharide: relatively constant

  • Lipid A: toxic, triggers immune response (e.g., septic shock in Salmonella, E. coli)

• Periplasmic space: Found in gram-negative bacteria, stores hydrolytic enzymes.

Cell Membrane

• Described by the fluid mosaic model: phospholipid bilayer with embedded proteins.

• Phospholipids: hydrophobic tails, hydrophilic heads.

• Proteins: intrinsic (70–80%), function in transport and enzymatic activity.

• Functions: selective barrier, enzyme housing, regulation of transport, site of respiration and ATP formation.

Transport Mechanisms

• Osmosis: Water moves to the side with higher solute concentration.

• Passive diffusion: Small molecules move from high to low concentration.

• Facilitated diffusion: Larger molecules move via permeases from high to low concentration.

• Active transport: Moves substances against the concentration gradient, requires energy and proteins.

Other Structures

• Chromatophores: Photosynthetic membranes in bacteria (e.g., cyanobacteria).

• Water: Makes up ~70% of cell, acts as solvent, reactant/product in biochemical reactions, and stabilizes temperature due to high specific heat.

• Nucleoid: Region containing the single, circular chromosome; protects DNA from degradation.

• Plasmids: Extra-chromosomal DNA, often encode antibiotic resistance, toxin production, or metabolic functions.

• Inclusions: Storage granules (e.g., volutin for phosphate, glycogen for energy, lipid for carbon/energy, sulfur for protein structure, magnetosomes for orientation).

• Ribosomes: 70S in prokaryotes (30S + 50S subunits); target for antibiotics like streptomycin and erythromycin.

• Vacuoles: Protein membranes, regulate buoyancy and protect against gas toxicity.

Motility and Surface Structures

Flagella

• Function: Motility (movement).

• Composed of flagellin; structure includes basal body (anchor), hook, and filament.

• Arrangements:

  • Atrichous: No flagella

  • Monotrichous: Single flagellum (polar or subpolar)

  • Lophotrichous: Tufts at one or both ends

  • Amphitrichous: Single flagellum at each end

  • Peritrichous: Flagella all over the surface

• Types of taxis: Chemotaxis (chemical), Phototaxis (light), Aerotaxis (oxygen), Magnetotaxis (magnetic fields).

Pili and Fimbriae

• Found mainly in gram-negative bacteria.

• Fimbriae: Short, numerous; function in attachment and pathogenicity (e.g., Neisseria gonorrhoeae, E. coli).

• Sex pili: Longer; involved in conjugation (DNA transfer between cells).

Bacterial Spores

Sporulation and Germination

• Sporulation: Formation of endospores in response to environmental stress (nutrient deprivation).

• Stages:

  1. DNA duplication

  2. Plasma membrane invagination (septum formation)

  3. Forespore formation

  4. Engulfment by mother cell, cortex formation (peptidoglycan), Ca-dipicolinate deposition

  5. Spore coat formation, release upon cell lysis

• Germination: Activation, degradation of spore layers, water uptake, and outgrowth into vegetative cell.

• Endospores are highly resistant to heat, desiccation, chemicals, and radiation.

Special Bacterial Groups

Rickettsia

• Gram-negative, non-motile, non-spore-forming bacilli (0.3–0.5 μm).

• Obligate intracellular parasites; transmitted by arthropod vectors (e.g., ticks, lice).

• Diseases: Rocky Mountain spotted fever, typhus, bubonic plague.

• Pathogenesis: Invade endothelial cells, cause vascular leakage (petechiae), necrosis of organs.

Chlamydia

• Obligate intracellular parasites with a complex life cycle.

• Infectious elementary body enters host cell by phagocytosis, transforms into reticulate body (reproductive form), then reverts to elementary body for release.

• Causes nongonococcal urethritis (NGU).

• Biosynthetically limited, more so than Rickettsia.

Mycoplasma

• Smallest free-living bacteria (0.125–0.25 μm), pleomorphic, lack cell wall.

• Membrane contains sterols for stability; sensitive to antibiotics targeting gram-negatives.

• Obligate symbionts, require sterols from environment; non-motile, non-spore-forming.

Viruses

Origin Theories

• Co-evolution with cells from self-replicating molecules.

• Reverse evolution (degeneration from cellular forms).

• Evolution from plasmids or viroids, acquiring genes for capsid formation.

Structure

• Capsid: Protein coat made of capsomeres; shapes include polyhedral (e.g., icosahedral) and helical.

• Spikes: Glycoproteins for host cell attachment.

• Nucleic acid: DNA or RNA (ss or ds), linear or circular.

• Envelope: Lipid membrane derived from host, present in some viruses.

• Simple viruses: head only; complex viruses: head and tail structures.

Classification

• By host: bacterial, plant, animal viruses.

• By tissue tropism in animals:

  • Dermatrophic: skin (e.g., warts)

  • Neurotrophic: nervous tissue (e.g., viral meningitis)

  • Viscerotrophic: organs (e.g., hepatitis)

  • Pneumotrophic: respiratory tract (e.g., cold viruses)

• By nucleic acid type, capsid shape, envelope presence, and size.

Viral Replication Strategies

• +ssRNA viruses: Genome acts as mRNA, directly translated by host ribosomes.

• -ssRNA viruses: Genome serves as template for complementary +RNA, must carry RNA-dependent RNA polymerase.

• Retroviruses: Use reverse transcriptase to convert RNA to DNA, integrate into host genome.

Examples of Viral Diseases

• Enterovirus (Picornavirus): Polio, transmitted via digestive tract, can cause paralysis.

• Hepatovirus: Hepatitis A, affects the liver.

• Rhinovirus: Common cold, infects upper respiratory tract.

• Herpesvirus: Latency, causes herpes, chickenpox, Epstein-Barr.

• Poxvirus: Smallpox.

• Papovavirus: Cervical cancer.

• Hepadovirus: Hepatitis B, associated with liver cancer.

Key Terms and Concepts

• Antigenicity: Ability of a molecule (e.g., O-antigen in LPS) to be recognized by the immune system.

• Septic shock: Dangerous drop in blood pressure due to immune response to bacterial endotoxins (Lipid A).

• Svedberg unit (S): Measure of sedimentation rate during centrifugation, used to describe ribosome size (e.g., 70S in prokaryotes).

Summary Table: Major Microbial Groups

Key Equations

• Osmosis: Water moves from low to high solute concentration across a semi-permeable membrane.

• Passive Diffusion Rate:

• Facilitated Diffusion (Michaelis-Menten kinetics):

• Active Transport (energy requirement):

Additional info: Some explanations and tables have been expanded for clarity and completeness based on standard microbiology textbooks.