The Microbial World Study Notes

The Microbial World

Overview

  • Prokaryotes: Comprising Bacteria and Archaea.

  • Eukaryotes: Includes all organisms with complex cells.

  • Viruses: Non-cellular entities.

  • Course: MICR1010: Introductory Microbiology & Molecular Biology.

Classifying Living Things

  • Biological Classification: Systematic grouping of organisms based on evolutionary relationships.

    • Methods of Evidence:

      • Fossil Record: Historical evidence of organisms.

      • Comparative Homologies: Similarity of anatomy/physiology based on common ancestry.

      • Comparative Sequencing: Analyzing Genetic Material (DNA & RNA) among different organisms.

Gene Encoding Ribosomal RNA

  • Steps in Phylogenetic Analysis:

    1. Isolate DNA from each organism.

    2. Make copies of the rRNA gene via PCR (Polymerase Chain Reaction).

    3. Sequence DNA.

    4. Analyze sequence.

    5. Generate phylogenetic tree based on sequences:

      • Example: Aligned rRNA sequences like A A A G T G T T C G C G G C G G G T T T T A A A G G G.

Three Domains of Life

Bacteria

  • Defined as true bacteria, which are prokaryotes.

    • Examples: Streptococcus pneumoniae, Lactobacillus.

Archaea

  • Initially classified with Bacteria, now recognized as distinct.

    • Examples: Extremophiles.

Eukarya

  • Comprises all eukaryotic organisms divided into four kingdoms:

    • Protista: e.g., algae.

    • Fungi: e.g., mushrooms.

    • Plantae: e.g., Ackee tree.

    • Animalia: e.g., humans.

Naming Living Things

Binomial Nomenclature

  • Developed by Carolus Linnaeus in the 1700s.

    • Each species has a unique two-part name in Latin:

      • Genus (capitalized): Refers to a group of species.

      • Species (lowercase): Specific identifier.

  • Example: Vibrio cholerae, Canis lupus, Acer pseudoplatanus, Homo sapiens.

Characteristics of Prokaryotes (Bacteria)

  • General Characteristics:

    • Very small, simple, single-celled organisms.

    • Genetic material is not enclosed in a nuclear membrane.

    • Main shapes include:

      • Bacillus: rod-shaped.

      • Coccus: spherical.

      • Spiral: corkscrew-shaped.

Bacteria Sizes

  • Range of Size:

    • Between 0.1 μm to 600 μm.

    • Examples:

      • Mycoplasma: 100-200 nm diameter.

      • Escherichia coli: 1.1-1.5 μm x 2-6 μm.

      • Spirochetes: up to 500 μm length.

      • Cyanobacterium (Oscillatoria): 7 μm diameter.

      • Epulopiscium fishelsoni: up to 600 μm x 80 μm.

      • Thiomargarita namibiensis: 750 μm diameter.

      • Thiomargarita magnifica: 1 cm in length.

Surface-to-Volume Ratio

  • A large surface-to-volume ratio allows for effective nutrient absorption and waste removal due to proximity of cell surface to internal structures, enhancing microbial success despite simple morphologies.

Bacterial Cell Morphology

  • Morphological Shapes:

    • Cocci: spherical cells.

    • Bacilli: rod-shaped.

    • Spiral-shaped: typically motile, including:

      • Vibrio: comma-shaped.

      • Spirillum: spiral-shaped.

      • Spirochete: tightly coiled.

Bacterial Arrangements

  • Grouping Types:

    • Diplococci: pairs.

    • Streptococci: chains.

    • Tetrads: groups of four.

    • Sarcinae: cubical packets.

    • Staphylococci: clusters.

    • Bacilli arrangements include:

      • Diplobacilli: pairs.

      • Streptobacilli: chains.

      • Coccobacilli: oval-shaped.

Prokaryotic Cell Structures

External Appendages

  • Flagella: for movement.

  • Pili: for adherence and genetic exchange.

  • Fimbriae: for attachment to surfaces.

  • Glycocalyx: slimy layer providing protection and adherence (includes capsules and slime layers).

Cell Wall and Envelope

  • Consists of peptidoglycan, providing structural support and maintaining shape, protecting against osmotic lysis.

  • Gram-Positive Bacteria: Thick peptidoglycan layer, contains teichoic acid.

  • Gram-Negative Bacteria: Thinner peptidoglycan layer, complex outer membrane including lipopolysaccharides (LPS).

Function of Prokaryotic Structures

  • Plasma Membrane: Selectively permeable, involved in nutrient transport and metabolic processes.

  • Gas Vacuoles: Provide buoyancy.

  • Ribosomes: Protein synthesis.

  • Inclusion Bodies: Storage of nutrients.

  • Nucleoid: Location of genetic material.

  • Periplasmic Space: Houses enzymes for nutrient processing.

  • Cell Wall: Maintains shape, prevents lysis.

  • Capsules and Slime Layers: Protects against phagocytosis.

  • Fimbriae and Pili: Aid in attachment and genetic exchange.

  • Flagella: Allows for motility.

  • Endospore: Ensures survival during adverse conditions.

Gram-Staining Property of Cell Wall

  • Gram-Positive:

    • Peptidoglycan thickness: 20-80 nm.

    • Composed predominantly of peptidoglycan (90% of cell wall weight).

  • Gram-Negative:

    • Peptidoglycan thickness: 5-20% of cell wall; additional outer membrane containing LPS.

Cell Wall Structure

Peptidoglycan

  • A mesh-like structure composed of alternating units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) with peptide cross-links, providing rigidity and protection.

  • Target for antibiotics due to its essential role in bacterial survival.

Gram-Negative Cell Wall

  • Components:

    • Outer Membrane: Characteristic of Gram-negative bacteria, containing LPS which functions as an endotoxin.

    • Peptidoglycan Layer: Thin compared to Gram-positive, about 15-20% of the cell wall.

    • Periplasmic Space: Contains proteins crucial for nutrient processing and resistance to antibiotics.

External Structures of Prokaryotes

Flagella

  • Definition and Function: Thin structures enabling motility through various arrangements (monotrichous, lophotrichous, amphitrichous, peritrichous).

  • Facilitate various types of taxis (chemotaxis, phototaxis, aerotaxis, magnetotaxis).

Fimbriae and Pili

  • Pili: Facilitate adhesion to host tissues and gene transfer during conjugation.

  • Fimbriae: Shorter, assisting in adherence and biofilm formation; present mainly in Gram-negative bacteria.

Glycocalyx

  • Definition: A sticky polymer layer surrounding cells composed of polysaccharides and/or polypeptides.

    • Types:

      • Slime Layer: Unorganized, loosely attached.

      • Capsule: Organized, firmly attached, playing a role in virulence.

Internal Structures of Prokaryotes

Cytoplasmic Membrane

  • Functions as a permeability barrier, host for energy-producing pathways (electron transport chain).

Cytoplasm

  • Contains a mixture of nucleic acids (nucleoid), ribosomes, and plasmids (circular DNA that may confer antibiotic resistance).

Endospores

  • Structures that enable bacteria to survive extreme conditions; contain essential cellular components and protective layers forming during sporulation, allowing for long-term dormancy and germination under favorable conditions.

Classifying Bacteria: Gram-Negative & Gram-Positive

  • Differences in cell wall composition and structure have significant implications for bacterial physiology, pathogenicity, and antibiotic susceptibility.