History of Microbiology

Early Discoveries and the Microbial World

The field of microbiology began with the invention and improvement of microscopes, allowing scientists to visualize cells and microorganisms. Key figures include Robert Hooke and Antonie van Leeuwenhoek, who made foundational observations of plant cells and bacteria, respectively.

• Robert Hooke: Used a primitive microscope to observe cork cells, coining the term cellulae (cells).

• Antonie van Leeuwenhoek: Improved microscopes and first documented bacteria in 1683.

Disproving Spontaneous Generation

Spontaneous generation (abiogenesis) was the belief that life could arise from non-living matter. The competing theory, biogenesis, posited that cells arise only from pre-existing cells. Several experiments provided evidence for biogenesis:

• Francisco Redi (1668): Showed that maggots do not develop on covered meat.

• Lazzaro Spallanzani: Demonstrated that sealed and heated broth did not support microbial growth.

• Louis Pasteur (1861): Used a swan-neck flask to show that microbes are trapped from air, disproving spontaneous generation. Also developed pasteurization to control microbial spoilage in food and beverages.

Germ Theory of Disease and Koch's Postulates

The germ theory states that specific microbes cause specific diseases. Robert Koch established guidelines (Koch's postulates) to link microbes to diseases:

1. Pathogen must be present in diseased organisms.

2. Pathogen can be isolated and grown in lab.

3. Pathogen causes disease when introduced to a healthy organism.

4. Pathogen can be re-isolated from the infected organism.

Microbial Control and Medical Advances

• Joseph Lister: Used carbolic acid (phenol) to reduce surgical infections.

• Alexander Fleming: Discovered penicillin, the first antibiotic, from Penicillium mold.

• Edward Jenner: Developed vaccination using cowpox to confer protection against smallpox.

Diversity in Microbiology

Taxonomy and Classification

Taxonomy is the science of classifying organisms. Modern classification is based on phylogenetic relationships determined by DNA evidence. The largest taxonomic group is the domain, followed by kingdom, phylum, class, order, family, genus, and species.

• Domains:

  • Archaea: Unicellular prokaryotes, unique cell walls (no peptidoglycan), unique membrane lipids.

  • Bacteria: Unicellular prokaryotes, cell walls with peptidoglycan, phospholipid bilayer membranes.

  • Eukarya: Unicellular and multicellular eukaryotes, nuclei, internal organelles.

• Binomial Nomenclature: Scientific names use genus and species (e.g., Escherichia coli).

Major Groups of Microbes

• Bacteria: Prokaryotic, peptidoglycan cell walls, diverse shapes and arrangements.

• Archaea: Prokaryotic, no peptidoglycan, unique membrane chemistry, resistant to antibiotics.

• Eukarya:

  • Kingdom Animalia: Multicellular, consume other organisms, includes helminths (flatworms, roundworms).

  • Kingdom Fungi: Multicellular (molds) and unicellular (yeasts), external digestion, spore formation.

  • Protists: Protozoans (heterotrophic, e.g., Entamoeba histolytica), algae (photosynthetic).

• Viruses: Subcellular parasites, require host cells for replication, contain proteins, lipids, nucleic acids.

Microbial Relationships and Importance

• Pathogens: Cause disease in humans and other organisms.

• Microbiota: Community of microbes in healthy individuals, outnumber human cells, contribute to health (vitamins, fatty acids).

• Microbiome: All microbial genetic material in humans.

• Fermentation: Yeasts and bacteria produce food products (yogurt, bread, alcohol).

Chemical Principles of Microbiology

Water and Its Properties

Water is essential for life, serving as the medium for biochemical reactions. Its bent molecular shape and polar covalent bonds create dipoles, allowing hydrogen bonding between molecules.

• Chemical formula:

• Hydrogen bonds: Each water molecule can form up to four hydrogen bonds.

Solutions and Dissociation

• Solution: Mixture of solute (dissolved substance) and solvent (liquid, usually water).

• Dissociation: Ionic compounds break into ions when dissolved (e.g., ).

• Ions: Cations (positive, lost electrons), anions (negative, gained electrons).

Acids, Bases, and Salts

• Acids: Release hydrogen ions ().

• Bases: Release hydroxide ions () or absorb hydrogen ions.

• Salts: Release ions other than or .

pH Scale

• pH: Measures hydrogen ion concentration; neutral water is pH 7.

• Acidic: pH < 7; higher concentration.

• Basic (alkaline): pH > 7; higher concentration.

Organic Compounds and Functional Groups

• Organic compounds: Contain carbon and hydrogen.

• Functional groups: Hydroxyl (-OH), amino (-NH2), carboxyl (-COOH), ester (-COO-), ether (-COC-).

Chemical Reactions

• Anabolic (biosynthetic): Build larger molecules; dehydration synthesis produces water.

• Catabolic: Break down molecules; hydrolysis uses water to split reactants.

Major Classes of Organic Molecules

• Carbohydrates: Energy source; composed of C, H, O in 1:2:1 ratio.

  • Monosaccharides: Single ring (e.g., glucose, fructose).

  • Disaccharides: Two monosaccharides (e.g., sucrose, lactose).

  • Polysaccharides: Long chains (e.g., starch, cellulose).

• Lipids: Energy storage, cell barriers, hormones; hydrophobic except phospholipids (amphipathic).

  • Triglycerides: Glycerol + 3 fatty acids.

  • Phospholipids: Glycerol + 2 fatty acids + hydrophilic group; form bilayers in membranes.

• Proteins: Built from amino acids; functions include enzymes, structure, transport.

  • Amino acids: 20 types, variable R group, hydrophilic/hydrophobic properties.

  • Peptide bonds: Covalent bonds between amino acids.

  • Protein folding: Essential for function; denaturation disrupts structure and function.

• Nucleic acids: DNA and RNA; store and transmit genetic information.

  • Nucleotide: Pentose sugar, nitrogenous base, phosphate group.

  • DNA: Double helix, four bases (A, T, G, C), complementary base pairing.

  • RNA: Single-stranded, ribose sugar, uracil replaces thymine.

Gene Expression

• Transcription: DNA base sequence copied to RNA.

• Translation: RNA sequence converted to polypeptide at ribosome.

Microscopes and Microbial Observation

Size Scale of Microbes

Microbes are measured using metric prefixes:

• Milli- (m):

• Micro- (µ):

• Nano- (n):

• Pico- (p):

Light Microscopy

• Brightfield: Standard technique; cells appear against a bright background.

• Darkfield: Filter minimizes background light; cells appear bright on dark background.

• Phase contrast: Specialized lenses reveal internal structures in living cells.

• Staining:

  • Positive stains: Basic dyes (e.g., crystal violet, safranin) color cells.

  • Negative stains: Acidic dyes (e.g., nigrosin) color background.

  • Differential stains: Distinguish cell types (e.g., Gram, endospore, acid-fast, capsule stains).

• Fluorescence microscopy: Uses fluorochromes and immunofluorescence to label specific cells.

Electron Microscopy

• SEM (Scanning Electron Microscopy): Surface structure, 10 nm–1 mm range.

• TEM (Transmission Electron Microscopy): Internal structure, 10 pm–100 µm range.

• Limitation: Cannot observe living samples due to vacuum and toxic stains.

Prokaryotic Cell Structures & Functions

Bacterial Cell Shapes and Arrangements

• Coccus: Round cells

• Bacillus: Rod-shaped cells

• Coccobacillus: Rounded rods

• Vibrio: Curved, comma-shaped

• Spirillum: Spiral with flagella

• Spirochete: Spiral with internal locomotion structures

Common arrangements: diplo (pairs), strepto (chains), staphylo (clusters), tetrad (four), sarcina (eight). Pleomorphic bacteria do not maintain consistent morphology.

Plasma Membrane

• Structure: Phospholipid bilayer, amphipathic molecules.

• Function: Regulates transport; integral proteins assist in transport of hydrophilic/charged solutes.

Motility Structures

• Flagella: Types include peritrichous, monotrichous, lophotrichous, amphitrichous, atrichous.

• Endoflagella (axial filaments): Internal movement in spirochetes (e.g., Treponema pallidum, Borrelia burgdorferi).

Attachment Structures

• Fimbriae: Short, used for attachment to surfaces.

• Pili: Used for attachment and genetic exchange (e.g., Neisseria gonorrhoeae).

Cell Wall Structure

• Peptidoglycan: Carbohydrate backbone (NAG-NAM), peptide cross-links.

• Gram-positive: Thick peptidoglycan, teichoic acids, pentaglycine cross-bridges.

• Gram-negative: Thin peptidoglycan, outer membrane with lipoproteins and lipopolysaccharide (LPS), tetrapeptide cross-links.

• LPS: Contains lipid A, potent endotoxin.

Gram Stain Steps

1. Primary stain (crystal violet)

2. Mordant (iodine)

3. Decolorizer (ethanol)

4. Counterstain (safranin)

Gram-positive cells retain crystal violet (purple); Gram-negative cells take up safranin (pink).

Mycobacterium Cell Wall

• Contains mycolic acid: Hydrophobic, prevents conventional staining.

• Acid-fast stain: Carbolfuschin dye, heat or time as mordant, acid-alcohol decolorizer, methylene blue counterstain.

Glycocalyx

• Capsule: Compact carbohydrate layer, aids in evasion and attachment.

• Biofilm: Broad glycocalyx, allows adherence to surfaces and tissue.

Nucleoid and Plasmids

• Nucleoid: Region containing circular chromosome (e.g., E. coli genome ~5 Mbp, 4,400+ genes).

• Plasmids: Small, non-essential DNA molecules, may confer advantages (e.g., antibiotic resistance).

Endospores

• Formation: Sporulation under unfavorable conditions; highly resistant structures.

• Genera: Bacillus, Clostridium.

• Structure: Core contains chromosome, ribosomes, enzymes, calcium, dipicolinic acid.

• Staining: Endospore stain (malachite green, safranin counterstain).

• Germination: Return to vegetative state under favorable conditions.

Comparison of Domains: Bacteria vs. Eukarya

Additional info: Table entries inferred from standard microbiology comparisons.