Introduction to Microbiology

Definition and Scope

Microbiology is the study of microorganisms, which are organisms too small to be seen with the unaided eye. Microbes are found in nearly every environment, from salt flats and acidic soils to oceans and potentially even extraterrestrial locations.

• Microorganisms: Include bacteria, archaea, fungi, protozoa, algae, viruses, and some multicellular parasites.

• Human Microbiome: The collection of microbes living stably on/in the human body, outnumbering human cells and playing roles in health, immunity, and disease prevention.

• Normal Microbiota: Acquired microorganisms on or in a healthy human, which may be permanent or transient depending on environmental suitability.

• Microbes in Unusual Environments: Examples include salt flats, acidic soils, and deep ocean habitats.

Classification of Organisms

The classification system developed by Carl Woese (1978) divides life into three domains based on 16S rRNA sequences:

• Bacteria: Prokaryotic, peptidoglycan cell walls, diverse metabolism, includes pathogens.

• Archaea: Prokaryotic, lack peptidoglycan, often extremophiles, none are pathogenic.

• Eukarya: Eukaryotic, includes protists, fungi, plants, and animals.

Types of Microorganisms

• Prokaryotic: Bacteria, Archaea

• Eukaryotic: Fungi, Protozoa, Algae

• Viruses: Acellular, DNA or RNA core, protein coat, replicate only in host cells

• Multicellular Animal Parasites: Helminths (flatworms, roundworms), some microscopic stages

Historical Observations

• Robert Hooke (1665): First described cells, beginning of cell theory.

• Anton van Leeuwenhoek (1673–1723): Observed "animalcules" (microbes) with magnifying lenses.

Disproving Spontaneous Generation

Spontaneous Generation vs Biogenesis

Spontaneous generation posited that life arises from nonliving matter, while biogenesis states that living cells arise only from preexisting cells.

• Francesco Redi (1668): Covered and uncovered meat jars; maggots appeared only in open jars.

• John Needham (1745): Boiled broth in covered flasks; microbial growth occurred.

• Lazzaro Spallanzani (1765): Boiled broth in sealed flasks; no microbial growth.

• Rudolf Virchow (1858): Proposed biogenesis.

• Louis Pasteur (1861): Swan-neck flask experiment; broth remained sterile unless exposed to air/dust, disproving spontaneous generation.

Golden Age of Microbiology (1857–1914)

• Relationship between microbes and disease

• Role of immunity

• Chemical activities of microorganisms

• Improved microscopy and culturing methods

• First vaccines and chemotherapeutic drugs

Microorganisms and Humans

Impact on Health and Disease

• Microbes can be beneficial (e.g., gut flora, bioremediation) or harmful (pathogens).

• Control of infectious diseases has shifted causes of mortality over the last century.

Applications in Agriculture and Industry

• Microbes in rumen digest cellulose for animal nutrition.

• Microbes participate in nitrogen and sulfur cycles.

• Applications in food industry, antibiotics, hormones, enzymes, bioremediation, biofuels, and biotechnology (e.g., designer jeans, plastics).

Prokaryotic Cell Structures & Functions

Prokaryotes vs Eukaryotes

• Prokaryotes: One circular chromosome, no nuclear membrane, histone-like proteins, no organelles, peptidoglycan cell walls (bacteria), pseudomurein (archaea), 70S ribosomes, binary fission.

• Eukaryotes: Paired chromosomes in nuclear membrane, histones, organelles, polysaccharide cell walls (plants/fungi), no cell wall (animals), 80S ribosomes, mitosis.

Bacterial Cell Size and Shape

• Average size: 0.2–1.0 µm × 2–8 µm

• Shapes: Bacillus (rod), Coccus (sphere), Spiral (vibrio, spirillum, spirochete), star-shaped, rectangular

• Arrangement: Single, diplo, chains, tetrads, sarcina, staphylo

• Some bacteria are pleomorphic (variable shapes)

Plasma Membrane

• Structure: Lipid bilayer, fluid mosaic model, amphipathic phospholipids, proteins (peripheral, integral, transmembrane), hopanoids (bacteria), sterols (eukaryotes)

• Functions: Encloses cytoplasm, selective permeability, ATP production (electron transport chain), photosynthetic pigments (chromatophores), anchors external structures

Transport Across the Membrane

• Passive Processes:

  • Simple diffusion: Movement from high to low concentration

  • Facilitated diffusion: Uses transporter proteins

  • Osmosis: Water movement across membrane; via lipid layer or aquaporins

• Active Processes:

  • Active transport: Requires transporter protein and ATP

  • Group translocation: Uses PEP; substance is chemically altered during transport

Osmosis in Solutions

• Isotonic: Equal solute concentration; no net water movement

• Hypotonic: Lower solute outside; water enters cell, may cause lysis

• Hypertonic: Higher solute outside; water leaves cell, causes plasmolysis

Energy Production and Photosynthesis

• Electron transport chain in plasma membrane generates ATP

• Photosynthetic pigments in chromatophores/thylakoids capture sunlight

Cell Wall & External Structures

Cell Wall Structure and Function

• Protects from osmotic lysis, gives shape

• Gram-positive: Thick peptidoglycan, teichoic acids

• Gram-negative: Thin peptidoglycan, outer membrane, periplasmic space

Peptidoglycan Composition

• Polymer of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM), linked by β-1,4 glycosidic bonds

• Rows linked by polypeptides; helical chains; peptide cross-bridges

Gram Staining Protocol

• Fixation → Crystal violet → Iodine treatment → Decolorization → Counterstain (safranin)

• Gram-positive: Retain crystal violet (purple)

• Gram-negative: Lose crystal violet, take up safranin (pink/red)

Gram-positive Cell Wall

• Teichoic acids (wall and lipoteichoic acids), negative charge, regulate cation movement

Gram-negative Cell Wall

• Outer membrane: O polysaccharide, core polysaccharide, lipid A (endotoxin), porins, lipoproteins

• Permeability barrier, surface attachment, biofilm formation

Cell Wall Damage

• Lysozyme hydrolyzes glycan bonds, weakening cell wall

• Penicillin inhibits peptide bridge formation

• Protoplasts (wall-less Gram-positive), spheroplasts (wall-less Gram-negative), L forms (irregular, wall-less)

Mycobacteria and Atypical Cells

• Mycobacteria: Mycolic acids, arabinogalactans, acid-fast stain, sticky cell walls, slow growth, resistance to digestion/desiccation

• Mycoplasmas: Lack cell wall, sterols in membrane

• Archaea: Wall-less or pseudomurein walls, S-layer (protein)

Glycocalyx: Capsule and Slime Layer

• Outside cell wall, mostly carbohydrate, sticky

• Capsule: Organized, protective, aids attachment, resists desiccation

• Slime layer: Unorganized, loose

• Capsules visualized by negative staining

External Structures

• Flagella: Filament, hook, basal body; made of flagellin; arrangement (peritrichous, monotrichous, lophotrichous, amphitrichous); function (motility, taxis); rotation driven by proton motive force

• Archaella: Archaeal motility structure, glycoproteins, rotation

• Eukaryotic Flagella/Cilia: Microtubule structure, flexible, wave/whip-like motion

• Axial Filaments: Endoflagella in spirochetes, corkscrew motion

• Fimbriae: Hair-like, attachment to host

• Pili: Longer, surface attachment, twitching/gliding motility, DNA transfer (sex pili)

Cytoplasm and Internal Structures

Cytoplasm

• Thick, aqueous, elastic, semitransparent; 80% water plus macromolecules

• Contains DNA (nucleoid), ribosomes, inclusions

• Cytoskeleton: Fibers for division, shape, growth, DNA movement

Bacterial Genome

• Nucleoid: Circular DNA, not membrane-bound, histone-like proteins, supercoiling, anchored to membrane

• Plasmids: Extrachromosomal DNA, independent replication, antibiotic resistance, pathogenesis, transferable

Cytoskeletal Proteins

• FtsZ: Division (spherical, rod, vibrioid)

• MreB: Elongation (rod, vibrioid)

• Crescentin: Curvature (vibrioid)

Ribosomes

• Sites of protein synthesis; made of protein and rRNA

• Prokaryotic: 70S (50S + 30S); Eukaryotic: 80S (60S + 40S)

• Antibiotics targeting prokaryotic ribosomes: Streptomycin, Gentamicin, Erythromycin, Chloramphenicol

Inclusions

• Storage granules: Phosphate (volutin), polyhydroxyalkanoate (PHA), glycogen

• Sulfur granules: Energy reserves

• Carboxysomes: CO2 concentrating mechanism (Calvin Cycle)

• Gas vacuoles: Buoyancy

• Magnetosomes: Iron oxide inclusions, destroy H2O2

Endospores

• Resting cells produced when nutrients are depleted; resistant to desiccation, heat, chemicals, radiation

• Produced by Bacillus and Clostridium

• Sporulation: Endospore formation; germination: return to vegetative state

• Structure: Spore septum, forespore, peptidoglycan layer, spore coat, release

• Resilience: Dipicolinic acid (DPA) and Ca2+

• Survival: Endospores can persist for millions of years

Endospore Formation Steps

1. Spore septum isolates DNA and cytoplasm

2. Membrane surrounds isolated portion

3. Forespore formed (two membranes)

4. Peptidoglycan layer forms

5. Spore coat forms

6. Spore released from mother cell

Endospore Staining

• Special stains (e.g., malachite green) used to visualize endospores

Comparison Table: Prokaryotes vs Eukaryotes

Key Formulas and Equations

• Diffusion Rate Equation: Where J is flux, D is diffusion coefficient, C is concentration, x is distance.

• Osmosis: Where \Pi is osmotic pressure, i is van 't Hoff factor, M is molarity, R is gas constant, T is temperature.

Additional info: Academic context was added to clarify mechanisms, historical experiments, and cell structure details. Table and equations were inferred for completeness.