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Fundamentals, History and Development of Microbiology – Vocabulary Flashcards

Definitions of Microbiology

  • Multiple complementary definitions exist; no single wording is considered sufficient.
  • Core ideas shared by all definitions:
    • Scientific study of microscopic agents/organisms (micro-organisms).
    • Focus on life too small to be seen unaided; observation requires microscopes.
    • Encompasses both cellular (prokaryotic & eukaryotic) and acellular (virus-like) entities.
  • Standard disciplinary breakdown (sub-fields):
    • Virology – viruses
    • Bacteriology – bacteria
    • Mycology – fungi
    • Parasitology – parasites (protozoa & helminths)
  • Applied/functional subdivisions include microbial physiology, genetics & evolution, environmental and industrial microbiology, food microbiology, etc.
  • Etymology: micro = "small", bio = "life", loge (logos) = "study" ➜ study of small life-forms.

Spectrum of Microbial Life

  • Acellular infectious agents:
    • Viruses – DNA or RNA within protein capsid, 20\text{–}450\,\text{nm}.
    • Viroids – circular ssRNA, no protein coat, plant pathogens.
    • Virusoids – ssRNA satellites requiring helper viruses.
    • Prions – proteinaceous infectious particles (~5\,\text{nm}), target CNS.
  • Cellular microscopic agents:
    • Eubacteria ("true" bacteria)
    • Archaea (ancient prokaryotes; many extremophiles)
    • Fungi – yeasts & moulds
    • Algae (protistan phototrophs)
    • Protozoa (heterotrophic protists)
    • Slime moulds (protists)

Prokaryotes vs Eukaryotes & Viral Exception

  • Criterion: presence/absence of membrane-bound nucleus.
    • Prokaryotes – Bacteria & Archaea (nucleoid only).
    • Eukaryotes – animals, plants, algae, fungi, protozoa.
  • Viruses are traditionally considered non-living yet treated operationally as microorganisms.

Representative Groups – Key Traits & Examples

  • Viruses: geometric capsid shapes; HIV, Yellow-fever, Polio, TMV.
  • Prions: unconventional viruses; cause mad-cow disease.
  • Viroids: PSTV (potato spindle-tuber) agent.
  • Bacteria: motile/non-motile; Gram ±; autotroph/heterotroph; Micrococcus, Staphylococcus.
  • Protozoa: uninucleate, flagellated/amoeboid; Giardia, Trypanosomes.
  • Algae: aquatic phototrophs; Spirogyra, brown/red algae.
  • Fungi: heterotrophic, spore-forming; yeast (Saccharomyces), moulds (Aspergillus, Penicillium), mushrooms.

General Characteristics of Microorganisms

  1. Invisibility
    • Require magnification: moulds at \times10; bacteria often \times1000 oil-immersion; viruses only by electron microscopy.
    • Smallest bacterium: Mycoplasma genitalium ~0.25\,\mu\text{m}.
    • Nanobacteria (controversial) ~0.05\,\text{µm}=50\,\text{nm}.
    • Viroids RNA as short as 248 nucleotides (<10\,\text{nm} diameter).
    • Unit conversion: 1\,\mu\text{m}=1\times10^{-6}\,\text{m}.
  2. Ubiquity
    • Present in air, water, soils, extreme niches (hydrothermal vents, high salinity, high pressure, acidic/alkaline sites) and on/in organisms (normal flora).
  3. Rapid Reproducibility
    • Binary fission yields exponential growth; generation time of many bacteria ≤ 25 min.
  4. Culturability
    • Growth on artificial media forms discrete colonies distinguished by colour, size, margin, elevation, opacity.
  5. Metabolic Impact
    • Biodegradation (beneficial), biodeterioration (economic loss), invasion (disease). Powered by intra/extra-cellular enzymes.
  6. Innumerability
    • Colony-forming unit (cfu) concept; one gram garden soil ≈ 10^{10} cells; global bacterial count estimated 5\times10^{30}.
  7. Indispensability
    • Ecosystem services: decomposition, elemental cycling (C, N, S), O$_2$ evolution (>50 % from cyanobacteria/algae), food-chain support, symbiotic digestion/vitamin synthesis, yet also pathogenic roles that regulate populations.

Branches & Specialties of Microbiology

  • Medical Microbiology – pathogens, pathogenesis, epidemiology, diagnostics, vaccines.
  • Environmental Microbiology/Microbial Ecology – community structure/function in soil, water, air; bioremediation.
  • Agricultural Microbiology – crop, livestock, aquaculture, soil fertility (e.g., N$_2$ fixation).
  • Pharmaceutical Microbiology – drug production, sterility, quality control.
  • Food Microbiology – fermentation, preservation, safety (infection/intoxication).
  • Water & Sanitary Microbiology – potable water, wastewater treatment.
  • Industrial Microbiology – large-scale production of antibiotics, enzymes, vitamins, bio-fuels.
  • Petroleum Microbiology – MEOR (microbial enhanced oil recovery), souring, corrosion, spill cleanup.
  • Fermentation Technology – starter cultures, bioreactors, downstream processing.
  • Microbial Physiology/Biochemistry – metabolic pathways, energy generation.
  • Microbial Genetics/Biotechnology – gene structure, recombinant DNA, GM microbes.
  • Immunology – host immune responses.
  • Epidemiology – disease distribution & control.
  • Microbial Metabolism – comparative anabolism/catabolism.
  • Analytical Microbiology & Quality Control – assays, standards.
  • Genetic Engineering & Biotechnology – cross-cutting application of microbial genetics.

Life & Its Origins – Microbiological Perspective

  • Defining life via attributes: complex organisation, metabolism, growth, responsiveness, reproduction, heredity.
  • Geological timeline:
    • Earth forms ≈ 4.6 billion y ago (Ga).
    • Life appears ≈ 3.5 Ga.
  • Cosmological theories:
  1. Solar nebular condensation of gas/dust.
  2. Planetary molten coalescence & cooling.
  3. Big Bang → stellar evolution → heavy elements (C, N, O) forged in stars ➜ "life from stardust".
    • Philosophical debate: natural self-organisation vs divine design.
  • Chemical evolution pathway (Haldane–Oparin “primordial soup”): hot, reducing atmosphere of \text{H}2\text{O}, \text{CH}4, \text{NH}3, \text{H}2; energy (UV, lightning) drives synthesis of amino acids, sugars, nucleobases.
  • Miller–Urey experiment (1952): recirculating gases + electric sparks produced aldehydes, carboxylic acids, amino acids within a week, supporting abiotic synthesis.
  • From molecules to protocells:
    • Coacervates/protenoids: membrane-like protein/lipid droplets that grow and split.
    • Hypothesis of RNA world: spontaneous polymerisation of RNA with self-replication → reverse transcriptase evolves → DNA replaces RNA as info store.
    • Carl Woese’s "progenote": ancestral cell with DNA genome & primitive ribosomes; ancestors diverged into Archaea, Bacteria, Eukarya.
    • Early metabolism possibly anaerobic heterotrophy or chemotrophy; later cyanobacteria adopted photosynthesis (initially using \text{H}2\text{S} before \text{H}2\text{O}).

Abiogenesis vs Biogenesis – Classic Experiments

  • Francesco Redi (1668) – meat in open vs gauze-covered jars showed maggots originate from fly eggs.
  • Louis Jablot (1745) – boiled hay infusions; covered (no growth) vs uncovered (turbid) ➜ microbes are airborne.
    • John Needham’s flawed repetition (unsterile, spore-formers) temporarily revived abiogenesis claims.
  • Schultze & Schwann (1830s) – air sterilised by heat/chemicals pumped into broth halted growth; argued against “vital force.”
  • Louis Pasteur (1861) – swan-neck flask: sterile broth remained clear while neck intact; breaking neck allowed dust → growth. Definitive refutation of spontaneous generation.

The Five I’s – How Microbes Are Grown & Studied

  1. Inoculation – introduce sample onto/into growth medium; viruses require live hosts (cells, eggs).
  2. Incubation – controlled temperature, humidity, gas conditions optimise multiplication.
  3. Inspection – macroscopic colony examination (number, colour, size, margin, elevation, texture).
  4. Isolation – select distinct colonies/pure cultures for study.
  5. Identification – microscopic morphology (shape, Gram reaction, spores, motility) + biochemical tests (enzyme activities, sugar fermentation, metabolic products) leading to taxonomic placement.

Systematics & Taxonomy of Microorganisms

  • Taxonomic hierarchy: Kingdom → Phylum/Division → Class → Order → Family → Tribe → Genus → Species → Sub-species.
  • Classification criteria:
    • Phylogenetic (evolutionary lineage)
    • Phenetic (overall similarity)
    • Phenotypic traits (morphology, physiology, biochemical reactions, Gram stain)
    • Genotypic traits (e.g., %G+C content; Actinomycetes have high GC).
  • Major domains/kingdoms recognised (Whittaker, Woese): Archaea, Bacteria, Eukarya (+ viruses as acellular link).
  • Bergey’s Manual remains the authoritative bacterial taxonomy reference.

Historical Milestones & Key Contributors (17th–19th C.)

  • Galileo Galilei (1610) – telescope; heliocentric support.
  • Robert Hooke (1665) – invented compound microscope; coined “cell.”
  • Francesco Redi (1668) – first experimental challenge to abiogenesis.
  • Anton van Leeuwenhoek (1674–1676) – single-lens microscopes; first to observe & report bacteria, protozoa (“animalcules”); founder of microbiology.
  • Carolus Linnaeus (1735) – binomial nomenclature.
  • John Needham (1745) – flawed support for abiogenesis.
  • Lazzaro Spallanzani (1767) – further refutation of abiogenesis.
  • Edward Jenner (1798) – smallpox vaccination using cowpox pus; birth of immunology.
  • Agostino Bassi (1829) – first fungal pathogen of animals (silkworm muscardine).
  • Ignaz Semmelweis (1840) – hand-washing reduced puerperal fever.
  • John Snow (1854) – epidemiology; cholera traced to contaminated water.
  • Louis Pasteur (1857–1861):
    • Germ theory of fermentation; role of yeast in wine.
    • Pasteurisation (heating to 68\,^{\circ}!\text{C} for 10 min, rapid cooling).
    • Swan-neck flask disproved abiogenesis.
    • Silkworm disease studies; rabies vaccine (first human trials on 16 Russians).
    • Father of Industrial Microbiology.
  • Rudolf Virchow (1858) – cellular biogenesis principle: "Omnis cellula e cellula".
  • Ernst Haeckel (1866) – proposed Protista kingdom.
  • Joseph Lister (1867) – antiseptic surgery (carbolic acid spray).
  • Ferdinand Cohn (1872) – bacterial classification by shape; described endospores; elemental cycling.
  • Robert Koch (1876–1884):
    • Anthrax studies led to germ theory of disease & Koch’s Postulates (4 conditions for causation).
    • Discovered Vibrio cholerae, Mycobacterium tuberculosis (grown on blood-serum slants at 37\text{–}39\,^{\circ}!\text{C}).
    • Introduced solid media methods; Nobel Prize 1905.
  • John Tyndall (1877) – fractional sterilisation (Tyndallisation).
  • Albert Neisser (1879) – identified N. gonorrhoeae.
  • Angelina & Walther Hesse (1882) – introduced agar as solidifying agent.
  • Friedrich Loeffler & Edwin Klebs (1883) – Corynebacterium diphtheriae; exotoxin concept.
  • Élie Metchnikoff (1884) – phagocytosis; cellular immunity.
  • Theodor Escherich (1884) – isolated Escherichia coli.
  • Hans Christian Gram (1884) – Gram staining technique (differential cell wall chemistry).

Twentieth & Twenty-First Century Advances & Challenges

  • G.W. Beadle (1958) – microbial genetics groundwork.
  • Jacob, Lwoff & Monod (1965) – gene regulation (operon model).
  • Temin et al. (1975) – reverse transcription in RNA viruses.
  • Recombinant human insulin (1978–1982) – E. coli expression, first FDA-approved GM drug.
  • Luc Montagnier & Robert Gallo (1983) – isolation/characterisation of HIV.
  • 1990s–2000s biotechnology revolution: sequencing, PCR, CRISPR, genome engineering, synthetic biology.
  • Contemporary issues:
    • Emergence of new pathogens (HIV, SARS-CoV, Lyme disease, toxic shock syndrome).
    • Re-emergence of old diseases (TB, mumps, pertussis).
    • Environmental pollution & ozone depletion → bioremediation solutions.
    • GMOs: enhanced crops, concerns over toxicity, ethics, resistance development.
  • Microbiology shifts from mere isolation/identification → molecular exploration, manipulation, and industrial exploitation.

Ethical, Philosophical & Practical Implications

  • Origin-of-life debates integrate science (big bang, chemical evolution) and philosophy/theology (design vs chance).
  • Biotechnology raises questions on biosafety, bioethics, gene therapy, cloning, bioterrorism.
  • Microbial indispensability positions microbes as both stewards (environmental cleanup, food production) and threats (pathogens, spoilage), influencing policy in health, agriculture, and industry.

Key Numerical Facts & Equations (LaTeX Format)

  • Size relationships:
    1\,\text{µm}=1\times10^{-6}\,\text{m}=1\times10^{-3}\,\text{mm}
    Virus range: 0.02\text{–}0.3\,\mu\text{m}=20\text{–}300\,\text{nm}
  • Global bacterial estimate:
    N_{bacteria}\approx5\times10^{30}
  • Soil load example:
    1\,\text{g soil}\to10^{10}\,\text{cells}
  • Generation time illustration (E. coli):
    Nt=N0\,2^{t/g} (doubling every g=25\,\text{min}).
  • Koch’s Postulates (logical sequence, not equation but important algorithmic criteria).

Conceptual Connections & Real-World Relevance

  • Pasteurisation parallels today’s food safety (milk, juices).
  • Germ theory foundational to antisepsis, antibiotic development, public-health interventions.
  • Bioremediation exploits ubiquity & metabolic diversity for oil spill cleanup, wastewater treatment.
  • Microbial model systems (fast growth, simple genomes) underpin molecular biology, CRISPR technology, vaccine production (mRNA platforms derived from viral replication knowledge).
  • Industrial fermentation (bread, beer, biofuels) derives from ancient practices refined through modern microbiology.
  • Normal flora research informs probiotics and gut-brain axis studies.