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BIOL3420-001-Introduction to microbiology

Goals and Objectives

  • Define microbes and microbiology
  • Explain taxonomic position of medically important groups of microbes
  • List the most important scientists in the field of microbiology and explain their achievements
  • Describe roles of microbes in different ecosystems
  • Provide examples of use of microbes in industry

What is Microbiology?

  • Microbiology is an area of biology that studies organisms too small to be seen without magnification
  • These organisms are known as microorganisms or microbes
    • Examples include: Viruses, Bacteria, Protozoa, Archaea, Fungi, Algae, Helminths

Tree of Life

  • Three domains: Bacteria, Archaea, Eukarya
  • Four eukaryotic kingdoms: Animalia, Plantae, Fungi, Protista
  • Protista includes two subkingdoms: Algae, Protozoa
  • Viruses are not living organisms
  • PATHOGENIC MICROBES – cause diseases

Prokaryotes vs. Eukaryotes

  • PROKARYOTES
    • Domains: Bacteria and Archaea
    • DNA position: in cytoplasm (nucleoid)
    • Membrane-bound organelles: absent
    • Cell size: 0.1-5.0\,\mu\text{M}
    • DNA molecules: circular
    • Organization: unicellular
  • EUKARYOTES
    • Domain: Eukarya
    • DNA position: in nucleus
    • Membrane-bound organelles: present
    • Cell size: 10-100\,\mu\text{M}
    • DNA molecules: linear
    • Organization: unicellular or multicellular

Taxonomy

  • Domain (Domains): Bacteria, Eubacteria, Eukarya
  • Example hierarchical levels and entities:
    • Domain: Bacteria → Phylum/Kingdom: Proteobacteria → Class: Gammaproteobacteria → Order: Enterobacteriales → Family: Enterobacteriaceae → Genus: Escherichia → Species: Escherichia coli
  • Example hierarchical levels and entities for Eukarya/Protista:
    • Domain: Eukarya → Kingdom: Protista → (Groups listed in slide) Sarcomastigophora, Zoomastigophora, Diplomonadida, Hexamitidae → Genus: Giardia → Species: Giardia lamblia

FOUNDATION OF MICROBIOLOGY

  • Robert Hooke (1660s): used a single-lens microscope and described molds on a book cover (first microbe descriptions)
  • Antonie van Leeuwenhoek (late 1600s): magnification ~300x; observed bacteria using self-designed microscope

ABIOGENESIS VS. BIOGENESIS

  • Redi's experiment (early skepticism of spontaneous generation) demonstrated that maggots did not arise spontaneously from decaying meat when protected from flies
  • Pasteur's Test of Spontaneous Generation (swan-neck flask experiment) showed that broth remained free of microorganisms unless the flask was exposed to preexisting microbes; curved neck prevents microbial entry
  • Summary: Evidence supports biogenesis (life from preexisting life) over abiogenesis in ordinary conditions

KEY EVENTS IN MEDICAL MICROBIOLOGY

  • 1665 – Robert Hooke depicted molds and published their description (first description of microbes)
  • 1675 – Antonie van Leeuwenhoek observed bacteria using a self-designed microscope
  • 1796 – Edward Jenner performed vaccination against smallpox
  • 1860s – Florence Nightingale established aseptic practices in nursing
  • 1864 – Louis Pasteur disproved spontaneous generation
  • 1876 – Robert Koch proved that microbes cause diseases
  • 1928 – Alexander Fleming discovered penicillin (first antibiotic)

MICROBES WERE THE FIRST ORGANISMS IN THE EARTH

  • Timeline of Planet Earth (illustrative):
    • 4.5 billion years ago: Earth formed
    • 4.0–0.5 BYA: First life appears; Precambrian Time: Time of Prokaryotes
    • Archaean Era: Era of Archaea
    • Proterozoic Era: Era of Cyanobacteria
    • Phanerozoic Time: Eukaryotic time; First Cyanobacteria; First Eukaryotes
  • Concept: Microbes were among the earliest life forms on Earth

DOMINANT LIVING FORM

  • The biomass of bacteria on Earth is estimated to be equal to the biomass of all plants combined
  • Microbes inhabit all available ecological niches
  • Implication: Microbes play a dominant role in global biogeochemical cycles and ecosystem functioning

PATHOGENIC (MEDICAL) MICROBIOLOGY

  • Less than 1% of all microorganisms live in symbiosis that benefits hosts; play important roles in digestion in humans
  • HUMAN MICROBIOME – all microorganisms living in the human body
  • Less than 10% of symbiotic microorganisms cause infectious diseases

HUMAN MICROBIOME

  • The collective genome and community of microorganisms living in the human body
  • Includes bacteria, archaea, viruses, and fungi across various body sites (gut, skin, oral cavity, etc.)

IMPORTANCE OF MICROORGANISMS

  • Photosynthetic microorganisms contribute more than 70% of the Earth's photosynthesis
  • Important in balancing decomposition and nutrient recycling
  • Live in associations with other living organisms
  • Nitrification – transformation of ammonia to inorganic salts that can be used by plants
  • Microbes are integral to ecosystem services, climate regulation, and agriculture

GENETIC ENGINEERING

  • Concept workflow:
    • Isolate chromosome → Desired gene
    • Use restriction enzyme to cut at specific sites
    • Isolate plasmid (vector) and cut with the same restriction enzyme
    • Ligation using DNA ligase to join complementary ends
    • Result: Recombinant plasmid DNA
  • Key steps (described in slide as):
    • Isolated chromosome; Desired gene; Restriction enzyme cutting; Plasmid (vector) isolation; Cutting with same restriction enzyme; Ligation with DNA ligase; Recombinant plasmid DNA

BIOREMEDIATION

  • Use of living organisms (usually microorganisms) in cleaning pollution
  • Concept illustrated by GoAnimate example (educational animation) depicting microbial cleanup of pollutants
  • Applications include degradation of hydrocarbons, heavy metals, and other contaminants in soil and water