The Evolution of Microorganisms and Microbiology

Introduction to Microorganisms

  • Definition of Microorganisms: Organisms that are typically too small to be clearly seen by the unaided eye.
  • Size Constraints: Generally, these organisms are measured at less than 1 mm1\,mm (<1 mm<1\,mm), although some, such as bread mold (macroscopic), can be seen with the naked eye.
  • Construction: These organisms are simple in their construction and lack differentiated tissues.
  • Class Divisions: Microbes are divided into two main categories: Cellular (living) and Acellular (non-living biological entities).

Classification and Types of Microbes

  • Cellular Microorganisms:
    • Fungi: Includes Yeasts (unicellular) and Molds (multicellular).
    • Protists: Includes Algae, Protozoa, and Slime molds.
    • Bacteria: Examples include Escherichia coli.
    • Archaea: Examples include Methanogens.
  • Acellular Biological Entities:
    • Viruses: Composed of Protein and nucleic acid (DNA or RNA).
    • Viroids: Composed purely of RNA.
    • Satellites: Composed of Nucleic acid enclosed in a protein shell.
    • Prions: Composed purely of Protein.

Microbial Habitats and Abundance

Microorganisms are found in nearly every environment on Earth. Their estimated abundances are as follows:

  • Major Habitats:
    • Atmosphere: 5×10235 \times 10^{23}
    • Soil: 3×10293 \times 10^{29}
    • Deep continental subsurface: 3×10293 \times 10^{29}
    • Humans: 4×10234 \times 10^{23}
    • Oceans: 1×10291 \times 10^{29}
    • Upper ocean sediment: 5×10285 \times 10^{28}
    • Deep ocean sediment: 4×10294 \times 10^{29}
    • Sea surface: 2×10232 \times 10^{23}
  • Other Habitats:
    • Groundwater: 5×10275 \times 10^{27}
    • Phyllosphere: 2×10262 \times 10^{26}
    • Cattle: 4×10244 \times 10^{24}
    • Termites: 6×10236 \times 10^{23}
    • Pigs: 7×10237 \times 10^{23}

Classification Schemes and the Three-Domain System

  • Three-Domain System: Developed based on research comparing ribosomal RNA (rRNA) genes.
    1. Bacteria: Referred to as true bacteria.
    2. Archaea.
    3. Eukarya: Includes all eukaryotes.

Comparison of Cell Types

  • Prokaryotic Cells: Described as having an "open floor plan" because they lack a membrane-enclosed nucleus.
  • Eukaryotic Cells:
    • Contain a membrane-enclosed nucleus.
    • They are typically larger and more morphologically complex than prokaryotic cells.

Characteristics of the Three Domains

  • Bacteria:
    • Usually single-celled organisms.
    • Most possess a cell wall containing peptidoglycan.
    • Most lack a membrane-bound nucleus.
    • Found ubiquitously, including extreme environments and the human body (known as the Microbiome).
    • Both disease-causing and non-disease-causing (beneficial/neutral) species exist.
  • Archaea:
    • Distinguished from Bacteria by unique ribosomal RNA (rRNA) sequences.
    • Contain unique membrane lipids.
    • Possess unusual metabolic characteristics.
    • Many are extremophiles (living in extreme environments).
    • Not known to directly cause disease in humans.
  • Eukarya:
    • Protists: Unicellular but generally larger than Bacteria and Archaea.
      • Protozoa: Possess animal-like metabolism.
      • Algae: Photosynthetic organisms.
    • Fungi: Can be unicellular or multicellular.
      • Yeasts: Unicellular forms.
      • Molds and Mushrooms: Multicellular forms.

The Evolution of Life and the RNA World

  • Definition of Life:
    • Orderly structure.
    • Metabolism: The ability to obtain and use energy.
    • Reproduction: The ability to produce offspring.
  • Molecular Relationships:
    • Proteins: Function as catalysts (enzymes) or structural components.
    • DNA: Stores hereditary information meant to be replicated and passed to the next generation.
    • RNA: Acts as a messenger by taking DNA information to synthesize proteins.
  • The Origins Paradox: The existence of proteins requires RNA and other proteins. DNA requires proteins for cellular work and replication. RNA requires DNA as a template and proteins as catalysts. While they rely on each other today, evidence suggests one molecule likely appeared first (often hypothesized as the RNA world).

Defining Microbiology and Its Tools

  • Microbiology: The study of microorganisms.
  • Essential Tools:
    • Microscopes.
    • Culture techniques (e.g., Pure culture: isolating a single strain).
    • Molecular genetics.
    • Genomics.

Chronological History of Microbiology and Significant Events

  • 1348: The Plague (Black Death) reaches England.
  • 1543: Copernicus publishes work on the heliocentric solar system.
  • 1620: Francis Bacon argues for inductive reasoning in the scientific method.
  • 1665: Robert Hooke publishes Micrographia, containing drawings of the fungus Mucor.
  • 1668: Francisco Redi refutes the spontaneous generation of maggots.
  • 1674–1676: Antony van Leeuwenhoek discovers "animalcules."
  • 1687: Isaac Newton’s Principia is published.
  • 1765–1776: Lazzaro Spallanzani attacks the theory of spontaneous generation.
  • 1775: The American Revolution begins.
  • 1798: Edward Jenner introduces cowpox vaccination for smallpox.
  • 1854: John Snow traces the cholera source to a specific water pump.
  • 1859: Charles Darwin publishes Origin of Species.
  • 1861: Louis Pasteur disproves spontaneous generation.
  • 1861–1865: The American Civil War occurs.
  • 1876: Alexander Graham Bell invents the telephone.
  • 1876: Robert Koch demonstrates that Bacillus anthracis causes anthrax.
  • 1879: Thomas Edison develops the first light bulb.
  • 1884: Publication of Koch's postulates; Elie Metchnikoff describes phagocytosis; the autoclave and Gram stain are developed.
  • 1885: Louis Pasteur develops the rabies vaccine.
  • 1887–1890: Sergei Winogradsky studies sulfur and nitrifying bacteria.
  • 1888: Martinus Beijerinck isolates root nodule bacteria.
  • 1889: The Eiffel Tower is completed.
  • 1893: Edvard Munch paints The Scream.
  • 1898: The Spanish-American War.
  • 1899: Martinus Beijerinck proves a virus causes tobacco mosaic disease.
  • 1900: Max Planck develops quantum theory.
  • 1903: Wright brothers’ first powered aircraft flight.
  • 1905: Albert Einstein proposes the theory of relativity.
  • 1908: The first Model T Ford is produced.
  • 1911: Peyton Rous discovers a virus can cause cancer.
  • 1914: World War I begins.
  • 1915–1917: Felix d’Herelle and Frederick Twort discover bacterial viruses (bacteriophages).
  • 1917: The Russian Revolution.
  • 1918: Influenza pandemic kills over 50 million people.
  • 1923: First edition of Bergey’s Manual is published.
  • 1927: Charles Lindbergh’s transatlantic flight.
  • 1928: Frederick Griffith discovers bacterial transformation.
  • 1929: The Stock Market Crash.
  • 1929: Alexander Fleming discovers penicillin.
  • 1932: Max Knoll and Ernst Ruska build the first electron microscope.
  • 1933: Adolf Hitler becomes chancellor of Germany.
  • 1937: Hans Krebs discovers the citric acid cycle.
  • 1939: World War II begins.
  • 1945: Atomic bomb dropped on Hiroshima.
  • 1950: The Korean War begins.
  • 1953: James Watson and Francis Crick propose the DNA double helix structure.
  • 1961: The first human travels into space.
  • 1961: Francois Jacob and Jacques Monod propose the lac operon.
  • 1969: Neil Armstrong walks on the moon.
  • 1970: Werner Arber and Hamilton Smith discover restriction endonucleases.
  • 1973: The Vietnam War ends.
  • 1977: Carl Woese divides prokaryotes into the domains Bacteria and Archaea.
  • 1980: First home computers appear.
  • 1981: First space shuttle launch.
  • 1983–1984: HIV isolated by Robert Gallo and Luc Montagnier; Kary Mullis develops the PCR technique.
  • 1990: First human gene therapy testing begins.
  • 1991: The Soviet Union collapses.
  • 1992: First human trials of antisense therapy.
  • 2001: World Trade Center attack; Anthrax bioterrorism attacks in the U.S.
  • 2003: Second war with Iraq; SARS outbreak in China.
  • 2005: Genome of the 1918 influenza virus is sequenced.
  • 2010: First bacterium with a synthetic genome constructed.
  • 2010: H1N1 influenza outbreak occurs.
  • 2014: Two-year Ebola outbreak begins.
  • 2019: The COVID-19 pandemic begins.

The Discovery of Microorganisms

  • Early Observations:
    • Francesco Stelluti: Observed bees and weevils using a microscope between 1625 and 1630.
    • Robert Hooke: Published Drawings of the fungus Mucor in his 1665 book, Micrographia.
    • Antony van Leeuwenhoek (1632–1723): Recognized as the first person to accurately observe microorganisms.

The Conflict over Spontaneous Generation

  • The Theory: The idea that living organisms can develop from non-living or decomposing matter.
  • Francesco Redi (1626–1697): Credited with discrediting spontaneous generation for larger organisms by showing that maggots on decaying meat resulted from fly eggs, not the meat itself.
  • John Needham (1713–1781): Boiled hay infusions and observed that they gave rise to microorganisms, concluding that some extracts confer life from non-living material.
  • Lazzaro Spallanzani (1729–1799): Disproved Needham's findings by proving that hay infusions did not produce microbes if they were boiled and then immediately sealed.

Louis Pasteur (1822–1895) and the Swan-Neck Flask Experiments

  • Methodology:
    • Pasteur created flasks with long, curved ("swan") necks.
    • Solutions in the flasks were boiled to achieve sterility.
    • The flasks remained exposed to the air.
  • Observation: Airborne microbes were trapped at the base of the curved neck.
  • Result: No growth occurred in the sterile broth as long as the neck remained intact. If the neck was broken, growth occurred rapidly.
  • Conclusion: Spontaneous generation was disproved.

The Final Disproof of Spontaneous Generation

  • John Tyndall (1820–1893):
    • Demonstrated that dust carries microorganisms.
    • Proved that nutrient broths remained sterile even when exposed to air, provided no dust was present.
    • Provided early evidence for exceptionally heat-resistant forms of bacteria.
  • Ferdinand Cohn (1828–1898): Discovered that heat-resistant bacteria could produce endospores.

Microorganisms and Their Role in Disease

  • Historical Context: Infectious disease was originally attributed to supernatural forces or an imbalance of the four bodily-fluid ‘humors’ (blood, phlegm, yellow bile [choler], and black bile [melancholy]).
  • Agostino Bassi (1773–1856): Proved a silkworm disease was caused by a fungus.
  • M. J. Berkeley (1803–1889): Proved the potato blight of Ireland was caused by a protozoan (water mold).
  • Heinrich de Bary (1831–1888): Demonstrated that fungi caused various crop diseases.
  • Louis Pasteur: Demonstrated that microorganisms are responsible for fermentation and developed pasteurization to prevent wine spoilage.
  • Joseph Lister (1827–1912): Developed an antiseptic surgery system to prevent microbes from entering wounds; his methods significantly reduced postoperative infections.
  • Robert Koch (1843–1910):
    • Established the causal link between Bacillus anthracis and Anthrax.
    • Established the link between Mycobacterium tuberculosis and Tuberculosis (TB).
    • Koch's Postulates: A set of criteria still used in modern microbiology to link a specific microorganism to a specific disease.

The Development of Vaccines

  • Pasteur and Roux: Discovered that pathogens lose their virulence (ability to cause disease) if they are incubated for long intervals between transfers.
  • Attenuated Cultures: These weakened pathogens were used to develop vaccines for diseases including chicken cholera, anthrax, and rabies.

Major Fields within Microbiology

  • Medical Microbiology: Focuses on diseases affecting humans and animals (e.g., COVID-19 studies).
  • Public Health Microbiology: Focuses on the control and spread of communicable diseases.
  • Immunology: Examines how the immune system protects hosts from pathogens.
  • Microbial Ecology: Studies the relationship of organisms with their environment.
  • Agricultural Microbiology: Studies the impact of microbes on food production.
  • Food Microbiology: Studies microbes used in food/beverage production and those responsible for spoilage.
  • Industrial Microbiology: Utilizes microbes to manufacture antibiotics, vaccines, steroids, alcohols, solvents, vitamins, amino acids, enzymes, and biofuels.
  • Microbial Physiology: Investigates the metabolic pathways of microorganisms.
  • Microbial Genetics, Molecular Biology, and Bioinformatics: Focuses on genetic information and the regulation of cell development and function.