2. Chapter Overview ● What is a microbe?
● How microbes have shaped human history
● The development of medical microbiology
● The development of microbial ecology
● The microbial family tree in all its splendor
● The advent of cell biology and the brilliant DNA revolution

3. What Is a Microbe?
A microbe is a living organism that requires a microscope to be seen.
- Microbial cells range in size from millimeters (mm) to 0.2 micrometer (mm).
- Viruses may be 10 times smaller.
Some microbes consist of a single cell.
Each microbe contains in its genome the capacity to reproduce its own kind.

4. Representative Microbes
Figure 1.2 4

5. What Is a Microbe?
The simple definition of a microbe, however, leaves us with contradictions.
1. Supersize microbial cells
- e.g.: Thiomargarita namibiensis
2. Microbial communities
- e.g.: Biofilms
3. Viruses
- e.g.: Mimivirus
The largest prokaryote, Thiomargarita namibiensis compared to a fruit fly, Drosophila. A single cell can reach a diameter of 0.75 mm. Thiomargarita namibiensis, which means 'sulfur pearl from Namibia
Figure 1.1
Figure 1.4

6. Thiomargarita namibiensis is found in the sulfur-rich sediments of the ocean floor along the west coast of Africa, where they play an important ecological role. By oxidizing sulfur they act as detoxifiers, removing the poisonous gas from the water and keeping it hospitable for the fish and other marine organisms.

7. Microbes include members of the three domains of life.
Figure 1.5

8. Microbial Genomes Are Sequenced
A genome is the total genetic information contained in an organism’s chromosomal DNA.
The first genome sequenced was that of a virus, bacteriophage fX174.
Nearly two decades passed before the first genome sequence of a cellular microbe was completed – Haemophilus influenzae.

9. Figure 1.8

10. Microbes Shape Human History
Microbes have shaped human culture since our earliest civilizations.
- Yeasts and bacteria = Foods and beverages
- “Rock-eating” bacteria = Lithotrophs enabled mining of metals
- Unfortunately, they also consume stones of ancient monuments.

11. Cement degrading bacteria

12. Figure 1.9 12

13. Microbial Diseases
Throughout history, microbial diseases have profoundly affected human demographics and cultural practices.
- 14th century = Bubonic plague caused by Yersinia pestis
- 19th century = Tuberculosis caused by Mycobacterium tuberculosis
- Today = Acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV)

14. Figure 1.10 The AIDs Memorial Quilt
Medieval church procession to ward off the Black Death (bubonic plague)
The AIDs Memorial Quilt
Figure 1.10 14

15. Discovery of Microbes Robert Hooke (1635–1703)
- Built the first compound microscope
- Used it to observe mold
Figure 1.12
- Published Micrographia, the first manuscript that illustrated objects under the microscope
- Coined the term cell 15

16. Discovery of Microbes Antoni van Leeuwenhoek (1632–1723)
- A cloth draper
- Built single-lens magnifiers, complete with sample holder and focus adjustment
- First to observe single-celled microbes
- He called them “small animals.” 16

17. Figure 1.13 17

19. Do Microbes Have Parents?
Spontaneous generation = The theory that living creatures could arise without parents
Francesco Redi (1660s) = Showed that maggots in decaying meat were the offspring of flies
Lazzaro Spallanzani (1760s) = Showed that a sealed flask of meat broth sterilized by boiling failed to grow microbes

21. Rudolf Virchow – Biogenesis theory
The alternative hypothesis, that the living organisms arise from preexisting life, is called biogenesis

22. Louis Pasteur (1861)
Microorganisms can be present in air, liquid, and solids and “heating will destroy them”
Basis for aseptic techniques, sterilization, and pasteurization.

23. Louis Pasteur (1860s) = Discovered the microbial basis of fermentation
- Devised “swan neck” flasks
Figure 1.14
- Showed that, after boiling, the contents remain free of microbial growth despite access to air

24. Germ Theory of Disease Robert Koch (1843–1910)
- Founder of the scientific method of microbiology
- Developed
pure-culture techniques
- Petri dish
- Agar
Figure 1.15
Figure 1.16

25. Figure 1.17 25

27. Immunization Prevents Disease
In the 18th century, smallpox infected a large fraction of the European population.
Lady Mary Montagu introduced the practice of smallpox inoculation to Europe in 1717.
Edward Jenner (1749–1823) deliberately infected patients with matter from cowpox lesions.
- The practice of cowpox inoculation was called vaccination (Latin vacca for “cow”). 27

28. Figure 1.18 28

29. Louis Pasteur (1822–1895) developed the first vaccines based on attenuated (weakened) strains.
- Fowl cholera
- Rabies
Figure 1.19
Immunization = The stimulation of an immune response by deliberate inoculation with an attenuated pathogen 29

30. Antiseptics
In 1847, Ignaz Semmelweis ordered doctors to wash their hands with chlorine, an antiseptic agent.
In 1865, Joseph Lister developed carbolic acid to treat wounds and clean surgical instruments.
In the 20th century, aseptic surgery was developed.
- Environments completely microbe-free 30

31. Antibiotics
In 1929, Alexander Fleming discovered that Penicillium mold generated a substance that kills bacteria.
In 1941, Howard Florey and Ernst Chain purified penicillin.
- The first commercial antibiotic to save human lives
Figure 1.20 31

32. The Discovery of Viruses
Martinus Beijerinck = The agent of tobacco mosaic disease is not a bacterium, because it passes through a filter that retains bacteria
The filterable agent was purified and crystallized by Wendell Stanley.
- Tobacco mosaic virus (TMV)
Figure 1.21 32

33. Microbial Ecology
Sergei Winogradsky (1856–1953) was among the first to study bacterial in natural habitats.
- Discovered lithotrophs
- Developed enrichment cultures
- Built the Winogradsky column
- A wetland model ecosystem
Figure 1.22 33

36. Winogradsky and others showed importance of bacteria in geochemical cycling.
Figure 1.23 36

37. The Microbial Family Tree
Ernst Haeckel (1834–1919) = Microbes are neither plant nor animal
- A third kind of life called Monera
Herbert Copeland (1902–1968) = Divided Monera into two groups
- Eukaryotic protists (protozoa and algae)
- Prokaryotes
Robert Whittaker (1920–1980) = Added Fungi as a fifth kingdom of eukaryotic microbes 37

38. The Microbial Family Tree
The five-kingdom system was modified dramatically by Lynn Margulis.
- She proposed that eukaryotic organelles, such as mitochondria and chloroplasts, evolved by endosymbiosis from prokaryotic cells engulfed by proto-eukaryotes. 38

39. Figure 1.26 39

40. - He called them Archaea.
Figure 1.27
In 1977, Carl Woese was studying recently discovered prokaryotes in hot springs.
Analysis of the 16S rRNA revealed that these prokaryotes were a distinct form of life.
- He called them Archaea. 40

41. Woese’s discovery replaced the five kingdoms with the three domains:
Figure 1.28
Woese’s discovery replaced the five kingdoms with the three domains:
- Bacteria
- Archaea
- Eukarya 41

42. Advances in Cell Biology
Two instruments had exceptional impact on the study of cell structure.
- The electron microscope
- Developed by Ernst Ruska
- Revealed internal structure of cells
- The ultracentrifuge
- Developed by Theodor Svedberg
- Enabled separation of subcellular parts 42

43. Microbial Genetics
In 1928, Frederick Griffith discovered transformation in bacteria.
In 1944, Oswald Avery et al. showed that the transforming substance is DNA.
In 1953, Rosalind Franklin used X-ray crystallography to determine that DNA is a double helix.
Later that year, James Watson and Francis Crick discovered the complementary bases and antiparallel nature of DNA. 43

44. Figure 1.31 44

45. The DNA Revolution Began with Bacteria
The promise of DNA was first fulfilled in bacteria and bacteriophages.
- Restriction endonucleases led to recombinant DNA.
- A heat-stable DNA polymerase was used for amplifying DNA via the polymerase chain reaction (PCR).
- Gene regulation discovered in bacteria provided models for animals and plants. 45

46. Research in Microbiology
Research in microbiology finds applications in diverse fields. 46

47. Chapter Summary - van Leeuwenhoek = Observation of microbes
● Most microbes are microscopic and include bacteria, archaea, fungi, algae, protists, and viruses.
● Microbes have affected human civilization.
● Many scientists have contributed to our understanding of microbiology. They include:
- van Leeuwenhoek = Observation of microbes
- Pasteur = Disproved spontaneous generation
- Koch = Developed the Four Postulates
- Jenner = Developed vaccination
- Fleming = Discovered antibiotics 47

48. Chapter Summary
● Microbes perform unique roles in geochemical cycling.
● The three domains of life are Bacteria, Archaea, and Eukarya.
● Advances in microscopy and biochemistry revealed the structure and function of the various cell components. 48