Microorganisms: Origin, Diversity, and Impact on Society

1. Chapter 1 Microbial Life: Origin and Discovery

2. What Is a Microbe? • Microbes are microscopic organisms • Through most of its lifespan • Can only be seen through a microscope • mm (10-3 m) to 0.2 μm (2x10-7 m) • Usually single-celled • Self-contained genome • Capacity to reproduce

3. What Is a Microbe? • Exceptions exist 1. Super-sized microbial cells • Thiomargarita namibiensis “sulfur pearl of Namibia” • Caulerpa taxifolia “killer algae” with acres of single cell 2. Microbial communities multicellular assemblages: biofilm, mushrooms microscopic worms and arthropods NOT microbes 3. Living? • viruses • viroids • prions

4. What Is a Microbe? • 6 major groups studied by microbiologists • Prokaryotes • Bacteria • Eukaryotes • Algae • Viruses • Archaea • Protists • Fungi

5. What Is a Microbe? • Microbial genomes are easily sequenced • Genome = organism’s total genetic content • Complete gene sequence known for many species • Over 1000 bacteria, archaea • Tens of thousands of viruses • First sequenced genomes • Bacteriophage ΦX174 (1977) • Haemophilus influenzae (1995) • Saccharomyces cerevisiae (1996) • Microbes have greatest diversity of genomes • Important for understanding evolution • Comparative genomics shows core genes

6. Why study microorganisms?

7. Microbes Shape Human History • Microbes affect food availability • Destroy crops, preserve food • bread, wine, cheese • Chocolate! • Microbial diseases change history • Black plague in Europe • Smallpox in Americas • HIV/AIDS worldwide

8. Discovery of Microbes • Light microscope invented in 1600s • Quality improved continuously • mid-1600s: Robert Hooke observes small eukaryotes (mold) • Saw “cells” in cork • 1676: Antoni van Leeuwenhoek discovers bacteria • First to see single-celled microbes

9. Microbes Are Living Organisms • Microbes arise only from other microbes • No spontaneous generation • 1688: Francesco Redi shows that maggots do not spontaneously generate • 1861: Louis Pasteur shows that microbes do not grow in liquid until introduced from outside • Contradiction by John Tyndall: • Boiled broth still spoil • Contaminated with endospores

10. Germ Theory of Disease • Observations: • Germs can infect and grow on food. • Hypothesis: • Can germs infect and grow on people? • i.e. Do germs cause disease? • Hypothesis is testable: • Are germs can be found in infected tissue? • Can transmission of germs cause disease?

11. Germ Theory of Disease • Pasteur’s Theory: • Transmission of germs causes disease • All Scientific Theories: • Explain many known observations • e.g. Transmission of rabies • Provide framework for understanding • Where do diseases come from? • Can be tested further • Do germs cause anthrax? • A scientific theory is NOT a “guess”

12. Koch’s Postulates • Provides means of testing hypothesis: • “Does this germ cause that disease?” • Organism must meet 4 criteria: • 1. Microbe always present in diseased • Absent in healthy • 2. Microbe is grown in pure culture • No other microbes present. • 3. Introduce pure microbe into healthy individual • Individual becomes sick • 4. Same microbe re-isolated from now-sick individual

14. Corollary to Germ Theory • Stop germ transmission, stop disease spread • Kill germ, prevent disease • Antiseptics • 1865: Antiseptic surgery • Joseph Lister • Antibiotics • 1929-1941: Penicillin • Alexander Fleming • Many newer antibiotics • Bacteria become resistant

15. Corollary to Germ Theory • Stop germ transmission, stop disease spread • Stop spread of germs • Epidemiology, public health measures • Resistant individuals prevent spread of germs • 1798: Vaccination with cowpox prevents smallpox • Turkish physicians, Lady Montagu, Edward Jenner

16. Microbial Ecology • Most microbes don’t grow on typical medium • Many live in varied conditions • Anaerobic • bottom of swamp, in our gut • High pressure • Bottom of ocean • Hot or cold temperatures • Below 0°C to 113°C • No organic carbon • Use light for energy, CO2 for carbon • Microbes existed before animals, plants • Early earth contained mainly reduced compounds, such as ferrous iron, methane, ammonia

17. Microbial Ecology • Culture some microbes in natural mud environment • Winogradsky column • Layers grow different species • Reflects different conditions • Can see variations in nature • Yellowstone geyser runoff • Colors reflect different species • Different growth temperatures >56°C <50°C

18. Microbial Ecology • Microbes cycle most elements on earth • Nitrogen cycle • Bacteria fix N2 to NH4+ • Nitrify NH4+ to NO3- • Carbon cycle • Photosynthetic microbes fix most carbon • Many other conversions • Sulfur cycle • Phosphorus cycle

19. The Microbial Family Tree • Microbial species are difficult to classify • Difficult to distinguish by shape • Often reproduce asexually • Pass DNA to each other without reproduction • Use biochemical properties to classify • Gram stain • Ability to metabolize different substrates • Use DNA sequence to classify • Bacterial genomes relatively small

20. The Microbial Family Tree • Archaea are not bacteria • Similar size, shape • Very different biochemistry • Different membranes • Archaeal ribosomes similar to eukaryotic ribosomes • Many archaea live in harsh environments • 16s rRNA gene sequence • Found in all creatures • Archaea is a separate domain

21. Endosymbiont Theory • How did eukaryotes arise? • DNA similar to archaea’s • Mitochondrial, chloroplast DNA • Similar to bacterial DNA • Endosymbiont theory: • Mitochondria WERE bacteria • Chloroplasts WERE cyanobacteria • Infected or eaten by other species • Ended up living together inside • Endo-sym-biosis

22. Cell Biology Techniques • Electron microscopy • Observation of cell components • Eukaryotic organelles • Membranes • Ultracentrifuge • Separation of cell components • Study of biochemistry of organelles • Fluorescence microscopy • Identification of cell components • Subcellular location of individual proteins

23. Genetics and DNA Revolution • Molecular genetics depends on bacteria • Concept of “gene” proposed for bacteria • DNA structure • Genetic code • Transcription, translation • Restriction enzymes • Recombinant DNA • Cloning • PCR reaction • E. coli has best understood genome