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, CO 2 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 <50°C >56°C

18. Microbial Ecology Microbes cycle most elements on earth  Nitrogen cycle Bacteria fix N 2 to NH 4 + Nitrify NH 4 + to NO 3 -  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