Quiz Me!	Introduction to Microbiology
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Last revised: Thursday, January 6, 2000
Reading: Ch. 1 in Prescott et al, Microbiology, 4th Ed.

Note: These notes are provided as a guide to topics the instructor hopes to cover during lecture. Actual coverage will always differ somewhat from what is printed here. These notes are not a substitute for the actual lecture!

Copyright 2000. Thomas M. Terry

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Unifying Themes

1. The invisible world of microbes underlies and shapes what we call the "visible world".
2. Microbes have extraordinary genetic and metabolic diversity.
3. Microbial metabolism can create anaerobic environments, and anaerobic microbes can exploit these environments.
4. Different microbes are adapted to survive and exploit an enormous range of environments, both inanimate and animate.
5. Among all life forms on earth, microbes have the widest range of genetic and evolutionary diversity.

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The Subject Matter of Microbiology

1. What are microbes?

• Microbes are small organisms, generally smaller than human eye can detect
• Typical microbes are
  • bacteria (in Kingdom Monera)
  • protists (in Kingdom Protista)
  • algae (in Kingdom Protista or Plantae, depending on taxonomy)
  • fungi (in Kingdom Fungi)
• Note: only members of the Kingdom Animalia (and most Plantae) are not considered microbes
• Viruses are also considered microbes. Viruses are not cells, but informational parasite ("piece of bad news wrapped up in protein"). Viruses are classified separately. Each Kingdom has its own associated viruses (e.g., HIV virus that causes AIDS cannot infect bacteria or plants, or for that matter other mammals).
• Many microbes live as single cells or cell clusters; some multicellular (e.g. filamentous multicells), but not as complex as animals, plants

2. The Structure of Microbes

Two basic cell architectures: prokaryotes & eukaryotes

Image drawn by Thomas M. Terry for The Biology Place. Used with permission.

1. Prokaryotes
   • "pro" = before, + "karyos" = nucleus
   • Includes bacteria and cyanobacteria (formerly blue-green algae)
   • Simple architecture not understood until EM technology in 1940's
   • Sample electron micrographs
   • Typical sizes: 1 um diameter
2. Eukaryotes
   • "eu" = true, + "caryos" = nucleus
   • Typically contain membrane-bounded organelles (e.g. mitochondria, lysosomes, endoplasmic reticulum, Golgi bodies)
   • Typical sizes: anywhere from 5 micrometers (yeast cells) to 50 or 100 micrometers. A few cells (such as bird eggs) are enormous, and some cells (such as animal nerve cells) can attain lengths of many meters, even though small in diameter.
   • Includes protists, fungi, animals and plants.

3. The variety of Bacteria

• Small variety of bacterial shapes
  1. Rods = bacilli (sing. bacillus).
     • View Pseudomonas aeruginosa, a common opportunistic pathogen and widely distributed soil bacillus.
     • View bacilli in a scanning electron micrograph (SEM), from Dennis Kunkel's Image Gallery
  2. Spheres = cocci (sing. coccus).
     • View stained Staphylococcus slide.
     • Study growth patterns of cocci
  3. Spiral forms = spirilla (sing. spirillum).
     • View Borrelia burgdorferi, the bacterium that causes Lyme disesase.
  4. Filamentous forms.
     • Common among actinomycetes. Many grow in branching filamentous network called mycelium.
     • View actinomycetes
  5. Pleiomorphic shapes.
     • Some bacteria lack distinct shape; typical of Mycoplasmas (also called Acholeplasmas). These organisms lack cell walls, so have no well defined shape.
       
       
  6. Square bacteria: discovered 1981, Red Sea shore (Halophiles)

• Bacterial Nomenclature
  • Named by the Linnaean system: Genus + species.
  • Examples:
    1. Escherichia (genus) coli (species). Named after Theodor Escherich, German bacteriologist who discovered this organism in intestinal tract in 1885. He called it Bacterium coli, but it was subsequently renamed in his honor.
    2. Bacillus megaterium; a large rod shaped organism, member of the Genus Bacillus.
    3. Enterococcus faecalis; fecal organism, coccus shape
  • Name often reveals some characteristic feature.
  • Note: Bacillus (one genus of bacteria, italicized) vs bacilli (general term for rods, not italicized)

4. History and Distribution of Bacteria

Where do bacteria come from, and where are they found?

1. History
   • Earth was formed about 4.5 billion years ago (BYA)
   • Fossil bacteria can be found in the oldest rocks (~ 3.8 billion years old)
   • Early Earth was anaerobic. Cyanobacteria evolved ability to use water as raw material in photosynthesis, produced oxygen gas O₂ as waste. This led to buildup of O₂ in atmosphere from 0% to 20% around 2 BYA.
   • Eearliest fossil eukaryotes are about 1.5 billion years old, and animals evolved about 0.6 billion BYA.
   • All present-day life evolved from bacteria.
2. Distribution
   • Bacteria are the most abundant organisms on earth, found everywhere; air, water, soil, rocks (live bacteria even found in rocks more than a mile below earth's surface)
   • Billions per gram of fertile soil (will measure this in lab)
   • Humans contain 10¹⁴ bacterial cells, 10¹³ human cells; 10% of dry weight of humans is bacterial (mostly in large intestine). Feces is 1/3 bacteria.
   • One of major human problems: getting rid of microbes, or preventing their growth. Practical problem for food, beverage, cosmetic, pharmaceutcals, other industries.
   • Where are microbes not found? Only inside tissues of organisms, kept at bay by defensive mechanisms. Even so, challenges common (cut finger, get infected).

5. What do microbes do?

1. When food is abundant, microbial "behavior" is very simple: EAT, GROW, AND DIVIDE.
2. Watch movie showing E. coli growing in time-lapse photography
3. Table showing rate of growth of different organims
   
   

   Organism	Time needed to consume body weight
   Human	180 Days
   Pig	20 Days
   Yeast	30 Minutes
   Lactobacillus	10 Minutes
   Micrococcus	3 Minutes

   
   
4. Growth rates can be phenomenally fast: e.g. some bacteria can reproduce every 20 min. under optimal conditions. 24 hours, could have 2⁷¹ bacteria = 2.4 x 10²¹. Bacterial cell weighs ca. 10^-12 g., so 24 hours growth weighs 2.4 x 10¹⁰grams = 2.4 x 10⁷ kg = 26,400 tons.
5. Physiology: what kinds of foods do they eat? How do they extract energy? Lots of extraordinary tricks: e.g. some bacteria can use up to 150 different chemicals as the ONLY source of carbon. Mothballs, starch, etc. Imagine your life if you could do this!
6. Bacteria in animal gut are important for animals to digest food. In some animals, bacteria are obligatory, animals cannot survive without them.
7. Many human foodstuffs are produced by bacteria or fungi: yogurt, cheese, and other sour milk products; saurkraut; beer, wine, and all other alcoholic beverages; vinegar.
8. Bacteria rarely enjoy continued ample food, so much time spent in dormant or near-dormant states. Bacteria can survive with minimal metabolism in very extreme environments, including antarctic ice, rocks (as far as a mile below earth's surface), boiling sulfur springs, and more.
9. Bacteria have many sophisticated mechanisms for handling lack of food, including secreting antibiotics and other toxins ("get rid of the competition"), modifying intracellular metabolism, and producing modified structures for dormancy (spores, cysts, endospores).

6. Why is microbiology important?

1. Disease. Since discovery of infectious microbes, most infectious diseases controlled by sanitation, preventive medicine, and chemotherapy.
2. Agriculture. microbes vital in processing materials in soil, e.g. nitrogen, sulfur, etc.
3. Food and drink. Microbial fermentations responsible for all alcoholic beverages, breads, pickles, cheeses, etc. Control of food and drink spoilage is major concern of food industry.
4. Chemical products. Microbes have incredible variety of metabolic tricks; can be used to produce acetone and other commercial solvents, pharmaceuticals, antibiotics, preservatives, etc.
5. Basic research. Microbes grow fast, produce enormous # of offspring. Easy to find events that occur only 1 in a billion times if have 100 billion bacteria in test tube. Crucial to modern biology.
6. Biotechnology. E.g. genetic engineering, ability to move genes freely from one organism to another, select genes of interest and amplify their expression. Bacteria are natural hosts for such activities.

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7. How did microbiology become a science? Major historical figures

• Good book on history: The Microbe Hunters (Paul De Kruif) available in paperback
• First careful descriptions of microbes by Antony van Leeuwenhoek (late 1600's) Amateur lens grinder. Made simple microscope. Drew bacteria, yeasts, etc.
• View facsimile of Van Leeuwenhoek's microscope (b&w); (color)
• View micrograph taken through Van Leeuwenhoek's microscope.

Spontaneous Generation controversy.

• From ancient times, belief that live could spring from inert matter
  
• After Leeuwenhoek, "beasties" believed to arise from water.
  
• Ex. 1748, Needham boiled mutton broth, sealed container. But clear broth became cloudy. Conclude: life arose from matter.
  
• Pasteur (mid 1800's) devised many ingenious expts. to show that air carried contaminating microbes.
  
• Expt: Filter air through cotton. Dissolve cotton, look at slide --> things like spores. Place cotton over sterile (boiled) medium - filters air, no growth occurs
  
• Swan neck flask expt.
  
• Tyndall (late 1800's); provided evidence that some bacteria had exceptionally heat resistant stage (= endospores).

Microbes cause Disease!

• First shown in plants, early 1800's. Slow to discover human disease agents
  
• Lister (late 1800's); impressed with Pasteur's work, developed antiseptic surgery; heat sterilize instruments, swab surfaces with strong acids. Dramatic reduction of post-surgical infections.
  
• Koch (late 1800's); first demonstrated direct causal link of single microbe to single disease: Anthrax.
  
• Koch's postulates: basic logical proof that disease is caused by a microbe
  1. Microbe must be present in every case of disease, but absent from healthy individuals
     
  2. suspected microbe must be isolated and grown in culture
     
  3. Same disease must result when isolated microbe introduced into healthy host
     
  4. Same microbe must be isolated again from diseased host
     

Late 1800's: "Golden Age" of Microbiology.

• Every year, new proof of particular disease caused by particular microbe: cholera, typhoid, tuberculosis, diphtheria, etc. (see Table 1.2)

Microbes transform organic and inorganic matter

• Pasteur established that microbes cause fermentation, produce wine, beer, etc.
  
• Winogradsky (early 1900's) studied soil microbes, showed bacteria change state of nitrogen, sulfur, iron, carbon. Many can "eat" inorganic matter, get necessary energy
  
• Beijerinck (early 1900's) showed root nodules of some plants contain bacteria that fix nitrogen, produce most ammonia on earth

Recent Developments

• Microbes used in research (fast growth, streamlined genetic systems, encyclopedic knowledge), easily manipulated. Major role in molecular biology
  
• Study of disease continues: new diseases, new problems with old diseases.
  
• Microbes important as producers of desired products (eg Pfizer)
  
• Biotechnology revolution largely dependent on microbes to move genes around

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