Introduction
Last revised: Tuesday, January 28, 2003
Reading: Ch. 1 in text

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What are microbes?

• Microbes are small organisms, generally smaller than human eye can detect
• Typical microbes are
  • bacteria (in Kingdom Monera); also archaea, which look like bacteria but are really very different (see below)
  • 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).
• Most microbes live as unicellular cells or cell clusters; some multicellular (e.g. filamentous multicells), but not as complex as animals, plants

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 called blue-green algae and thought to be plants), as well as archaea (see below)
   • Simple architecture not understood until EM technology in 1940's. View electron micrograph of bacteria.
   • Bacteria have a single circular DNA molecule ("chromosome"), divide by binary fission, not by mitosis or meiosis.
   • Typical sizes: 0.5-5 µm (micrometer) diameter.
2. Eukaryotes
   • "eu" = true, + "karyos" = nucleus
   • Typically contain membrane-bounded organelles (e.g. mitochondria, lysosomes, endoplasmic reticulum, Golgi bodies) -- see text pp. 10-16 for more details.
   • 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.
   • Eucaryotes divide by mitosis (asexual reproduction), or sometimes meiosis (in preparation for sexual reproduction)

The variety of Bacteria

• There is only a small variety of bacterial shapes
  1. Rods = bacilli (sing. bacillus).
     • View Pseudomonas aeruginosa [light micrograph, gram stain], a common opportunistic pathogen and widely distributed soil bacillus.
     • View E. coli bacilli in a scanning electron micrograph [SEM].
  2. Spheres = cocci (sing. coccus).
     • View Staphylococcus [light micrograph, gram stain].
     • 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. Also common among cyanobacteria.
     • View light micrograph of actinomycete
     • View SEM of filamentous cyanobacteria ("protected" image.) Why is this protected?
  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.
     • View TEM of Mycoplasma cells.
  6. Square bacteria: discovered 1981, Red Sea shore (Halophiles). View micrograph showing square cells of Haloarcula.

Microbial Nomenclature

• Named by the Linnaean system: Genus + species. Always italicized (substitute by underlining if italics is not available), Genus always begins with Upper Case, species lower case.
• 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. Usually abbreviated E. coli.
  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)
• Question: what does it mean to call different isolates of similar bacteria a species? Can they interbreed?

Life's Diversity

• It's easy to compare different animals or plants -- lots of structural features, also fossils to help reconstruct ancestors. But how do you assess diversity of microbes? Very few structural differences, yet many different types of metabolism, ecological roles.
• "Molecular Phylogeny" -- a new approach. Based on a few assumptions:
• Genes mutate randomly
• Many mutations are "neutral" -- do not lead to any obvious disadvantage to the strain.
• Once a mutation is established, all progeny of parent cell carry that particular mutation. For example, in figure below, if template "A" is erroneously replicated to a "C" in the opposite strand instead of T, then one generation later the error will be "locked into place", and all progeny with that DNA will be forever altered (unless a reversion mutation occurs at some later time).
  
  
  
  
• Over long periods of time, assume mutations occur with roughly predictable frequency. This is the "molecular clock" hypothesis.
• View conversion of gene differences to evolutionary tree ("protected" image.) Why is this protected?
• To compare microbes that have evolved over billions of years, need to find some molecule that is found in all cells, accumulates mutations only very slowly.
• Carl Woese (U. of Illinois), spent years sequencing and comparing gene sequence of small ribosomal subunit:
• 16S RNA is found in small ribosomal subunit (30S) of procaryotic ribosomes. Eucaryotic ribosomes have 40S subunit with 18S RNA.
• Most ribosomal RNA mutations are deleterious. Very few mutations are neutral.
• Therefore evolution of 16S RNA is very slow. It is a very good molecule to use to compare organisms that may have diverged as far back as 3 or 4 billion years ago.
• See "Molecular Phylogeny" for more information about comparative gene sequencing to establish phylogenies.
• Astonishing result: Woese discovered that organisms can be separated into 3 major evolutionary groups, each as different from each other. Archaea and Bacteria (also called Eubacteria) are as different from each other as either is from Eukarya.





• (Optional): Visit the Tree of Life Web site for a comprehensive, on-going global collaboration to create an accurate phylogeny for life on earth
• (Optional): Visit Major Groups of Prokaryotes page for further information (from Univ. of Wisconsin-Madison)

Evolution of Prokaryotes

• Earth was formed about 4.5 billion years ago (BYA)
• Origin of life itself is speculative. Some experiments by Oparin, and Miller & Urey, show that simple inorganic molecules exposed to energy (heat, electric discharge, UV, etc.) can reorganize to form more complex molecules, even primitive bubbles resembling cells. See diagram of Miller-Urey experiment. See The Origin of Cells and your text for further ideas.
• Oldest sedimentary rocks (~ 3.8 billion years old) found so far on this planet in Isua area near Nuuk, Greenland. See figure of oldest rocks.
  Fossils recognizable as bacteria have been found in rocks dating back to 3.5 BYA; see figure of fossil bacteria. Also see text Fig. 1.1 and Milestone box 1.1. See fossils of cyanobacteria.
• View stromatolites, fossilized remains of ancient cyanobateria. These microbes grew as mats, still a predominant feature of intertidal communities today.
• Aside from fossil cells, ancient sedimentary rocks contain fossilized organic materials called kerogens, remains of ancient microbes -- see text p. 6. Kerogens under metamorphic compression, heating become oil, coal, etc., but some sediments have remained unchanged. Chemical analyses of kerogens from these rocks provides evidence of more microbial diversity than is visible from fossils. (Optional example: Archean Molecular Fossils and the Early Rise of Eukaryotes
• Early Earth was anaerobic (devoid of free oxygen). Cyanobacteria evolved ability to use water as raw material in photosynthesis, produced oxygen gas O₂ as waste. This led to slow buildup of O₂ in atmosphere starting around 2 BYA.
  
  

  Buildup of atmospheric O in geological time (PAL is present atmospheric level.) From "Engineering Initial Conditions in a Self-Producing Environment" by R. Swenson, in M. Rogers and N. Warren (Eds.) A Delicate Balance: Technics, Culture and Consequences (p. 71), 1989d, Los Angeles Institute of Electrical and Electronic Engineers (IEEE). Copyright 1989 by IEEE. Reprinted by permission. Data originally fro Cloud (1976) and Runnegar (1982).

• Banded iron formations in geological strata provide evidence of first oxygen appearance. View figure and see text p. 18. Ancient rocks had high iron content, leading to high Fe⁺⁺ ions in water. When cyanobacteria produced oxygen, this reacted with Fe⁺⁺ to form magnetite (Fe₃O₄), an iron oxide, leading to removal of iron and accumulation of magnetite in sediment. But continued growth of cyanobacteria led to more O₂ than could be removed, resulting in toxic effects that killed cyanobacteria and stopped free oxygen production. Gradually Fe⁺⁺ levels increased again, and eventually cyanobacteria started new population growth as iron was available to remove O₂, until once again the O₂ production outstripped iron ions and population died off. These cycles resulted in alternating band patterns of magnetite and no magnetite that kept cycling for nearly 800,000,000 years! Eventually, microbes evolved protective measures against oxygen and were able to grow even when O₂ was present.
  View figure showing how banded iron formations develop (from Banded Iron Formation lecture).
• Possible exam Question: explain how banded iron formations arose, and why this is considered evidence for the origin of bacterial oxygenic photosynthesis. Use the text and web materials provided to learn more.

Evolution of Eukaryotes

• Origins of eukaryotes remain obscure and very speculative.
• Oldest eukaryotic fossil is roughly 1.5 billion years old, but this is a complex fossil so it is likely eukaryotes evolved earlier still.
• Eukaryotes almost certainly evolved from prokaryotic ancestors, for several reaons:
• Both use RNA and DNA as genetic material
• Both use the same 20 amino acids
• Both have ribosomes and DNA and RNA
• Many features of Archaea are intermediate between Bacteria and Eukaryotes
• One popular theory for the origin of eukaryotes is the Endosymbiont Hypothesis, championed by Lynn Margulis. Theory seeks to explain how organelles such as mitochondria and chloroplasts became established.
• Large cells can engulf smaller cells, forming endosymbiotic partnerships. Phenomenon is common even today (e.g. algae inside fungus = lichen).
• Mitochondria could have began when a large prokaryote ("protoeukaryote") engulfed smaller aerobic prokaryote, with progressive increase of dependence obligate dependence.
  
  Image source
• Chloroplasts could have begun by engulfment of smaller cyanobacterium by larger cell.
  
  Image source
• For more extensive background, see Endosymbiosis and The Origin of Eukaryotes (from Kimball's Biology Pages).
• Possible exam question: what evidence supports the endosymbiotic theory of the origin of eukaryotes? (You'll need to do some more reading and/or browsing to collect this information).
• Other possibilities for evolution of life on earth include astrobiology: life forms traveling to earth on meteors from other planets. See "Is There Life Beyond Earth?" for one spin on this idea.

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