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Microbial Taxonomy & Evolution

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Last revised: Tuesday, March 28, 2000
Ch. 19 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

Introduction: Two different possible goals

(1) Convenient ordering scheme. Use of a "key"

(2) Scheme displaying evolutionary relationships.

Numerical Taxonomy

Note: dendrogram is just a graphical display of similarity coefficients; but one often assumes that these are representative of a deeper evolutionary relationship. This may or may not be legitimate conclusion, depending on the traits used. The diagram below is a hypothetical evolutionary diagram, superficially similar to a dendrogram but actually quite different, since it seeks to portray an accurate picture of how and when organisms diverged from common ancestors over time.

To get accurate phylogeny, must decide which characteristics give best insight. DNA and RNA sequencing techniques are considered to give the most meaningful phylogenies.



type strain:

many similar strains = species

strain, species, genus, family, order, class, division, kingdom


Genus: Escherichia
Species: coli
Family: Enterobacteriaceae
Class: Scotobacteria
Division: Gracilicutes
Kingdom: Procaryotae

"Classical Taxonomy"

Bergey's Manual: a phenetic system

"Molecular Taxonomy"

Basic assumptions

Molecular "clocks"

Use of 16S RNA sequence homology

But how do you actually do it?

The Bacterial Phylogenetic Tree

16S RNA results have produced remarkable results!

Bacteria consist of approximately 10 distinct groups

see MCB 409: Microbial Diversity at NC State University for more detail
  1. Gram + (including Mycoplasmas)
    • Two major subdivisions:
      1. high G+C group (Actinomycetes, Mycobacteria, Micrococcus, others)
      2. low G+C group (Bacillus, Clostridia, Lactobacillus, Staphylococci, Streptococci, Mycoplasmas)
      3. For more information....
  2. Proteobacteria = Purple photosynthetic + non-photosynthetic Gram-negative
    • includes most "common" Gram-negative bacteria
    • For more information....
    • ancestral species was a photosynthetic purple bacterium
  3. Cyanobacteria: oxygenic phototrophs
  4. Spirochetes and relatives

  5. Planctomyces
    • Have never been cultivated, but common in pond water.
    • Distant cousins of Chlamydia, also lack peptidoglycan
    • Free-living aquatic oligotrophs; divide by budding, not binary fission.
    • All have fimbriae & flagella.
    • At least some have nuclear envelopes, like eukaryotes.
  6. Bacteroides, Flavobacteria
    • intracellular parasites, no peptidoglycan
  7. Green sulfur bacteria

    • anaerobic phototrophs
  8. Green non-sulfur bacteria
    • also anaerobic phototrophs
  9. Radioresistant micrococci and relatives
    • Very resistant to radiation, including gamma rays, X-rays, and UV. More than 20x as resistant as E. coli. Cells have very efficient DNA repair systems, multiple copies of DNA.
    • Often show up in the spoilage of radiation-pasteurized food. Dose of gamma-rays used in food sterilization is very high precisely because of the need to kill Deinococcus. Compare with use of very high temperatures to preserve food, because of need to kill heat-resistants spores.
  10. Thermotoga and Thermosipho
    • thermophiles from marine vents

Archaea consist of 3 distinct groups

Web sites for further exploration: Microbial Diversity course at North Carolina State University

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