Microbial Taxonomy
Last revised: Monday, March 31, 2003
Reading: Ch. 17 in text: for further details, see Microbial Diversity class notes from N. C. State Univ.

---

Taxonomy and Diversity

• Purpose of taxonomy is to provide useful ways for identifying and comparing organisms. Another goal is to assess the extent of diversity of different types of organisms.
• Two very different ways to construct a taxonomy:
1. Phenetic system: groups organisms based on mutual similarity of phenotypic characteristics. May or may not correctly match evolutionary grouping. Example: group (motile) organisms in one group, non-motile organisms in another group. This is useful, but does it reflect underlying evolutionary ancestry?
• Numerical Taxonomy: a common approach to phenetic taxonomy
• Use a variety of characteristics: e.g., Gram stain, cell shape, motility, size, aerobic/anaerobic capacity, nutritional capabilities, cell wall chemistry, immunological characteristics, etc.
• Relies on similarity coefficients
• If use 10 characteristics, then match organisms.
• Ex. A and B share 8 characters out of 10: similarity coefficient S_ab is 8/10 = 0.8
• Can use many such values to establish similarity matrix
• Dendrograms help display this information clearly.
  
  
  
  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.
2. Phylogenetic system: groups organisms based on shared evolutionary heritage. Example: Mycoplasma (no wall) and Bacillus (walled Gram+ rods) are not obviously similar, would not be grouped together phenetically. But evolutionarily they are similar, more so than either to Gram- organisms.
• 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.

---

Terminology

• Strain
• descended from a single organism
• different isolates may be same species but are different strains; often have slight differences
• Type strain
• often the first strain isolated or best characterized
• kept in collections; e.g., ATCC (American Type Culture Collection) maintains the following frozen or freeze-dried stocks: (number of species in parentheses)
  • Algae (120)
  • Bacteria (14400)
  • Fungi (20200)
  • Yeasts (4300)
  • Protozoa (1090)
  • Cell lines: animal (2300)
  • Cell lines: plant (25)
  • Viruses: animal (1350)
  • Viruses: plant (590)
  • Viruses: bacteria (400)
• Species
• Species concept in eukaryotes is based grouping organisms that can reproduce into species category
• Species concept is applied in microbiology as well, but harder to define. In practice, strains that share certain type properties can be called the same species even if they differ by up to 30% in DNA variation.
• Linnaean hiearchy
• Sequence from smaller to larger levels of organization
• strain, species, genus, family, order, class, division, kingdom
• Example:
• Genus: Escherichia
  
• Species: coli
  
• Family: Enterobacteriaceae
  
• Class: Scotobacteria
  
• Division: Gracilicutes
• Kingdom: Procaryotae
• Note: for bacteria, it is challenging to decide where to draw boundaries such as genus and family.

---

Bergey's Manual of Systematic Bacteriology: The definitive guide to procaryotic taxonomy

• First edition published in 1923, now in 9th edition.
• Uses both morphological and Physiological characteristics
• Very practical system. Use successive "key" features to narrow down identification
• Ex. Gram + or -? Then shape? Then motile or not? etc. Eventually only a few organisms match the process of elimination.
• Second edition now being published, a major reorganization
• Primary emphasis is phylogenetic, not phenetic
• Example: pathogens are not grouped together, instead they are scattered in different
• Five volumes have instructive titles:
1. The Archaea, and the Deeply Branching and Phototrophic Bacteria
2. The Proteobacteria
3. The Low G + C Gram-positive Bacteria
4. The High G + C Gram-positive Bacteria
5. The Planctomyces, Spirochaetes, Fibrobacters, Bacterioidetes, and Fusobacteria

---

Types of Diversity

• Metabolic diversity: heterotrophs vs autotrophs.
  We have seen major differences between the metabolic needs of heterotrophic and autotrophic microorganisms, and between catabolic styles such as fermentation vs respiration (aerobic and anaerobic).
• Structural diversity: we have seen major differences between gram-positive and gram-negative bacteria, and even more profound structural differences between bacteria and archaea. Other differences include presence or absence of walls, external appendages, endospores, etc.
• Morphological diversity: bacilli, cocci, and spirals are 3 common shapes, but we've also seen filamentous forms, pleiomorphic forms. Although most bacteria are tiny, there are many varieties of size, ranging from submicroscopic up to a few bacteria that can be seen with the naked eye.
• Genetic diversity: small ribosomal subunit sequencing has profoundly altered our perception of the extent of genetic diversity. Now that genomes are being sequenced for many microbes, the full extent of this diversity is being understood as never before. The great bulk of life's diversity is not in the eukaryotes, but in the bacteria and archaea.

---

Bacteria consist of approximately 12 distinct groups
Note: most of these groups appear to have radiated from the same point. These are called the "main radiation" groups. A few branches are deeper and earlier, and appear to represent more primitive bacterial groups.

1. Aquifex-Hydrogenobacter group. Thermophilic bacteria. A. pyrophilus is the most thermophilic bacterium known, 85-95^o C. optimal growth temp. View TEM of Aquifex.
2. Thermotoga and relatives. View EM of thermotoga. All are thermophilic, anaerobic, fermentative rods. Cells enclosed in a sheath.
3. Green non-sulfur bacteria. Also thermophilic. Includes Chloroflexus, Thermomicrobium, Thermoleophilum, Herpetosiphon. These organisms are filamentous and move by gliding. Choloroflexus grows as anaerobic phototrophs or aerobically by fermentation; other groups are typically heterotrophic.
   
   Note: these 3 groups are all thermophilic, suggesting that the ancestors of the bacterial domain were thermophiles.
   
   
4. Deinococcus, Thermus and relatives: micrococci
   • Deinococci are 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.
   • See "Meet Conan the Bacterium" article
   • Thermus is another thermophilic genus. Thermus aquaticus is the source of Taq polymerase used in PCR, an enzyme with great commercial success. View phase micrographs of thermus bacteria.
5. Spirochaetes and relatives. Only 9 genera, including Borrelia (cause of Lyme disease) and Treponema (cause of syphillis). All have an axial fiber around which the cell is "wound", producing spiral shape. View micrographs of borrelia and treponema.
6. Cytophaga group. Includes genera Cytophaga, Flavobacterium, Bacteroides. All heterotrophic, rod-shaped. Common in soils and waters, not pathogenic and relatively poorly studied. Cytophaga move by interesting gliding motility.
7. 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.
   • Some have nuclear envelopes, like eukaryotes.
8. Chlamydia.
   • Obligate intracellular parasites, unable to grow outside host cells because they cannot synthesize many basic biomolecules (e.g., amino acids, ATP) and require these from their host cell.
   • Can exist in two states: metabolically inert elementary body (EB) and as metabolically active reticulate body (RB) found only inside host cells.
   • EB is analogous to virion stage of virus, a transmissible form that can travel to different body regions, must be ingested by phagocytosis to enter a cell.
   • Once ingested, organism grows and divides inside host cell in RB form. When cell is completely wasted, EB forms accumulate, cell lyses, and EBs are released for possible infection of other cells.
   • Includes Chlamydia trachomatis, the most common STD.
   • Chlamydia do not have peptidoglycan, but are sensitive to beta-lactam antibiotics (mechanism not understood).
   • View micrographs of Chlamydia in host cells.
9. Purple bacteria and relatives (aka Proteobacteria).
   • Includes Purple photosynthetic + non-photosynthetic Gram-negative bacteria.
   • Most common gram-negative heterotrophs are in this group: Escherichia, Salmonella, Pseudomonas, etc.
   • Also called "Proteobacteria" because of broad range of phenotypes.
   • Thousands of species, many diverse forms.
   • includes most "common" Gram-negative bacteria.
   • For more information....
10. Gram-positive (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)
    • For more information....
11. Cyanobacteria: oxygenic phototrophs -- carry out photosynthesis much like plants, split water and produce oxygen as waste product.
    View schematic diagram of cyanobacterial cell.
    Electron transport and pigments are located on thylakoid membranes. Membranes are lined with particles called phycobilisomes
    Cells vary greatly in shape. For more information....
12. Green sulfur bacteria. Ex: Chlorobium , a few related genera. Photosynthetic, use sulfide as electron donor, not water like cyanobacteria.

---

Archaea consist of 3 distinct groups

• Archaea means "ancient" because use ancient energy mechanisms
• Many found in harsh, early earth-like environments.
• Introduction to the Archaea
  1. Thermal vents at bottom of ocean
  2. extreme salt conditions (Great Salt Lake, Dead Sea).
  3. high acid conditions.
  Major Archaeal groups
  1. halophiles
     • Example: Halobacterium --
     • Found only in very concentrated brines, evaporating salt basins, Dead Sea, etc.
     • Brightly colored due to purple pigments (bacteriorhodopsin)
     • Use light energy to pump protons across cell membrane, generate proton gradient; make ATP from this
  2. methanogens
     • Example: Methanococcus jannaschii , the first archaeal organism to have its genome sequenced
  3. extreme thermophiles. Example: Pyrococcus furiosis; grows well at temperatures above boiling!

---

[ top] [ MCB 229 home page ] [ Dr. Terry home ] [ UConn MCB Department ] [ Univ. of Conn. ]