Last Update: 4 November 2017 Part II

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Microbial Taxonomy
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. There are 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?
o Numerical Taxonomy: a common approach to phenetic taxonomy
o Use a variety of characteristics: e.g., Gram stain, cell shape, motility, size, aerobic/anaerobic
capacity, nutritional capabilities, cell wall chemistry, immunological characteristics, etc.
o Relies on similarity coefficients
o If use 10 characteristics, then match organisms.
o Ex. A and B share 8 characters out of 10: similarity coefficient Sab is 8/10 = 0.8
o Can use many such values to establish similarity matrix
o 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.
o 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.

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 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
o descended from a single organism
o different isolates may be same species but are different strains; often have slight differences
Type strain
o often the first strain isolated or best characterized
o 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
o Species concept in eukaryotes is based grouping organisms that can reproduce into species
category
o 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
o Sequence from smaller to larger levels of organization
o strain, species, genus, family, order, class, division, kingdom
o Example:
Genus: Escherichia
Species: E. coli
Family: Enterobacteriaceae
Class: Scotobacteria
Division: Gracilicutes
Kingdom: Procaryotae
o 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 prokaryotic

taxonomy
First edition published in 1923, now in 9th edition.
o Uses both morphological and Physiological characteristics
o Very practical system. Use successive "key" features to narrow down identification
o 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
o Primary emphasis is phylogenetic, not phenetic
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 o Example: pathogens are not grouped together, instead they are scattered in different
o 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, 85-95o 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.

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 Choloroflexus grows as anaerobic phototrophs or aerobically by fermentation; other groups are
typically heterotrophic.

4. Note: these 3 groups are all thermophilic, suggesting that the ancestors of the bacterial domain were
thermophiles.
5. Deinococcus, Thermus and relatives: micrococci
o 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.
o 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.
o See "Meet Conan the Bacterium" article
o 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.
6. 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.
7. 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.
8. Planctomyces
o Have never been cultivated, but common in pond water.
o Distant cousins of Chlamydia, also lack peptidoglycan
o Free-living aquatic oligotrophs; divide by budding, not binary fission.
o All have fimbriae & flagella.
o Some have nuclear envelopes, like eukaryotes.
9. Chlamydia.
o 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.
o Can exist in two states: metabolically inert elementary body (EB) and as metabolically active
reticulate body (RB) found only inside host cells.

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 o 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.
o 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.
o Includes Chlamydia trachomatis, the most common STD.
o Chlamydia do not have peptidoglycan, but are sensitive to beta-lactam antibiotics
(mechanism not understood).
o View micrographs of Chlamydia in host cells.
10. Purple bacteria and relatives (aka Proteobacteria).
o Includes Purple photosynthetic + non-photosynthetic Gram-negative bacteria.
o Most common gram-negative heterotrophs are in this group: Escherichia, Salmonella,
Pseudomonas, etc.
o Also called "Proteobacteria" because of broad range of phenotypes.
o Thousands of species, many diverse forms.
o includes most "common" Gram-negative bacteria.
o For more information....
11. Gram-positive (including Mycoplasmas)
o Two major subdivisions:
1. high G+C group (Actinomycetes, Mycobacteria, Micrococcus, others)
2. low G+C group (Bacillus, Clostridia, Lactobacillus, Staphylococci, Streptococci,
Mycoplasmas)
o For more information....
12. Cyanobacteria: oxygenic phototrophs -- carry out photosynthesis much like plants, split water and
produce oxygen as waste product. Electron transport and pigments are located on thylakoid
membranes. Membranes are lined with particles called phycobilisomes. Cells vary greatly in shape.
13. 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
4. 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
5. methanogens
Example: Methanococcus jannaschii , the first archaeal organism to have its genome
sequenced
6. extreme thermophiles. Example: Pyrococcus furiosis; grows well at temperatures above
boiling!

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