Transcript Classification and Taxonomy

Classification and Taxonomy
Phylogeny
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The most recent model for the basic divisions of life is
the “three domain model”, first put forth by Carl Woese
in the 1970’s.
He compared the sequences of 16S ribosomal RNA
genes, which are fundamentally important for protein
synthesis and found in all known living organisms.
He discovered that “bacteria” could be divided into 2
very different groups, the Eubacteria (often just called
Bacteria) and the Archaea
The third group is the eukaryotes, organisms in which
the DNA is contained within a membrane-bound
nucleus.
Eubacteria and Archaea are the two type of prokaryote,
organisms in which the DNA is loose within the
cytoplasm and not contained within a nucleus.
Archaea usually live in extreme environments: very
hot, acidic, salty, etc. They use quite different
information processing machinery than the bacteria.
We are going to mostly ignore them.
Classifying Bacteria
• Classically, bacteria have been characterized by
their staining pattern, shape, reaction to oxygen,
pH, temperature, and salt optima, and their ability
to metabolize various compounds.
– good functional classification: what they look like, and
where they live, but often evolutionary relationships are
not accurate
• More recent classification schemes are based in
16S ribosomal RNA., which is found in all
(known) cells. Also, the percentage of G and C
(G+C content) is used for classification.
Gram Stain
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A major distinction between groups
of bacteria is based on the Gram
stain. In this method, bacteria are
treated with the dye “crystal
violet”, then washed. Often a
second stain, “safranin” is applies
to make the unstained bacteria
visible.
Gram stain causes bacteria with a
lot of peptidoglycan and very little
lipid in their cells walls to stain
purple. The presence or absence of
peptidoglycan is a fundamental
biochemical difference between
groups of bacteria
Another stain, the “acid-fast stain”
is used to identify Mycobacteria,
such as the tuberculosis agent
Mycobacterium tuberculosis.
Bacterial Morphology
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Bacteria only take a few basic shapes, which are
found in many different groups. Bacterial cells
don’t have internal cytoskeletons, so their shapes
can’t be very elaborate.
Shape: coccus (spheres) and bacillus (rods).
Spirillum (spiral) is less common.
– note: “bacillus” is a shape, but “Bacillus” or
(better) Bacillus is a taxonomic group, a
genus containing such species as Bacillus
subtilis, Bacillus anthracis, and Bacillus
megaterium. The bacillus shape is NOT
limited to the Bacillus genus.
Aggregation of cells: single cells, pairs (diplo),
chains (strepto), clusters (staphylo).
Thus we have types such as diplococcus (pair of
spheres) and streptobacillus (chain of rods).
Relationship to Oxygen
• For more than half of Earth’s history, oxygen
wasn’t present in the atmosphere. Many bacteria
evolved under anaerobic conditions.
• Classification:
– strict aerobes (need oxygen to survive)
– microaerobes need oxygen, but at reduced
concentration (such as in cow guts)
– strict anaerobes (killed by oxygen)
– aerotolerant (don’t use oxygen, but survive it).
– facultative anaerobes (use oxygen when it is present,
but live anaerobically when oxygen is absent).
Temperature
• thermophiles have an optimum growth
temperature above 50oC
• hyperthermophiles have an optimum growth
temperature above 80oC. Many of these are
Archaea, not Bacteria
• psychrophiles (cryophiles) have an optimum
growth temperature below 15oC
• mesophiles are those with optima between 15oC
and 50oC.
Metabolic Classification
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All living organisms need to obtain energy from the environment, and they need to
obtain or make reduced, organic carbon compounds.
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CO2 (carbon dioxide) is the most oxidized form of carbon, and it is not considered “organic”
Energy comes from 2 sources, sunlight or chemical bonds
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an organism that uses light for energy is a phototroph
an organism that uses chemical bonds for energy is a chemotroph
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chemotrophs are sub-divided:
• if the chemical bonds used for energy come from organic molecules, it is a
chemoorganotroph.
• If inorganic compounds are used, it is a chemolithotroph (litho = rock)
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Organic carbon compounds are often obtained from other organisms: heterotroph.
Or, organic compounds can be made by reducing carbon dioxide: autotroph.
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Humans are thus chemoorganoheterotrophs. Plants are photoautotrophs. Various
bacteria are found in all 6 roles.
Tree of Life: Bacterial Phyla
http://tolweb.org/tree?group=Eubacteria&contgroup=Life_on_Earth