Classification and Taxonomy

1. Classification and Taxonomy

2. Phylogeny • 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.

3. 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.

4. Gram Stain • 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.

5. Bacterial Morphology • 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).

6. 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).

7. 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.

8. Metabolic Classification • All living organisms need to obtain energy from the environment, and they need to obtain or make reduced, organic carbon compounds. • 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 • an organism that uses light for energy is a phototroph • an organism that uses chemical bonds for energy is a chemotroph • 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) • Organic carbon compounds are often obtained from other organisms: heterotroph. • Or, organic compounds can be made by reducing carbon dioxide: autotroph. • Humans are thus chemoorganoheterotrophs. Plants are photoautotrophs. Various bacteria are found in all 6 roles.

9. Tree of Life: Bacterial Phylahttp://tolweb.org/tree?group=Eubacteria&contgroup=Life_on_Earth