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 50 o C hyperthermophiles have an optimum growth temperature above 80 o C. Many of these are Archaea, not Bacteria psychrophiles (cryophiles) have an optimum growth temperature below 15 o C mesophiles are those with optima between 15 o C and 50 o C.

8. Metabolic Classification All living organisms need to obtain energy from the environment, and they need to obtain or make reduced, organic carbon compounds. –CO 2 (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 Phyla http://tolweb.org/tree?group=Eubacteria&contgroup=Life_on_Earth