1. Prokaryotic Microbial Diversity
Early attempts at taxonomy: all plants and animals
Whitaker scheme (late 20th century): Five kingdoms
Animalia, Plantae, Fungi, Protista, and Monera
Monera comprised of prokaryotes
Classification of bacteria difficult
Plants, animals can be distinguished from each other by physical characteristics; backed up by DNA
Bacteria look very similar
Convergent evolution a problem
Unrelated bacteria develop similar physical and biochemical traits

2. Goal: Evolutionary classification
In order to understand relatedness, organisms must be viewed at the DNA level
Similar sequences, mutations should give clues
Which genes? Bacteria readily swap genes around.
Carl Woese and 16S RNA
Ribosomal RNA genes cannot afford to mutate much
Changes would interfere with protein synthesis
Change in rRNA genes over time very gradual
Useful for looking at large differences among organisms

3. Domains Sequencing rRNA genes reveal differences
Bacteria, Archaea, Eukarya all different from each other
Despite Bacteria, Archaea both being prokaryotes
Differences in Bacteria, Archaea backed up
Aspects of molecular biology
Membrane lipid chemistry
Cell wall chemistry
Extreme environments

4. What’s a Species? Eukaryotes: plants and animals
Generally, 2 organisms are of same species if they can successfully interbreed
Definition based on sexual reproduction
Bacteria don’t reproduce sexually
Bacterial species: a group of strains that are more closely related to each other than to another group.
Members of a species have DNA that can hybridize
Because of gene exchange, mutation, phase variation, there are no sharp boundaries between species.

5. Metagenomics Mixed population studies
Using molecular techniques (PCR, sequencing) we find various unique DNA sequences
Most of these bacteria have not/ cannot be cultured
Using molecular techniques to classify unculturable bacteria is called metagenomics
Identification techniques can be molecular or traditional
Traditional techniques require isolation into pure culture, biochemical tests, sometimes serological tests.

6. Major groups of Bacteria-1
Hyperthermophilic Gram negatives
Grow at >70 degrees
Green Sulfur and Green Non-sulfur bacteria
Photosynthetic, anoxygenic
Deinococcus and relatives
Highly radiation resistant; great DNA repair
Gram negative or positive? Odd mixture of traits
Cyanobacteria
“blue-green algae”; oxygenic photosynthesis

7. Major groups of Bacteria-2
Proteobacteria
Largest group of Gram negative bacteria
Enteric bacteria (E.coli, Salmonella, Shigella)
Vibrio (related to enterics; V. cholerae; curved rods)
Pseudomonads (strictly respiratory)
Various groups affecting N and sulfur cycles
Purple sulfur and Purple non-sulfur anoxygenic phototrophs
Rickettsia: obligate intracellular parasites
Bacteroides and Cytophaga
First is strict anaerobic; 2nd aerobic and gliding

8. Major groups of Bacteria-3
Gram Positive bacteria
Endospore formers (Bacillus, Clostridium)
Cocci (Staph, Strep, Micrococcus)
Other rods (Mycobacteria, Listeria, etc.)
Actinomycetes (filamentous, antibiotic producers)
Mycoplasma (DNA says G+, but no cell wall)
Spirochetes
Tight spirals, internal flagella, G-
Chlamydia
Obligate intracellular parasites; 2 stage life cycle

9. Archaea Methanogens and Halophiles Mostly hyperthermophiles
Methanogens strict anaerobes, make methane
Halophiles need at least 1.5 M salt
Mostly hyperthermophiles
Growth from 80 upwards to 120 degrees C
Third major group has one species!