1. Chapter 17 Prokaryotic Taxonomy How many species of bacteria are there? How many species can be grown in culture? Bergey’s Manual Classification Schemes Artificial, using morphological or physiological traits as a means of comparing organisms Phylogenetic, comparing evolutionary relatedness using differences in rRNA, DNA, or protein sequences

2. Artificial Taxonomy: Numerical Taxonomy, using an arbitrary scale of values for measurable traits to compare relatedness --- all traits have the same weight S AB = a/a+b+c where: a  traits common to A & B b  traits for a only c  traits for b only Problems for Prokaryotes: --- comparing metabolic differences difficult, many are not equal --- few morphological differences --- no fossil record

3. Phylogenetic Taxonomy --- looks at differences in the sequence of rRNA, DNA, and protein of different organisms --- first done (on a large scale) with 16S rRNA --- all cells have 16S rRNA --- 16S rRNA has constant and variable regions --- has some problems --- also done using gene sequence and sometimes protein seq. Types of Phylogenetic Analysis Distance Matrix, looks at the total number of differences between the sequences being compared and ranks (groups) organisms with the fewest differences closest together Maximum Parsimony, uses difference data to create a large number of random groupings and then chooses the one with the fewest branches

4. A Complication for Prokaryotic Phylogeneitcs Horizontal Gene Transfer, transfer of genes from one species of bacteria to another --- looking at single genes is particularly dangerous among the bacteria due to the chance that the gene in question may have been “borrowed” directly from another bacterium --- 16S rRNA sometimes cannot more than roughly group bacteria by genus --- attempts are under way to sequence enough bacterial genomes that phylogeny can be done using all the genes in a genome

5. Prokaryote Identification Metabolic --- classical (i.e. what we will do in lab), still used, still useful --- micro-tube based (Bio-Log) Structural --- 2-D gel electrophoresis (look at proteins) --- Mass-spectrometry (protein based, fast) --- fatty acid analysis (use gas chromatograph to identify bacteria, fast) Nucleic Acid --- FISH (Fluorescence In Situ Hybridization), use flourescently labeled probe DNA to look for complementary sequences in sample --- Real Time PCR, also fluorescence technique combined with PCR

6. Selected Groups of Prokaryotes Archaea --- a separate domain from the bacteria --- have divergent rRNA sequences (from bacteria) and actually share a number of essential proteins with eukaryotes --- most bacterial antibiotics do not affect the achaea --- are vitally important to numerous geochemical cycles Groups: Crenarchaeota, extremophiles and ocean dwellers Euryarchaeota, methanogens, important in global carbon cycling Korarchaeota, some extemophiles

7. Proteobacteria --- include most of the common human disease organisms and the enterics --- generally considered to be the most recently evolved bacteria --- mostly Gram (-) aerobic, mixed acid fermenters Enterics

8. Serovars: --- strains of bacteria (below species level) identified by the binding of specific antibodies to bacterial cell surface molecules O antigen  LPS H antigen  flagellum (flagellin protein) Vi antigen  outer membrane polysaccharide example: E. coli O157:H7 Indicator species --- an easy to grow organism that can serve as a marker for a larger group example: E. coli is an indicator bacterium for the enterics in general and an indicator of fecal contamination (water assays)