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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
Artificial Taxonomy:
Numerical Taxonomy, using an arbitrary scale of values
for measurable traits to compare relatedness
--- all traits have the same weight
SAB= 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
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
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
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
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
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
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)