Microbial taxonomy and phylogeny

1
Microbial taxonomy and phylogeny Taxonomy - the
science of biological classification Phylogeny
- the evolutionary development of a species
2
Taxonomy Consists of three parts Classification
- arrangement of organisms into groups or
taxa Nomenclature - assignment of names to
taxonomic groups Identification - determining
which group an organism belongs in
3
Importance of taxonomy Allows for the
organization of a large amount of
knowledge Allows scientists to make predictions
and form hypotheses about organisms
4
Importance of taxonomy Facilitates communication
by placing organisms into groups with precise
names Essential for the accurate identification
of organisms (e.g. clinical
laboratories)
5
Microbial evolution
Earth is about 4.6 billion years old Fossilized
prokaryotes 3.5-3.8 billion years old
found First cells likely anaerobic
6
Microbial evolution
Diversity increased dramatically as oxygen
became more plentiful Oxygen-producing cells
evolved about 2.5-3 billion years ago
(cyanobacteria)
7
Microbial diversity Studies using rRNA sequences
have divided organisms into three domains Carl
Woese - prokaryotes divided into bacteria and
archaea (1970s)
8
Microbial diversity Domains placed above phylum
and kingdom levels Domains differ markedly from
each other
9
Microbial diversity
10
Microbial diversity
11
Microbial evolution Bacteria and archaea
diverged early Eukaryotes developed
later Different theories regarding evolution of
eukaryotes
12
Evolution of eukaryotes
One theory states that organelles developed as
invaginations of membrane Endosymbiotic theory
states that eukaryotes developed from a
collection of prokaryotes living symbiotically
13
Taxonomic ranks Organisms placed in a small
homogenous group that is itself a member of a
larger group Most commonly used levels (or ranks)
are Species, Genus, Family, Order, Class,
Phylum, Domain
14
Taxonomic ranks
15
Species Often defined as organisms that are
capable of interbreeding Prokaryotes reproduce
asexually, therefore another definition is
required
16
Prokaryotic species A group of strains that are
share many stable properties and differ
significantly from other groups of strains A
group of strains that have similar G C
composition and 70 sequence
similarity A collection of strains that share
the same sequences in their core housekeeping
genes
17
Strains A population of organisms that is
distinguishable from other populations within a
taxon Considered to have descended from a
single organism or a pure culture
isolate Strains within a species may vary in
different ways
18
Strains Biovars - differ biochemically or
physiologically Morphovars - differ
morphologically Serovars - differ antigenically
19
Type strain Usually one of the first strains of
a species studied Usually the most well
characterized example of the species Not
necessarily representative of the species
20
Binomial system of nomenclature Devised by Carl
von Linné (Carolus Linnaeus) Italicized name
consists of two parts Genus name/generic name
(capitalized) Species name/specific epithet
(uncapitalized)
21
Binomial system of nomenclature Genus name may
be abbreviated by first letter
e.g. Escherichia coli E.
coli Approved bacterial names published in the
International Journal of Systematic Bacteriology
22
Classification systems Natural classification
systems arrange organisms into groups based on
shared characteristics Two methods for
construction Phenetic classification - organisms
grouped based on overall similarity Phylogenetic
classification - organisms grouped based on
evolutionary relationships
23
Phenetic classification Groups organisms
together based on phenotypic similarities May
reveal evolutionary relationships but not
dependent on phylogenetic analyses Best systems
compare as many attributes as possible
24
Numerical taxonomy Used to create phenetic
classification systems Information about
different properties of organisms converted into
numerical form and compared (usually 50
properties)
25
Numerical taxonomy Used to construct a
similarity matrix Used to identify phenons
(organisms with great similarity) Used to
construct dendrograms (tree-like diagram used to
display relationships between organisms)
26
Numerical taxonomy Similarity matrix
Phenons Dendrogram
27
Phylogenetic classification Also known as
phyletic classification Usually based on direct
comparison of genetic material and gene products
28
Major characteristics used in taxonomy Classical
characteristics Molecular characteristics
29
Classical characteristics Morphological
characteristics Physiological and metabolic
characteristics Ecological characteristics Genet
ic analysis
30
Morphological characteristics
31
Physiological and metabolic characteristics
32
Physiological and metabolic characteristics Are
directly related to the nature and activity of
enzymes and transport proteins Provides an
indirect comparison of microbial genomics
33
Ecological characteristics Life-cycle
patterns Symbiotic relationships Ability to
cause disease in a particular host Habitat
preferences (temp., pH, oxygen and osmotic
concentrations)
34
Genetic analysis Study of chromosomal gene
exchange by transformation or conjugation Proces
ses rarely cross the genus level Plasmid-borne
traits can introduce errors into the analysis
35
Genetic analysis Transformation Rarely occurs
between genera Conjugation Can be used to
identify closely related genera