Microbial taxonomy and phylogeny
Taxonomy - the science of biological classification
Phylogeny - the evolutionary development of a species
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
Importance of taxonomy
Allows for the organization of a large amount of knowledge
Allows scientists to make predictions and form hypotheses about
organisms
Importance of taxonomy
Facilitates communication by placing organisms into groups with
precise names
Essential for the accurate identification of organisms
(e.g. clinical laboratories)
Microbial evolution
Earth is about 4.6 billion years
old
Fossilized prokaryotes 3.5-3.8
billion years old found
First cells likely anaerobic
Microbial evolution
Diversity increased dramatically
as oxygen became more plentiful
Oxygen-producing cells evolved
about 2.5-3 billion years ago
(cyanobacteria)
Microbial diversity
Studies using rRNA sequences have divided organisms into three
domains
Carl Woese - prokaryotes divided into bacteria and archaea (1970s)
Microbial diversity
Domains placed above phylum and kingdom levels
Domains differ markedly from each other
Microbial diversity
Microbial diversity
Microbial evolution
Bacteria and archaea diverged early
Eukaryotes developed later
Different theories regarding evolution of eukaryotes
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
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
Taxonomic ranks
Species
Often defined as organisms that are capable of interbreeding
Prokaryotes reproduce asexually, therefore another definition is
required
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
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
Strains
Biovars - differ biochemically or physiologically
Morphovars - differ morphologically
Serovars - differ antigenically
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
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)
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
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
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
Numerical taxonomy
Used to create phenetic classification systems
Information about different properties of organisms converted
into numerical form and compared (usually ≥ 50 properties)
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)
Numerical taxonomy
Similarity matrix
Phenons
Dendrogram
Phylogenetic classification
Also known as phyletic classification
Usually based on direct comparison of genetic material and gene
products
Major characteristics used in taxonomy
Classical characteristics
Molecular characteristics
Classical characteristics
Morphological characteristics
Physiological and metabolic characteristics
Ecological characteristics
Genetic analysis
Morphological characteristics
Physiological and metabolic characteristics
Physiological and metabolic characteristics
Are directly related to the nature and activity of enzymes and
transport proteins
Provides an indirect comparison of microbial genomics
Ecological characteristics
Life-cycle patterns
Symbiotic relationships
Ability to cause disease in a particular host
Habitat preferences (temp., pH, oxygen and osmotic
concentrations)
Genetic analysis
Study of chromosomal gene exchange by transformation or
conjugation
Processes rarely cross the genus level
Plasmid-borne traits can introduce errors into the analysis
Genetic analysis
Transformation
Rarely occurs between genera
Conjugation
Can be used to identify closely related genera