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