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