Microbial taxonomy and phylogeny Taxonomy - the science of biological classification Phylogeny - the evolutionary development of a species

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