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 billion years old found
First cells likely anaerobic

6. Microbial evolution
Diversity increased dramatically as oxygen became more plentiful
Oxygen-producing cells evolved about 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
Genetic 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
Processes 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