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TaxonomyContent
TaxonomyContent
Why Taxonomy?Why Taxonomy?
How to determine & classify a species
Domains versus KingdomsDomains versus Kingdoms
Phylogeny and evolution
Wh T ?Why Taxonomy?• Classification – Arrangement in groups or taxa g g p
(taxon = group)
• Nomenclature – Assigning names to taxa
• Identification – Determination of taxon to which an• Identification – Determination of taxon to which an
isolate belongs
(Most practical part of taxonomy)
Making sense of Nature
Classification
Comparison of species based on:
• Natural – anatomical characteristics• Phenetic – phenotypic characteristics• Genotypic – genetic characteristics• Genotypic – genetic characteristics• Phylogenetic – evolutionary links
Polyphasic TaxonomyPolyphasic Taxonomy
• used to determine the genus and species of a newly discovered procaryote
• incorporates information from genetic, h t i d h l ti l iphenotypic and phylogenetic analysis
genus – well defined group of one or more species that is clearly separate from other generathat is clearly separate from other genera
Defining procaryotic species & strains
• Definition species:– collection of strains that share many stable properties and
differ significantly from other groups of strains
• Alternative definition:ll ti f i th t h th i– collection of organisms that share the same sequences in
their core housekeeping genes
• Strain:descended from a single pure microbial culture- descended from a single, pure microbial culture
- Type strain: usually one of first strains of a species studied
Fig. 19.7 Hierarchical arrangement in Taxonomy.g. 9.7 e c c ge e o o y.
Binomial System of Nomenclature(Carl von Linné)
Numerical TaxonomyNumerical Taxonomy• To create phenetic classification systemsTo create phenetic classification systems• multistep process
– code information about properties of organismscode information about properties of organisms• e.g., 1 = has trait; 0 = doesn’t have trait
– use computer to compare organisms on 50 characters
– determine association coefficientt t i il it t i– construct similarity matrix
– identify phenons and construct dendograms
Association coefficients
• Simple matchingSimple matching coefficient (SSM)
• Jaccard coefficient– ignores characters g
that both lack
• dendogram – treelike diagram used to display resultsdendogram treelike diagram used to display results
• phenon – group of organisms with great similarity– phenons with 80% similarity = bacterial species– phenons with 80% similarity = bacterial species
similaritymatrix
rearranged andjoined to show l t
dendogrammatrix clusters
Figure 19.6
Techniques for Determining Microbial Taxonomy and Phylogeny
• Classical Characteristics• Classical CharacteristicsMorphological
EcologicalPh i l i lPhysiologicalBiochemical
Genetic
The largest bacterium: 600 μm by 80 μmThe largest bacterium: 600 μm by 80 μm
Ecological CharacteristicsEcological Characteristics
life-cycle patternslife-cycle patternssymbiotic relationshipsability to cause disease
habitat preferenceshabitat preferencesgrowth requirements
API 20E system for several physiological testsAPI 20E system for several physiological tests
Figure 35.6
Figure 35.5a. Classic dichotomous keys for clinically important genera.
Molecular CharacteristicsMolecular Characteristics
Comparison of proteinsNucleic acid base compositionNucleic acid base composition
Nucleic acid hybridizationyNucleic acid sequencing
N l i id b itiNucleic acid base composition
G + C content
- Mol% G + C = (G + C/G + C + A + T)100( )
Often determined from melting temperature (T )- Often determined from melting temperature (Tm)
- Variation within a genus usually < 10%
as temperature slowlyincreases, hydrogen bondsb k d t d
DNA issinglebreak, and strands
begin to separate
singlestranded
Figure 19.8 DNA melting curve.
Nucleic acid hybridizationNucleic acid hybridization
f h l• measure of sequence homology• common procedure:
bind nonradioacti e DNA– bind nonradioactive DNAto nitrocellulose filterincubate filter with radioactive– incubate filter with radioactivesingle-stranded DNA
– measure amount of radioactivemeasure amount of radioactiveDNA attached to filter
Figure 19.9
Nucleic acid sequencingNucleic acid sequencing
• most powerful and direct method for comparing genomesp g g
• sequences of 16S & 18S rRNA (SSU rRNAs) are used most often in phylogenetic studiesare used most often in phylogenetic studies
• complete chromosomes can now be sequenced and compared(BIOINFORMATICS !)(BIOINFORMATICS !)
Genetic AnalysisGenetic Analysis
• study of chromosomal gene exchange by transformation and conjugationtransformation and conjugation– these processes rarely cross genera
• plasmids can help to solve confusion in theplasmids can help to solve confusion in the analysis of phenotypic traits
Fig. 19.11 Overview Genomic fingerprinting technique.
Relative Taxonomic Resolution of Various Molecular Techniques
Figure 19.12
The Major Divisions of LifeThe Major Divisions of Life
• Currently held: 3 domains of life:–BacteriaBacteria–Archaea–Eucarya
• Scientists do not all agree aboutScientists do not all agree aboutthis way of the “Tree of Life”
The suggestedKingdomsKingdoms
Figure 19.14 Variations in Design of “Tree of Life”.
Figure 19.3 Universal Phylogenetic Tree.
Comparative Analysis of 16S rRNA sequences
• Oligonucleotide signature sequences– short conserved sequences specific for a phylogenetically
defined group of organisms
• Organisms relatedness = association coefficient (Sab)
th hi h th S l th l l l t d th– the higher the Sab value, the more closely related the organisms
Small Ribosomal Subunit rRNA
Fig. 19.10
Frequently used to create trees showing broad relationships
Universal PhylogeneticUniversal Phylogenetic Tree with Lateral Gene
TransferTransfer