Why Taxonomy?Why Taxonomy? How to determine & classify a ...· Taxonomy Content Why Taxonomy?Why Taxonomy?

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  • Taxonomy Content

    Taxonomy Content

    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 coefficient t 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

    similarity matrix

    rearranged and joined to show l t

    dendogram matrix clusters

    Figure 19.6

  • Techniques for Determining Microbial Taxonomy and Phylogeny

    • Classical Characteristics• Classical Characteristics Morphological

    Ecological Ph i l i lPhysiological Biochemical

    Genetic

  • The largest bacterium: 600 μm by 80 μmThe largest bacterium: 600 μm by 80 μm

  • Ecological CharacteristicsEcological Characteristics

    life-cycle patternslife-cycle patterns symbiotic relationships ability to cause disease

    habitat preferenceshabitat preferences growth 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 proteins Nucleic acid base compositionNucleic acid base composition

    Nucleic acid hybridizationy Nucleic 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 slowly increases, hydrogen bonds b k d t d

    DNA is singlebreak, and strands

    begin to separate

    single stranded

    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 DNA to nitrocellulose filter incubate filter with radioactive– incubate filter with radioactive single-stranded DNA

    – measure amount of radioactivemeasure amount of radioactive DNA 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 about this way of the “Tree of Life”

  • The suggested KingdomsKingdoms

  • 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

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