Taxonomy Content Why Taxonomy? How to determine & classify a species Domains versus Kingdoms Phylogeny and evolution
Why Taxonomy? Classification Arrangement in groups or taxa (taxon = group) Nomenclature Assigning names to taxa 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 Phylogenetic evolutionary links
Polyphasic Taxonomy used to determine the genus and species of a newly discovered procaryote incorporates information from genetic, phenotypic and phylogenetic analysis genus well defined group of one or more species that 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: collection of organisms that t share the same sequences in their core housekeeping genes Strain: - descended from a single, pure microbial culture - Type strain: usually one of first strains of a species studied
Fig. 19.7 Hierarchical c arrangement e in Taxonomy. o Binomial System of Nomenclature (Carl von Linné)
Numerical Taxonomy To create phenetic classification systems multistep process code 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 construct tsimilarity il it matrix identify phenons and construct dendograms
Association coefficients Simple matching coefficient (S SM ) Jaccard coefficient ignores characters g that both lack
dendogram treelike diagram used to display results phenon group of organisms with great similarity phenons with 80% similarity = bacterial species similarity matrix rearranged and joined to show clusters dendogram Figure 19.6
Techniques for Determining Microbial Taxonomy and Phylogeny Classical Characteristics Morphological Ecological Physiological i l Biochemical Genetic
The largest bacterium: 600 μm by 80 μm
Ecological Characteristics life-cycle patterns symbiotic relationships ability to cause disease habitat preferences growth requirements
API 20E system for several physiological tests Figure 35.6
Figure 35.5a. Classic dichotomous keys for clinically important genera.
Molecular Characteristics Comparison of proteins Nucleic acid base composition Nucleic acid hybridization Nucleic acid sequencing
Nucleic acid base composition G + C content -Mol% G + C = (G + C/G + C + A + T)100 - Often determined from melting temperature (T m ) - Variation within a genus usually < 10%
as temperature slowly increases, hydrogen bonds break, and strands begin to separate DNA is single stranded Figure 19.8 DNA melting curve.
Nucleic acid hybridization measure of sequence homology common procedure: bind nonradioactive DNA to nitrocellulose filter incubate filter with radioactive single-stranded DNA measure amount of radioactive DNA attached to filter Figure 19.9
Nucleic acid sequencing most powerful and direct method for comparing ggenomes sequences of 16S & 18S rrna (SSU rrnas) are used most often in phylogenetic studies complete chromosomes can now be sequenced and compared (BIOINFORMATICS!)
Genetic Analysis study of chromosomal gene exchange by transformation and conjugation these processes rarely cross genera plasmids 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 Life Currently held: 3 domains of life: Bacteria Archaea Eucarya Scientists do not all agree about this way of the Tree of Life
The suggested Kingdoms
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 (S ab ) the higher h the S ab value, the more closely l related dthe organisms
Small Ribosomal Subunit rrna Fig. 19.10 Frequently used to create trees showing broad relationships
Universal Phylogenetic Tree with Lateral Gene Transfer