Taxonomy

Science of Classification, Nomenclature, Identification

Organisms are named and arranged into taxa

Provides:
universal names reference

facilitates research, scholarship and communication

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Taxonomy
Systematics or phylogeny Provides tools for clarifying evolution of organisms as well as their interrelationships All Species Inventory (2001-2025)

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Scientific Nomenclature
Scientific binomial Kbebsiella pneumoniae Pfiesteria piscicida Source of Genus name Honors Edwin Klebs Honors Lois Pfiester Source of Specific epithet The disease Disease in fish

Salmonella typhimurium
Streptococcus pyogenes Penicillium notatum Trypanosoma cruzi

Honors Daniel Salmon

Chains of cells (strepto-) Tuftlike (penicill-)

Stupor (typh-) in mice (muri-)

Forms pus (pyo-) Spores spread in wind (nota)

Corkscrew-like (trypano-, Honors Oswaldo Cruz borer; soma-body)

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History of Taxonomy
1735
1857 1866

Carlous Linnaeus: 2 Kingdoms

Bacteria & fungi put in the Plant Kingdom Ernst Haeckel: 3 Kingdoms

1937
1959

"Prokaryote" term introduced

Kingdom Fungi

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History of Taxonomy
1961 1969 Current definition of prokaryote introduced Robert Whittaker: 5 kingdoms Plantae; Animalia; Fungi; Protista; Monera 1978 Carl Woese: 3 Domains Eukarya, Bacteria and Archaea Based on variation in cellular composition Primary evidence to support comes from differences in rRNA sequences
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The Three-Domain System

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Figure 10.1

Three Domains

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Table 10.1

Nested Taxonomical Hierarchy

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Figure 10.5

Species Definition

Eukaryotic species:

Prokaryotic species:
Clone Strain Viral species:

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References for Prokaryote Identification

Bergeys Manual of Determinative Bacteriology Provides identification schemes for identifying bacteria and archaea Morphology, differential staining, biochemical tests

Bergeys Manual of Systematic Bacteriology Provides phylogenetic information on bacteria and archaea

Based on rRNA sequencing

Approved Lists of Bacterial Names Lists species of known prokaryotes

Based on published articles

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Methods of Identifying Microorganisms

1. Morphological characteristics 2. Differential and structural stains 3. Biochemical tests 4. Serology based on antigenic nature of microbes 5. Phage typing determines to which phages a bacteria is susceptible 6. Analysis of nucleic acids

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Acid fast bacilli and non-acid fast cocci

Gram - bacilli and Gram + cocci

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Flagella stain

Endospore stain

Dichotomous key for biochemical tests based on enzyme activity

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Rapid Identification Tests

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Figure 10.9

 Microbes are antigenic

Combine known antiserum + unknown bacterium

Slide agglutination

ELISA
Western blot

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Figure 10.10

Phage Typing

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Figure 10.13

Analysis of nucleic acids

DNA base composition DNA fingerprinting Electrophoresis of RFLPs Nucleic acid hybridization rRNA sequencing

PCR

Copyright 2004 Pearson Education, Inc., publishing as Benjamin Cummings