Ch 10 Classification of Microorganisms. Copyright © 2006 Pearson Education, Inc., publishing as...

Ch 10Classification

of Microorganisms

Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

Student Learning Outcomes

Define taxonomy, taxon, and phylogeny.

List the characteristics of the Bacteria, Archaea, and Eukarya domains.

Differentiate among eukaryotic, prokaryotic, and viral species.

Explain the scientific naming

Differentiate between culture, clone, and strain.

Compare and contrast classification and identification.

Explain the purpose of Bergey’s Manual.

Describe how staining and biochemical tests are used to identify bacteria.

Explain how serological tests and phage typing can be used to identify an unknown bacterium.

Describe how a newly discovered microbe can be classified by ribotyping, DNA fingerprinting, and PCR.

Describe how microorganisms can be identified by nucleic acid hybridization, DNA chips, and FISH.

Explain and apply a dichotomous key


Taxonomy and Phylogeny

Taxonomy: Science of classifying organisms. Provides universal names for organisms.

Taxonomic categories: Taxon / Taxa

Phylogeny or Systematics: Evolutionary history of group of organisms.

Taxonomic hierarchy shows phylogenetic (evolutionary), relationships among organisms.

1969: Living organisms divided into five kingdoms.

1978: Two types of prokaryotic cells found. Prokaryotic relationships determined by rRNA sequencing.

All Species Inventory (2001–2025)


The Three-Domain SystemFoundation Fig 10.1


Level Above Kindom: The Three-Domain System

CarlWoese

1978

Eubacteria (virtuosos)Archaea (weirdoes)

Eukarya (predators and thieves)


Endosymbiotic Theory: Origin of Eukaryotes

Cyanophora paradoxa: modern example of possible evolutionary process

Figs 10.2, 10.3


Scientific Nomenclature

Common names

Vary with languages

Vary with geography

Binomial Nomenclature (genus + specific epithet)

Used worldwide

Escherichia coli

Homo sapiens

Scientific Names

Scientific Binomial Source of Genus Name

Source of Specific Epithet

Klebsiella pneumoniae Honors Edwin Klebs The disease

Pfiesteria piscicida Honors Lois Pfiester Disease in fish

Salmonella typhimurium Honors Daniel Salmon Stupor (typh-) in

mice (muri-)Streptococcus pyogenes

Chains of cells (strepto-) Forms pus (pyo-)

Penicillium chrysogenum Tuftlike (penicill-) Produces a yellow

(chryso-) pigment

Trypanosoma cruziCorkscrew-like (trypano-, borer; soma-, body)

Honors Oswaldo Cruz


Classification: Species Definition

Eukaryotic species: A group of closely related organisms that breed among themselves

Prokaryotic species: A population of cells with similar characteristics (Bergey’s Manual of Systematic Bacteriology is standard reference on bacterial classification). Culture: Grown in laboratory media Clone: Population of cells derived from a single cell Strain: Genetically different cells within a clone

Viral species: Population of viruses with similar characteristics occupying a particular ecological niche. Viruses: not placed in kingdom nor domain – not composed of cells – cannot grow without a host cell.

Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 10.6

Phylogenetic Relationships of Prokaryotes


Domain Eukarya

Animalia: Multicellular; no cell walls; chemoheterotrophic

Plantae: Multicellular; cellulose cell walls; usually photoautotrophic

Fungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments

Protista: A catchall kingdom for eukaryotic organisms that do not fit other kingdoms

Grouped into clades based on rRNA


Classification: Placing organisms in groups of related species. Lists of characteristics of known organisms.

Identification: Matching characteristics of an “unknown” to lists of known organisms.

Fig 10.8

Classification and Identification


Applications, p. 283

Identifying Bacteria


Bergey’s Manual:Classifying and Identifying Prokaryotes

Bergey’s Manual of Determinative BacteriologyProvides identification schemes for identifying bacteria and archaea

Morphology, differential staining, biochemical tests

Bergey’s Manual of Systematic BacteriologyProvides phylogenetic information on bacteria and archaea

Based on rRNA sequencing


Clinical Lab Identification

Morphological characteristics Useful for identifying eukaryotes

Differential staining Gram staining, acid-fast staining

Biochemical tests Determines presence of bacterial enzymes

Numerical Rapid Identification


Serology Involves reactions of

microorganisms with specific antibodies: Combine known anti-serum with unknown bacterium

Useful in determining the identity of strains and species, as well as relationships among organisms.

Fig 10.10: Slide Agglutination

Examples: Slide agglutination ELISA (see lab) Western blot (no details)


Phage Typing Fig 10.13

Identification of bacterial species and strains by determining their susceptibility to various phages.

More details on bacteriophages in Ch 13


Genetics DNA fingerprinting:

Number and sizes of DNA fragments (fingerprints) produced by RE digests are used to determine genetic similarities.

Ribotyping: rRNA sequencing

Polymerase chain reaction (PCR) can be used to amplify a small amount of microbial DNA in a sample. The presence or identification of an organism is indicated by amplified DNA. (see lab)

Fig 10.14: Electrophoresis of RE digest of plasmid DNA


Nucleic Acid Hybridization

Fig 10.15

Single strands of DNA or RNA, from related organisms will hydrogen-bond to form a double-stranded molecule; this bonding is called nucleic acid hybridization.

Examples of Applications:

• Southern blotting, • DNA chips, and• FISH

Nucleic Acid Hybridization: DNA Chip

Fig 10.17

Fluorescent In Situ Hybridization (FISH)

Fig 10.18a–b

Add DNA or RNA probe attached to fluorescent dyefor S. aureus

Dichotomous Key

ANIMATION Dichotomous Keys: Practice

ANIMATION Dichotomous Keys: Sample with Flowchart

ANIMATION Dichotomous Keys: Overview

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