Ch 10

Classification of Microorganisms

LEARNING OBJECTIVES

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, Southern blotting, DNA chips, and FISH.

Differentiate a dichotomous key from a cladogram.

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

Taxonomy and Phylogeny

Taxonmoy

: science of classifying organisms with goal of showing relationships among organisms.

 Taxonomic categories: Taxon / Taxa  Provides universal names for organisms and a means of identifying them.

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

Level Above Kindom: The Three-Domain System Carl Woese 1978

Eubacteria (virtuosos) Archaea (weirdoes)

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).

 Clone: Population of cells derived from a single cell   Strain: Genetically different cells within a clone Closely related strains constitute a bacterial species.



Viral species

: Population of viruses with similar characteristics occupying a particular ecological niche. Viruses: not placed in a kingdom – not composed of cells

Scientific Nomenclature

Scientific Binomial

Klebsiella pneumoniae

Source of Genus Name

Honors Edwin Klebs

Source of Specific Epithet

The disease

Pfiesteria piscicida

Honors Lois Pfiester Disease in fish

Salmonella typhimurium Streptococcus pyogenes

Honors Daniel Salmon Chains of cells (

strepto

-) Stupor (

typh

-) in mice (

muri

-) Forms pus (

pyo

-)

Saccharomyces cerevisiae

Fungus

(-myces)

that uses sugar

(saccharo)

Makes beer

(cerevisiae) Trypanosoma cruzi

Corkscrew-like ( Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

trypano

borer;

soma

-, body) -, Honors Oswaldo Cruz

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 for eukaryotic organisms

Identification Methods 

Morphological characteristics:

Useful for identifying eukaryotes

Fig 10.8



Differential staining:

staining Gram staining, acid-fast 

Biochemical tests:

bacterial enzymes Determines presence of Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

Bergey’s Manual: Classifying and Identifying Prokaryotes

Bergey’s Manual of Determinative

Bacteriology:

Is standard reference for laboratory identification of bacteria. Morphology, differential staining, biochemical tests to test for presence of various enzymes.

Bergey’s Manual of Systematic Bacteriology

Provides phylogenetic information on bacteria and archaea Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Based on rRNA sequencing

Identification Methods cont.:

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)

Identification Methods cont.:

Phage Typing

Figure 10.13

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

More details on bacteriophages in Ch 13 Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

Identification Methods cont.:

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

Identification Methods cont.:

Nucleic Acid Hybridization

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

Figs. 10.17 and 10.18

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

Fig 10.15

Putting Identification/Classification Methods Together 

Dichotomous keys

are widely used for identification of organisms. They are based on successive questions that each have two possible answers 

Cladograms

are maps that show phylogenentic (evolutionary) relationship.

Method used to establish cladogram for microorganisms?

Animation: Dichotomous Keys (The Microbiology Place)

Microbiology in the News

(p. 294): Mass Death of Marine Mammals

Dichotomous Key