Ch 10 Classification of Microorganisms. Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings LEARNING OBJECTIVES Define taxonomy,

Ch 10Classification of Microorganisms

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

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.


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 relationships determined by rRNA sequencing.


Level Above Kindom: The Three-Domain System

CarlWoese

1978

Eubacteria (virtuosos)Archaea (weirdoes)

Eukarya (predators and thieves)


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 – cannot grow without a host cell.


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-)

Saccharomyces cerevisiae Fungus (-myces) that uses sugar (saccharo)

Makes beer (cerevisiae)

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

Scientific Nomenclature


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 that do not fit other kingdoms


Identification Methods

Morphological characteristics: Useful for identifying eukaryotes

Differential staining: Gram staining, acid-fast staining

Biochemical tests: Determines presence of bacterial enzymes

Fig 10.8


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 BacteriologyProvides phylogenetic information on bacteria and archaea

Based on rRNA sequencing

Bergey’s Manual:Classifying and Identifying Prokaryotes


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 TypingFigure 10.13

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

More details on bacteriophages in Ch 13


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

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

Figs. 10.17 and 10.18


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.

PLAY Animation: Dichotomous Keys (The Microbiology Place)

Method used to establish cladogram for microorganisms?

Microbiology in the News (p. 294): Mass Death of Marine Mammals

Dichotomous Key

Documents

Ch 10 Classification of Microorganisms. Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings LEARNING OBJECTIVES Define taxonomy,