Chapter 5: Classification of Microorganisms

• Taxonomy

  the science of biological classification

  • describing, identifying, classifying, and naming of

  organisms
• Classification

  -grouping organisms into taxa

  based on mutual similarity or

  evolutionary relatedness
• Identification

  • characterization of an isolate to determine what species it is
• Nomenclature

  • assignment of names to taxonomic groups in agreement

  with published rules
• Systematics

  study of the diversity of life (both past and present) and

  the relationships among living things through time

  • uses taxonomy as a means to understand organisms
• Species (in eukaryotes)

  • a group of closely related organisms that breed among themselves
• Species in prokaryotes: collection of strains that share stable properties in common and differ significantly from other group of strains
• Strain: population of organisms that descends from a pure culture isolate or from a species

  • while different strains may be nearly identical genetically, they can have very different attributes.
• Haeckel Tree: 1st attempt to depict the common

  evolutionary history of all living

  cells (by Ernst Haeckel in 1866)

  • Three Kingdom Tree

  • Protista- for unicellular organisms

  • Monera (fourth kingdom tree) - unicellular organisms

  whose cells lack nuclei; ancestral

  to other forms of life
• Whittaker Tree: Five-Kingdom Tree

  • Proposed adding another Kingdom (Fungi)

  • Prokaryota contained just the Kingdom

  Monera. Eukaryota contained the other four

  kingdoms: Fungi, Protista, Plantae, and

  Animalia

  • Unicellular or multicellular organization is

  also a key feature in the system, although

  the fungi are not truly multicellular.
• Carl Woese (6 Kingdoms)

  • Eubacteria, Archaebacteria, Protista,

  Fungi, Plantae, Animalia

  • Genetics-based tree of life

  • Archaebacteria (simply known as

  Archaea) are significantly different

  from other bacteria and eukaryotes

  in terms of 16S rRNA gene

  sequences.
• Three Domains of Life: Introduced by Carl Woese in

  1990

  
  

  • Divides cellular life forms into

  Archaea, Bacteria, and

  Eukaryote domains.

  
  

  • Differences in ribosomal RNAs

  (16S rRNA gene) = synthesize

  new proteins

  
  

  • Revolutionized the

  understanding of microbial

  evolution
• Generic Name: can change if the organism is assigned to

  another genus because of new information
• Specific Name: stable; the oldest epithet for a particular

  organism takes precedence and must be used
• Characterization and Identification

  Involves the study, not of a single cell, but of a population of identical cells

  Prerequisite: pure culture
• Reasons for doing characterization

  • identification purposes

  • comparison with other organisms

  • exploit characteristics which may be beneficial
• Cultural characteristics: is affected by the nutrients required for growth and the physical conditions of an environment that will favor growth
• Based on E source

  Phototrophs

  Chemotrophs
• Based on C source

  Autotroph

  Heterotroph (organotroph)
• Acidophile opt pH below 5.5
• Neutrophile opt pH 5-8
• Alkaliphile opt pH above 8.5
• obligate aerobes: dependent on o2
• obligate anaerobes: o2 is toxic to the cells
• facultative anaerobes: grows w/ or without o2
• aerotolerant anaerobes: grows equally well with or without o2
• microaerophiles: require o2 at low levels
• Examples of cultural characteristics: form, elevation, margin, growth patterns on slants
• Morphological characteristics: Microscopic characteristics include size, arrangement, ID of structures,

  internal structures, organization
• Antigen: is a molecule that binds to a specific antibody, often stimulating a

  response in the immune system as a result.
• Dna Hybridization: DNA Probes will bind to the gene of interest if it is present in the sample
• Examples of Identification :

  • Examining Agar Cultures, Gram Staining, Endospore Staining
• Example of Strain: Flu Strain vs Influenza Virus
• Examples of Morphological: Checking internal structures such as shape or arrangement
• Examples of Cultural Characteristics: checking temp, ph, and oxygen
• Metabolic: physiological characteristics
• Example of Metabolic: presence of enzymes or fermentation of sugar
• Given Antigen: several motifs recognized by immune cells
• Typical protein antigen: multiple epitopes
• Example of antigen: virulence factors in salmonella. checking genes that encode the virulence factors