Classification of Microorganisms

Classification of Microorganisms

1. Three Domains

   • Domain Eukarya
     • Animals, Plants, Fungi
   • Domain Bacteria
     • Early Cell
       • Eukaryotes originated from infoldings of prokaryotic plasma membranes around DNA
         • Formed Nucleoplasm
       • Engulfed bacterial cells
         • Endosymbiotic Relationship
         • Bacterial became organelles
           • Mitochondira and chloroplasts
   • Domain Archaea
     • Methanogens, Extreme Halophiles, Hyperthermophiles

2. History

   • Taxonomy
     • Study of classifying organisms
     • Taxa or Taxon (singular)
       • Organisms are put into these catergories

3. A Phylogenetic Tree

   • Not many fossil remains
     • Stromatolies
       • fossilized remains of bacteria
         • 0.5 - 2 million years ago
     • Cyanobacteria-like
       • fossils found in rocks
         • 3 - 3.5 million years ago
     • Instead, based around genomic evidence
       • Molecular clocks
         • Based on nucleotide sequences in the genomes
           • rRNA seqencing

4. Scientific Nomenclature

   • Binomial
     • Genus
     • Speific Epithet
       • Species
   • More information
     • Genus may be subdivided

5. Taxonomic Hierachy

   • Series of subdivsions made by Linnaeus
     • Genus
       • Species that differ from each other but related by descent
     • Species
       • group of closely related
         • Can breed with themselves
     • Domain
       • Kingdom
         • Phylum
           • Class
             • Order
               • Family
                 • Related Genera
               • Similar Families
             • Group of similar Order
           • Related Classes
         • Related Phyla
       • Related Kingdoms

6. Classification of Prokaryotes

   • Haploid
   • Asexual
   • Prokaryotic species
     • pop of cells with similar characteristics
     • Culture
       • Bacteria grown in a lab media
     • Clone
       • pop of cells from a single parent cell
         • Pure culture
       • Strain
         • Genetically different cells within a clone
     • contains subspecies and serovars

7. Classification of Eukaryotes

   • Kingdom Protista
     • everything kingdom
     • Mostly unicellular simple eukaryotes
       • Nutrient diverse: autotrophs, heterotrophs, parastic
     • being grouped into clades
       • based on rRNA seqencing
   • Kingdom Fungi
     • Unicellular Yeasts
     • Multicellular Molds
     • Macroscopic mushrooms
     • cell walls of chitin
     • develop from spores or hyphal fragments
   • Kingdom Plante
     • Mulitcellular
     • Cellulose Cell walls
     • Photosynthesis
   • Kingdom Animalia
     • Multicellular
       • Animals with backbones
     • No cell walls
     • Chemotrophic
       • ingest organic matter

8. Classification of Viruses

   • Not composed of cells
     • needs a host cell
   • Obligate intracellular parasites

9. Methods of Classifying and Identifying Microorganisms

   • Classification
     • placing organisms in groups of related species
   • ID
     • matching characteristics to known organisms
   • Morphological
     • Useful to ID eukaryotes
     • Most are Rod or circle shaped
     • no info on phylogenetic relationships
   • Differential staining
     • Not useful for bacteria with no cell walls or archaea
   • Biochemical tests
     • Determines the presence of enzymes
       • used to seperate into distinct genera or species
     • EnteroPluri Test
       • Rapid Test
       • 15 biochemical test in one

10. Serology

    • The study of serum and the immune reposnes in serum
    • Serum
      • Liquid component of blood w/o clotting factors
      • Antibodies form when an antigen is present
    • Antiserum
      • solution of antibodies
    • Slide aggulation test
      • Bacteria clumps together when mixed with antibodies
    • Serological Testing
      • used to differentiate between species and strains within species
        • Serotypes, serovars, or biovars
          • have different antigens
    • Enzyme-linked immunosorbent assay
      • ELISA
        • Fast
        • A reaction color changed happens when a known antibody binds to an unknow antigen
    • Western blotting
      • Used to ID antibodies in a patient's serum
      • Confirms HIV and Lyme

11. Flow Cytometry

    • ID bacteria without culturing
      • Measure electric conductivity between species
      • Also Use fluorescence

12. DNA Fingerprinting

    • Uses resriction enzymes to digest DNA
      • cuts DNA when a specific sequence is present
        • Analyzed by Electrophoresis gel
          • Creates the DNA fingerprint

13. Nucleic Acid Hybridization

    • Measures the ability of DNA to hybridize another DNA strand
      • Higher hybridization = closer relatedness

14. Southern Blotting

    • Uses Nucliec Hybridization to ID
      • Using DNA probes

15. DNA Chips

    • Also known as Microarray
      • Contains DNA probes
    • Detects pathogens by hybridization between probes and the DNA

16. rRNA Seqencing

    • Used to determine phylogenetic relationships
    • Pros
      • All cells have ribosomes
        • RNA genes rarely mutate
          • Signature sequnce
      • No culturing
    • rRNA is found in the small subunit 30s or 40s
      • 16s in Prokaryotes
        • Use polymerase chain reaction to amplify the gene
          • Then sequence the gene
            • create phylogenetic tree
      • 18s in EU

17. Diachotomous Keys

    • Widely used for ID
    • ID keys are based on successive questions
    • no phylogenetic tree

18. Cladograms

    • Maps showing relationships among organisms
    • Steps
      • Sequence the rRNA genes
        • Align the sequences
          • Calculate % of similarities
            • length of lines dictate %
              • branch point (node) represent common ancestory