Classification of Microorganisms

Three Domains
1. Domain Eukarya
  1. Animals, Plants, Fungi
2. Domain Bacteria
  1. Early Cell
    1. Eukaryotes originated from infoldings of prokaryotic plasma membranes around DNA
      1. Formed Nucleoplasm
    2. Engulfed bacterial cells
      1. Endosymbiotic Relationship
      2. Bacterial became organelles
        Mitochondira and chloroplasts
3. Domain Archaea
  1. Methanogens, Extreme Halophiles, Hyperthermophiles
History
1. Taxonomy
  1. Study of classifying organisms
  2. Taxa or Taxon (singular)
    1. Organisms are put into these catergories
A Phylogenetic Tree
1. Not many fossil remains
  1. Stromatolies
    1. fossilized remains of bacteria
      1. 0.5 - 2 million years ago
  2. Cyanobacteria-like
    1. fossils found in rocks
      1. 3 - 3.5 million years ago
  3. Instead, based around genomic evidence
    1. Molecular clocks
      1. Based on nucleotide sequences in the genomes
        rRNA seqencing
Scientific Nomenclature
1. Binomial
  1. Genus
  2. Speific Epithet
    1. Species
2. More information
  1. Genus may be subdivided
Taxonomic Hierachy
1. Series of subdivsions made by Linnaeus
  1. Genus
    1. Species that differ from each other but related by descent
  2. Species
    1. group of closely related
      1. Can breed with themselves
  3. Domain
    1. Kingdom
      1. Phylum
        Class
        Order
        Family
        Related Genera
        Similar Families
        Group of similar Order
        Related Classes
      2. Related Phyla
    2. Related Kingdoms
Classification of Prokaryotes
1. Haploid
2. Asexual
3. Prokaryotic species
  1. pop of cells with similar characteristics
  2. Culture
    1. Bacteria grown in a lab media
  3. Clone
    1. pop of cells from a single parent cell
      1. Pure culture
    2. Strain
      1. Genetically different cells within a clone
  4. contains subspecies and serovars
Classification of Eukaryotes
1. Kingdom Protista
  1. everything kingdom
  2. Mostly unicellular simple eukaryotes
    1. Nutrient diverse: autotrophs, heterotrophs, parastic
  3. being grouped into clades
    1. based on rRNA seqencing
2. Kingdom Fungi
  1. Unicellular Yeasts
  2. Multicellular Molds
  3. Macroscopic mushrooms
  4. cell walls of chitin
  5. develop from spores or hyphal fragments
3. Kingdom Plante
  1. Mulitcellular
  2. Cellulose Cell walls
  3. Photosynthesis
4. Kingdom Animalia
  1. Multicellular
    1. Animals with backbones
  2. No cell walls
  3. Chemotrophic
    1. ingest organic matter
Classification of Viruses
1. Not composed of cells
  1. needs a host cell
2. Obligate intracellular parasites
Methods of Classifying and Identifying Microorganisms
1. Classification
  1. placing organisms in groups of related species
2. ID
  1. matching characteristics to known organisms
3. Morphological
  1. Useful to ID eukaryotes
  2. Most are Rod or circle shaped
  3. no info on phylogenetic relationships
4. Differential staining
  1. Not useful for bacteria with no cell walls or archaea
5. Biochemical tests
  1. Determines the presence of enzymes
    1. used to seperate into distinct genera or species
  2. EnteroPluri Test
    1. Rapid Test
    2. 15 biochemical test in one
Serology
1. The study of serum and the immune reposnes in serum
2. Serum
  1. Liquid component of blood w/o clotting factors
  2. Antibodies form when an antigen is present
3. Antiserum
  1. solution of antibodies
4. Slide aggulation test
  1. Bacteria clumps together when mixed with antibodies
5. Serological Testing
  1. used to differentiate between species and strains within species
    1. Serotypes, serovars, or biovars
      1. have different antigens
6. Enzyme-linked immunosorbent assay
  1. ELISA
    1. Fast
    2. A reaction color changed happens when a known antibody binds to an unknow antigen
7. Western blotting
  1. Used to ID antibodies in a patient's serum
  2. Confirms HIV and Lyme
Flow Cytometry
1. ID bacteria without culturing
  1. Measure electric conductivity between species
  2. Also Use fluorescence
DNA Fingerprinting
1. Uses resriction enzymes to digest DNA
  1. cuts DNA when a specific sequence is present
    1. Analyzed by Electrophoresis gel
      1. Creates the DNA fingerprint
Nucleic Acid Hybridization
1. Measures the ability of DNA to hybridize another DNA strand
  1. Higher hybridization = closer relatedness
Southern Blotting
1. Uses Nucliec Hybridization to ID
  1. Using DNA probes
DNA Chips
1. Also known as Microarray
  1. Contains DNA probes
2. Detects pathogens by hybridization between probes and the DNA
rRNA Seqencing
1. Used to determine phylogenetic relationships
2. Pros
  1. All cells have ribosomes
    1. RNA genes rarely mutate
      1. Signature sequnce
  2. No culturing
3. rRNA is found in the small subunit 30s or 40s
  1. 16s in Prokaryotes
    1. Use polymerase chain reaction to amplify the gene
      1. Then sequence the gene
        create phylogenetic tree
  2. 18s in EU
Diachotomous Keys
1. Widely used for ID
2. ID keys are based on successive questions
3. no phylogenetic tree
Cladograms
1. Maps showing relationships among organisms
2. Steps
  1. Sequence the rRNA genes
    1. Align the sequences
      1. Calculate % of similarities
        length of lines dictate %
        branch point (node) represent common ancestory

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