ch 10

  • Introduction to Microbial Classification

    • Microbiology focuses on the classification of microorganisms.
    • Historically, organisms were categorized as either plants or animals.
    • In 1937, prokaryotic (no membrane-bound nucleus) and eukaryotic (organisms with a nucleus) cells were first distinguished.
    • Various taxonomic systems have been proposed over time, with emphasis on phenotypic relationships (observable characteristics).

  • The Five Kingdom System

    • Proposed by Robert Whittaker in 1969.
    • Suggests that eukaryotes evolved from prokaryotes based on observable traits.
    • Classifies organisms into five kingdoms:
    1. Prokaryotae (Monera)
      • Includes all prokaryotic cells (Bacteria and Archaea).
    2. Protista
      • Comprises unicellular eukaryotes such as algae and protozoa.
    3. Fungi
      • Encompasses molds and yeasts.
    4. Animalia
      • Represents all multicellular animals.
    5. Plantae
      • Covers all plants.

  • The Three Domain System

    • Proposed by Carl Woese in 1978, focusing on evolutionary (phylogenetic) relationships based on nucleotide sequences of rRNA (16S rRNA for prokaryotes and 18S rRNA for eukaryotes).
    • Significance of rRNA:
    1. Present in all living cells.
    2. Functions similarly across life forms.
    3. Highly conserved molecule.
    • Molecular Phylogeny:
    • Reveals three major domains, which differ from Whittaker's five kingdoms.
    • Domains are higher than kingdoms in biological classification.
    • The three domains are:
      1. Bacteria
      2. Archaea
      3. Eukarya

  • Comparison of Ribosomes

    • Prokaryotic Ribosome (70S):
    • 30S and 50S subunits
    • Composed of 21 different proteins, mainly 16S rRNA.
    • Eukaryotic Ribosome (80S):
    • 40S and 60S subunits
    • Approximately 30 proteins and 18S rRNA.

  • Bergey's Manual

    • A resource that categorizes prokaryotes under two domains: Archaea and Bacteria using molecular phylogeny based on 16S rRNA.
    • Organizes biological classifications into domains, phyla, classes, orders, families, etc.
    • Provides identification schemes (e.g., dichotomous keys) based on various criteria:
    • Cell wall structure, morphology, staining properties, oxygen requirements, and biochemical test results.

  • Traditional Classification Methods

    • Morphological Characteristics:
    • Size, shape, and structural features of organisms.
    • Ecological Niche:
    • Environment or habitat where organisms are typically found.
    • Biochemistry:
    • Differences in metabolic processes; includes differential and selective growth conditions.
    • Differential Staining:
    • Techniques like Gram staining to identify cellular structures.

  • Molecular Classification Methods

    • Involves biochemical analysis and DNA analysis techniques:
    • G/C Ratios: Measure DNA base composition.
    • DNA Sequencing/Fingerprinting:
      • Techniques like ribotyping (16S & 18S rRNA).
    • Polymerase Chain Reaction (PCR): A method to amplify DNA segments.
    • Microarray Technology:
      • Involves screens for thousands of gene expressions.
    • Southern Blotting & FISH: Other molecular methods for identifying genetic material.

  • ### Molecular Identification Methods

    • Serological Techniques:
    • Measure antibodies or cytokine production in response to microbial antigens (e.g., ELISA).
    • Enzyme Assays:
    • Assessing enzyme activities such as reverse transcriptase for HIV.
    • Soft-Ionization Mass Spectroscopy (MALDI): Used for detailed microbial identification.
    • Phage Typing & Fatty Acid Profiles: Emerging methods for identifying and classifying bacteria.