Microbiology Exam Review: Taxonomy, Viruses, and Fungi

Posted on Oct 10, 2025 in Biology

Historical Shifts in Biological Taxonomy (1900–Present)

Significant changes in biological classification systems since 1900:

  • The earliest change started with Carl von Nägeli in the 1800s, who proposed bacteria and fungi be placed in the Plant Kingdom. However, in 1959, they were given their own kingdoms.
  • In 1937, the term prokaryote was introduced, and Robert G. E. Murray proposed the Kingdom Prokaryotae.
  • In the 1960s, the molecular clock was proposed, establishing an evolutionary timeline based on observations of nucleotide sequences in organisms.
  • In 1969, Robert H. Whittaker created the Five-Kingdom System. This system placed prokaryotes in the Kingdom Prokaryotae and eukaryotes in the other four kingdoms.
  • Also in 1969, simple eukaryotes that were mostly unicellular were grouped in the Kingdom Protista, as there was no other suitable kingdom for them.
  • In 1978, Carl R. Woese proposed the Three-Domain System. He observed that Archaea and Bacteria, despite looking similar, had fundamental differences in rRNA, membrane lipid structure, tRNA molecules, and sensitivity to antibiotics, necessitating separate domains.
  • In 1995, Raul Cano and his team contributed to the use of the molecular clock by successfully growing organisms that survived in amber for millions of years. The genomes of these organisms provided valuable evolutionary information.

Comparative Microbiology and Classification

Archaea, Eukarya, and Bacteria Comparisons

Similarities and Differences Between Key Domains

  • Archaea and Eukarya: Share similarities in transcription and translation enzymes. Both lack a peptidoglycan cell wall.
  • Archaea and Bacteria: Both lack nucleus-bound organelles, are typically small, and reproduce asexually. Bacteria, however, possess a cell wall containing peptidoglycan, which Archaea lack.
  • Eukaryotic Organelles and Prokaryotes: Prokaryotes lack the complex internal membrane structures (organelles) found in eukaryotes.

Taxonomic Hierarchy: Correct Order

The correct order of the taxonomic hierarchy (from broadest to most specific):

  1. Domain
  2. Kingdom
  3. Phylum
  4. Class
  5. Order
  6. Family
  7. Genus
  8. Species

Microbiological Techniques: Hybridization and Serology

Molecular and Serological Identification Methods

DNA Hybridization Techniques

  • Southern Blotting
  • Northern Blotting
  • Microarrays
  • Fluorescence in situ Hybridization (FISH)
  • In situ Hybridization (ISH)

Serological Methods

  • Agglutination
  • Precipitation
  • Enzyme-Linked Immunosorbent Assay (ELISA)
  • Western Blot
  • Immunofluorescence Assay (IFA)

Steps in Blotting Procedures

Southern Blot Steps (DNA Detection)

  1. DNA extraction
  2. Gel electrophoresis
  3. Denaturing
  4. Transfer (to membrane)
  5. Hybridization (with probe)
  6. Washing
  7. Detection

Western Blot Steps (Protein Detection)

  1. Protein extraction
  2. SDS-PAGE (Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis)
  3. Transfer (to membrane)
  4. Blocking
  5. Primary antibody incubation
  6. Secondary antibody incubation
  7. Washing
  8. Detection

Specific Characteristics of Bacteria and Prokaryotes

Key Genera and Unique Traits

  • Genus characterized by swarming ability: Proteus
  • Distinguishing feature of Bdellovibrio: It is an obligate predator, Gram-negative, exhibiting distinct attack and growth phases. Found in aquatic environments and soil, it is a potential antimicrobial agent.
  • Where are heterocysts found? In certain filamentous cyanobacteria (used for nitrogen fixation).
  • Which genera use reduced sulfur compounds as an electron donor? Beggiatoa, Thiobacillus, Acidithiobacillus, Thiomargarita, Thiothrix.
  • How can some prokaryotes grow to larger than normal bacteria sizes? By using special adaptations such as a large vacuole, thin cytoplasm, multiple copies of the genome, or existing in symbiotic or specialized niches.

Fungal Biology and Reproduction

Fungal Morphology and Classification

  • Genus best known for conidiospore formation: Aspergillus
  • Hyphae involved in reproduction: Aerial Hyphae
  • Asexual spore within a hyphal segment: Arthroconidium
  • Fungi where sexual reproduction has not been observed: Deuteromycota (imperfect fungi) or Microsporidia
  • Which fungi produces basidiospores? Basidiomycota (club fungi)

Protists, Algae, and Symbiosis

Key Protist and Algal Concepts

  • Lichens are a mutualistic combination of: A fungus and a photosynthetic partner (either green algae or cyanobacteria).
  • Algae that stores oil: Diatoms
  • Examples of chemoheterotrophic algae: Oomycota, Euglena, Chlamydomonas.
  • Slime mold that exhibits cytoplasmic streaming: Myxomycota or Myxogastria (Acellular slime molds).

Parasitology: Cestodes and Disease Transmission

  • Cestodes (Tapeworms) using humans as definitive host: Taenia species, Diphyllobothrium latum, Hymenolepis nana.
  • Difference between biological and mechanical transmission:
    • Biological Transmission: The pathogen develops or multiplies inside the vector before it is transmitted to the host.
    • Mechanical Transmission: The pathogen is carried passively on the body surface of the vector and transferred to the host without biological involvement.

Virology: Structure, Replication, and Disease

Viral Classification and Genetics

  • Viral Species Definition: Viral species share similar genetic information and often occupy the same ecological niche. They are also similar in replication methods and structural characteristics.
  • Specialized vs. Generalized Transduction: Both are methods of interchanging genetic material using bacteriophages.
    • Generalized Transduction: Occurs when the bacteriophage accidentally picks up random fragments of host DNA and transfers them to a new bacterium.
    • Specialized Transduction: Occurs when a lysogenic bacteriophage excises itself imperfectly from the bacterial chromosome, accidentally taking a small, specific piece of adjacent bacterial DNA with it.

Viral Replication and Life Cycles

  • Major differences between bacteriophages and animal viruses: Differences include host type, entry method, uncoating process, and replication site.
  • Where does DNA virus replicate in the host cell? Typically in the nucleus (except Poxviruses).
  • Enzyme that produces DNA from a viral RNA genome: Reverse Transcriptase (characteristic of retroviruses).
  • Distinguishing latent from persistent viral infections:
    • Latent Virus: The virus remains dormant in the host for long periods, often without symptoms (e.g., Herpes simplex).
    • Persistent Virus: The infection gradually increases or continues over a long period, often leading to chronic disease (e.g., Hepatitis C).
  • How do plant viruses enter plant cells? Through wounds or via plant parasites (e.g., insects).
  • In what ways can PrPSc (Prion protein scrapie) be transmitted? Ingestion, medical procedures, inherited genetic predisposition, direct contact, or experimental inoculation.