Taxonomy, Domains of Life, and Acellular Infectious Agents

Carl Linnaeus and the Birth of Modern Taxonomy

• Swedish taxonomist & physician (18th century)
• Published Systema Naturae
  • First comprehensive attempt to classify, describe & identify living organisms (practice now called taxonomy)
  • Originally recognized three kingdoms:
  • Animal
  • Plant
  • Mineral → later dropped
• Introduced a formal hierarchical scheme:
  • Kingdom \rightarrow Class \rightarrow Order \rightarrow Family \rightarrow Genus \rightarrow Species
  • Designed so each successive rank is a subdivision of the one above it

Binomial Nomenclature (Two-Word Naming System)

• Each species receives two Latin or Latinized names: Genus\;name + Specific\;epithet
  • Example: Homo\;sapiens
    • Homo = genus (capitalized)
    • sapiens = specific epithet (lower-case)
• Formatting rules
  • Always italicized (or underlined when handwritten)
  • Full name spelled out at first mention; thereafter genus may be abbreviated (e.g., H. sapiens)
• Naming rationales
  • May reflect a unique trait (morphology, habitat, physiology)
  • May honor the discoverer or another individual

From Kingdoms to Domains

• Modern molecular phylogeny separates all cellular life into three domains:
  1. Archaea
  2. Bacteria
  3. Eukarya
• Distinction hinges on cell structure & molecular signatures (e.g., rRNA sequences)
• All three domains contain microorganisms

Cellular Architecture Primer

• Prokaryotes (Archaea & Bacteria)
  • No membrane-bound nucleus
  • Lack membrane-bound organelles
• Eukaryotes (Eukarya)
  • Possess membrane-bound nucleus & organelles
  • Range from unicellular (yeasts, some algae, protozoa) to complex multicellular organisms (plants, animals)

Domain Archaea

• Composed of highly specialized prokaryotes often inhabiting extreme environments
• Major ecological/physiological groups
  • Extreme thermophiles – thrive at very high T
  • Thermoacidophiles – tolerate high T & low pH
  • Methanogens – produce CH4; require anoxic niches (no O2)
  • Halophiles – require/survive high salinity
  • Acidophiles – flourish at pH<3 or in high H2SO4
• Cell wall contains pseudo-peptidoglycan (distinct from bacterial peptidoglycan)

Domain Bacteria

• Also prokaryotic but cell wall built mainly from peptidoglycan + lipopolysaccharide (LPS)
• Some lineages form endospores (dormant, resistant forms) – a capability lacking in Archaea
• Exhibit remarkable morphological & metabolic diversity
  • Shapes: cocci, bacilli, spirilla, filamentous, etc.
  • Energy strategies:
  • Photosynthetic (e.g., cyanobacteria)
  • Chemolithotrophic – oxidize inorganic compounds (e.g., NH3, H2S)
  • Chemoorganotrophic – metabolize organic molecules

Domain Eukarya

• Encloses all organisms with eukaryotic cell structure
• Microbial members
  • Fungi (yeasts, molds)
  • Algae (photosynthetic protists)
  • Protozoa (heterotrophic protists)
• Multicellular eukaryotes (plants, animals) share the same fundamental cell plan but organize into specialized tissues & organs

Acellular Infectious Agents

1. Viruses

• Not true living cells – lack cytoplasmic membrane, cytosol & metabolic machinery
• Structure: nucleic acid (DNA or RNA) + protein coat (capsid); sometimes an envelope
• Replication
  • Obligate intracellular parasites: must infect a living host cell
  • Viral genome commandeers host metabolism, produces progeny virions, often lyses or damages host
• Life-criteria failings – no independent energy generation, metabolism, or response to environment outside a host

2. Viroids

• Small, circular RNA molecules (≈250–400 nt)
• No capsid or encoded proteins
• Replicate using host RNA polymerase; RNA itself serves as both genome & template
• Cause plant diseases; mechanism of transmission & environmental survival still under study

3. Prions

• Infectious misfolded proteins; contain no nucleic acids
• Misfolded conformation induces normal proteins (usually brain glycoprotein PrP^{C}) to adopt pathogenic form PrP^{Sc}
• Lead to Transmissible Spongiform Encephalopathies (TSE)
  • Humans: Creutzfeldt–Jakob disease, variant CJD, kuru
  • Animals: bovine spongiform encephalopathy (BSE, “mad-cow”), scrapie in sheep
• Hallmarks: sponge-like brain, loss of motor control, dementia; invariably fatal; no cure
• May arise via inherited mutation, spontaneous misfolding, or ingestion/iatrogenic exposure

Comparative Highlights & Key Takeaways

• Hierarchy & Nomenclature ensure universal communication; Latinization avoids linguistic bias
• Domains vs. Kingdoms: domains reflect fundamental molecular lineages; older “three-kingdom” (animal, plant, mineral) obsolete for biology
• Archaea vs. Bacteria: superficially similar (prokaryotic) but chemically & genetically distinct (cell-wall chemistry, membrane lipids, rRNA)
• Eukarya bridges microbial (yeast, protozoa) & macroscopic (plants, animals) biology
• Acellular agents challenge the definition of life; depend wholly (viruses, viroids) or partly (prions) on host biology yet can cause profound disease