Five Kingdom and Three Domain Systems

As biology advanced, the simple plant/animal division of Linnaeus gave way first to the Five Kingdom system (1969) and then to the Three Domain system (1990). Each revision reflected new evidence about the diversity of life — especially the discovery that what look like "bacteria" actually comprise two ancient and distantly related groups. OCR A-Level Biology A specification 4.2.2 (c)–(d) requires you to know both systems and explain why the Three Domain system has replaced the older Five Kingdom framework.

Key Definitions:

• Kingdom — a major division of life.
• Domain — an even broader category above kingdom.
• Prokaryote — organism with no membrane-bound nucleus.
• Eukaryote — organism with a membrane-bound nucleus.
• Archaea — single-celled prokaryotes distinct from bacteria at the molecular level.

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The Five Kingdom System (Whittaker, 1969)

flowchart TD
    A[All Life] --> B[Prokaryotae]
    A --> C[Protoctista]
    A --> D[Fungi]
    A --> E[Plantae]
    A --> F[Animalia]

In 1969, the American ecologist Robert Whittaker proposed five kingdoms to capture the diversity revealed by 20th-century biology:

1. Prokaryotae (= Monera)

• Prokaryotic cells (no nucleus, no membrane-bound organelles).
• Circular DNA; may have plasmids.
• Peptidoglycan cell wall (in bacteria; archaea use different molecules).
• Reproduce by binary fission.
• Examples: E. coli, Bacillus subtilis, cyanobacteria (e.g. Anabaena), extremophiles like Thermus aquaticus.

2. Protoctista

• Eukaryotic, mostly single-celled (but some multicellular forms like kelp).
• Extremely diverse — effectively, "everything eukaryotic that isn't a plant, animal or fungus".
• Include protozoans (e.g. Amoeba, Paramecium, Plasmodium), algae (diatoms, dinoflagellates) and slime moulds.
• A "rag-bag" kingdom that modern taxonomy has split into many groups.

3. Fungi

• Eukaryotic, usually multicellular (but includes unicellular yeasts).
• Heterotrophic — obtain nutrients by absorption, often secreting enzymes onto food.
• Chitin cell walls (different from plant cellulose).
• Reproduce by spores.
• Examples: mushrooms (Agaricus), moulds (Penicillium), yeasts (Saccharomyces), ringworm (Trichophyton).

4. Plantae

• Eukaryotic, multicellular.
• Autotrophic by photosynthesis (contain chloroplasts).
• Cellulose cell walls.
• Alternation of generations in life cycle.
• Examples: mosses, ferns, conifers, flowering plants.

5. Animalia

• Eukaryotic, multicellular.
• Heterotrophic by ingestion (consume other organisms).
• No cell wall.
• Nervous system (in most) permitting rapid movement.
• Examples: sponges, jellyfish, worms, molluscs, arthropods, chordates.

Advantages of Five Kingdoms

• Reflected the major differences in cell structure (prokaryotic vs eukaryotic) and mode of nutrition (autotrophic vs heterotrophic).
• Separated fungi from plants, which had previously been lumped together.
• Gave single-celled eukaryotes their own kingdom rather than wedging them into Plantae or Animalia.

Limitations

• Prokaryotes turned out to be deeply divided into two evolutionarily distant groups (bacteria and archaea), which the Five Kingdom system failed to recognise.
• Protoctista is clearly not a natural group — it lumps together organisms more closely related to plants, animals and fungi than to each other.
• Based on morphology and biochemistry rather than molecular data.

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The Three Domain System (Woese, 1990)

In the late 1970s, the American microbiologist Carl Woese pioneered the use of ribosomal RNA (rRNA) to reconstruct evolutionary relationships. Because rRNA is present in every cell and changes slowly over time, differences in its sequence reveal deep evolutionary splits. Woese's analysis showed something astonishing: "prokaryotes" were not a single group at all. Certain single-celled organisms previously lumped with bacteria were in fact as distantly related from bacteria as they were from animals and plants. Woese named them Archaea.

He proposed a new, higher level — the Domain — above kingdom:

flowchart TD
    A[Life] --> B[Bacteria]
    A --> C[Archaea]
    A --> D[Eukarya]
    B --> B1[E. coli, Cyanobacteria, Lactobacillus]
    C --> C1[Methanogens, Thermophiles, Halophiles]
    D --> D1[Protoctista]
    D --> D2[Fungi]
    D --> D3[Plantae]
    D --> D4[Animalia]

1. Domain Bacteria

True bacteria — the familiar prokaryotes. Characteristics:

• Peptidoglycan cell walls.
• Ester-linked membrane lipids (glycerol ester lipids).
• Sensitive to most antibiotics.
• RNA polymerase with 4–5 subunits.
• Include pathogens (Salmonella, Vibrio), symbionts (gut flora) and environmental species (cyanobacteria, nitrogen-fixing bacteria).

2. Domain Archaea

Previously called "archaebacteria". At first glance they look like bacteria — single cells, no nucleus — but their molecular biology is strikingly different:

• No peptidoglycan in cell walls (instead pseudopeptidoglycan, S-layers, or no wall).
• Ether-linked membrane lipids (more stable at extreme temperatures).
• Different ribosomal RNA sequences.
• More eukaryote-like RNA polymerase (often with 8+ subunits) and DNA replication machinery.
• Histone-like proteins package DNA in many archaea.
• Not sensitive to most antibacterial antibiotics.

Many archaea are extremophiles:

• Thermophiles live in hot springs and hydrothermal vents (Pyrococcus survives above 100 °C).
• Halophiles live in saturated salt (Halobacterium in the Dead Sea).
• Acidophiles live at very low pH.
• Methanogens produce methane in anaerobic environments (cow rumens, marshes, rice paddies).