Introduction to Classification

Lessons

Senior 4 · Biology

Introduction to Classification

5 lessons

Lesson 2 of 5

The three domains and the five kingdoms

25 min

Methane from the bottom of Lake Kivu

Deep in Lake Kivu, below about 300 m, the water holds dissolved methane, enough for the lake's methane to be pumped up and burned to generate electricity for Rwanda's grid. Much of that methane is thought to be made by microorganisms that reduce volcanic carbon dioxide. Every organism known to make methane in this way belongs to a group that looks, under a light microscope, just like bacteria: tiny cells with no nucleus.

In 1977 the American microbiologist Carl Woese compared the sequence of the RNA in the small subunit of the ribosome (16S rRNA) in many microorganisms. The methane-makers turned out to be as different from ordinary bacteria as bacteria are from humans. He called them archaea, and in 1990 he and his colleagues proposed that all life falls into three domains. This lesson compares that system with the older five-kingdom system that you met in S1.

Definition

Prokaryote: an organism whose cell has no nucleus and no membrane-bound organelles; its DNA lies free in the cytoplasm. Example: Escherichia coli.

Eukaryote: an organism whose cells have a nucleus surrounded by a double membrane and membrane-bound organelles such as mitochondria. Example: a maize plant.

Domain: the highest rank in classification, above kingdom. There are three: Bacteria, Archaea and Eukarya.

Archaea: prokaryotes that differ from bacteria in their rRNA sequences, membrane lipids and cell walls, and resemble eukaryotes in several features of their genes. Many are extremophiles, organisms that live in extreme conditions such as hot springs, very salty lakes or places with no oxygen.

Kingdom: the rank below domain. The five-kingdom system recognises Prokaryotae, Protoctista, Fungi, Plantae and Animalia.

The three domains compared

Feature	Bacteria	Archaea	Eukarya
Nucleus and membrane-bound organelles	Absent	Absent	Present
Cell wall	Contains peptidoglycan (murein)	No peptidoglycan; proteins or other polymers	Cellulose (plants), chitin (fungi) or none (animals)
Membrane lipids	Unbranched fatty acids joined to glycerol by ester bonds	Branched chains joined to glycerol by ether bonds	Unbranched fatty acids joined by ester bonds
Ribosomes	70S	70S	80S in the cytoplasm (70S in mitochondria and chloroplasts)
Histone proteins with DNA	Absent	Present in many	Present
Introns in genes	Rare	In some genes	Common
RNA polymerase	One, simple	Several types, complex, eukaryote-like	Several types, complex
Growth stopped by the antibiotics streptomycin and chloramphenicol	Yes	No	No

Archaea share the prokaryote body plan with bacteria but share many genetic features with eukaryotes. That is why the tree in Figure 1 shows Archaea and Eukarya sharing a more recent common ancestor with each other than either shares with Bacteria. The ether-linked lipids of archaea make their membranes more stable at high temperatures, one reason many live in hot springs.

Worked example 1: which domain?

An organism isolated from a hot spring at 85 °C has these features: single cells about 1 µm across; no nucleus; a cell wall with no peptidoglycan; membrane lipids with ether bonds; 70S ribosomes; its growth is not affected by streptomycin. Assign it to a domain, using evidence.

No nucleus and 70S ribosomes: it is a prokaryote, so it is not in Eukarya.
No peptidoglycan, ether-linked lipids and resistance to streptomycin all match Archaea and not Bacteria.
Its home, a hot spring, fits, but is not evidence on its own: some bacteria also live in hot springs.
Conclusion: domain Archaea, on the evidence of its cell wall, membrane lipids and antibiotic response.

The five kingdoms

The American ecologist Robert Whittaker proposed five kingdoms in 1969; the form below, with the kingdoms Prokaryotae and Protoctista, was set out later by Lynn Margulis and Karlene Schwartz.

Kingdom	Cell type and body	Nutrition	Cell wall	Examples
Prokaryotae	Prokaryotic; single cells, chains or clusters	Autotrophic (photosynthetic or chemosynthetic) or heterotrophic	Usually present	Lactobacillus (souring milk), Rhizobium (root nodules), cyanobacteria
Protoctista	Eukaryotic; mostly single-celled, or multicellular without specialised tissues	Autotrophic (algae) or heterotrophic (protozoa); some both	Cellulose in many algae; absent in protozoa	Amoeba, Plasmodium (malaria), Euglena, Spirogyra, seaweeds
Fungi	Eukaryotic; thread-like hyphae forming a mycelium, or single cells (yeasts)	Heterotrophic: secrete enzymes onto food and absorb the products (saprotrophic or parasitic)	Chitin	Yeast, Rhizopus (bread mould), mushrooms
Plantae	Eukaryotic; multicellular with tissues and organs	Photoautotrophic, with chlorophyll in chloroplasts; store starch	Cellulose	Mosses, ferns, conifers, flowering plants such as cassava
Animalia	Eukaryotic; multicellular with tissues and, in most, nervous coordination	Heterotrophic: ingest food and digest it inside the body; store glycogen	None	Sponges, worms, insects, fish, cattle, humans

Fungi were once placed with plants because both are fixed in place and have cell walls. The evidence now says otherwise: fungal walls are chitin, not cellulose; fungi store glycogen, as animals do; and DNA comparisons show that fungi share a more recent common ancestor with animals than with plants.

Worked example 2: awkward organisms

Assign each organism to a kingdom and justify your choice: (a) Euglena, a single cell with chloroplasts, a flagellum and no cell wall, which can also absorb food in the dark; (b) baker's yeast, single cells with chitin walls that absorb sugar; (c) a slime mould, a yellow, many-nucleate mass that creeps over rotting wood and engulfs bacteria.

(a) Protoctista. It has a nucleus, so it is a eukaryote; it is single-celled with no cellulose wall and no tissues, so it is not a plant, even though it photosynthesises.
(b) Fungi. Being single-celled does not make it a protoctist: its chitin wall and absorptive heterotrophic nutrition are the features of fungi.
(c) Protoctista. Slime moulds were once called fungi because they produce spores, but the feeding stage has no chitin wall and engulfs its food, and molecular evidence places them away from true fungi.
Lesson: classify by a combination of features, and check against molecular evidence; a single feature (single-celled, green, makes spores) can mislead.

Several Euglena cells seen through a light microscope: long, flexible green cells packed with chloroplasts, each with a small red eyespot near one end. Euglena photosynthesises like a plant but swims and has no cell wall, one reason it is placed in the Protoctista. Photo: Deuterostome, CC BY-SA 3.0, via Wikimedia Commons

CrashCourse: "Old & Odd: Archaea, Bacteria & Protists" (Crash Course Biology #35). Note the features that set archaea apart from bacteria, and why the video calls the protists a group of leftovers.

Warning

Common mistakes

Calling archaea "a kind of bacteria". They are prokaryotes, but they form a separate domain.
Putting every single-celled eukaryote in Protoctista. Yeasts are single-celled fungi.
Putting every green organism in Plantae. Cyanobacteria are prokaryotes, and many algae are protoctists.
Forgetting that viruses fit in neither system: they are not cells (Lesson 4).

Tip

Memory hook. For the domains, think "wall, lipid, ribosome": peptidoglycan wall means Bacteria; ether lipids mean Archaea; 80S ribosomes mean Eukarya. For the kingdoms, ask three questions in order: nucleus? many cells with tissues? how does it feed (makes, absorbs or ingests)?

✦

Practice: domains and kingdoms

Give three features shared by bacteria and archaea, and three that differ between them.
Explain why the evidence that led Woese to propose the domain Archaea came from rRNA rather than from microscope observations.
State the kingdom of each: (a) Plasmodium; (b) a mushroom; (c) Rhizobium; (d) a fern; (e) a sponge.
An organism is multicellular, has cell walls made of chitin and digests food outside its body. Name its kingdom and give one way it differs from a plant.
Figure 1 shows Fungi closer to Animalia than to Plantae. Give two pieces of evidence for this.
Explain why antibiotics such as streptomycin, which act on 70S ribosomes, can harm bacteria in the body without stopping the body's own protein synthesis in the cytoplasm.
Evaluate the five-kingdom system in the light of the three-domain system.

Show answersHide answers

Shared: no nucleus, no membrane-bound organelles, 70S ribosomes (also circular DNA, small size). Different: peptidoglycan in the wall (bacteria only); ester-linked versus ether-linked membrane lipids; histones absent in bacteria but present in many archaea (also RNA polymerase type, response to streptomycin).
Bacteria and archaea look almost identical under a microscope, so structure could not separate them. rRNA is present in all cells and changes slowly, so comparing its sequence measures how distantly related organisms are.
(a) Protoctista; (b) Fungi; (c) Prokaryotae; (d) Plantae; (e) Animalia.
Fungi. A plant has cellulose walls, chlorophyll and makes its own food by photosynthesis; the fungus has chitin walls and absorbs food made by other organisms (and stores glycogen, not starch).
Fungi and animals both store glycogen, and their DNA sequences are more similar to each other's than to plants' (chitin also occurs in the exoskeletons of some animals).
Body cells have 80S ribosomes in the cytoplasm, which the drug does not bind to; bacteria have 70S ribosomes, so their protein synthesis is blocked.
It works well for eukaryotes, whose four kingdoms survive inside Eukarya. Its weakness is Prokaryotae, which lumps together two groups (Bacteria and Archaea) that are as different from each other as either is from eukaryotes; and Protoctista is not a natural group but many separate lineages. The three-domain system reflects evolutionary relationships better, because it is based on molecular evidence.

Quick check

A prokaryote has a cell wall without peptidoglycan and membrane lipids with ether bonds. Which domain is it in?

Key points

Three domains: Bacteria and Archaea (prokaryotes) and Eukarya; they differ in cell walls, membrane lipids, ribosomes, histones and RNA polymerase.
rRNA sequences revealed that archaea are a separate domain, closer to eukaryotes than to bacteria.
Five kingdoms: Prokaryotae, Protoctista, Fungi, Plantae, Animalia, told apart by cell type, body organisation, nutrition and cell wall.
The four eukaryote kingdoms sit inside Eukarya; Prokaryotae is split into two domains, and Protoctista is a mixed group.

Sources and credits

5.2.3: Structure of Prokaryotes: Bacteria and Archaea and 4.3.4: Perspectives on the Phylogenetic Tree, from Biology 2e by OpenStax (Mary Ann Clark, Matthew Douglas, Jung Choi), via LibreTexts Biology, licensed under CC BY 4.0. Used for the comparison of bacteria and archaea, and Woese's three domains. Adapted by Ganzaa.
Lake Kivu and Three-domain system, Wikipedia contributors, licensed under CC BY-SA 4.0. Used for the methane of Lake Kivu and its microbial origin, and the history of the domains. Adapted by Ganzaa.
Figure 1, the worked examples, practice and quick check: written by Ganzaa.
Photos: Albatros4825, CC BY-SA 4.0; Deuterostome, CC BY-SA 3.0; HelenGinger, CC BY-SA 3.0; all via Wikimedia Commons.
Video: "Old & Odd: Archaea, Bacteria & Protists - CrashCourse Biology #35", CrashCourse, embedded from YouTube.

This lesson adapts CC BY-SA material and is shared under CC BY-SA 4.0.

1Methane from the bottom of Lake Kivu

2The three domains compared

3The five kingdoms

Methane from the bottom of Lake Kivu

The three domains compared

The five kingdoms