The Three-Domain System: Bacteria, Archaea, and Eukarya

The three-domain system divides all cellular life into Bacteria, Archaea and Eukarya, based mainly on differences in ribosomal RNA and cell chemistry. In brief: Bacteria and Archaea are both single-celled prokaryotes without a nucleus, but Archaea differ from Bacteria in their cell membranes, cell walls and gene machinery, and in these respects they are more similar to eukaryotes. Eukarya includes all organisms whose cells have a nucleus: animals, plants, fungi and protists.

The system was proposed by Carl Woese in 1990 and changed the way biologists see the tree of life. This guide explains how the domains differ, describes each in turn with examples, compares them in a table, works through an identification example and corrects common mistakes.

Why three domains?

Until the 1970s, living things were divided into two groups: prokaryotes (cells without a nucleus) and eukaryotes (cells with a nucleus). Carl Woese compared the sequences of ribosomal RNA (rRNA), a molecule found in all cells, and found that the prokaryotes include two very different groups. The differences between Bacteria and Archaea are as great as the differences between either group and eukaryotes. A domain is the highest taxonomic rank, above the kingdom.

What are Bacteria?

Bacteria are single-celled prokaryotes, typically 1 to 5 micrometers long. They are the best-known prokaryotes and live nearly everywhere: soil, water, air and the bodies of other organisms. A human body contains about as many bacterial cells as human cells, and they are mostly harmless or useful.

• The cell wall contains peptidoglycan.
• The cell membrane is made of phospholipids with ester-linked, unbranched fatty acids.
• The DNA is a single circular chromosome, often with plasmids.
• Shapes: cocci (spheres), bacilli (rods) and spirilla (spirals).

Bacteria are very diverse in the way they get energy: some are photosynthetic (cyanobacteria), some obtain energy from inorganic chemicals (chemoautotrophs), and many consume organic matter (heterotrophs). Examples are Escherichia coli in the gut, Streptococcus (some species cause strep throat), Rhizobium (fixes nitrogen in legume roots) and cyanobacteria, which produced much of the oxygen in the atmosphere. Some cause diseases such as tuberculosis and cholera.

What are Archaea?

Archaea are also single-celled prokaryotes, and they look similar to bacteria under the microscope. They were first thought to be unusual bacteria, because many were found in extreme environments, but they are also found in oceans, soil and the human gut.

• The cell walls lack peptidoglycan. They are made of other polymers, such as pseudomurein or proteins.
• The cell membrane lipids have ether linkages and branched chains, and some archaea have a monolayer membrane. These features allow them to withstand high temperatures.
• Their gene expression machinery (RNA polymerase, ribosomal proteins) is more similar to that of eukaryotes than to that of bacteria.
• The DNA is circular, but is wrapped around histone-like proteins.

Many archaea are extremophiles. Thermophiles live in hot springs and hydrothermal vents, such as Pyrolobus fumarii, which can grow at temperatures above 100 °C. Halophiles thrive in very salty water such as the Dead Sea, and acidophiles grow in acid. Methanogens produce methane and live in oxygen-free places, such as swamps, the guts of cattle and termites, and sewage. No archaeon is known to cause a human disease with certainty.

What is Eukarya?

Eukarya includes all organisms with cells that have a nucleus and membrane-bound organelles. Four groups are usually recognized:

• Protists: mostly single-celled eukaryotes, such as Amoeba, Paramecium and algae. This is not a natural group, but a collection of organisms that do not fit in the other three.
• Fungi: they absorb food from their surroundings and have chitin cell walls. Examples are mushrooms, molds and yeasts.
• Plants: multicellular photosynthetic organisms with cellulose cell walls.
• Animals: multicellular heterotrophs that digest food internally and have no cell walls.

The detailed features of these kingdoms are discussed in the next article.

The three domains compared

Worked example: placing organisms in domains

Use the questions below to assign each organism to a domain.

1. Does the cell have a nucleus? If yes, it is Eukarya. If no, it is prokaryotic: go to question 2.
2. Does the cell wall contain peptidoglycan, and are the membrane lipids ester-linked? If yes, it is Bacteria. If not, and if the lipids are ether-linked, it is Archaea.

Apply this to three samples:

• Sample A: a 2-micrometer rod without a nucleus, with a peptidoglycan wall, from yogurt. It is a bacterium (Lactobacillus).
• Sample B: a 1-micrometer sphere without a nucleus, from a hot spring at 90 °C, with no peptidoglycan and ether-linked membrane lipids. It is an archaeon, probably a thermophile.
• Sample C: a 20-micrometer cell from pond water, with a nucleus and chloroplasts. It is a eukaryote (an alga, which is a protist).

In a practical situation, microscope shape and size alone are not enough, because bacteria and archaea look alike. Identification requires chemical tests or DNA sequencing. The 16S rRNA gene, a section of ribosomal RNA, is widely used for this purpose.

How was the system discovered?

In 1977, Carl Woese and George Fox published the finding that methanogens have a ribosomal RNA that is as different from that of bacteria as from that of eukaryotes, and proposed a separate group of “archaebacteria”. In 1990, Woese, Otto Kandler and Mark Wheelis proposed the formal domains Bacteria, Archaea and Eukarya. Later gene studies suggested that eukaryotes arose from a merger involving an archaeon, probably related to the Asgard archaea, and an alphaproteobacterium that became the mitochondrion. The details of this origin are still being debated.

Why does it matter?

The distinction between Bacteria and Archaea matters for medicine and biotechnology. Antibiotics target bacterial structures such as peptidoglycan, which archaea do not have. Enzymes from thermophilic archaea and bacteria, such as Taq polymerase (from the bacterium Thermus aquaticus), are used in PCR, a technique that copies DNA at high temperatures. Methanogens are used in biogas production and contribute to atmospheric methane.

Which mistakes are common?

Mistake 1: Assuming that archaea are a type of bacteria

They are a separate domain. They differ in membrane lipids, cell walls and gene machinery.

Mistake 2: Saying that all archaea live in extreme environments

Many live in oceans, soils and the human body.

Mistake 3: Believing all prokaryotes are harmful

Most are harmless, and many are useful, in digestion, nutrient cycles and food production.

Mistake 4: Using kingdoms as the highest rank

Domains are above kingdoms. Domain Eukarya contains the kingdoms Animalia, Plantae and Fungi, as well as protists.