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Extended reading: the three domains of life

The five kingdoms put all bacteria in Monera. By comparing the ribosomal RNA genes, Carl Woese found that the archaebacteria differ from the true bacteria as much as from the eukaryotes. In 1990 the three domains were proposed: Bacteria, Archaea and Eukarya. Archaea and Eukarya share a more recent ancestor. Monera splits into two domains, and the other four kingdoms are all in Eukarya.

This is the first lesson of Biological Classification: Three Domains, Microbes in the Laboratory and NEET Practice, free for everyone to read.

A system is a tool

You have met three systems. Aristotle and Linnaeus used two kingdoms; Whittaker used five. A system changes when a new kind of evidence is found. In this lesson we meet the evidence that led to the next change.

Other biologists tried other numbers. Haeckel (1866) added a third kingdom, Protista, for the single-celled organisms. In the 1950s Copeland took the bacteria out as a separate kingdom, Monera, and so had four. Each change came from looking at more features.

The problem in Monera

The five kingdoms put all bacteria in Monera. But the archaebacteria are special: they live in extreme places, and they have a different cell wall. How different are they? The answer came from the genes.

The ribosomal RNA gene

In 1977, Carl Woese and George Fox compared the ribosomal RNA (rRNA) of many organisms, from the small part of the ribosome. There are three good reasons to use it.

Every cell has ribosomes, from a bacterium to a human, so any two organisms can be compared.
The gene changes slowly. So the number of differences tells how long ago two lines separated: more differences, longer ago.
The sequence can be read and counted, so the result does not depend on an opinion.

You should find that two lines that split $2000$ million years ago differ at $80$ places in $1000$ , or $8\%$ . That is at $2$ changes per $1000$ places per $100$ million years on each line. A slow clock is what lets us look so far back.

They found that the methanogens, which every book then called bacteria, were as different from the true bacteria as from the eukaryotes. They named the group Archaea. In 1990, Woese and others proposed three domains: Bacteria, Archaea and Eukarya. A domain is a rank above the kingdom.

A tree of the three domains of life. From one last common ancestor, the line splits into Bacteria (true bacteria and cyanobacteria) and a second line that later splits into Archaea (halophiles, methanogens and thermoacidophiles) and Eukarya. Eukarya holds the four eukaryotic kingdoms: Protista, Fungi, Plantae and Animalia. A note says that Archaea and Eukarya share a more recent ancestor.

The tree says that Archaea and Eukarya share a more recent ancestor than either shares with Bacteria. Archaea are not eukaryotes, but in some ways they are more like us than like the true bacteria.

How the domains differ

Feature	Bacteria	Archaea	Eukarya
Nucleus with a membrane	no	no	yes
Cell wall	peptidoglycan	no peptidoglycan	cellulose, chitin or none
Histone-like proteins on the DNA	no	yes	yes (histones)
The first amino acid of a protein	formylmethionine	methionine	methionine
Examples	Escherichia coli, cyanobacteria	Halobacterium salinarum, Methanococcus jannaschii	yeast, mango, human

Methanococcus jannaschii, from a hot vent on the sea floor, was the first archaeon whose whole set of genes was read, in 1996.

Five kingdoms, three domains

The two systems answer different questions.

Monera is split between two domains: the true bacteria in Bacteria, and the archaebacteria in Archaea.
Protista, Fungi, Plantae and Animalia, the four kingdoms of eukaryotes, are all in Eukarya.

Your NCERT book and the examinations use the five kingdoms. Research papers often use the three domains, so it is good to know both.

Try it in Python

This program compares short pieces of rRNA genes of four organisms, and counts the places where each pair differs. The sequences are made up for this lesson, but the method is the real one.

Practise with new numbers

Common mistakes

Calling Archaea eukaryotes. They have no nucleus with a membrane.
Putting Archaea closest to Bacteria. By rRNA, Archaea share a more recent ancestor with Eukarya.
Thinking a fast-changing gene is best for old splits. A slow gene keeps a record over billions of years.
Thinking the domains replace the kingdoms. A domain is a rank above the kingdom.

Remember these

Systems change with new evidence: two kingdoms, three (Haeckel), four (Copeland), five (Whittaker).
Woese and Fox compared ribosomal RNA genes (1977). Every cell has them, and they change slowly.
Three domains: Bacteria, Archaea and Eukarya. Archaea and Eukarya share a more recent ancestor.
Monera is split between Bacteria and Archaea. The other four kingdoms are all in Eukarya.

Check yourself

Try each one on your own first. If you are stuck, open a hint. Then check with Show the answer.

In which domain are the methanogens?

Why is the rRNA gene a good one to compare?

How many domains hold the organisms of Monera?

Which two domains share a more recent ancestor?

Liked this lesson? There is more

Biological Classification: Three Domains, Microbes in the Laboratory and NEET Practice is a Standard course. It adds 2 more lessons, practice and tests on top of the free chapter.

12Problems3Python Labs1Question Set1Mock Test

Extended reading: bacteria in the laboratory: In the Gram stain, a bacterium with a thick peptidoglycan wall keeps the purple crystal violet (Gram-positive). One with a thin wall inside an outer membrane loses it and takes the pink safranin (Gram-negative). A culture grows through a lag, log, stationary and death phase. The number of live bacteria in a sample is found by dilution and plating: CFU per mL = colonies ÷ (dilution × volume plated in mL), using a plate with 30 to 300 colonies.