Biodiversity: The Three Domains of Life
April 4, 2001

BioInquiry: Chapter 8: 209-222

"The incredible diversity of life on this planet, most of which is microbial, can only be understood in an evolutionary framework" -- Carl Woese, 2000

How is Life Classified?

Before 1969: Life was classified into two kingdoms: Plant Kindgom – Animal Kingdom

From 1969 – 1990: Life was classified into 5 Kingdoms: Monera, Protista, Plantae, Fungi, Animalia, by R.H. Whittaker [Science 163, 150 (1969)] using classification according to Linnaeus – based on anatomy, morphology, embryology, and cell structure.

(PS. Viruses are not in ANY of these kingdoms...remember that scientists do not classify them as 'alive').

– the traditional 5 Kingdom system says nothing about how organisms within Kingdoms or between kingdoms may be related to each other via evolutionary relationships among the kingdoms.

A New Proposal:
The Three Domains of Life (Carl Woese, 1990)

Starting in the early 1970s, Dr. Carl Woese, a professor in the Department of Microbiology, University of Illinois, Urbana-Champaign, and other scientists began to find evidence for a previously unknown group of prokaryotic organisms. These organisms lived in extreme environments - deep sea hydrothermal vents, "black smokers", hot springs, the Dead Sea, acid lakes, salt evaporation ponds - environments that scientists had never suspected would contain a profusion of life!

Because they appeared prokaryotic, they were considered bacteria and named "archaebacteria" ('ancient' bacteria). However, became obvious from biochemical characteristics and DNA sequence analysis that there were numerous differences between these archaebacteria and other bacteria. Before long, it was realized that these archaebacteria were more closely related to the eukaryotes (including ourselves!) than to bacteria. Today, these bacteria have been renamed Archaea.

From this work, Dr. Woese proposed that there should be a new caterogy of classification of life - the Domain, a classification category above Kingdom. The Historic Paper: Woese, C.R., O. Kandler, & M.L. Wheelis (1990). "Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya." Proc. Natl. Acad. Sci. USA 87:4576-4579. [Image]

PS. Carl Woese won the National Medal of Science in November 2000. Is there a Nobel prize in his future???? Dr. Marrs says YES! (Not that the Nobel Committee asks for my opinion...).

Each one of these Domains shares some features with the others and also has unique characteristics of its own. Some examples:

  Bacteria Archaea Eukarya








Ribosomal RNA
small subunit




in cell wall




RNA polymerase




Histone proteins
around DNA




Initiator amino acid
in protein synthesis




Introns in genes




Sensitivity to antibiotics




How was the 'Three Domain' Classification of Life Determined?

Woese (and many other scientists involved in this project) used the nucleotide sequence of Ribosomal rRNA (the small subunit) and other RNA and protein sequences as an “Evolutionary Chronometer” – an evolutionary time clock.

What makes rRNA (or another sequence) a good ‘chronometer’?

1. It is universally distributed across group chosen – all organisms have rRNA
2. It is functionaly similar between organisms – rRNAs all participate in protein synthesis
3. Its sequence changes slowly - good for looking across long periods of time
4. The rRNA sequences can be aligned, or matched up, between 2 organisms

Evolutionary distance (ED) =
between 2 organisms
Number of differences (% change) in nucleotide
sequnce of a gene between 2 organisms

Other sequences that can be used are the large rRNA subunit, or the gene for cytochrome c oxidase, ferredoxin.
The Ribosomal Database project: A central database for rRNA sequences
Want to know more about
ribosomes? Click here!

The Three domains - Some Characteristics:

Bacteria: Domain Bacteria is familiar to most people when associated with human or animal disease. However, most bacterial species do not (and cannot) cause disease. Many species even play beneficial roles by producing antibiotics and food. The soil teems with free-living bacteria that perform many essential functions in the biosphere, e.g. nitrogen fixation. Our bodies are covered with bacteria that make up our normal flora. [Quote]

Fun Fact: There are more bacteria in one person's mouth than there are people in the world. Many are decomposers, some are photosynthesizers, and a few cause disease. Most bacteria cause disease by producing exotoxins that harm human cells, while others cause illness as a result of glycoproteins found on the outside of their capsules. There are many shapes that bacteria can come in, but three of the main ones are cocci (spherical), bacilli (rods) and spirochete (spiral bacteria). [Quote]

At least 5 major Phyla:

Proteobacteria: Enteric bacteria like E. coli, Salmonella typhus, Legionella, Heliobacter pylorii (cause of many ulcers), Neisseria gonorrhea (cause of gonorrhea). These bacteria are very closely related to eukaryotic mitochondria.

Cyanobacteria: Photosynthetic ‘blue-green’ bacteria = produce O2 gas. Over 2 billion years ago, these bacteria made the O2 rich atmosphere in which we live!!! These bacteria are very closely related to eukaryotic chloroplasts. [Image]

Eubacteria: Clostridium (tetanus, botulism), Bacillus, mycoplasma (walking pneumonia).

Chlamydias: Parasites: Giardia, Chlamydia (STD)

Spirochaetes: Spiral bacteria: cause syphilis, Lyme disease

To read more about bacteria we don't like, see the "Bad Bug Book".

Archaea: Life's Extremists...!

1. Methanogens: “methane-makers”
Use only CO2, H and N to produce energy to live, and as a result give off methane gas.
[Image]. Live in swamps, marshes, gut of cattle, termites, etc. Methanococcus jannaschii, isolated from the deep sea Alvin probe, was the first Archaean whose genome was sequenced. Methanogens are decomposers; and can be used in sewage treatment. Methanogens may someday be used to produce methane as fuel!

2. Extreme Halophiles: “salt lovers”
Require an environment as salty or even10x saltier than ocean water. Some prefer up to 30% salt concentrations! These bacteria live in the Dead Sea, the Great Salt Lake, salt evaporation ponds.

3. Extreme Thermophiles: “heat / cold lovers”
Prefer temperatures above 60C (up to 110C for hyperthermophiles!) or near or below freezing. (Some thermophiles will die at roon temperature).
Thermophiles ive in hot sulfur springs, Yellowstone Park, deep sea hydrothermal vents “black smokers”, geothermal power plants. Also live in ocean waters around Antarctica, under the polar ice caps, etc. Thermus aquaticus and Pyrococcus furiosis and two species.

More Extremophiles here!!!
Extremophiles - Scientific American 1997 (PS. Written by Barry Marrs - but no relation!)


1. Protista – Single celled eukaryotes – Euglena, Amoeba, Paramecium etc

Protists can be found on land, in water, or living inside other organisms. Some protists are photosynthetic, like "phytoplankton", and produce more oxygen than all land plants put together. Other protists are parasites or predators. The protozoan Trypanosoma brucei causes African Sleeping Sickness. This parasite it transmitted to man by the bite of the tsetse fly. Another protozoan, Entameba histolytica is a parasite of the stomach which kills cells and drinks blood (but do not actually kill their host). The protozoan Plasmodium vivax causes malaria, carried by female mosquitos. Most protozoans move by means of pseudopodia ("false feet") or by cilia (little hairs). [Quote]

Fungi – Mushrooms, bread molds, water molds, yeasts ,etc

The Kingdom Fungi includes some of the most important organisms on Earth. By breaking down dead organic material, they cycle nutrients through ecosystems. Other fungi provide drugs such as penicillin and other antibiotics, foods like mushrooms, truffles and morels, and the bubbles in bread, champagne, and beer.

Fungi also cause plant and animal diseases: in humans, ringworm, athlete's foot, and several more serious diseases are caused by fungi. Plant diseases caused by fungi include rusts, smuts, and leaf, root, and stem rots, and may cause severe damage to crops. However, a number of fungi, in particular the yeasts, are important "model organisms" for studying problems in genetics and molecular biology.

Plantae – Flowering plants, gymnosperms (conifers), ferns, mosses, etc

Kingdom Plantae includes all land plants - an amazing range of diverse forms with more than 250,000 species. Plants first appeared on Earth in the Ordovician period approximately 510 million years ago. The most striking, and important, feature of plants is their green color, the result of a pigment called chlorophyll. Plants use chlorophyll to capture light energy, which fuels the manufacture of food—sugar, starch, and other carbohydrates. [Quote]

4. Animalia – [There is so much to say about this Kingdom - please visit the links if you want more information!!!] [Image]

First appeared on Earth ~650 million years ago. Includes sponges, jellyfish, corals, fish (etc etc) and a special mention to: Arthropods (includes insects):

"By nearly any measure, the most successful animals on the planet are the arthropods. They make up over three-fourths of all currently known living and fossil organisms, or over one million species in all. Since many arthropod species remain undocumented or undiscovered, the true number of living arthropod species is probably in the tens of millions. One recent conservative estimate puts the number of arthropod species in tropical forests at 6 to 9 million species (Thomas, 1990).

"Arthropods range in distribution from the deep sea to mountain peaks, in size from the king crab with its 12-foot armspan to microscopic insects and crustaceans. Despite this unbelievable diversity, the basic body plan of arthropods is fairly constant. Arthropods have a stiff cuticle made largely of chitin and proteins, forming an exoskeleton. They have segmented bodies to form integrated units (heads, abdomens, and so on). The phylum takes its name from its distinctive jointed appendages, which may be modified in a number of ways to form antennae, mouthparts, and reproductive organs."

And another special mention to Tetrapods (amphibians, reptiles, birds and mammals):

"Tetrapods were the first vertebrates to truly walk the land. Before tetrapods existed, vertebrates (like fish) were all confined to living in aquatic habitats. The tetrapods began moving to land in the Paleozoic around 360 million years ago. Tetrapods are a name that we have given to anything with four feet (tetra=four, pod=feet). Therefore all land dwelling vertebrates can be considered tetrapods. Tetrapods, whose closest living relatives are lungfish, have two main groups: amphibians and amniotes. The amniotes in turn have two main groups: the synapsids (including mammals) and the sauropsids (including reptiles and their fossil relatives)." [Quote]

End of Exam 3 Material; we will finish this last bit (below) after Exam 3!

A universal phylogenetic tree:(handout)

Who was the Universal Ancestor?
Carl Woese and others have proposed that at one point in time (3.3 - 3.5 billlion years ago), there was a Universal Ancestor that gave rise to all life on Earth. However, this ancestor would not have been a single organism, but a community of organisms. It is hypothesized that these organisms would have had inaccurate DNA replication, inaccurate protein synthesis (lots of genetic diversity), and could exchange their genes freely (more genetic diversity). We will talk more about this in our next discussion.

This group of organisms - sometimes referred to as the
Last Universal Common Ancestor (LUCA) could be considered the universal ancestors of all life on Earth. These organisms would are hypothesized to have had common properties of all three domains:

Nucleic acids as genetic material (DNA or RNA)
Ribosomes and tRNAs for making proteins
The universal genetic code (AUG = Met)
Amino acids for making proteins

The universal phylogenetic tree suggests that the Last Universal Common Ancestor of all life on Earth was a hyperthermophile.


1. What are the names of the 3 Domains? Who is Carl Woese and what was his role developing the concept of 3 Domains?
Explain the similatities and differences in cell structure between Bacteria, Archaea, and Eukarya.
What is an Evolutionary Chronometer? How is E
D (evolutionary distance) calculated?
4. What is rRNA and why was did scientists choose it as an Evolutionary Chronometer? ()
5. Bacteria:
What is the significance of the Proteobacteria and the Cyanobacteria in the development of eukaryotic organelles?
6. Archaea:
Distinguish between the three groups. Why are thay called 'extremeophiles'?
7. Eukarya: Be able to list the 4 Kingdom within Eukarya and give 1 representative organisms for each. (You do not need to know dates, numbers of species, or other facts provided in the quotes).

8. (Not on Exam 3) What might have been the characteristics of the Last Universal Common Ancestor?