What is Three Domain System – Key Things You Need To Know

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By Lokesh Joshi

The three-domain system classifies biological organisms. It was developed by Carl Woese in the year 1990. That is why it is coined Carl Woese’s Classification as well. The three-domain system is further subdivided into 6 kingdoms.

The earlier kingdom model of classification is founded on the basis of principles created by Carolus Linnaeus, a Swedish scientist. It comprised 2 kingdoms namely “Animal” and “Plant”. He classified organisms into hierarchical system groups derived from commonly observed physical characteristics.

The Existing System

Existing System

The systems to classify organisms have been evolving continuously. This happens as scientists continue learning about more and more organisms. With the discovery of the genetic sequencing process, researchers have come to know about an entirely novel way by which relationships among organisms can be analyzed.

Groups of organisms that comprise the currently existent three-domain system are categorized mainly on the basis of dissimilarities in their ribosomal RNA (rRNA) structure, which adds up to a molecular block to build ribosomes.

The three-domain system categorizes organisms into 3 domains and 6 kingdoms that are as follows:


  1. Archaea
  2. Bacteria
  3. Eukarya


  1. Animalia
  2. Archaebacteria (archaic or ancient bacteria)
  3. Eubacteria (real bacteria)
  4. Fungi
  5. Plantae
  6. Protista

The three-domain system together with the kingdom classification typifies life depending on variations in the structure of rRNA and membrane of the constituent cells and sensitivity to antibiotics. This classification primarily differs from the previous one in terms of how archaea are separated from bacteria.

The evaluation of rRNA structure can be really useful. Because of the presence of rRNA molecules, organisms can perform somewhat identical functions all through the natural ambiance. Also, rRNA molecules enable organisms to carry out structural modifications in very little time. As a consequence, the differences and similarities that characterize rRNA nucleotide sequences amply indicate to what extent cells and organisms are related or unrelated.

In this particular system classification, there are 16S ribosomal RNAs (rRNA) used by Carl Woese to define a Chronometer, which is:

  • Universally distributed among all species
  • Functionally identical in all organisms
  • Capable of slowly changing its sequence
  • Capable of matching its sequences between two organisms

system classification

Defining Each Domain

1. Archaea Domain

The organisms making up the archaea domain are looked upon as the oldest species on Earth. They are formed of a single cell. The genes inherited by these organisms have similarities with those of bacteria as well as eukaryotes. Archaea have a very strong resemblance with bacteria because of which they were initially misconstrued as bacteria.

Akin to bacteria, organisms belonging to the archaea domain do not possess any membrane-enclosed nucleus. That is why they are referred to as prokaryotic organisms.

They are devoid of any internal cell organelles. They have unique biochemistry. Plus, their shape and size are similar to that of bacteria. Reproduction of archaea organisms takes place through binary fission. They are endowed with a single circular chromosome. Also, just like bacteria, they make use of flagella to hover around the environment.

The composition of the cell wall in archaea is different from that found in bacteria. It lacks peptidoglycan, a kind of polymer composed of amino acids and sugars and responsible for creating a mesh-like plasma membrane. Even the cell wall in archaea is made up of ether leakage.

And, as far as the composition of the membrane and type of rRNA are concerned, organisms of the archaea domain differ from bacteria and eukaryotes. All these differences are adequately significant to classify archaea in a different domain.

The organisms that are members of the archaea domain exist amid harsh environmental conditions such as Arctic and Antarctic ice, acidic springs, and hydrothermal vents.

There are 3 phyla of archaea organisms that are as follows:

  • Crenarchaeota

These organisms can be both hyperthermophiles and hypothermophiles meaning that they can survive in extremely high and low temperatures respectively. Sulfolobus, Acidianus, Pyrolobus are examples of Crenarchaeota that can successfully thrive above water’s boiling point. A few of the hypothermophiles can even survive the cold, frigid waters of the Arctic and Antarctic oceans.

They can likewise survive amidst excessively acidic environments because of which they are also thermoacidophilic in nature.

  • Euryarchaeota

This phylum of archaea is also called methanogens. They are capable of producing methane gas as an after-effect of their metabolism. Examples of methanogens are Methanobacterium and Methanosarcina. They need an environment free of oxygen for their survival.

A few of them are believed to be acute halophiles that colonize and thrive in extremely saline environments. An example of a typical halophile is Halobacterium.

A few Euryarchaeota are found to successfully survive in very acidic environments. They are known as acidophiles. Examples of acidophiles include Thermoplasma, Picrophilus, and Ferroplasma.

  • Korarchaeota

This phylum is relatively more unknown. It is still not taxonomically recognized. Some of the species from this phylum are found surviving in places around hydrothermal vents, hot springs, and obsidian pools that have their beds covered by volcanic, black, sandy materials.

accumulation of archaea

The picture above shows the accumulation of archaea around the Dead Sea.

2. Bacteria Domain

Even bacteria, like archaea, are microbes with a single cell. They have a simple cell structure. Bacterial cells are also prokaryotic in nature with organelles having no nucleus or membrane. Instead, they survive through a single-loop DNA control center that contains genetic information. A few bacteria comprise an additional circle of a genetic substance called a plasmid. The genes inhabited in plasmid make bacteria resistant to certain antibiotics even though they are sensitive to conventional antibiotics.

Bacteria are omnipresent in all earthly habitats such as rock, soil, oceans, snow, etc. A few of them are parasites and dwell in other organisms like animals, plants, and humans. The number of bacterial cells inhabiting a human body is estimated 10 times more than the total number of cells the human body possesses.

Bacteria are dreadful organisms as a few of them are pathogenic in nature and have the capability to cause diseases and illnesses.

But, at the same time, bacteria are considered an essential part of life as many of them are integral to the human microbiota. These types of bacteria are responsible for performing important bodily functions like proper digestion of and assimilation of the nutrients from the food we consume.

A few bacterial organisms live on the human skin. They prevent the inhibition of pathogenic microbes and help in the stimulation of the human immune system.

Because of them being primary decomposers, the presence of bacteria is also essential to recycle nutrients within the global ecosystem. They are found to be astonishingly helpful in producing fermented foods like yogurt and soya sauce.

Their cell wall membrane is composed of diacylglycerol diester lipids. The membrane contains peptidoglycan. It is also made of chains of unbranched fatty acids coupled with glycerol ester linkage.

The bacterial cell wall composition is done with an rRNA which is uniquely different from the rRNA present in archaea and eukarya.

phyla of bacterial organisms

Here are the 5 phyla of bacterial organisms:

1. Proteobacteria

It comprises the maximum number of groups of bacteria. Examples include Salmonella typhus (they cause typhoid), E.coli, Legionella, Helicobacter pylori (they cause many ulcers), Neisseria gonorrhea (they cause gonorrhea disease), Vibrio, etc.

2. Cyanobacteria

This phylum of bacteria is known to get energy from photosynthesis. Because of their distinctive color, they are also called blue-green algae.

3. Firmicutes

This phylum is alternatively called Eubacteria or true bacteria. These organisms are known to yield a positive result in the Gram stain test. That is why they are called gram-positive bacteria. They have thick cell walls. Examples include Clostridium (they cause tetanus and botulism), Bacillus, and Mycoplasma (they have no cell walls and cause walking pneumonia).

4. Chlamydia

These bacteria are parasitic in nature. They reproduce within the cells of the host from which they live off. Examples include Giardia, Chlamydia trachomatis (they cause Chlamydia, a sexually transmitted disease), and Chlamydophila pneumoniae (they cause pneumonia).

5. Spirochetes

This phylum of bacteria has the shape of a corkscrew. They move in a uniquely twisted fashion. Examples include Treponema pallidum (they cause syphilis) and Borrelia burgdorferi (they cause Lyme disease).

3. Eukarya Domain

These cells have a nucleus enclosed by a membrane containing ester linkages. The linkages are constituted by glycerol and chains of unbranched fatty acids. Like archaea, these organelles have cell walls that are devoid of any peptidoglycan composition. However, the rRNA structure in eukaryotes is dissimilar when compared with archaea and bacteria.

Eukaryotic cells have the most complex structures when it comes to their internal and external constitutions, physiology, and the reproductive process.

Eukarya are parasitic to antibacterial antibiotics. However, they are not resilient to antibiotics that attack eukaryotic cells.

The domain of Eukarya is further subdivided into 4 kingdoms that are as follows:

1. Protista

They are simple in structure and are predominantly single-celled. Protista is found on land and water and can also reside in other organisms as parasites. Examples of protista include algae, protozoans, amoeba, slime molds, and euglenoids.

2. Fungi

These organisms have eukaryotic cell types and may be unicellular or multicellular in nature. Their cell walls do not have any tissue formation. They obtain nutrients to survive through the process of absorption. They are incapable of performing photosynthesis. Examples of fungi include mushrooms, water molds, bread molds, sac and club fungi, and yeasts.

3. Plantae

These organisms are multicellular in composition with membrane-enclosed nuclei. They have defined cell walls. They also have perfect tissue formation. They acquire nutrients to thrive by carrying out photosynthesis or through absorption. Examples include flowering plants and gymnosperms like conifers, ferns, mosses, etc.

4. Animalia

This kingdom consists of organisms each having multiple, eukaryotic cells. Even though the cells do not have cell walls, still, they have definite tissue formation. The organisms cannot execute photosynthesis. They derive nutrients mainly through the process of ingestion. Sponges, worms, jellyfish, corals, insects, worms, and vertebrates are typical examples.

Eukarya Domain


Originally, it was thought that microorganisms undergo changes or adopt their harm-inflicting abilities in a slow, gradual manner to adjust to varying environmental conditions. The changes involved mutations, gene deletions and duplications, and chromosomal rearrangements. These changes were then passed on to the progeny of microbes leading to the occurrence of a natural selection. This process of transfer of genes to an offspring from its parent organism is termed “vertical gene transmission”.

However, recent studies reveal that the transfer of microbial genes from a parent to its offspring does not happen only in a vertical way. It also happens horizontally especially with distant relations such as other species and genera. This process is called “horizontal gene transfer”.

There are several mechanisms by virtue of which chromosomal DNA and genetic elements like plasmids, integrons, and transposons can be directly transferred between microorganisms. These include:

  • Transformation
  • Transduction
  • Conjugation

Consequently, the three-domain system of microorganisms is now more apparently a “mesh of life”. Each of the cell types belonging to the three domains tends to fit into recurrent roles or specialties.

  • Bacteria have the most prolific reproduction ability, at best, amid moderate environments.
  • Archaea have the competence to quickly adapt to extreme environments. They can also acclimatize to wide-ranging food sources.
  • Eukaryotes exhibit maximum flexibility in relation to building cooperative colonies. This is obvious in the case of multicellular organisms such as humans. As a matter of fact, the cell structure in a eukaryote has most probably come into being by merging various cell types and subsequently forming organelles.


Of late, several fusion hypotheses have been formulated and put forward to stand over the existing literature. One such hypothesis suggests that the occurrence of the diploid or 2N eukaryotic genome took place after the fusion of 2 prokaryotic cells of haploid or 1N nature. Others come up with a theory that the emergence of archaea and eukarya domains happened out of a common ancestor which in turn had its origin from a member of the bacteria domain. This particular hypothesis is backed by evidence that states a certain bacterial superphylum known as PVC consists of members whose characteristics are similar to those of archaea and eukaryotes. Also, numerous pieces of evidence have brought forward the likelihood of the origin of eukaryotes from an archaeal subset.

Regardless of all these propositions and their veracities, today, it is universally accepted that 3 distinct domains of organisms that exist in nature are archaea, bacteria, and eukarya.

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