Classification of Life: The Three Domain System

The word Liferefers to the process of organisms which grow by a metabolic system. Generally, organisms are metabolized, have an ability to grow, react, reproduce, move, adjust and evolve .

The Earth is 4.6 billion years old and microbial life is thought to have first appeared between 3.8 and 3.9 billion years ago; in fact, 80% of Earth’s history was exclusively microbial life. Microbial life is still the dominant life form on Earth. It has been estimated that the total number of microbial cells on Earth on the order of 2.5 X 1030 cells, making it the major fraction of biomass on the planet.

In biological taxonomy, a domain, also superkingdom, realm or empire, is the highest taxonomic rank of organisms in the three domain system of taxonomy. Again,phylogeny refers to the evolutionary relationships between organisms. The Three Domain System, proposed by Woese and others, is an evolutionary model of phylogeny based on differences in the sequences of nucleotides in the cell’s ribosomal RNAs (rRNA), as well as the cell’s membrane lipid structure and its sensitivity to antibiotics. Comparing rRNA structure is especially useful. Because rRNA molecules throughout nature carry out the same function, their structure changes very little over time. Therefore similarities and dissimilarities in rRNA nucleotide sequences are a good indication of how related or unrelated different cells and organisms are.

There are various hypotheses as to the origin of prokaryotic and eukaryotic cells. Because all cells are similar in nature, it is generally thought that all cells came from a common ancestor cell termed the last universal common ancestor (LUCA). These LUCAs eventually evolved into three different cell types, each representing a domain.Before Woese’s discovery of archaea as distinct from bacteria in 1977, scientists believed there were only two types of life: eukarya and bacteria. Woese believed that the archaea and the bacteria although similar in appearances, should form their own separate domains on the evolutionary tree. Comparing the sequence of nucleotides in ribosomal RNA from different kinds of cells shows that there are three distinctly different cell groups-

They are-

  • The Archaea
  • The Bacteria
  • The Eukarya

life: three-domain classification

Well,the evolutionary relationship of the three domains is the subject of current research by biologists. Originally, archaea were thought to be the most primitive group, whereas bacteria were assumed to be more closely related to the eukaryotes. Studies of rRNA indicate that a universal ancestor split into three lineages. That split led to the Archaea, the Bacteria, and what eventually became the nucleoplasm of the eukaryotes. The oldest known fossils are the remains of prokaryotes that lived more than 3.5 billion years ago. Eukaryotic cells evolved more recently, about 1.4 billion years ago.

A rooted phylogenetic tree resembles a living tree, with a common ancestor indicated as the base of the trunk. Two branches form from the trunk. The left branch leads to the domain Bacteria. The right branch branches again, giving rise to Archaea and Eukarya. Smaller branches within each domain indicate the groups present in that domain.

More recently various fusion hypotheses have begun to dominate the literature. One proposes that the diploid or 2N nature of the eukaryotic genome occurred after the fusion of two haploid or 1N prokaryotic cells. Others propose that the domains Archaea and Eukarya emerged from a common archaeal-eukaryotic ancestor that itself emerged from a member of the domain Bacteria. Some of the evidence behind this hypothesis is based on a “superphylum” of bacteria called PVC, members of which share some characteristics with both archaea and eukaryotes. There is growing evidence that eukaryotes may have originated within a subset of archaea. In any event, it is accepted today that there are three distinct domains of organisms in nature: Bacteria, Archaea, and Eukarya.

The Three Domains- Some Characteristics

Domain Archaea

Archaea, Domain; Archaea, Kingdom; Euryarchaeota, Phylum;...
Domain Archaea

Archaea, (domain Archaea), any of a group of single-celled prokaryotic organisms (that is, organisms whose cells lack a defined nucleus) that have distinct molecular characteristics separating them from bacteria (the other, more prominent group of prokaryotes) as well as from eukaryotes (organisms, including plants and animals, whose cells contain a defined nucleus). Archaea is derived from the Greek word archaios, meaning “ancient” or “primitive,” and indeed some archaea exhibit characteristics worthy of that name. Members of the archaea include: Pyrolobus fumarii, which holds the upper temperature limit for life at 113 °C (235 °F) and was found living in hydrothermal vents; species of Picrophilus, which were isolated from acidic soils in Japan and are the most acid-tolerant organisms known—capable of growth at around pH 0; and the methanogens, which produce methane gas as a metabolic by-product and are found in anaerobic environments, such as in marshes, hot springs, and the guts of animals, including humans.

The Archaea possess the following characteristics:

  1. Archaea are prokaryotic cells.
  2. Unlike the Bacteria and the Eukarya, the Archaea have membranes composed of branched hydrocarbon chains (many also containing rings within the hydrocarbon chains) attached to glycerol by ether linkages.
  3. The cell walls of Archaea contain no peptidoglycan.
  4. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are sensitive to some antibiotics that affect the Eukarya.
  5. Archaea contain rRNA that is unique to the Archaea as indicated by the presence molecular regions distinctly different from the rRNA of Bacteria and Eukarya.

Domain Archaea include three major groups-

  • Methanogens– strict anaerobes that produce methane (CH4) from carbon dioxide and hydrogen.
  • Extreme halophiles– which require high concentratation of salt for survival.
  • Hyperthermophiles– which normally grow in extremely hot environments.

Domain Bacteria

Bacteria are single celled microbes. The cell structure is simpler than that of other organisms as there is no nucleus or membrane bound organelles. Instead their control centre containing the genetic information is contained in a single loop of DNA. Some bacteria have an extra circle of genetic material called a plasmid. The plasmid often contains genes that give the bacterium some advantage over other bacteria. For example it may contain a gene that makes the bacterium resistant to a certain antibiotic.

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Bacteria are found in every habitat on Earth: soil, rock, oceans and even arctic snow. Some live in or on other organisms including plants and animals including humans. There are approximately 10 times as many bacterial cells as human cells in the human body. A lot of these bacterial cells are found lining the digestive system. Some bacteria live in the soil or on dead plant matter where they play an important role in the cycling of nutrients. Some types cause food spoilage and crop damage but others are incredibly useful in the production of fermented foods such as yoghurt and soy sauce. Relatively few bacteria are parasites or pathogens that cause disease in animals and plants.

The Bacteria possess the following characteristics:

a. Bacteria are prokaryotic cells.

b. Like the Eukarya, they have membranes composed of unbranched fatty acid chains attached to glycerol byester linkage.

c. The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain peptidoglycan.

d. Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to most antibiotics that affect Eukarya.

e. Bacteria contain rRNA that is unique to the Bacteria as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Eukarya.

Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-negative bacteria.

Classification of Bacteria on the Basis of Shape

Classification of Bacteria on the Basis of Shape

Bacterial cells can exist as single cells, in pairs, chains or clusters. In the year 1872 scientist Cohn classified bacteria to 4 major types depending on their shapes are as follows:

A) Cocci: These types of bacteria are unicellular, spherical or elliptical shape. Either they may remain as a single cell or may aggregate together for various configurations. They are as follows:

  • Monococcus:– they are also called micrococcus and represented by single, discrete round      Example: Micrococcus flavus.
  • Diplococcus:– the cell of the Diplococcus divides ones in a particular plane and after division, the cells remain attached to each other. Example: Diplococcus pneumonia.
  • Streptococcus: – here the cells divide repeatedly in one plane to form chain of cells. Example: – Streptococcus pyogenes.
  • Tetracoccus: – this consists of four round cells, which defied in two planes at a right angles to one another. Example: – Gaffkya tetragena. Staphylococcus: – here the cells divided into three planes forming a structured like bunches of grapes giving and irregular configuration. Example: – Staphylococcus aureus.
  • Sarcina: -in this case the cells divide in three planes but they form a cube like configuration consisting of eight or sixteen cells but they have a regular shape. Example: –Sarcina lutea.

B) Bacilli: These are rod shaped or cylindrical bacteria which either remain singly or in pairs. Example: Bacillus cereus.

C) Vibro: The vibro are the curved, comma shaped bacteria and represented by a single genus. Example: Vibro cholerae.

D) Spirilla: These type of bacteria are spiral or spring like with multiple curvature and terminal flagella. Example: Spirillum volutans.


Actinomycetes are branching filamentous bacteria, so called because of a fancied resemblance to the radiating rays of the sun when seen in tissue lesions (from actis meaning ray and mykes meaning fungus).

Mycoplasmas are bacteria that are cell wall deficient and hence do not possess a stable morphology. They occur as round or oval bodies and as interlacing filaments.

Domain Eukarya

Coming from the Greek words “eu“, which means “true“, and “karyon” which means, “nut“, the domain Eukarya is composed of organisms having “true nucleus“. The domain Eukarya consists of eukaryotes which are an organism with a true nucleus and every organelle in them is membrane bound. Eukaryotes are made up of cells that have a nucleus and membrane-bound organelles.

Learn Three Domains of Life in 4 minutes.

 The cells of eukaryotes are more complex than the cells of prokaryotes. For this reason, the cells of eukaryotes are usually larger than the cells of prokaryotes.Eukaryotic cells, as their cells are called, are perhaps the most complex in terms of both external and internal structures, and physiological and reproductive process. Among all domains in the biological world, members of the domain Eukarya have the most significant body size and body mass. Some eukaryotes, such as many protists and fungi, are single-celled. Many eukaryotes are multicellular organisms. Some protists and many fungi, plants, and animals are multicellular eukaryotes. Domain Eukarya is made up of all eukaryotes.

Where Did Eukaryotes Come From?

According to various archeological evidences, eukaryotic cells have started to exist more than 0.6 billion years ago. Up until now, their evolution is viewed by many as one of the most unusual events in biological history.

To explain such a bizarre event, scientist Lynn Margulis proposed the so-called “Endosymbiotic Theory“.

  • This theory states that the Mitochondria (the powerhouse of the cell), and the chloroplasts (structure for photosynthesis) were once single-celled organisms that have been engulfed by “proto-eukaryotic” cells.
  • The eukaryotic mitochondria and chloroplasts have a different set of genetic materials as compared to the cell itself. Hence it proves that they were once bacterial cells.
  • Their continuous and maintained symbiosis required both cells to reproduce at the same rate and not to digest each other.
  • As a result, the resulting cells could now produce their energy and fix carbon through the use of light.

The Eukarya possess the following characteristics:

1. Presence of membrane bounded organelles

The eukaryotic cell contains various internal membrane-bound structures referred to as the “organelles“.

  • In cells, the job of organelles is to carry out physiological and metabolic processes that are important for the survival of the cell.
  • Other organelles function for support and motility. Such were the intracellular filaments, cilia, and flagella.

2. Presence of a double membrane nucleus

Unlike other organisms of other domains (which have their genetic material suspended in the cytoplasm), the DNA of eukaryotic organisms is stored in the nucleus.

The nucleus of eukaryotes is surrounded by the nuclear envelope, a double membrane, which has pores to allow the movement of the DNA in and out of it.

3. Cell division is different

Another distinguishing feature of eukaryotes is that they have a different mode of replicating themselves. Instead of merely dividing themselves and copying their genetic materials (like what other domains do), cell division in eukaryotes involves two processes: mitosis and cytokinesis.

  • During mitosis, the nucleus of the cell divides into two while the genetic material, present as chromosomes are equally distributed to each opposite of the cell.
  • Following that step is the cytokinesis, which is when the cytoplasm of the cell divides, developing it the equal division of the genetic material.

4. Mode of reproduction may vary

Eukaryotic cells can reproduce themselves in two ways: asexual (through mitosis) or sexual reproduction (through meiosis).

  • During asexual reproduction, the cell divides through mitosis followed by cytokinesis.
  • On the other hand, they may also reproduce sexually by involving their sex cells called the gametes. In this type of reproduction, the offspring inherits a chromosome from each of its parents.

The Eukarya are subdivided into the following four kingdoms:

  1. Kingdom Protista: Protista are simple, predominately unicellular eukaryotic organisms. Examples includes slime molds, euglenoids, algae, and protozoans.
  2. Kingdom Fungi: Fungi are unicellular or multicellular organisms with eukaryotic cell types. The cells have cell walls but are not organized into tissues. They do not carry out photosynthesis and obtain nutrients through absorption. Examples include sac fungi, club fungi, yeasts, and molds.
  3. Kingdom Plantae: Plants are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and have cell walls. They obtain nutrients by photosynthesis and absorption. Examples include mosses, ferns, conifers, and flowering plants.
  4. Kingdom Animalia: Animals are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and lack cell walls. They do not carry out photosynthesis and obtain nutrients primarily by ingestion. Examples include sponges, worms, insects, and vertebrates.

It used to be thought that the changes that allow microorganisms to adapt to new environments or alter their virulence capabilities was a relatively slow process occurring within an organism primarily through mutations, chromosomal rearrangements, gene deletions and gene duplications. Those changes would then be passed on to that microbe’s progeny and natural selection would occur. This gene transfer from a parent organism to its offspring is called vertical gene transmission.

It is now known that microbial genes are transferred not only vertically from a parent organism to its progeny, but also horizontally to relatives that are only distantly related, e.g., other species and other genera. This latter process is known as horizontal gene transfer. Through mechanisms such as transformation, transduction, and conjugation, genetic elements such as plasmids, transposons, integrons, and even chromosomal DNA can readily be spread from one microorganism to another. As a result, the old three-branched “tree of life” in regard to microorganisms now appears to be more of a “net of life.”

Microbes are known to live in remarkably diverse environments, many of which are extremely harsh. This amazing and rapid adaptability is a result of their ability to quickly modify their repertoire of protein functions by modifying, gaining, or losing their genes. This gene expansion predominantly takes place by horizontal transfer.


  1. Phylogeny refers to the evolutionary relationships between organisms.
  2. Organisms can be classified into one of three domains based on differences in the sequences of nucleotides in the cell’s ribosomal RNAs (rRNA), the cell’s membrane lipid structure, and its sensitivity to antibiotics.
  3. The three domains are the Archaea, the Bacteria, and the Eukarya.
  4. Prokaryotic organisms belong either to the domain Archaea or the domain Bacteria; organisms with eukaryotic cells belong to the domain Eukarya.
  5. Microorganism transfer genes to other microorganisms through horizontal gene transfer – the transfer of DNA to an organism that is not its offspring.

Photo source

  1. The Three Domain System- https://www.britannica.com/science/archaea
  2. Phylogenetic Tree of Life- https://courses.lumenlearning.com/wmopen-nmbiology1/chapter/phylogenetic-trees/
  3. Domain Archaea- https://www.thinglink.com/scene/762535547766833154
  4. Dead Sea- https://www.britannica.com/science/archaea
  5. Domain Bacteria- https://www.shutterstock.com/search/enterica
  6. Shapes of bacteria- https://microbenotes.com/classification-of-bacteria/
  7. Domain Eukarya- https://www.toppr.com/content/story/amp/three-domains-of-life-86033/


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About Armany Arju Lubna

Armany Arju Lubna
A curious girl with many questions.Want to discover life in a different way.And lastly,"Miles to go before i sleep."

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