What are the 3 domains of the 3 domain system

Hypothesis for classification of life

The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990[2][1] that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryote or Eukarya. The key difference from earlier classifications such as the two-empire system and the five-kingdom classification is the splitting of archaea from bacteria as completely different organism. It has been challenged by the two-domain system that divides organisms into Bacteria and Archaea only, as eukaryotes are considered as one group of archaea.[3][4][5]





Woese argued, on the basis of differences in 16S rRNA genes, that bacteria, archaea, and eukaryotes each arose separately from an ancestor with poorly developed genetic machinery, often called a progenote. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. Originally his split of the prokaryotes was into Eubacteria (now Bacteria) and Archaebacteria (now Archaea). Woese initially used the term “kingdom” to refer to the three primary phylogenic groupings, and this nomenclature was widely used until the term “domain” was adopted in 1990.[1]

Acceptance of the validity of Woese’s phylogenetically valid classification was a slow process. Prominent biologists including Salvador Luria and Ernst Mayr objected to his division of the prokaryotes.[6][7] Not all criticism of him was restricted to the scientific level. A decade of labor-intensive oligonucleotide cataloging left him with a reputation as “a crank,” and Woese would go on to be dubbed “Microbiology’s Scarred Revolutionary” by a news article printed in the journal Science in 1997.[8] The growing amount of supporting data led the scientific community to accept the Archaea by the mid-1980s.[9] Today, very few scientists still accept the concept of a unified Prokarya.[10]





The three-domain system adds a level of classification (the domains) “above” the kingdoms present in the previously used five- or six-kingdom systems. This classification system recognizes the fundamental divide between the two prokaryotic groups, insofar as Archaea appear to be more closely related to Eukaryotes than they are to other prokaryotes – bacteria-like organisms with no cell nucleus. The three-domain system sorts the previously known kingdoms into these three domains: Archaea, Bacteria, and Eukarya.[3]

Domain Archaea




The Archaea are prokaryotic, with no nuclear membrane, but with biochemistry and RNA markers that are distinct from bacteria. The Archaeans possess unique, ancient evolutionary history for which they are considered some of the oldest species of organisms on Earth, most notably their diverse, exotic metabolisms.

Some examples of archaeal organisms are:

  • methanogens – which produce the gas methane
  • halophiles – which live in very salty water
  • thermoacidophiles – which thrive in acidic high-temperature water

Domain Bacteria




The Bacteria are also prokaryotic; their domain consists of cells with bacterial rRNA, no nuclear membrane, and whose membranes possess primarily diacyl glycerol diester lipids. Traditionally classified as bacteria, many thrive in the same environments favored by humans, and were the first prokaryotes discovered; they were briefly called the Eubacteria or “true” bacteria when the Archaea were first recognized as a distinct clade.

Most known pathogenic prokaryotic organisms belong to bacteria (see[11] for exceptions). For that reason, and because the Archaea are typically difficult to grow in laboratories, Bacteria are currently studied more extensively than Archaea.

Some examples of bacteria include:

  • “Cyanobacteria” – photosynthesizing bacteria that are related to the chloroplasts of eukaryotic plants and algae
  • Spirochaetota – Gram-negative bacteria that include those causing syphilis and Lyme disease
  • Actinomycetota – Gram-positive bacteria including Bifidobacterium animalis which is present in the human large intestine

Domain Eukarya




Eukarya are organisms whose cells contain a membrane-bound nucleus. They include many large single-celled organisms and all known non-microscopic organisms. A partial list of eukaryotic organisms includes:

Kingdom Fungi or fungi

  • Saccharomycotina – includes true yeasts
  • Basidiomycota – includes mushrooms

Kingdom Plantae or plants

  • Bryophyta – mosses
  • Magnoliophyta – flowering plants

Kingdom Animalia or animals

  • Chordata – includes vertebrates as a subphylum

Kingdom Protista or protozoans

  • Euglenoids – includes euglena as an organism





Each of the three cell types tends to fit into recurring specialities or roles. Bacteria tend to be the most prolific reproducers, at least in moderate environments. Archaeans tend to adapt quickly to extreme environments, such as high temperatures, high acids, high sulfur, etc. This includes adapting to use a wide variety of food sources. Eukaryotes are the most flexible with regard to forming cooperative colonies, such as in multi-cellular organisms, including humans. In fact, the structure of a eukaryote is likely to have derived from a joining of different cell types, forming organelles.

Parakaryon myojinensis (incertae sedis) is a single-celled organism known to be a unique example. “This organism appears to be a life form distinct from prokaryotes and eukaryotes”,[12] with features of both.





Alternative versions of the three domains of life’s phylogeny

Parts of the three-domain theory have been challenged by scientists including Ernst Mayr, Thomas Cavalier-Smith, and Radhey S. Gupta.[13][14][15]

Recent work has proposed that Eukarya may have actually branched off from the domain Archaea. According to Spang et al. Lokiarchaeota forms a monophyletic group with eukaryotes in phylogenomic analyses. The associated genomes also encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities.[16] This work suggests a two-domain system as opposed to the three-domain system.[4][5][3] Exactly how and when archaea, bacteria, and eucarya developed and how they are related continues to be debated.[17][3][18]

See also








The Three Domain System, developed by Carl Woese in 1990, is a system for classifying biological organisms.

Before Woese’s discovery of archaea as distinct from bacteria in 1977, scientists believed there were only two types of life: eukarya and bacteria.

The highest ranking previously used had been “kingdom,” based on the Five Kingdom system adopted in the late 1960s. This classification system model is based on principles developed by Swedish scientist Carolus Linnaeus, whose hierarchical system groups organisms based on common physical characteristics.

The Current System

As scientists learn more about organisms, classification systems change. Genetic sequencing has given researchers a whole new way of analyzing relationships between organisms.

The current Three Domain System groups organisms primarily based on differences in ribosomal RNA (rRNA) structure. Ribosomal RNA is a molecular building block for ribosomes.

Under this system, organisms are classified into three domains and six kingdoms. The domains are

  • Archaea
  • Bacteria
  • Eukarya

The kingdoms are

  • Archaebacteria (ancient bacteria)
  • Eubacteria (true bacteria)
  • Protista
  • Fungi
  • Plantae
  • Animalia

Archaea Domain

This Archaea domain contains single-celled organisms. Archaea have genes that are similar to both bacteria and eukaryotes. Because they are very similar to bacteria in appearance, they were originally mistaken for bacteria.

Like bacteria, archaea are prokaryotic organisms and do not have a membrane-bound nucleus. They also lack internal cell organelles and many are about the same size as and similar in shape to bacteria. Archaea reproduce by binary fission, have one circular chromosome, and use flagella to move around in their environment as do bacteria.

Archaea differ from bacteria in cell wall composition and differ from both bacteria and eukaryotes in membrane composition and rRNA type. These differences are substantial enough to warrant that archaea have a separate domain.

Archaea are extreme organisms that live under some of the most extreme environmental conditions. This includes within hydrothermal vents, acidic springs, and under Arctic ice. Archaea are divided into three main phyla: Crenarchaeota, Euryarchaeota, and Korarchaeota.

  • Crenarchaeota include many organisms that are hyperthermophiles and thermoacidophiles. These archaea thrive in environments with great temperature extremes (hyperthermophiles) and in extremely hot and acidic environments (thermoacidophiles.)
  • Archaea known as methanogens are of the Euryarchaeota phylum. They produce methane as a byproduct of metabolism and require an oxygen-free environment.
  • Little is known about Korarchaeota archaea as few species have been found living in places such as hot springs, hydrothermal vents, and obsidian pools.

Bacteria Domain

Bacteria are classified under the Bacteria Domain. These organisms are generally feared because some are pathogenic and capable of causing disease.

However, bacteria are essential to life as some are part of the human microbiota. These bacteria preform vital functions, such as enabling us to properly digest and absorb nutrients from the foods we eat. Bacteria that live on the skin prevent pathogenic microbes from colonizing the area and also aid in the activation of the immune system.

Bacteria are also important for the recycling of nutrients in the global ecosystem as they are primary decomposers.

Bacteria have a unique cell wall composition and rRNA type. They are grouped into five main categories:

  • Proteobacteria: This phylum contains the largest group of bacteria and includes E.coli, Salmonella, Heliobacter pylori, and Vibrio. bacteria.
  • Cyanobacteria: These bacteria are capable of photosynthesis. They are also known as blue-green algae because of their color.
  • Firmicutes: These gram-positive bacteria include Clostridium, Bacillus, and mycoplasmas (bacteria without cell walls.)
  • Chlamydiae: These parasitic bacteria reproduce inside their host’s cells. Organisms include Chlamydia trachomatis (causes chlamydia STD) and Chlamydophila pneumoniae (causes pneumonia.)
  • Spirochetes: These corkscrew-shaped bacteria exhibit a unique twisting motion. Examples include Borrelia burgdorferi (cause Lyme disease) and Treponema pallidum (cause syphilis.)

Eukarya Domain

The Eukarya domain includes eukaryotes or organisms that have a membrane-bound nucleus.

This domain is further subdivided into the kingdoms

  • Protista
  • Fungi
  • Plantae
  • Animalia

Eukaryotes have rRNA that is distinct from bacteria and archaeans. Plant and fungi organisms contain cell walls that are different in composition than bacteria. Eukaryotic cells are typically resistant to antibacterial antibiotics.

Organisms in this domain include protists, fungi, plants, and animals. Examples include algae, amoeba, fungi, molds, yeast, ferns, mosses, flowering plants, sponges, insects, and mammals.

Comparison of Classification Systems

Systems for classifying organisms change with new discoveries made over time. The earliest systems recognized only two kingdoms (plant and animal.) The current Three Domain System is the best organizational system we have now, but as new information is gained, a different system for classifying organisms may later be developed.

Here is how the Five Kingdom System compares to the Three Domain System, which has six kingdoms:

Five Kingdom System:

  • Monera
  • Protista
  • Fungi
  • Plantae
  • Animalia

Archaea DomainBacteria DomainEukarya DomainArchaebacteria KingdomEubacteria KingdomProtista KingdomFungi KingdomPlantae KingdomAnimalia KingdomThree Domain System



Your Citation

Bailey, Regina. “Three Domain System.” ThoughtCo, Sep. 7, 2021, thoughtco.com/three-domain-system-373413.

Bailey, Regina. (2021, September 7). Three Domain System. Retrieved from https://www.thoughtco.com/three-domain-system-373413

Bailey, Regina. “Three Domain System.” ThoughtCo. https://www.thoughtco.com/three-domain-system-373413 (accessed November 23, 2022).

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Written by Jane