Three Domain Classification

Introduction:

From Carl Linnaeus’s two-kingdom classification(plant kingdom and animal kingdom) to Robert Whittaker’s five kingdom classification(kingdom monera, kingdom Protista, kingdom fungi, kingdom Plantae and kingdom Animalia), we have come a long way. Scientists have broadened our spectrum of vision for the world we live in. Icing to the cake is the three-domain system by Carl Woese. In the year 1990, Carl Woese introduced the three-domain system. The three-domain system is actually a three-domain and six kingdom classification. It is also called Carl Woese’s classification, after the scientist who devised this idea.

What was the basis of this classification?

Carl Woese took into consideration three factors that led to the division of the living world into three domains and six kingdoms. The three factors were

• 16s rRNA(Ribosomal RNA) structure: He primarily argued on the differences in the nucleotide sequences in the 16sRNA as one’s genetic sequence says much about how different and how closely related we are to our ancestors

But why only 16s rRNA?

• It is universally present in all species
• Although, it is different in all species. But it is functionally similar. That makes it suitable for classification
• The 16s rRNA undergoes mutation very slowly
• The nucleotide sequences in 16s rRNA can be aligned for matching up between two organisms
• Cell’s membrane lipid structure and organism’s sensitivity to antibiotics: He took into consideration the cell membrane and sensitivity to antibiotics. As modern-day microbiology uses gram stain to stain the cell membrane, to divide bacteria into gram-positive and gram-negative organisms. Also, many modern-day antibiotics work primarily on the bacteria’s cell membrane

Classification

Every living organism on the earth can be classified into 7 levels, those are kingdom, phylum, class, order, family, genus and species. Carl Woese added another level to this, that is the domain. He first classified the entire living world into three domains and six kingdoms.

The three domains were:

• Domain Archaea
• Domain Bacteria
• Domain Eukarya

The six kingdoms were:

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

Robert Whittaker’s five kingdom classification included domain archaea and domain bacteria in a single kingdom, that is monera. If they are all bacterias, then why did Carl Woese distinguish them into two different domains? It is indeed true that domain archaea and domain bacteria primarily consist of bacteria, which are all prokaryotes. Like all other prokaryotes, they lack a nuclear membrane, but they were distinguished based on their biochemistry and RNA markers. Their distinct genetic material and unique metabolism are the reason why scientists believe these to be one of the oldest organisms on the planet. Some organisms included in this domain are:

• Methanogens: These are methane-producing organisms, they produce methane through a process called methanogenesis. The process of methanogenesis requires a completely anaerobic environment, hence these organisms are obligate anaerobes(organisms that live in the complete absence of oxygen). Based on their methanogenesis, they’re divided into two groups:
• Obligate chemolithotrophic methanogens: They utilize CO₂ and H₂ to produce methane.
• Methylotrophic methanogens: They utilize methyl-group-containing compounds to produce methane. Like methanol, acetate, etc.

These organisms are found in the digestive tract of herbivores, marshes, and lake bottoms. And also in sewage treatment plants where the anaerobic condition is artificially made.

• Thermoacidophiles: As the name suggests, heat(thermos) and acid-loving(philes). These are the organisms that prefer living in extremely hot and acidic waters like hot springs and deeper parts of the ocean. These are facultative anaerobes(they can live both in aerobic as well as the anaerobic environments), but they need sulfur for their metabolism.
• Halophiles: The term halophiles is a Greek word where halos mean salt and philes mean loving. These are organisms that can thrive in extremely high salt concentrations. They require NaCl concentrations between 15-35% to thrive. Based on their salt tolerating capacity they are further divided into:
• Slightly halophilic or halotolerant
• Moderate halophiles
• Extreme halophiles
• Domain Bacteria

These are also the prokaryotes with no nuclear membrane, but with a genetic sequence distinct from that of domain archaea. Carl Woese also took into consideration the cell membrane while devising the three-domain classification. Organisms in the domain bacteria possess diacyl glycerol diester lipids in their cell membrane, which is absent in organisms of the domain archaea whereas these contain phytanyl. Organisms belonging to the domain bacteria are also referred to as eubacteria or true bacteria. These were the first prokaryotes to be discovered by humans. Most pathogens that cause infections in the human body belong to this group.

• Domain Eukarya

The domain Eukarya consists of everything, but the Monerans from Robert Whittaker’s five kingdom classification. That is kingdom Protista, kingdom Fungi, kingdom Plantae and kingdom Animalia. While Robert Whittaker segregated them based on cell structure, body organization, and certain other factors, Carl Woese united them all under one roof that is Domain Eukarya. Phylogenetically, these were the first organisms to have a nuclear membrane and other membrane-bound organelles. These were named eukaryotes, in contrast to prokaryotes which possessed the primitive cell type. It has three kingdoms:

• Kingdom Fungi: This kingdom includes organisms like yeasts, molds and mushrooms. Based on their method of reproduction, they were further divided into four classes. Those are:
• Phycomycetes
• Ascomycetes
• Basidiomycetes
• Deuteromycetes
• Kingdom Plantae: This kingdom includes all the plants that we see around us. From the big banyan tree(Ficus benghalensis) to the lotus(Nelumbo nucifera), all of them belong to the kingdom Plantae.
• Kingdom Animalia: This kingdom consists of all the animals.

Conclusion

The biological world is all about mysteries and possibilities. No one in the 17th-18th century ever imagined organisms living their life with just a single cell, till the father of microscopy, Antonie van Leeuwenhoek saw them through the eyepiece of his microscope. After more than a hundred years, a third kingdom was brought to light. Today we know about organisms that can survive even in the harshest of environments like hot springs and marshes. You never know, if 100 years down the line a new kingdom would be introduced that would entirely change our view about the world we live in.