1.5: The Tree of Life – Bacteria, Archaea, Eukaryotes

The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both extant and extinct, are organized into three domains: bacteria, archaea, and eukaryotes. However, the distinctions between these domains and the classification of organisms is debated continuously, resulting in a ‘living’ tree of life that changes as more information is uncovered.

The History of the Tree of Life

The tree of life, itself, has evolved, much like the organisms it contains. Shortly after Charles Darwin published On the Origin of Species in 1859, Ernst Haeckel proposed three “kingdoms” of life: plants, animals, and protists - which were simply organisms that were neither plant nor animal. The distinctions between these kingdoms were based entirely on easily observable phenotypes.

In 1937 Edouard Chatton divided the tree of life into two vast ‘empires’ instead: eukaryotes and prokaryotes. Simply put, the eukaryotes possessed membrane-bound nuclei, and the prokaryotes did not. During the 1970’s, Woese found that a group under the bacteria classification, called archaea, differed from the bacteria in several ways: an absence of peptidoglycan in their cell walls, differences in coenzymes, and differences in their 16S rRNA gene sequence. All of these differences suggested that archaea originated from a line of descent separate from bacteria.

The Three Domains of Life

The modern tree of life consists of three ‘branches’: bacteria, archaea, and eukaryotes. The domain bacteria consists of unicellular, prokaryotic organisms that lack a membrane-bound nucleus. Bacteria can take many shapes, from spherical cocci to rod-shaped bacilli. Members of this domain are found in almost every place on Earth, including on and in the human body.

Similar to bacteria, archaea are also unicellular, prokaryotic organisms. Phenotypically, archaea are very difficult to differentiate from bacteria. At the molecular level, archaea resemble eukaryotes in terms of their machinery for replication, transcription, and translation. However, archaea resemble bacteria in terms of metabolism and energy conversion. Archaea are often found in the most inhospitable of habitats: bogs, wastewater treatment plants, the deepest parts of the ocean, and hot acid springs.

Charles Darwin famously compared the evolutionary relationships between different species to the branches of a tree, all originating from a common ancestor.

Historically, an organism’s position on the tree was simply determined based upon its observable characteristics or phenotype, such as the presence of leaves, a spine, or eyes.

Extinct species could be placed on the tree in a similar fashion – using phenotypic traits preserved in the fossil record.

Shortly after Darwin published On the Origin of Species, Haeckel proposed three ‘kingdoms’ of life in 1866, plants, animals, and protists – which were neither plant nor animal - based on easily observable phenotypes.

Eventually, the distinction between plants and animals was found to be less important than previously proposed.

Thus, in 1937, the tree of life evolved to contain two large ‘empires’ – the eukaryotes with membrane-bound nuclei and the prokaryotes without.

This paradigm, however, resulted in some difficulty when it came to placing prokaryotes on the tree: one rod-shaped microbe is phenotypically hard to distinguish from another.

Advancements in genetic analysis, particularly 16S rRNA sequencing, soon toppled this tree when organisms traditionally classed together as prokaryotes were found to have genetically divergent evolutionary origins.

So, the tree of life evolved once more in 1990 and the prokaryotes were divided into two domains - giving us the three domains of the modern tree of life: bacteria, archaea, and eukaryotes.

The first of these domains, bacteria, consists of unicellular, prokaryotic organisms that lack a membrane-bound nucleus.

The next domain, archaea, is also made up of unicellular, prokaryotic organisms distinguished from bacteria by their unique evolutionary history.

Finally, the eukaryotes consist of uni- and multicellular organisms distinguished by their membrane-bound nucleus. This domain includes fungi, plants, and animals.

The evolutionary tree of life, much like an actual tree, is a ‘living’ metaphor and the classification of many organisms, even the distinction between archaea and bacteria, is often contested and occasionally changed.