The classification system for life on Earth reflects the deepest splits in evolutionary history. At the highest level of organization are the domains of life, a rank above the traditional kingdom classification. This system changed how scientists view the diversity and relationships among all organisms. All cellular life forms are grouped into three distinct domains: Bacteria, Archaea, and Eukarya.
The Shift in Biological Classification
The three-domain system significantly changed the older five-kingdom model, which lacked the resolution to classify microscopic life. American microbiologist Carl Woese proposed this new classification in the late 1970s, basing the framework on genetic evidence rather than physical appearance. The division was established by comparing the sequences of ribosomal RNA (rRNA), specifically the 16S subunit, a molecule found in all cells. Sequencing this conserved molecule revealed fundamental molecular differences among groups previously lumped together as simple microbes.
Domain Bacteria
Domain Bacteria encompasses a vast and diverse group of single-celled organisms, all of which are prokaryotes. Their cells lack an organized nucleus and other internal membrane-bound structures. A defining characteristic is their cell wall composition, which is largely made of the unique polymer peptidoglycan. This macromolecule forms a mesh-like layer surrounding the cell membrane, providing mechanical strength and protecting the cell from osmotic pressure. Bacteria perform ecologically important functions, such as nitrogen fixation, producing oxygen through photosynthesis (cyanobacteria), and acting as both pathogens and crucial components of the human microbiome.
Domain Archaea
Domain Archaea members are also prokaryotes, but they are genetically and biochemically distinct from Bacteria. Their cell membranes are a primary distinction, as their lipids feature ether linkages to glycerol, contrasting with the ester linkages found in Bacteria and Eukarya. Furthermore, Archaea lack peptidoglycan in their cell walls, often possessing cell walls made of proteins or a similar polymer called pseudopeptidoglycan. These structural features allow many species to thrive as extremophiles in environments with high temperatures, salinity, or acidity, though they are also abundant in moderate habitats like soils and oceans.
Domain Eukarya
The Domain Eukarya contains all organisms whose cells are defined by the presence of a true, membrane-bound nucleus housing the genetic material. Eukaryotic cells also contain a complex network of internal membrane-bound organelles, such as mitochondria and chloroplasts, which compartmentalize cellular functions. These cells are typically much larger and more structurally complex than those of the other two domains. This domain includes the four familiar kingdoms: Animalia, Plantae, Fungi, and the diverse, mostly unicellular Protista.
Tracing the Evolutionary Tree
Molecular sequencing techniques revealed that the three domains represent the deepest evolutionary divergence points in life’s history. Phylogenetic analysis of ribosomal RNA sequences indicates that all life evolved from a single common ancestor, with Bacteria diverging earliest. Evidence suggests that Archaea and Eukarya share a more recent common ancestor with each other than either does with Bacteria. This shared ancestry is reflected because the genetic machinery for processes like transcription and translation in Archaea more closely resemble those in Eukarya. The resulting “Tree of Life” model shows that the two prokaryotic domains, Bacteria and Archaea, are two separate, ancient evolutionary lineages, not one unified group.