The classification of life on Earth is organized into three domains: Bacteria, Archaea, and Eukarya. Both Bacteria and Archaea are single-celled organisms that lack a nucleus and other membrane-bound internal structures, leading to their collective grouping as prokaryotes. However, their superficial resemblance is misleading, as they represent distinct evolutionary lineages that diverged billions of years ago. A closer examination of their internal machinery and physical structures reveals fundamental biological distinctions. These differences, particularly in their cellular walls, genetic processes, and unique metabolism, separate them into two ancient and separate domains of life.
Fundamental Cellular Architecture
The cell wall of nearly all Bacteria contains a complex polymer called peptidoglycan, which provides structural integrity and protection against osmotic pressure. Peptidoglycan is a unique molecular structure composed of sugar chains cross-linked by short peptides.
Archaea completely lack peptidoglycan in their cell walls. Instead, they utilize a variety of other materials for structural support, such as pseudopeptidoglycan, which is chemically different but structurally similar to the bacterial version. Other archaeal species use a layer of protein or glycoprotein known as an S-layer. This difference in cell wall composition is a major factor in the vulnerability of Bacteria to certain antibiotics that target peptidoglycan synthesis, while Archaea remain unaffected.
Another defining difference is found in the composition of the cell membrane lipids. Bacterial membranes are constructed from fatty acids linked to a glycerol backbone by an ester bond, typically forming a lipid bilayer. This type of linkage is also found in the membranes of Eukaryotes.
The lipids in the archaeal membrane are distinct, featuring phytanyl chains, which are branched hydrocarbons, linked to glycerol via an ether bond. This ether linkage is significantly more chemically stable than the ester linkage found in Bacteria, providing exceptional resilience. Furthermore, these unique lipids can form a single, fused monolayer structure rather than a bilayer. This structure is thought to contribute to the ability of many Archaea to survive in extremely high temperatures.
Genetic and Transcriptional Mechanisms
The differences between the two domains extend deep into the cell, affecting the very machinery that manages and expresses genetic information. Transcription, the process of copying DNA into RNA, is managed by an enzyme called RNA polymerase. Bacterial cells possess a relatively simple RNA polymerase made up of four protein subunits.
The RNA polymerase found in Archaea is far more complex, consisting of multiple subunits that often number between eight and twelve. This complex structure closely resembles the RNA Polymerase II used by Eukaryotes, which transcribes messenger RNA. The process of initiating transcription in Archaea also mirrors that of Eukaryotes, relying on basal transcription factors, whereas Bacteria use a specialized sigma factor.
Another genetic distinction is the presence of non-coding sequences, or introns, within the genes of some archaeal species. Introns are genetic segments that must be removed from the initial RNA transcript before a protein can be made. This process is common in Eukaryotes but is generally absent in Bacteria. The existence of these splicing mechanisms in Archaea further highlights their evolutionary kinship with the Eukaryotic domain.
The initial step of protein synthesis, known as translation, also features a difference in the initiating amino acid used to start the polypeptide chain. Bacteria begin the synthesis of all their proteins with the modified amino acid Formylmethionine. In contrast, Archaea use the unmodified amino acid Methionine to start protein production, a feature they share with Eukaryotes. These molecular differences in transcription and translation support the view that Archaea are genetically closer to Eukaryotes than they are to Bacteria.
Metabolic Diversity and Habitat
The distinct cellular structures and genetic mechanisms of Archaea enable them to inhabit environments that would be lethal to most other life forms, including Bacteria. Bacteria are geographically pervasive, found in virtually every habitat on the planet, from soil and water to the human body, and show a vast metabolic diversity. While Archaea are also found in many common environments, a significant number are classified as extremophiles, thriving in conditions such as boiling hot springs, highly acidic waters, and super-salty lakes.
These extremophiles include halophiles, which require extremely high salt concentrations, and thermophiles, which grow optimally at temperatures well above 80 degrees Celsius. The exceptional stability of the archaeal ether-linked membrane lipids is thought to be a factor that permits their survival under these harsh physical conditions. This ability to tolerate environmental extremes represents a major ecological difference between the domains.
The metabolic capabilities of Archaea also include a unique process not found in any Bacteria: methanogenesis. Methanogens are a group of Archaea that produce methane gas as a byproduct of their energy metabolism under strictly anaerobic conditions. This process is a fundamental part of the global carbon cycle, occurring in environments such as wetlands, the digestive tracts of ruminant animals, and deep-sea hydrothermal vents.