Historically, all single-celled organisms without a membrane-bound nucleus were grouped into a single category known as prokaryotes. This classification was based on the simple physical structure visible under a microscope. However, groundbreaking molecular analysis of ribosomal RNA in the 1970s revealed that this single group actually consisted of two fundamentally distinct life forms: Bacteria and Archaea. The discovery, championed by Carl Woese, necessitated the creation of the three-domain system of life—Archaea, Bacteria, and Eukarya. The genetic and biochemical differences between the two prokaryotic groups were profound, justifying their separation into entirely different domains.
The Shared Prokaryotic Blueprint
Both Archaea and Bacteria are microscopic, single-celled organisms that share a basic cellular architecture lacking the internal compartmentalization seen in eukaryotic cells. They both function without a true, membrane-enclosed nucleus, which is the defining characteristic of a prokaryote. This means their genetic material is typically contained within a region of the cytoplasm known as the nucleoid.
The genetic information in both domains is usually organized into a single, circular chromosome of double-stranded DNA. Many species also possess smaller, independently replicating circular DNA molecules called plasmids. Furthermore, they reproduce asexually through binary fission, where a single cell grows and divides into two identical daughter cells.
Defining Chemical Differences (Cell Walls and Membranes)
The most fundamental distinctions between the two domains lie in the chemical composition of their cell envelopes, particularly the cell wall and the plasma membrane. Bacterial cell walls are uniquely characterized by the presence of peptidoglycan, a complex polymer composed of sugar chains cross-linked by short peptides. This rigid layer provides structural integrity and protection against osmotic pressure, and its composition is used to classify bacteria through the Gram stain.
Archaea completely lack peptidoglycan in their cell walls. Instead, some archaeal species have a similar structure called pseudopeptidoglycan, while others use a cell wall made of protein sheets or polysaccharides. The plasma membrane lipids also show a profound difference in chemical bonding. Bacterial lipids are constructed from fatty acids attached to a glycerol molecule by an ester bond, similar to those found in Eukarya.
The cell membranes of Archaea are distinctly built from long, branched hydrocarbon chains, derived from isoprene units, that are linked to glycerol via an ether bond. This ether linkage is chemically more stable than the ester bond and contributes to the ability of many Archaea to withstand extreme temperatures and harsh chemical environments. Additionally, some archaeal membranes form a lipid monolayer instead of a bilayer, providing greater structural stability.
Genetic and Transcription Machinery
The machinery that handles genetic information also separates the two domains, with Archaea exhibiting a surprising similarity to Eukarya. Bacteria possess a relatively simple RNA Polymerase (RNAP), the enzyme responsible for transcribing DNA into RNA, which is composed of only four polypeptide subunits. This simplicity contrasts sharply with the archaeal RNAP, which is a complex enzyme made up of multiple polypeptide subunits, often more than eight, resembling the structure of the eukaryotic RNAP II.
This complexity suggests that Archaea and Eukarya share a more recent common ancestor than either does with Bacteria. Further evidence lies in the organization of the DNA itself. While bacterial DNA is relatively “naked,” the DNA of Archaea is often wrapped around specialized proteins called histones, a feature once thought to be exclusive to Eukarya. The presence of non-coding DNA segments, known as introns, within the genes of some Archaea is another eukaryotic-like trait that is rare or absent in Bacteria.
Specialized Habitats and Metabolism
The unique characteristics of Archaea allow them to thrive in environments that are hostile to most other life forms, leading to their initial classification as extremophiles. While they are also found in common environments like soil and the ocean, a significant number of Archaea inhabit extreme conditions such as highly saline lakes, acidic hot springs, or deep-sea hydrothermal vents. The stability conferred by their ether-linked lipids is an adaptation for survival in these high-temperature or high-salt habitats.
Bacteria, although immensely diverse and found almost everywhere, generally do not exhibit the same tolerance for such extremes. Metabolically, Archaea possess one unique pathway not found in any other domain: methanogenesis, the production of methane gas as a metabolic byproduct. This process is carried out exclusively by methanogenic Archaea and is a significant component of the global carbon cycle in anaerobic environments. Conversely, Bacteria are known for their vast and varied metabolic pathways, including oxygen-generating photosynthesis, a process not performed by Archaea.