Two of the three domains of life are classified as prokaryotes: Bacteria and Archaea. The third domain, Eukarya, includes all organisms whose cells contain a nucleus, from single-celled protists to plants, fungi, and animals. Despite sharing the prokaryotic label, Bacteria and Archaea are fundamentally different from each other in their genetics, biochemistry, and evolutionary history.
What Makes a Cell Prokaryotic
The word prokaryote means “before nucleus,” and that single feature defines the group. Prokaryotic cells have no membrane-bound nucleus. Their DNA floats in the main compartment of the cell rather than being sealed off in its own envelope. They also lack the internal membrane-bound compartments (organelles) that eukaryotic cells use to separate different chemical tasks.
Beyond the missing nucleus, prokaryotic cells share several structural traits. Their ribosomes, the molecular machines that build proteins, are smaller than those in eukaryotic cells (measured at 70S compared to the 80S ribosomes in eukaryotes). Their genomes are typically organized as circular chromosomes packed into a region called the nucleoid, and their genes are often bundled into units called operons, where several related genes are read and regulated together. The average operon contains three to four genes, and this arrangement lets the cell coordinate the production of proteins that work together.
One important caveat: “prokaryote” is a label of convenience, not a true evolutionary group. Bacteria and Archaea don’t share a single exclusive common ancestor that excludes eukaryotes. The two domains evolved separately, and their similarities reflect a shared simplicity rather than a close family relationship.
Domain Bacteria
Bacteria are the most abundant and diverse organisms on Earth, found in every habitat from deep ocean vents to the human gut. A defining chemical feature of bacterial cells is peptidoglycan, a mesh-like polymer that forms the structural backbone of their cell walls. This material acts like a pressure-resistant cage, preventing the cell from bursting due to water flowing in through osmosis.
Bacteria are broadly split into two structural types based on their cell walls. Gram-positive bacteria have thick peptidoglycan layers (30 to 100 nanometers) threaded with long, charged polymers called teichoic acids. Gram-negative bacteria have only a thin peptidoglycan layer but compensate with an additional outer membrane containing a molecule called lipopolysaccharide. This structural difference affects everything from how bacteria respond to antibiotics to how the immune system detects them.
Metabolically, bacteria are remarkably versatile. Some harvest energy from sunlight, others from inorganic chemicals like ammonia or sulfur compounds. Bacteria are the only organisms capable of true autotrophy through direct oxidation of inorganic compounds without sunlight. They also drive critical processes in the global nitrogen cycle, including nitrogen fixation (converting atmospheric nitrogen into a form plants can use), nitrification, and denitrification.
Domain Archaea
Archaea were not recognized as a separate domain until 1977, when Carl Woese and George Fox compared sequences of ribosomal RNA across microorganisms and discovered that some “bacteria” were genetically as different from true bacteria as either group was from eukaryotes. This finding was formalized into the three-domain system in the early 1990s, after more than 1,500 species of Bacteria and Archaea had been characterized by ribosomal RNA sequencing.
The most striking biochemical difference between Archaea and Bacteria is in their cell membranes. Bacterial and eukaryotic membranes are built from lipids linked together by ester bonds. Archaeal membranes use ether bonds instead, which are far more resistant to heat, mechanical stress, and high salt concentrations. Some heat-loving and acid-loving archaea go further, producing lipids that span the entire membrane to form a rigid single layer rather than the usual double layer. This makes their membranes nearly impermeable to ions, which is a major advantage in boiling hot springs or extremely acidic pools.
Archaea are subdivided into several major groups: the Euryarchaeota (which include methane-producing archaea and extreme salt lovers), the TACK superphylum (which includes heat-loving crenarchaeotes and ammonia-oxidizing thaumarchaeotes), the DPANN superphylum (very small-celled archaea, many of which depend on other microbes to survive), and the recently discovered Asgardarchaeota, which have attracted enormous attention because they appear to be the closest living relatives of eukaryotes.
Methane production, or methanogenesis, is an exclusively archaeal process. Methanogens are among the most oxygen-sensitive organisms known and thrive in environments like waterlogged soils, animal digestive tracts, and deep sediments. They use carbon dioxide as a final destination for electrons during energy production, releasing methane gas as a byproduct.
How Archaea Blur the Line With Eukaryotes
Despite being prokaryotes by cell structure, archaea share surprising molecular similarities with eukaryotes. Their RNA polymerase, the enzyme that reads DNA and produces RNA copies, closely resembles the version found in eukaryotic cells in both its architecture and the number of protein subunits it contains. Bacteria use a simpler version of this enzyme and rely on a completely different set of helper proteins (sigma factors) to start reading genes. Archaea instead use initiation factors that are direct counterparts of the ones eukaryotes use.
This pattern extends to other parts of the gene-reading and protein-building machinery. When archaeal RNA polymerase stalls or makes an error, it uses a cleavage factor closely related to the one eukaryotes use, while bacteria solve the same problem with an entirely unrelated protein. These molecular parallels suggest that the eukaryotic information-processing system evolved from an archaeal ancestor rather than being invented from scratch.
Some researchers now advocate a “two-domain” model of life rather than three. Under this hypothesis, eukaryotes arose from within a diversified archaeal lineage, specifically from a group related to the Asgardarchaeota. Analyses of combined ribosomal RNA datasets have produced evolutionary trees consistent with this view, placing certain archaea as the direct sister group of eukaryotes. If this model holds, there would be only two primary branches of life: Bacteria and a larger group that includes Archaea and all eukaryotes nested within it.
Bacteria vs. Archaea at a Glance
- Cell wall: Bacteria build walls from peptidoglycan. Most archaea lack peptidoglycan entirely, using other polymers instead.
- Membrane chemistry: Bacteria use ester-linked lipids. Archaea use ether-linked lipids, which are more heat and acid resistant.
- Gene-reading machinery: Bacteria use a simple RNA polymerase with sigma factors. Archaea use a complex, multi-subunit RNA polymerase with eukaryote-like initiation factors.
- Habitats: Both domains are found everywhere, but archaea dominate the most extreme environments, including superheated vents, hypersaline lakes, and highly acidic springs.
- Unique metabolisms: Nitrogen fixation is found in bacteria. Methanogenesis is exclusive to archaea.