Two of the three domains of life are prokaryotic: Bacteria and Archaea. The third domain, Eukarya, includes all organisms whose cells contain a nucleus, from single-celled protists to plants, fungi, and animals. Bacteria and Archaea share the fundamental trait of lacking a nucleus, but they differ from each other in surprising and significant ways.
The Three-Domain System
All life on Earth falls into three domains: Bacteria, Archaea, and Eukarya. This classification system was established by Carl Woese and George Fox in 1977, based on comparisons of a specific component of ribosomal RNA that acts as a molecular fingerprint for evolutionary relationships. Before their work, scientists grouped all prokaryotes together as a single category. The ribosomal RNA analysis revealed that Archaea are so genetically distinct from Bacteria that they deserve their own domain entirely. The formal three-domain system wasn’t widely accepted until the early 1990s.
What Makes a Cell Prokaryotic
Prokaryotic cells are defined by what they lack. They have no nucleus, so their DNA floats in a region of the cell called the nucleoid rather than being sealed inside a membrane-bound compartment. They also lack the internal organelles found in eukaryotic cells. Both Bacteria and Archaea are single-celled, typically carry a single circular chromosome, and reproduce asexually through binary fission, where one cell copies its DNA and splits into two identical daughter cells.
Both domains also have smaller ribosomes than eukaryotes. Prokaryotic ribosomes measure 70S (a unit of size based on how fast they settle in a centrifuge), compared to the larger 80S ribosomes in eukaryotic cells. This size difference is actually the reason certain antibiotics can target bacterial infections without harming human cells. Nearly all prokaryotes also have a cell wall outside their membrane, which helps them survive in harsh or rapidly changing conditions.
How Bacteria and Archaea Differ
Despite looking similar under a microscope, Bacteria and Archaea are as genetically different from each other as either is from Eukarya. The differences show up at the molecular level in ways that matter.
Their cell walls are built from completely different materials. Bacteria use a mesh-like molecule called peptidoglycan, made of sugar chains cross-linked by short chains of amino acids. Archaea lack peptidoglycan entirely. Some archaeal species, particularly methane-producing ones, build their walls from a lookalike called pseudomurein, which has a similar structure but different chemical building blocks, including different sugars and only the left-handed forms of amino acids (bacteria use unusual right-handed forms in their peptidoglycan).
Their cell membranes are also fundamentally different. Bacterial membranes are made of fatty acids attached to a glycerol backbone through ester bonds. Archaeal membranes use branching, chain-like molecules called isoprenoids attached through ether bonds instead. This difference runs so deep that scientists still debate whether the last common ancestor of all life had one membrane type or the other. The ether-linked membranes of archaea tend to be more stable at extreme temperatures and pH levels, which helps explain why so many archaea thrive in extreme environments.
Archaea’s Genetic Machinery Resembles Eukarya
One of the most surprising findings about Archaea is that their gene-reading machinery looks far more like that of complex eukaryotic cells than like Bacteria. The enzyme archaea use to copy DNA into RNA is composed of 11 to 13 subunits that closely match those of the equivalent enzyme in eukaryotes. Bacteria use a much simpler version.
Archaea also use eukaryotic-style promoter elements, the DNA sequences that signal where to start reading a gene. They rely on proteins called TBP and TFB that are direct counterparts to the proteins eukaryotic cells use. Bacteria, by contrast, use a completely different system involving sigma factors. Some archaea even package their DNA with histone proteins, creating a structured DNA landscape similar to what’s found in human cells. This mosaic of bacterial and eukaryotic traits makes archaea a fascinating window into how complex life may have evolved.
Where Prokaryotes Live
Bacteria are found in virtually every environment on Earth and are the most abundant life form on the planet. Current estimates suggest the Earth harbors roughly one trillion microbial species, with 99.999% still undiscovered. Bacteria dominate most of these niches, from soil and oceans to the human body.
Archaea are famous for thriving in extreme environments, though they also live in more moderate habitats. Some archaea hold the records for life at the limits: one species grows at 122°C (252°F), the highest temperature recorded for any organism, while another can grow at a pH of 0.06, more acidic than battery acid. Prokaryotes have been found 6.7 kilometers deep in the Earth’s crust and more than 10 kilometers deep in the ocean. Archaea include the most extreme heat-lovers, acid-lovers, alkali-lovers, and salt-lovers known to science. Among bacteria, cyanobacteria are the most versatile extremophiles, tolerating high salt, high metal concentrations, and desert-dry conditions, though they rarely survive in highly acidic environments below pH 5.
Prokaryotes in the Human Body
Your gut microbiome is overwhelmingly bacterial, but archaea are there too. Studies find archaea in every human gut sample tested, though they make up a small fraction of the total prokaryotic community, ranging from as little as 0.001% to about 7.2%. The dominant archaea in the human gut are methane producers, with one species being the most common in the majority of people sampled. These methanogens consume hydrogen and carbon dioxide produced by bacterial fermentation and release methane as a byproduct. They’re thought to help regulate the overall balance of the gut microbial ecosystem by removing hydrogen, which can otherwise slow down bacterial fermentation.
How Prokaryotes Share Genes
Beyond simple cell division, prokaryotes have a powerful trick that eukaryotes largely lack: horizontal gene transfer. This is the ability to pass genes sideways to unrelated organisms, not just downward to offspring. It happens through three main routes. In transformation, a bacterium picks up free-floating DNA fragments from dead cells in its environment and incorporates them into its own chromosome. In transduction, a virus accidentally packages a piece of bacterial DNA and delivers it to a new cell. In conjugation, two living bacteria make physical contact, often through a tiny bridge-like structure, and one transfers a copy of a DNA segment to the other.
Horizontal gene transfer is a major reason bacteria can adapt so quickly to new threats, including antibiotics. A resistance gene that evolves in one species can spread to entirely unrelated species through any of these three mechanisms, which is why antibiotic resistance can move through bacterial populations much faster than you’d expect from simple mutation alone.