The classification of life into three domains—Bacteria, Archaea, and Eukarya—established that the microscopic world of single-celled organisms is far more diverse than previously thought. Previously, Bacteria and Archaea were grouped simply as prokaryotes, defined by their shared lack of a membrane-bound nucleus and internal organelles. Deep molecular analysis of their ribosomal RNA genes revealed that these two groups represent fundamentally distinct evolutionary lineages. Understanding the differences between these two domains is necessary for comprehending the full spectrum of microbial life on Earth. Both domains consist of single-celled organisms that are structurally simple, yet their underlying biochemistry, genetic mechanisms, and ecological roles are profoundly varied.
Cellular Architecture and Composition
A key difference between the two domains lies in the composition of the cell envelope, the protective layers surrounding the cell. Bacterial cell walls are defined by the presence of peptidoglycan, a sturdy meshwork of sugars and amino acids. This polymer provides structural integrity and resistance to osmotic pressure, making it a definitive characteristic of the domain Bacteria.
Archaea completely lack peptidoglycan in their cell walls, a feature that distinguishes them biochemically from Bacteria. Instead, they utilize a diverse range of materials for their outer layer, which may include S-layers (paracrystalline surface layers of proteins or glycoproteins), various polysaccharides, or pseudopeptidoglycan. Pseudopeptidoglycan is similar in function to the bacterial version but is composed of different sugars and linkages, rendering it immune to the enzymes that break down bacterial cell walls.
The composition of the cell membrane lipids also represents a deep evolutionary split. Bacterial and eukaryotic membranes are built from fatty acids linked to glycerol via ester bonds to form a standard lipid bilayer. Archaea possess lipid chains constructed from repeating isoprene units, attached to glycerol using a chemically distinct ether bond. This ether linkage is significantly more stable than the ester bond, contributing directly to the survival of many Archaea in harsh environments.
In addition to the bond type, the arrangement of these lipids differs. Archaeal membranes sometimes consist of a single lipid monolayer rather than the typical bilayer structure found in Bacteria and Eukarya. In this monolayer, the isoprenoid chains span the entire width of the membrane, fusing the two sides and providing exceptional rigidity and stability under extreme conditions of heat or acidity. This molecular variation highlights a fundamental divergence in their ancestry and adaptation strategies.
Genetic Processing and Replication
The processes of transcription and translation reveal that Archaea share surprising similarities with Eukarya, despite their prokaryotic cell structure. The enzyme responsible for transcribing DNA into RNA, RNA Polymerase (RNAP), is a single, relatively simple molecule in Bacteria, composed of four main protein subunits. The archaeal RNAP is a much more complex machine, featuring multiple subunits that are structurally analogous to the complex RNAP found in Eukarya.
This complexity extends to how transcription is initiated, the process of starting gene expression. Bacteria rely on simple protein subunits called sigma factors to guide their single RNAP to the correct starting point on the DNA. Archaea, mirroring the eukaryotic system, utilize a suite of sophisticated general transcription factors, specifically a TATA-binding protein (TBP) and Transcription Factor B (TFB), to assemble the initiation complex. These factors are required to recruit the complex RNAP to the promoter region, a mechanism analogous to the eukaryotic method.
Further genetic differences appear in the structure of the genes themselves. While Bacteria generally have continuous coding sequences, some Archaea possess non-coding DNA segments within their genes, known as introns. These introns must be removed through a splicing process before the messenger RNA can be translated into protein, a feature that is common in Eukarya but almost entirely absent in Bacteria. The cellular machinery for protein synthesis, the ribosome, also shows subtle structural variations between the two domains, despite both possessing a 70S size.
Habitat and Metabolic Strategies
The architectural and genetic differences between the domains have allowed them to colonize vastly different ecological niches and develop unique ways of sustaining life. Bacteria are ubiquitous, thriving in virtually every conceivable habitat on Earth, from soil and water to the inside of other organisms, including humans. Archaea were initially studied primarily as extremophiles, organisms that flourish in environmental conditions considered hostile to most life.
Many Archaea are hyperthermophiles that inhabit boiling hot springs or deep-sea hydrothermal vents, while halophiles thrive in highly saline environments like salt lakes, and acidophiles grow in extremely acidic waters. This ability to withstand environmental stress is directly linked to the enhanced stability provided by their ether-linked membrane lipids and unique cell wall components. Although many Archaea are extremophiles, they are also abundant in non-extreme environments, including oceans and soil.
The metabolic pathways utilized by the two domains show a profound divergence in energy generation. Methanogenesis, the biological production of methane gas, is a unique characteristic of certain groups of Archaea known as methanogens. These organisms are obligate anaerobes that generate energy by reducing one-carbon compounds into methane. This process does not occur as an energy-conserving pathway in any known Bacteria.
The relationship of each domain to larger organisms provides a stark contrast. The domain Bacteria includes countless species that are human, animal, or plant pathogens, causing infectious diseases. Archaea are generally considered to be non-pathogenic to humans. While they are part of the human microbiome, any association with disease is typically indirect, influencing the environment to favor pathogenic bacterial species.