Bacteria and archaea are two fundamental and distinct domains of life. Both are single-celled organisms that lack a true nucleus and other membrane-bound organelles. Despite these shared prokaryotic characteristics, bacteria and archaea exhibit profound differences in their underlying biology, separating them into two distinct evolutionary lineages.
Cellular Structure and Composition
Significant distinctions exist in the cellular architecture and chemical makeup of bacteria and archaea. The cell membranes of bacteria are primarily composed of lipids with fatty acids linked to glycerol by ester bonds. These fatty acids often vary in length and saturation, contributing to membrane fluidity. In contrast, archaeal cell membranes feature lipids with phytanyl chains attached to glycerol by ether bonds, which are chemically more stable. Some archaea even possess unique lipid monolayers instead of the typical bilayers, providing increased stability in extreme conditions.
The cell wall, a protective layer outside the cell membrane, also varies considerably between the two domains. Bacterial cell walls are characterized by the presence of peptidoglycan, a complex polymer made of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) sugars cross-linked by short peptide chains. This peptidoglycan layer provides structural strength and maintains cell shape. Archaea, however, do not possess peptidoglycan in their cell walls. Instead, their cell walls are structurally diverse, often composed of S-layers, which are crystalline arrays of proteins or glycoproteins, or in some cases, pseudopeptidoglycan, polysaccharides, or various proteins.
Genetic Processes and Machinery
Differences in the machinery responsible for genetic processes further highlight the divergence between bacteria and archaea. Both typically house their primary genetic material as a single circular chromosome located in a region called the nucleoid, and many also contain smaller, circular DNA molecules known as plasmids. However, the enzymes involved in transcribing genetic information differ markedly.
Bacterial RNA polymerase, the enzyme that synthesizes RNA from a DNA template, is a relatively simple structure composed of four polypeptides. Archaeal RNA polymerase, conversely, is more complex, consisting of eight or more polypeptides. Its structure and function bear a closer resemblance to RNA polymerase II found in eukaryotes, indicating a shared evolutionary heritage.
Similarly, while both organisms possess 70S ribosomes for protein synthesis, archaeal ribosomes exhibit structural and sequence similarities to eukaryotic ribosomes, despite their prokaryotic size. The initiation of protein synthesis also differs, with bacteria using formyl-methionine as the initiator transfer RNA, whereas archaea use methionine, similar to eukaryotes.
Metabolic Pathways and Habitats
The metabolic diversity and preferred habitats of bacteria and archaea also show distinct patterns. Bacteria exhibit a vast array of metabolic capabilities, including photosynthesis, nitrogen fixation, and various forms of respiration. This allows them to thrive in nearly every environment on Earth, participating in nutrient cycling and decomposition.
Archaea are particularly recognized for their ability to inhabit extreme environments. These include hot springs, hydrothermal vents with temperatures exceeding 100°C, highly saline environments, and acidic conditions.
A unique metabolic process found only in some archaea is methanogenesis, where they produce methane as a byproduct of their energy metabolism in anaerobic conditions. This adaptation allows archaea to exploit ecological niches unavailable to most other life forms.
Evolutionary History and Classification
The recognition of bacteria and archaea as separate domains of life is a significant outcome of molecular biology. Early classifications grouped all single-celled organisms without a nucleus into a single category called prokaryotes. However, in the late 1970s, pioneering work by Carl Woese and colleagues, primarily through the analysis of ribosomal RNA (rRNA) gene sequences, revealed profound genetic differences.
This molecular evidence demonstrated that archaea were as genetically distinct from bacteria as they were from eukaryotes, leading to the establishment of the three-domain system: Bacteria, Archaea, and Eukarya. This classification suggests that while all life shares a last universal common ancestor, the bacterial and archaeal lineages diverged very early in Earth’s history. Their unique molecular and metabolic characteristics reflect this deep evolutionary separation, rather than superficial similarities based on their simple cellular structure.