Differences between Archaea and Bacteria

Archaea vs. Bacteria

Archaea and Bacteria are two of the three primary domains of life, alongside Eukarya. Both consist of single-celled prokaryotic organisms, meaning they lack a cell nucleus and other membrane-bound organelles. For many years, archaea were classified as bacteria. However, research beginning in the 1970s revealed that archaea have a distinct evolutionary history and biochemistry. Genetic analysis of ribosomal RNA (rRNA) shows that archaea and bacteria are separate lineages. In fact, archaea share a more recent common ancestor with eukaryotes than with bacteria.

While they appear similar in size and shape under a microscope, their fundamental cellular and genetic structures exhibit key differences. These distinctions are significant enough to place them in separate domains in the tree of life.

Comparison Table

Category	Archaea	Bacteria
Cell Wall	Composed of pseudopeptidoglycan or other substances; lacks peptidoglycan.	Contains peptidoglycan.
Cell Membrane Lipids	Glycerol-ether lipids with branched isoprenoid chains; can form monolayers.	Glycerol-ester lipids with unbranched fatty acid chains; bilayer only.
RNA Polymerase	One complex type, similar to eukaryotes, with multiple subunits (10+).	One simple type with fewer subunits (around 4).
Genetic Material	Chromosomes contain introns, and DNA is associated with histone-like proteins.	Introns are absent from chromosomes, and DNA is not associated with histones.
Metabolism	Diverse pathways; methanogenesis (methane production) is unique to some archaea. No chlorophyll-based photosynthesis.	Diverse pathways, including glycolysis and chlorophyll-based photosynthesis.
Reproduction	Asexual reproduction through fission, budding, or fragmentation. No spores are formed.	Primarily asexual fission; some species can form dormant endospores.
Habitat	Often found in extreme environments (extremophiles) such as hot springs, salt lakes, and deep-sea vents, but also present in moderate habitats.	Ubiquitous, found in soil, water, and living on or inside other organisms.
Pathogenicity	No known human pathogens.	Some species are pathogenic and can cause disease.

Venn diagram comparing Differences between Archaea and Bacteria

Cellular Composition

The most fundamental differences between archaea and bacteria are found in the composition of their cell wall and cell membrane. Bacterial cell walls contain peptidoglycan, a polymer of sugars and amino acids that provides structural integrity. This substance is absent in archaea. Instead, their cell walls may be composed of pseudopeptidoglycan or various proteins and polysaccharides.

The lipids that form the cell membrane also differ significantly. In bacteria, unbranched fatty acid chains are linked to glycerol by ester bonds. In archaea, branched isoprenoid chains are linked to glycerol by ether bonds. This chemical difference makes archaeal membranes more stable in the extreme environments they often inhabit. Some archaea possess a lipid monolayer instead of the bilayer found in bacteria and eukaryotes.

Genetics and Metabolism

At the genetic level, archaea show more similarities to eukaryotes than to bacteria. Archaeal DNA is associated with histone proteins, which help to package the DNA, a feature shared with eukaryotes but not bacteria. Furthermore, archaeal genes contain introns, which are non-coding DNA sequences that are removed before protein synthesis; introns are absent in bacteria. The enzymes involved in reading the genetic code (transcription and translation) in archaea are also more closely related to their eukaryotic counterparts.

Metabolically, both groups are diverse. Bacteria utilize well-known pathways like glycolysis for energy. While some archaea use modified versions of these pathways, they also possess unique metabolic capabilities. A notable example is methanogenesis, the production of methane, which is a process found only among certain archaea and plays a significant role in the global carbon cycle. While some bacteria are photosynthetic and produce oxygen, no known archaea perform chlorophyll-based photosynthesis.