Archaea

You have probably seen images of the colorful hot springs in Yellowstone National Park. The orange, yellow, pink, or red coloration is given by the microorganisms that live in these extremely hot and acidic environments. Most of these microorganisms are archaea, single-cell organisms that resemble bacteria but are actually more related to you! We describe the archaea traits that allow them to live in these harsh environments and make them unique, the similarities with bacteria and eukaryotes, and why they are important to understand our own origins.

Prokaryotes: Archaea and Bacteria

Despite the great diversity of life forms on earth and the enormous number of species, we currently classify all of them into two major groups based on the type of cell that forms an organism: the prokaryotes and the eukaryotes.

• Prokaryotes consist mostly of single-cell organisms formed by relatively simple prokaryotic cells,
• while eukaryotes include single-cell, colonial, and multicellular organisms formed by more complex eukaryotic cells.

Thus, archaea have the four features found in all cells: plasma membrane, cytoplasm, ribosomes, and DNA. They also have the general features of prokaryotic cells: DNA organized in a single circular strain of DNA, not enclosed but only concentrated in a region called a nucleoid, absence of organelles surrounded by a membrane, and they can have a cell wall externally surrounding the cell membrane. They can also have appendices that serve in locomotion.

Archaea definition

Until the 1970s archaea were thought to be bacteria, due to the similarities in general structure and appearance and because they were much less studied than bacteria. Then in 1977, Woese and Fox used the 16s ribosomal RNA (rRNA) gene, a molecular marker that helps to determine evolutionary relationships among organisms, and found that several of these “bacterial microorganisms” were actually more closely related to eukaryotes than to bacteria. Later studies revealed that archaea do share some traits with bacteria and others with eukaryotes, while also having unique characteristics.

Fig. 1: Scanning electron microscopic image of Metanohalophilus mahii strain SLP.

Archaea characteristics

Prior to being classified as Archaea, one of the characteristics that initially led to putting these organisms as a different type of bacteria was the observation that many archaea are extremophiles.

They live in environments with extreme conditions. While some bacteria can also live in extreme environments, archaea are most commonly found under these conditions and are the only ones found in the most extreme habitats.

Archaea structure and composition

Cell membrane: archaeal membranes have a similar structure to bacterial and eukaryote ones but have important differences in composition:

• Archaea membranes can be composed of a phospholipid bilayer (two layers of lipid molecules, like bacteria and eukaryotes) or have monolayers, only one layer of lipids (the tails of opposing phospholipids are fused). The monolayer might be a key to survival at high temperatures and/or extremely low acidity².

• They have isoprene chains as the side chains in membrane phospholipids instead of fatty acids.

• The isoprene chains are linked to the glycerol molecule by an ether linkage (it has only one oxygen atom, bound to the glycerol) instead of an ester linkage (it has two oxygen atoms attached, one bound to the glycerol, one sticking out from the molecule).

• Some of the isoprene chains have side branches, that enable the main chain to curl upon itself and form a ring, or to join with another main chain. It is thought that these rings give more stability to membranes, especially in extreme environments. Fatty acids do not form side branches.

• Archaea can have one or more appendages similar to flagella for movement. However, they are structurally different from bacterial and eukaryotic flagella.

Fig. 2: Archaeal membrane structure and composition. Top: archaeal membrane: 1-isoprene sidechain, 2-ether linkage, 3-L-glycerol, 4-phosphate molecule. Medium: bacterial and eukaryotic membrane: 5-fatty acid, 6-ester linkage, 7-D-glycerol, 8-phosphate molecule. Bottom: 9-lipid bilayer in bacteria, eukarya and most archaea, 10-lipid monolayer in some archaea.

Cell wall: there are four types of archaeal cell walls, but unlike bacteria, none have peptidoglycan. They can be composed of:

• pseudopeptidoglycan (similar to peptidoglycan but with different sugars in the polysaccharide chains),
• polysaccharides,
• glycoproteins,
• or only protein.

Archaea nutritional modes

Archaea can use a wide variety of energy and carbon sources, as prokaryotes in general do. They can be photoheterotrophs (use light as an energy source and break down organic molecules to obtain carbon), chemoautotrophs, or chemoheterotrophs (both use chemical sources of energy, but the autotrophs use inorganic sources for carbon, like CO₂, and heterotrophs break down organic molecules).

Archaea distribution

Although many archaea are lovers of extreme conditions, it was later found that the group is actually widely distributed and is also found in more normal environments (like soil, lake sediments, sewage, and the open ocean) as well as associated with a host. While some archaea are just really good for tolerating these conditions, the more extreme ones have a specific cell composition that can only function properly in these extreme conditions. Archaea can live in extreme environments such as habitats with high salinity (hyperhalophiles or extreme halophiles), temperature (hyperthermophiles or extreme thermophiles), acidity (acidophiles), or a mix of these conditions.

Fig. 3: Aerial view of Grand Prismatic Spring, Yellowstone National Park. The brilliant orange color in the border is given by microorganisms including bacteria and archaea.

They are part of the microbial community (which includes bacteria, fungi, and protists) that live in animal guts, especially in herbivores (cattle, termites, and others), but have also been found in humans.

Archaea examples

Let's see some examples of archaeal species and their main traits^2,3,4:

Table 1: Examples of archaeal organisms and description of some of their traits.

Source: Schäfer, 1999; Bräsen et al. 2014, and Kim, 2020.

Importance of Archaea

Archaea, like bacteria, are a vital part of the carbon and nitrogen cycles. As chemoautotrophs, they convert these inorganic compounds to ways readily available for other organisms that would not be able to reuse them otherwise. Methane is also a key compound in the biogeochemical cycle of carbon and, as mentioned earlier, the only organisms capable of producing methane are methanogenic archaea.

Archaea are also being subject of numerous evolutionary studies, as it is an important key in the origin of eukaryotes. The most accepted hypothesis (the endosymbiosis theory) indicates that eukaryotes originated from the fusion of an ancestral Archaean organism (or closely related to archaea) and an ancestral bacterium that eventually evolved into the organelle mitochondrion.

Archaea vs Bacteria vs Eukaryotes

We summarize the main similarities and differences between Archaea and the two other domains of life in table 2^6,7. As mentioned, Archaea share many prokaryotic traits with Bacteria. However, note how the machinery for genetic information processing (replication, transcription, and translation), represented here by tRNA and RNA polymerase types and ribosome composition, is more closely related to Eukarya.