ARCHAEA DOMAIN: ORIGIN, CHARACTERISTICS, CLASSIFICATION, NUTRITION - BIOLOGY - 2025

The archaea domain or archaea kingdom represents one of the three domains of life. It is composed of microscopic unicellular prokaryotic organisms very similar and at the same time very different from bacteria and eukaryotes in many respects.

The existence of this group was demonstrated a short time ago, more or less in the late 1970s, by a group of researchers led by Carl Woese, who considered that life could be divided into eukaryotes and two types of prokaryotic organisms: bacteria and archaea, also called archaebacteria.

"Morning Glory" hot springs in Yellowstone National Park, USA, whose color is given by archaea (Source: ZYjacklin via Wikimedia Commons) The studies by Woese and collaborators were based on comparative phylogenetic analyzes between the ribosomal RNA sequences of all the living beings, and the notion of the three domains is maintained, despite the immense quantity of sequences that continues to be added to ribosomal RNA catalogs (databases).

These studies managed to glimpse the possibility that archaea are a sister group to eukaryotes, despite their similarities with their prokaryotic counterparts (bacteria), so they could represent the "missing link" between prokaryotes and eukaryotes.

Although few are those who are dedicated to the study of archaea and this group is quite ignored by many students of biology, it is believed that these microorganisms represent more than 20% of all prokaryotes existing in oceanic waters, between 1 and 1 5% in soils, and the most dominant group in marine sediments and geothermal habitats.

In addition, archaea are characterized by living in "extreme" conditions such as hot springs, salines, environments with very high temperatures and very acidic pH, inhospitable places where the oxygen concentration is very low or null, etc.

These microorganisms are of great ecological importance as they participate in many of the biogeochemical cycles, contributing to the carbon, nitrogen and sulfur cycle, for example.

Evolutionary origin and phylogenetic relationships

There are three theories about the possible origin of the three domains of life proposed by Woese and colleagues:

1. Bacteria diverged first, forming a lineage that produced archaea and eukaryotes.
2. A "proto-eukaryotic" lineage diverged from a completely prokaryotic lineage (that of bacteria and archaea)
3. Archaea diverged from a lineage that later gave rise to eukaryotes and bacteria

In 1989, two researchers, Gogarten and Iwabe, independently proposed a way to analyze all living organisms phylogenetically (which is impossible to do from single gene sequence studies).

Iwabe used the analysis of the sequences of genes produced in "early" events of gene duplication, "rooting" the tree of life from the comparison of the sequence of the paralogue genes that encode elongation factors.

Elongation factors are GTP-binding proteins that participate in translation, specifically in the binding of amyoacylated transfer RNA molecules to ribosomes and in the translocation of peptidyl transfer RNA.

According to the results of the comparisons between the sequences of the three groups, the genes that code for the elongation factors in archaea are more similar to those of eukaryotic organisms than to those of bacteria.

The tree of life (Source: File: Collapsed tree labels simplified.png The original uploader was TimVickers at English Wikipedia.Translation to galician by Elisardojm via Wikimedia Commons) Gogarten, on the other hand, compared the sequences of other genes produced by events of duplication, specifically of those that code for the type V and type F subunits of the ATPase enzyme found in archaea / eukaryotes and bacteria, respectively.

The results obtained by Gogarten, like those noted above, demonstrate that these genes in archaea (which presumably arose from genetic duplication events) are more closely related to eukaryotes than to their bacterial counterparts.

These arguments were also supported by the analysis conducted by other researchers many years later, who used sequences from another family of duplicated genes, that of the aminoacyl synthetases transfer RNAs, strengthening the conception of the "closeness" between archaea and eukaryotes.

Woese's tree

Woese's Tree of Life

Woese used the analyzes carried out by Gogarten and Iwabe and other studies related to ribosomal RNA sequences to propose his “version” of the tree of life, where it becomes clear that archaea and eukaryotes constitute “sister” groups, separate from the ones. bacteria even though the ribosomal RNA sequences between archaea and bacteria are more similar to each other.

General characteristics of the archaea domain

Archaea are known for some very particular characteristics (their own) and also for presenting "combinations" of characteristics that were once thought to be exclusive to bacteria or eukaryotic organisms.

- Like bacteria, archaea are prokaryotic organisms, that is, inside the genetic material is not enclosed by a membrane (they do not have a nucleus) and there are no membranous cytoplasmic organelles.

- Generally, they are microorganisms of a similar size to bacteria, their DNA is in the form of a circular chromosome and some smaller circular fragments known as plasmids.

- They share the presence of similar topoisomerase and gyrase enzymes with bacteria, which represents “indirect” evidence of the “closeness” in terms of the chromosomal structure of both groups of organisms.

- However, archaea genes show great homology with many eukaryotic genes, especially those whose discovery derives from studies with antibiotics.

- The machinery for replication, transcription and translation of eukaryotes and archaea is very similar, especially with regard to the DNA polymerase enzyme.

- Their genes coding for proteins do not have introns (but others do), otherwise the eukaryotic genes. Furthermore, archaea have histone-like proteins associated with their DNA, present in eukaryotes and absent in bacteria.

- They are characterized by the presence of isoprenyl ether-lipids in their cell membranes, as well as by the absence of acyl-ester lipids and a fatty acid synthetase.

- One of the subunits of its RNA polymerase enzyme is divided and its messenger RNAs, as in bacteria, do not have “hoods” (from English cap) at their 5 'ends.

- They have a very specific range of sensitivity to antibiotics and have type II restriction enzymes very similar to those that have been described for bacteria.

- Another important characteristic has to do with the fact that a large part of archaea have a cell wall, but unlike bacteria, this is not composed of peptidoglycan.

Characteristics of its membrane lipids

The membrane lipids of archaea differ considerably from those found in bacteria and eukaryotic organisms, and this has been considered a very important differential characteristic.

The main difference between these amphipathic molecules (with a hydrophilic polar end and a hydrophobic apolar one) is that the bond between the glycerol portion and the fatty acid chains in archaea lipids is through an ether bond, while in the bacteria and eukaryotes corresponds to an ester bond.

Another important difference is that archaea have lipids with fatty acids characterized by the presence of highly branched isoprenyl chains with methyl groups, while eukaryotes and bacteria have predominantly unbranched chain fatty acids.

The lipids of eukaryotes and bacteria are "built" on a glycerol backbone to which the fatty acid chains are esterified at the positions corresponding to carbon atoms 1 and 2, but in archaea glycerol ethers contain acids fatty in positions 2 and 3.

Another difference with respect to membrane lipids has to do with their biosynthetic pathway, since some enzymes are also different in archaea.

For example, some species of archaea have a bifunctional prenyl transferase enzyme, which is responsible for providing the precursors both for the synthesis of squalene and for the synthesis of glyceryl-lipid isoprenoids. In bacteria and eukaryotes these functions are carried out by separate enzymes.

Classification of archaea

According to the data of the sequences of the small subunits of the ribosomal RNAs of the archaea, this group has been divided mainly into two "phyla", which are known as the phylum Crenarchaeota and the phylum Euryarchaeota, whose members are, above all, archaea grown in vitro.

However, many of the recently described archaea have not been cultured in vitro and are only distantly related to sequences that have been isolated from species maintained in laboratories.

Phylum Crenarchaeota

This group is mainly formed by species of hyperthermophilic and thermoacidophilic archaea, that is, those genus of archaea that inhabit inhospitable environments with extreme thermal and pH conditions.

It is composed of a single taxonomic class, known as Thermoprotei, within which are the following five taxonomic orders: Acidilobales, Desulfurococcales, Fervidicoccales, Sulfolobales and Thermoproteales.

Examples of some of the genera belonging to said classes can be the genera Sulfolobus, Desulforococcus, Pyrodictium, Thermoproteus and Thermofilum.

Phylum Euryarchaeota

The members of this group have a somewhat broader ecological range, being able to be found in it some hyperthermophilic, methanogenic, halophilic and even thermophilic methanogenic species, denitrifying archaea, sulfur reducing, iron oxidizing and some organotrophs.

The taxonomic classes described for Euriarcheotes are eight and are known as Methanopyri, Methanococci, Methanobacteria, Methanomicrobia, Archaeglobi, Halobacteria, Thermococci and Thermoplasmata.

Many of the archaea belonging to this group are widely distributed, found in soils, sediments and marine waters, as well as in the extreme environments described.

Phylum Thaumarchaeota

This phylum was defined relatively recently and very few of the species belonging to it have been cultivated in vitro, so little is known about these organisms.

All the members of the cutting edge obtain their energy from the oxidation of ammonia and are distributed globally in bodies of fresh water, soils, sediments and thermal waters.

Phyla Korarchaeota , Aigarchaeota and Goarchaeota

Some researchers skilled in the art, based on the analysis of genomic sequences, have recently determined the existence of three additional phyla in the kingdom Archaea, although the species proposed for these phyla have not yet been isolated in a laboratory.

In general, members of these phyla have been found under the surface of many terrestrial and marine ecosystems, but also in hot springs and deep sea hydrothermal systems.

Nutrition

Most species of archaea with chemotrophic organisms, that is, they are capable of using highly reduced inorganic compounds to get the energy they need to "move" their metabolic machinery, especially that which has to do with respiration.

The "specificity" for the inorganic molecules that they use as substrates to produce energy depends on the environment where each particular species develops.

Other archaea, as well as plants, algae, bryophytes and cyanobacteria, are capable of photosynthesis, that is, they use and convert the light energy of the sun's rays into usable chemical energy.

Some archaea have been shown to inhabit the stomach (rumen) of some ruminant animals (among which are cows, sheep, goats, etc.), which is why these are classified as "mutualistic archaea", since they consume part of the fiber that these animals ingest and collaborate with the digestion of some of its components.

Reproduction

Like bacteria, archaea are single-celled organisms whose reproduction is exclusively asexual. The main mechanisms described from the species maintained in vitro are:

- Binary fission, where each arch is "split" in half to create two identical cells

- Budding or "fragmentation", where cells shed "fragments" or "portions" of themselves that are capable of forming new, genetically identical cells.

Habitat

Archaea have been mainly related to “extreme” environments, that is, those natural places that impose serious restrictions for the normal development of living beings, especially in terms of temperature, pH, salinity, anaerobiosis (absence of oxygen), etc.; which is why their study is extremely interesting, as they have unique adaptations.

However, the most recent molecular analysis techniques for the identification of non-cultured microorganism species (isolated and kept in vitro in a laboratory) have made it possible to detect the presence of archaea in such everyday environments as the soil, the rumen of some animals, ocean waters and lakes, among others.

However, most of the archaea that have been identified in nature are classified according to the habitat they occupy, the terms "hyperthermophiles", "acidophiles" and "extreme thermoacidophiles", "extreme halophiles" are familiar in the literature. and "methanogens".

The environments occupied by hyperthermophilic archaea are those characterized by very high constant temperatures (well above the "normal" temperatures to which most living beings are subjected).

The environments where extreme acidophiles live, on the other hand, are those where the pH is very low and these can also be distinguished by high temperatures (extreme thermoacidophils), meanwhile the environments of extreme halophiles are those where the concentration of salts is very high.

Methanogenic archaea live in the absence of oxygen or anaerobiosis, in environments where they can use other molecules as electron acceptors in their metabolism and are capable of producing methane as a metabolic "waste" product.

Examples of archaea species

There are numerous known species of archaea, but only a few of them will be mentioned here.

Ignicoccus hospitalis and Nanoarchaeum equitans

I. hospitalis belongs to the genus of crenarqueotes known as Ignicoccus and is a chemolithoautotrophic organism that uses molecular hydrogen as an electron donor for sulfur reduction. This species has the smallest genome of all the archaea described in vitro so far.

I. hospitalis behaves like a "parasite" or "symbiont" of another species: Nanoarchaeum equitans. The latter has not been cultured in vitro and its genome is the smallest of all the uncultured archaea that have been described.

It lives mainly in marine environments and does not have genes for lipid, amino acid, nucleotide or cofactor biosynthesis, so experimental evidence suggests that it obtains these molecules thanks to its interaction with I. hospitalis.

Acidilobus saccharovorans

This is a species of thermoacidophilic anaerobic archaea, that is, it lives in poor environments or completely devoid of oxygen, with high temperatures and extremely low pH. It was first found in terrestrial hot spring bodies in Kamchatka.

Staphylothermus hellenicus

This archa belongs to the edge of the Crenarqueotas, specifically to the Desulfurococcales order. It is a hyperthermophilic heterotrophic archaea (it lives in very hot environments) and requires sulfur for energy.

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