Archaebacteria: Definition And Examples

by Daniel Nelson

Archaebacteria are similar in form to bacteria, but they are different from the normal bacteria that biologists often study. In fact, the differences between regular bacteria and archaebacteria are so great that they are classified apart from other forms of life and have challenged the way scientists classify life into different kingdoms.

Though archaebacteria and a regular bacteria were once considered part of the same kingdom, molecular biology and genetics have shown that these prokaryotic organisms have many unique features that merit their own branch on the phylogenetic tree of life.

Halobacteria, an example of archaea. Photo: By NASA – en:Image:Halobacteria.jpg(Taken from [1]), Public Domain, https://commons.wikimedia.org/w/index.php?curid=2979987

Some texts will refer to these organisms as archaea rather than archaebacteria, to make the distinction between them and bacteria more clear, and there is some disagreement about the exact terms used to classify archaea – whether or not they should be called archaea or archaebacteria. This article will use the terms interchangeably.

The Classification Of Archaea

Photo: Sting via Wikimedia Commons, Public Domain

One of the ways that scientists categorize life forms is by dividing them into different kingdoms, which are based on the cell structure of the organism. The different kingdoms include Fungi, Planitia, Animalia, Protista, and Monera. The kingdom Protista contained single-celled eukaryotic organisms while the kingdom Monera was believed to encompass all different varieties of prokaryotic organisms.

However, biochemical and genetic studies of bacteria have shown that certain types of prokaryotes, those referred to as a “archaebacteria”, have unique biochemistry that places them on their own section of the tree of life. The name of archaebacteria comes from the root “archaea”: meaning “ancient”, which reflects the hypothesis that modern archaebacteria have descended from ancient populations of bacteria which evolved to thrive in the sulfur-rich, high-temperature environments surrounding deep-sea vents.

Due to advances in biochemistry and genetics, the phylogenetic tree of life contains a new order of classification, the concept of domains. Domains encompass an even larger section of life than kingdoms do. Under the system of domains, all eukaryotic organisms including protists, fungi, plants, and animals are considered part of the Eukaryota domain. Meanwhile, most bacteria fall under the domain “eubacteria“. Finally, the domain of “archaea” belongs entirely to archaea/archaebacteria.

Archaebacteria Theories

The study of the unique biochemistry possessed by archaebacteria could give researchers more insight into how life worked during ancient, primordial times. Some scientists hypothesize that archaebacteria such as the bacteria Thermoplasma could be the predecessors of the nuclei found within the cells of eukaryotes, having evolved into nuclei through a process known as endosymbiosis.

Archaea are often found in hot springs as well as around hydrothermal vents. Photo: ZYjacklin via Wikimedia Commons, Public Domain

Archaea have the ability to not only survive, but thrive, in environments most other organisms would not be able to live in. These include high-temperature environments, highly acidic environments, and high salt environments. The bacteria can potentially survive temperatures as high as 190°F, and substances with acidity as high as 0.9 pH.

Beyond this, archaebacteria engage in horizontal gene transfer quite frequently. Horizontal gene transfer is when one individual transfers a gene to another individual within the lifetimes of those individuals. This makes it difficult to precisely determine how closely archaebacteria cells are related to one another. In fact, it’s difficult to ascertain if the bacteria even have the kinds of stable traits that a biologist might typically use to classify a species. For this reason, archaebacteria have challenged the traditional methods of species classification.

Traits Of Archaebacteria

The ancient cells that comprise archaea/archaebacteria display a number of traits or attributes not present in more modern types of cells. Eukaryotes and regular bacteria have cell membranes composed of ester-linked phospholipids, but in the case of archaebacteria, their cell membranes are made out of ether-linked phospholipids. Archaea create their cell membranes with a sugar that is different from the peptidoglycan sugar which composes the cells of traditional bacteria, though the sugar used by archae is similar in composition.

While archaebacteria have a single round chromosome like regular bacteria, their method of genes transcription is different from that of most other bacteria. Rather, gene transcription in archaebacteria is more like the transcription that happens in eukaryotic cells. In other words, gene transcription methods are similar in between archaea and eukarya, and the creation of the cell membrane is most similar in bacteria and archaea. This strange reflection of gene transcription and cell membrane creation methods has led some biologists to theorize that the evolution of eukaryotic cells was driven by the fusion of bacteria and archaebacteria.

Archaea may have merged with a different form of bacteria at one point and began living inside that bacterial cell in an example of a symbiotic relationship, eventually transforming into the nuclei that are present in the cells of other organisms, the cells eukaryotes have today. An organism known as Lokiarcheota may be evidence of this evolutionary path, representing a transitional form between archaea and early eukaryotes.
Some archaebacteria are capable of surviving in conditions of extremely high salinity, which usually has a desiccating effect on cells, killing them. Halobacterium is an example of such salt-tolerant archaebacteria. Halobacterium has the pigment bacteriorhodopsin in it, which provides it with chemical energy and gives halobacterium a purple coloration. Bacteriorhodopsin also pushes protons to the outside of the cell membrane, and when the protons flow back into the cell they start the synthesis of ATP. The bacteriorhodopsin pigment is quite similar to rhodopsin, another pigment found in the retinas of vertebrates.
There are both aerobic and anaerobic species of archaea, and the bacteria can be found in extreme environments as well as in common environments like regular soil. Archaebacteria are capable of practicing anaerobic respiration, specifically a form of anaerobic respiration dubbed methanogenesis as it produces methane as a byproduct of respiration. Archaebacteria also utilize other forms of cellular respiration, but methanogenesis via cellular respiration is exclusive to archaebacteria. Bacteria and eukaryotic cells cannot carry out methanogenesis.
Finally, the ribosomal RNA of archaebacteria suggests that eukarya and bacteria split off from archaea in the far distant past.

Different Kinds Of Archaea

Archaebacteria are divided into three different types and are classified based upon how close they are to one another on the phylogenetic tree or their level of genetic relationship to one another. Each type of archaebacteria has its own unique features.

Crenarchaeota

A Sulfolobus, a type of crenarchaeota, infected with an STSV-1 virus. Photo: By Xiangyux – English Wikipedia, Public Domain, https://commons.wikimedia.org/w/index.php?curid=1675914

The primary distinguishing characteristic of this type of archaebacteria is that it can survive at extremely high temperatures, temperatures as high as 230°F. Many species of this archaea have been found living near hydrothermal vents deep in the ocean, areas where magma emerging from beneath the crust of the Earth heats the water to extremely high temperatures. They have also been discovered in hot springs. Some theories regarding the origin of life hypothesized that deep-sea vents could have been the site where life first evolved, with the formation of the first cells occurring due to the unusual chemical interactions that occur at such high-temperature areas. This type of archaea is also capable of surviving in highly acidic environments.

Euryarchaeota

This type of archaea Is one of the previously mentioned types that can produce methane through cellular respiration, and they are the only lifeforms are known to use carbon as the electron acceptor when performing cellular respiration. This unique trait allows them to break down extremely complex carbon-based molecules, and it means that they fulfill an important ecological niche degrading carbon into methane and facilitating the carbon cycle of the earth. (Archaea may also play a role in the nitrogen cycle, as researchers have found some examples of marine archaea capable of carrying out nitrification.)

Methanogen archaea have been located in deep-sea sediment deposits, where they are responsible for producing isolated pockets of methane that lay beneath the floor of the ocean. They are also found in wetlands and marshes, and their chemical breakdown of carbon and production of methane is what accounts for the distinct smell associated with marshes, and for swamp gas. They are even found in the stomachs of other animals like cows, where they help the cow digest certain types of sugars that eukaryotic cells cannot digest.
Methanobacterium ruminatium is one example of the archaebacteria found in the digestive system of ruminating (mammals capable of getting nutrients from plant-food) animals. Humans even have some of these bacteria living within our digestive tract and they perform a similar function that cow archaebacteria do.

Korarchaeota

Korarchaeota are possibly the oldest type of archaea and therefore they could be the oldest organisms on the entire planet. Like the Crenarchaeota, they can be found near hydrothermal vents. They also share many genes with Crenarchaeota. In fact, Korarchaeota not only shares genes with Crenarchaeota, but they also share genes with Euryarcheaota. This implies that they could be a common ancestor close to Korarchaeota on the phylogenetic tree from which Crenarchaeota and Euryarcheaota descended. While Korarchaeota are amongst the oldest lifeforms on the planet, they are rather rarely found in nature apart from the selective niches of hot springs and deep-sea vents.

New life form answers question about evolution of cells

March 19, 2018, University of Groningen

The left panel shows: EM image of a normal E. coli cell. Right panel: an engineered cell with a mixed membrane, which shows an elongated form. Credit: Photo's University of Wageningen / Van der Oost laboratory

Bacteria and Archaea are two of the three domains of life. Both must have evolved from the putative last universal common ancestor (LUCA). One hypothesis is that this happened because the cell membrane in LUCA was an unstable mixture of lipids. Now, scientists from the University of Groningen and Wageningen University have created such a life form with a mixed membrane and discovered it is, in fact, stable, refuting this hypothesis. The results will be published in the journal Proceedings of the National Academy of Sciences in the week of 19 March.

There are many ideas on how cellular life could have evolved billions of years ago. Protocells may have formed in clay minerals, or as simple lipid vesicles. In the latter scenario, something called the 'lipid divide' would have occurred, creating the separate domains of bacteria and archaea, explains University of Groningen Professor of Molecular Microbiology Arnold Driessen. "The lipid membranes of both domains are different, composed of phospholipids that are each other's mirror image."

Mixed membranes

In technical terms, the lipids in the membranes of bacteria are made up of straight-chain fatty acids that are ester-linked to a backbone of glycerol-3-phosphate. But the lipids in the archaeal membrane have a backbone of glycerol-1-phosphate, to which isoprenoids are linked by ether bonds.

The idea behind the lipid divide is that a common ancestor of both bacteria and archaea had a cell membrane in which both types of lipid were mixed. "This mixed membrane would be less stable than a homogenous membrane of just one type of phospholipid, so eventually a split occurred, resulting in the two domains of Bacteria and Archaea," says Driessen.

All this would have happened over 3.5 billion years ago, so hard evidence is lacking. Driessen and his co-workers therefore decided to "reverse-engineer" a micro-organism with a mixed membrane. "This has been tried before, but these experiments resulted in bacteria with only very small amounts (< 1 percent) of archaeal lipids."

Left panel: EM image of a normal dividing E. coli cell. Right panel: an engineered cell with high archaeal lipid production, showing lobular irregularities in the cell membrane. Credit: Photo's University of Wageningen / Van der Oost laboratory

However, in the new study, this increased to 30 percent. Two key breakthroughs made this possible: "In previous research we discovered an enzyme crucial to the production of archaeal membrane lipids. This takes three steps, and before that, only two of the enzymes involved were known." The other breakthrough came from scientists at Wageningen University, explains Driessen. "They managed to increase the production of isoprenoids in the bacterium E. coli." Isoprenoids are a ubiquitous class of organic compounds which includes many natural flavours, colours or fragrances.

Both discoveries were transferred to a normal E. coli bacterium, which was a major feat of genetic engineering.

"And we didn't know if the end result would be a viable cell," says Driessen. But in the end, it worked out well. With some fine tuning, the scientists created a cell in which all phosphatidylglycerol, the lipids forming the basic bilayer of the bacterial membrane, were replaced by their archaeal equivalent (archaetidylglycerol).

This accounts for 30 percent of the lipids in the membrane. "This bacterium grew at normal speed and was stable," says Driessen. "So this result does not support the hypothesis that a mixed membrane is inherently instable and could thus have created the lipid divide."

Driessen notes that the archaeal enzymes for membrane lipid production are less specific in the reactions they catalyze than their bacterial equivalents. "They appear to be more "primordial." So the evolution of enzyme specificity could have been a driver for the divide." There is, of course, one major caveat—the experiments were done in modern E. coli bacteria, which have evolved 3.5 billion years beyond the original split with the archaea.

"The robustness of these mixed cells surprised us. We expected more problems keeping them alive. After all, what we have engineered does amount to a new life form." The engineered cells were more elongated than the original E. coli. And when the production of archaeal lipids was very high, growth slowed and the membrane developed lobular appendages.

Apart from the evolutionary implications, this discovery could spawn new research: "For example, we could engineer a bacterial expression system for archaeal membrane proteins, such as those produced by hyperthermophiles that grow at extremely high temperatures and pressure."
The work by the two Dutch universities is part of the Origins Center, a national programme dedicated to research into the origin of life on our planet.

Explore further: Formation of cell membrane component domains in artificial lipid bilayer

 

More information: Antonella Caforio el al., "Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane," PNAS (2018). www.pnas.org/cgi/doi/10.1073/pnas.1721604115
 

Journal reference: Proceedings of the National Academy of Sciences
Provided by: University of Groningen