Archaea: A microbiological world yet to be discovered

It is a group of prokaryotic morphology unicellular microorganisms (without nucleus), which are part of one of the three great living beings’ domains: archaea, bacteria and eukaryotes. Archaea are microscopic organisms, (size between 0.1 μm to more than 15 μm), which may have flagella. Their cells are surrounded by a cover (cell wall) with membrane lipids very different from other life forms, such as bacteria or eukaryotes, which gives them high resistance to extreme conditions. Their diet is also very different from that of bacteria, since they benefit from inorganic compounds such as hydrogen, carbon dioxide, alcohols, sulphur, iron, among others.

In the past, archaea were classified as bacteria, as prokaryotes, framed in the ancient Monera kingdom and were known as archaebacteria, but this classification is no longer used. Actually, archaea have an independent evolutionary history and show many differences in their biochemistry compared to other life forms, so they were classified in a separate domain.

The relationship between the three domains is of great importance when it comes to understanding the origin of life. Most metabolic pathways, which involve most genes of an organism, are common among archaea and bacteria, and most genes involved in genome expression are common among archaea and eukaryotes. In prokaryotes, the archaea membrane structure is very similar to Gram-positive bacteria, mainly because both have a lipid bilayer. In phylogenetic trees based on the sequences of different genes/proteins of prokaryotic equivalents, archaeal homologs are closer to those of Gram-positive bacteria.

S. Gupta suggests that archaea evolved from Gram-positive bacteria in response to a selective pressure exerted by antibiotics released by other bacteria. This idea is supported by the fact that archaea are resistant to a wide variety of antibiotics mainly produced by Gram-positive, and these antibiotics largely act on genes that distinguish archaea. His proposal is that the selective pressure towards antibiotic resistance generated by the Gram-positive antibiotics was finally enough to cause important changes in many of the genes targeted by the antibiotic, and that these microorganisms’ strains represented the common ancestor of the current archaea.

The archaea evolution in response to the selection by antibiotics, or any other competitive selective pressure, could also explain its adaptation to extreme environments (such as high temperature or acidity) as a result of a search for unoccupied ecological niches to escape from antibiotic producing organisms. Gupta’s proposal on the relationship between structural proteins and studies suggesting that Gram-positive bacteria may be one of the lineages that first branched into prokaryotes is also supported by other researches.

In the archaea domain, the existence of five evolutionary groups is admitted (according to the ribosomal RNA analysis). Out of these groups, Crenarchaeota (including hyperthermophiles, acidophiles, reducers and/or sulphur oxidizers and chemolithoheterotrophs) and Euryarchaeota (including methanogenic, thermoacidophilic and hyperhalophilic microorganisms), are being studied with greater intensity. The archaea classification is still difficult, because most of them were never studied in the laboratory and were only detected after analysing their nucleic acids in samples taken from the environment.

Archaea and bacteria are quite similar in size and shape, although archaea have very unusual, round, flattened, elongated or filamentous shapes up to 200 μm, or can even form macroscopic filamentous colonies. Despite this visual similarity with bacteria, archaebacteria have genes and several metabolic pathways that are closer to those of eukaryotes, especially in enzymes involved in transcription and translation. Other aspects of the archaebacteria biochemistry are unique, such as the lipid ethers of their cell membranes, which give them a much higher resistance, for example, at high temperatures. Archaea exploit as nutrients a variety of resources much greater than eukaryotes, from common organic compounds such as sugars, to ammonia, sulphur, metal ions or even hydrogen. Salt-tolerant archaea (halobacteria) use sunlight as a source of energy, and other archaea species sequester carbon. However, unlike plants and cyanobacteria, there is no known archaea capable of both. Archaea reproduce asexually and are divided by binary fission, fragmentation or budding. Unlike bacteria and eukaryotes, no species of archaea that forms spores is known.

Archaea can live in many habitats and it has been estimated that they could form up to 20% of the Earth’s biomass. Initially, archaea were all considered extremophiles that lived in hostile environments, such as thermal waters and salt lakes, acidic, alkaline environments… but the reality is that archaea are found in the most diverse habitats, such as soil, oceans, swamps and in the human colon (mesophilic archaea). Archaea are especially numerous in oceans, and plankton archaea could be one of the most abundant groups of organisms on the planet. They are currently considered an important part of life on Earth and could play an important role in both the carbon and nitrogen cycles.

No clear examples of pathogenic or parasitic archaea are known, but they are usually mutualists or eaters. Methanogenic archaea are examples that live in human intestines (Methanobrevibacter smithii), where they could act as mutualists interacting with other microorganisms to contribute to food digestion, as it happens in ruminants, where they are present in large quantities and contribute to food digestion. They have also been found in termites, corals… As with pathogenic microorganisms in living beings, only the archaea involvement with oral infections has been considered.

What can archaea be used for?

Archaea have their significance in technology. The extreme conditions in which these microorganisms can develop have been studied in depth, and it has been observed that this is possible thanks to certain enzymes. For this reason, some of these enzymes are nowadays being used to conduct reactions under extreme conditions. Some methanogenic archaea are used to treat wastewater in treatment plants, performing waste anaerobic digestion, producing biogas. Extremophile archaea enzymes are capable to withstanding high temperatures. They can do their function at over 100ºC, so foods can be processed at high temperatures (low-lactose milk or whey). Thermophilic archaea enzymes also tend to be very stable in organic solvents, so they can be used in a wide range of environmentally friendly processes for organic compounds synthesis.

Thanks to biotechnology, new microorganisms producing enzymes capable of withstanding the drastic conditions of industrial processes are constantly being sought. Less than 1% of the microorganisms that exist have been studied, so it is estimated that there are millions of them yet to be discovered, most of them found in environments in which growth conditions are extreme and impossible for other organisms (extremophile, psychrophilic, hyperthermophilic, osmophilic, alkalophilic microorganisms…). These microorganisms are undoubtedly a potential source of new enzymes. For example, psychrophiles synthesise enzymes with biochemical modifications that enable them operating at low temperatures, as well as molecules that reduce the water’s freezing point within the cell. A new class of potentially useful antibiotics is derived from this group of organisms. Eight of these substances have already been characterised, but there could be many more, especially in Halobacteria. These compounds are important because they have a structure different from that of bacterial antibiotics, so they can have a different mode of action. In addition, they could allow creating new selectable markers to be used in archaebacterial molecular biology. Discovering new substances depends on recovering these organisms from the environment and their culture.

The great biodiversity existing between extremophile microorganisms and their capacity to synthesise proteins and enzymes, active in these extreme conditions, has opened a promising panorama in biotechnology, since a large proportion of industrial processes take place under extreme temperature, pressure, ionic strength, pH and organic solvents conditions. Moreover, these enzymes can be used as a model to design and construct proteins with new useful properties for certain industrial applications, through the genetic manipulation of microorganisms.

The main industries that have benefited from using these extreme enzymes are detergent, food, textiles, leather, paper and pharmaceutical producers. Thermophiles and hyperthermophiles are the most studied extremophiles groups. Enzymes that have been isolated from them have been the subject of several researches and industrial and biotechnological applications, as they are extremely thermostable and generally resistant to the action of denaturing agents, detergents, organic solvents, and exposure to extreme pH values.

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