Archaea : General concepts - Culture; Molecular identification (PCR and sequencing)  

Information 14-10-2016.  

Archaea (Archaea) are unicellular microorganisms similar to bacteria cell structure, but with some differences, so previously were considered as ancient bacteria (Aqueobacterias). They are now considered a group of independent of the other two groups of living bacteria (Bacteria domain) and eukaryotes (Eukaria domain) independent living (Archeae domain). In the latter domain animals, plants, fungi and protozoa they are included.

Although being similar in size and shape to bacteria, some have very different shapes, and square cells with flat. Sometimes their genes and metabolic pathways, are more similar to those of eucaryotes, as with enzymes for transcription and translation. Also they possess different molecules in structure (ether lipids in their cell membranes), and used many sources of energy (organic compounds, ammonia, metal or hydrogen ions). They tolerate high salinities, use sunlight as an energy source, and can fix carbon. They divide by binary fission, fragmentation or budding, unlike other living beings.

Are considered extremophiles, ie that can develop in "extreme" conditions, as in hot water of high temperature, salt water, but can also be found in soil, oceans, swamps and in the human intestine or ruminants , which helps digest food.

Euryarchaeota, Crenarchaeota, Korarchaeota, Nanoarchaeota and thaumarchaeota of which are frequently the first two: using ribosomal RNA analysis the existence of five evolutionary groups supported. The Euryarchaeota include microorganisms varied as methanogens, thermoacidophiles and hiperhalófilos. The Crenarchaeota include hyperthermophilic, acidophilic, reducing and / or oxidizing the sulfur and quimiolitoheterótrofos. The Korarchaeota are very rare and are found in hot springs. The Nanoarchaeota are hyperthermophilic acidophilus or very small, with a size of 300 nm in diameter would be the smallest prokaryotes. The thaumarchaeota are chemolithoautotrophs nitrifying marine and terrestrial environments.

Archaea size may be from 0.1 .mu.m to more than 15 .mu.m, flat round, elongated shapes, filamentous, spirals, or lobed. Some form aggregates or filaments of up to 200 .mu.m, or may even form filamentous macroscopic colonies. Its structure is similar to that of bacteria, with no internal structures, their cell membrane is surrounded by a cell wall and may have flagella. They resemble Gram positive bacteria with the cytoplasmic membrane and cell wall, without periplasmic space, with some exceptions in which there is a periplasmic space in which can be found membrane vesicles.

However, the lipid membranes of archaea are very different from those that exist in other life forms such as bacteria or eukaryotes and therefore probably more resistant to extreme conditions. In bacteria and eukaryotes are phospholipids, which are composed of a nonpolar hydrophobic part (fatty acid unbranched or rings), a hydrophilic polar part attached to glycerol (D-glycerol) and phosphate through a link type ester forming layered structures (lipid bilayer). The most common esters by binding of an acid and an alcohol (-OH and -COOH) so formed that the hydroxyl radical -OH is replaced by -COO fatty acid. The hydrogen atom (H) of the acid group is attached to the hydroxyl radical of the alcohol to form water (H 2 O).

In archaea, phospholipids are also composed of a hydrophobic part (structure isoprenoid branched long, sometimes with cyclohexane rings or cyclopropane) and a polar glycerol (L-glycerol) and phosphate, but united by a ether linkage, whose resistance is much higher, for example at elevated temperature. Isoprenoids, terpenes or are C 5 hydrocarbon-methylbutane-1 2, 3-diene derived carbon. The ether linkage type is a type ROR' group, R and R'alkyl groups, for example two alcohols (ROH + HOR'à ROR' + H 2 O). These groups are very hydrophobic and tend not to be hydrolyzed. Some archaea, instead of having a lipid bilayer having a monolayer resulting from the merger of two hydrophobic chains, forming a single molecule with two hydrophilic polar groups that could confer rigidity to the extreme conditions, such as heartburn.

Most archaea have a cell wall composed of proteins that form a rigid assembly (S layer) covering the outside of the cells forming a mesh protects chemical and physical cell membrane. They lack peptidoglycan, except methanogenic archaea of having a pseudopeptidoglycan lacking N-acetylmuramic acid and amino acid

Archaea can obtain their energy from inorganic compounds such as sulfur or ammonia (litótrofas archaea as nitrifying, methanogens and anaerobic methane oxidizing) and a source of inorganic carbon or nitrogen fixation. Other use sunlight as an energy source (phototrophic archaea, but photosynthesis) and used as a carbon source organic compounds. Finally, other energy obtained organic compounds (organótrofas archaea) and carbon source obtained from organic compounds or carbon fixation.

Archaea can live in many habitats and could form 20% of the biomass on Earth. Many are extremophiles and thought this was his only ecological niche. For example, some live at very high temperatures (thermophilic archaea -> 45ºC- and hipetermófilas -> 80ºC-), even higher than 100 ° C; others are in very cold habitats, in, very acidic brines (halophilic) (acidophilic archaea, even at pH 0) or alkaline (alkaliphilic archaea). Others develop milder temperatures (mesophilic archaea) and live in mild and humid conditions as in oceans and soils.

Archaea relationship with other living things  

Archaea are found in the wild in nature in soil, water, extremophile environments such as hot springs and acidic or alkaline waters. They have also been found regarding living in situations of mutualism or commensalism beings. Situations regarding pathogenicity has only been suggested involvement in oral infections.

In situations of mutualism methanogenic archaea found in the digestive system of animals that digest cellulose as ruminants and termites, associated with protozoa. Protozoa would digest plant cellulose for energy, releasing hydrogen, but this would reduce the energy released. However, the presence of archaea convert the hydrogen to methane (CH 4) when using CO 2 as final electron acceptor (4H 2 + CO 2 CH 4 + 2H 2 O), benefiting protozoa. Some archaea would live in the interi or protozoan consuming the hydrogen produced by them hydrogenosomes, and the same would occur in some marine sponges. In the human intestinal flora Methanobrevibacter smithii there methanogen, which as in termites, may be mutualistic interacting with other microbes to contribute to the digestion of food. Similarly you have been found associated with coral and plant roots.

Interest in technology and industry

The extreme conditions in which these microorganisms can grow are possible because they have enzymes may function in these conditions. For this reason some of the enzymes are being used to perform reactions under extreme conditions. It is the case of some thermostable DNA polymerases such as Pfu DNA polymerase (Pyrococcus furiosus) used in molecular biology. The same applies to amylases, galactosidases, etc., other species of Pyrococcus that perform their function more than 100, which can be processed food at elevated temperatures (low - lactose milk or whey). Methanogenic archaea are the use for wastewater treatment to perform anaerobic digestion of waste producing biogas. Acidophilic archaea are used in mining for obtaining metals such as gold, cobalt and copper. It is considered obtaining antibiotics of these microorganisms.  

Tests in IVAMI:

 

  • Culture and molecular identification of archaea (Achaea) isolated in culture.

As possible coexistence of different species of archaea in any of the environmental conditions in which they are, we must cultivate the sample instead of going directly to molecular detection. For example in hypersaline environments may be Haloarcula spp., Haloterrigena spp., Haloferax spp., Halorubrum spp, Halobacterium spp, Halonotius spp, Haloquadratum spp, etc.). In some environments they can be found coexisting halophilic methanogenic archaea with archaea.

The customer must indicate the conditions under which the sample was to guide cultivation in the laboratory salinity and concentration if known; temperature; acidity; alkalinity, intestinal; ....

 

  • Molecular detection only: when only want to know if there archaea, molecular detection could be performed.

Recommended sample:

 

  • The sample will depend on where it is desired to detect its presence: water, soil, animal intestines, ...
  • About 100 grams or 100 mL are required as appropriate.

Preservation and shipment of sample:

 

  • Environmental conditions in which the sample is usually, unless it is samples receivables that are at elevated temperature can refer to room temperature.

Delivery term:

 

  • 10 to 15 days according to have to identify or not. The culture is prolonged as an enrichment should be performed with subcultures at 48 hours and 7 days, with the molecular identification when present.  

Cost of the test: