Essay on Archaebacteria

In this essay we will discuss about Archaebacteria. After reading this essay you will learn about:- 1. Origin of Archaebacteria 2. General Characters of Archaebacteria 3. Typical Characters 4. Important Representatives.

Contents:

1. Essay on the Origin of Archaebacteria
2. Essay on the General Characters of Archaebacteria
3. Essay on the Typical Characters of Archaebacteria
4. Essay on the Important Representatives of Archaebacteria

Essay # 1. Origin of Archaebacteria:

The archaebacterial have existed on Earth longer than any other organism of any type as their fossils have been located in Africa and Australian rocks 3.5 billion years old. They are such microorganisms which are prokaryotic in their cell organization but possess a strikingly different cell-chemistry when compared with the bacteria.

They are genetically as distantly related to bacteria as both are to eukaryotic organisms. This distinction among the archaebacteria, bacteria and karyotes is so profound that archaebacteria have been given the rank of a domain with a completely different status in the history of organisms’ classification.

Archaebacteria have become present-day’s central dogma of microbiological studies because they are being considered as having much significance:

(i) In relation to the origin and evolution of life, and

(ii) In determining the nature of life.

The archaebacteria are the microorganisms that appear to be relics of such a primitive group which transformed initial environment (which was highly anaerobic and warm) by using variety of compounds as source of carbon and energy before the evolution of the complex photosynthetic process.

It is so said because many of the present-day archaebacteria have been found using organic compounds like formate, acetate, methylamine, methanol, etc., and mostly thrive and prosper in such environmental conditions which can, to some extent, be compared with the environment during the early evolution of life (i.e., the prebiotic environment) on earth.

Archaebacteria, therefore, may prove to be a good test material for analysing various biochemical and biophysical events that might have been associated with the earliest life forms and may help tracing the mysteries of the origin and evolution of life.

Recent studies on enriched water-samples collected from submarine hydrothermal vents reveal that these samples contained cells exhibiting blue-green auto fluorescence (a typical feature of methanogenic archaebacteria) as well as they showed active methane-production at 102°C and some samples even at 300°C.

This is one of the most amazing discoveries related to archaebacteria as their ultrathermophilic existence destroys all current concepts on the upper temperature limits of life. The future studies on these microorganisms, therefore, may lead to new informations on the nature of life itself.

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Essay # 2. General Characters of Archaebacteria:

These prokaryotes often occur in extreme aquatic and terrestrial habitats which may be anaerobic, hyper-saline or hyper-thermophilic. Some archaebacteria have been found as symbionts in animal digestive system. Recently, these have also been collected from very low temperature environments and are thought to constitute upto 34% of the prokaryotic biomass in coastal Antarctic surface waters.

Archaebacteria may be spherical, rod-shaped, spiral, Iobed, plate-shaped, irregularly shaped or pleomorphic. Some are unicellular whereas others are filamentous or aggregates. They range in diameter from 0.1 to over 15 µm. Some filamentous archaebacteria even can grow upto 200 µm in length.

Archaebacteria are both Gram-positive and Gram-negative and reproduce by means of binary fission, fragmentation, budding and as yet unknown mechanisms. They may be aerobic, facultatively anaerobic or obligately anaerobic and, nutritionally, range from chemolithotrophs to organotrophs.

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Essay # 3. Typical Characters of Archaebacteria:

Although archaebacteria are prokaryotic and possess most of the basic features of prokaryotes, they have some very typical characters, which are unique to them and are not found in any other group of organisms. These characters are, cell wall structure, plasma membrane structure, RNA-polymerase structure, tRNA nucleotide sequence, novel coenzymes and cofactors, carbon assimilation pathway, and protein synthesis.

Cell Wall Structure:

Some archaebacteria such as Thermo-plasma species lack cell wall while most others do contain cell walls. The cell wall containing archaebacteria are morphologically almost similar to bacteria, the chemistries of the cell walls of the two are strikingly different.

(i) Morphology:

Archaebacterial cell wall may be gram-positive or gram-negative with respect to gram- staining. The wall of many archaebacteria is thick and homogenous resembling those of Gram-positive bacteria and thus stain Gram-positive (Fig. 7.1 A).

The wall of gram-negative archaebacteria lacks the outer membrane and complex peptidoglycan network present in gram-negative bacteria and, instead, they usually possess a surface layer of protein or glycoprotein subunits (Fig. 7. 1B).

(ii) Chemistry:

Peptidoglycan is the main constituent of the cell wall of all bacteria, but it completely lacks in the cell walls of archaebacteria. The latter shows great biochemical diversity; gram-positive archaebacterial cell walls are made up principally of pseudomurein and polysaccharides, gram-negative ones mainly of protein subunits and glycoproteins.

Methanobacterium, Methanobrevibacter, Methanothermus, and Methanopyrus contain pseudomurein [glycans (sugars) and peptides] in their cell walls.

But, the glycan portion of pseudomurein contains N- acetyltalosaminuronic acid (instead of N-acetylmuramic acid of bacterial glycan) and N-acetylglucosamine which are linked to each other by β (1 → 3) glycosidic bonds instead of β (1 → 4) glycosidic bonds of bacterial cell wall (Fig. 7.2) and alternate to form the cell wall backbone.

Lysozyme cannot digest β (1 → 3) glycosidic bonds. Peptides are short amino acid chains attached to N-acetyltalosaminuronic acid (NAT) and these amino acids are L-amino acids. Penicillin is ineffective in infibiting the cell wall peptide bridge formation.

The walls of some gram-positive archaebacteria contain polysaccharides. Methanosarcina contains non-sulfated polysaccharide similar to chondroitin sulfate of animal connective tissue. Halococcus cell wall is composed of sulfated polysaccharide.

The cell walls of Methanococcus, Thermococcus, Methanomicrobium, Methanogenium, etc. are exclusively made up of protein subunits (protein S-layer), whereas the cell wall of Methanospirillium consists of a protein sheath.

Halobacterium cell wall is made up of glycoproteins but also contains negatively charged acidic amino acids which counteract the positive charges of the high Na⁺ environment. The cell walls of Methanolobus, Sulfolobus, Thermoproteus, Desulfurococcus and Pyrodictium consist of glycoproteins (glycoprotein S-layer).

Plasma Membrane Structure:

The basic molecular architecture of the plasma membrane is the same in all cellular organisms; it contains lipids whose hydrophobic portion is a long, generally, ‘un-branched’ hydrocarbon chain linked to glycerol by ester linkages (—O—C—).

In contrast to plasma membranes of all cellular organisms, those of archaebacteria contain lipids having ‘branched’ hydrocarbon chains linked to glycerol by ether-linkages (—O—) (Fig. 7.3).

This uniqueness of plasma membrane lipids of archaebacteria is considered as one of the key features that distinguishes them from all other cellular organisms. Since many of the archaebacteria live under very high temperature (up to nearly 100°C) and low pH (up to below 2.0) environments, it is advocated that the unusual lipids of their plasma membrane help them survive under such extreme conditions.

The ether-linkages provide stability to them against thermal breakage and the branching of the hydro­carbon chains decrease membrane fluidity; therefore, plasma membranes are stable under high temperature conditions.

Two types of lipid structures are found among the archaebacterial plasma membranes: glycerol diphytanyl diethers and diglycerol dibiphytanyl tetraethers (Fig. 7.4). Usually the diether side chains are 20 carbons in length and the tetraether chains are 40 carbons.

In general, the coccoid cells of methanogenic archaebacteria contain only glycerol diphytanyl diethers, while the rest contain both glycerol diphytanyl diethers and diglycerol dibiphytanyl tetraethers. The halophilic archae­bacteria contain mainly glycerol diphytanyl diethers, while the thermoacidophilic ones contain mainly diglycerol dibiphytanyl tetraethers.

Archaebacterial plasma membranes containing digycerol dibiphytanyl tetraether give an appearance of a monolayer rather than the usual bilayer because lipid chains are long enough to extend from one side of the membrane to the other (Fig. 7.5). This makes these plasma membranes very resistant to extreme environmental conditions of their habitats.

Genome:

The archaebacterial chromosome, like bacteria, are single closed DNA circles. The latter, in some cases, are significantly smaller than the normal bacterial DNA. Thermoplasma acidophilum DNA is about 0.8 x 10⁹ daltons and Methanobacterium thermoautotrophicum DNA is about 1.1 x 10⁹ daltons in comparison to the DNA of Escherichia coli which are about 2.5 x 10⁹ daltons in size.

In archaebacterial genome the G + C content percentage is high (about 21-68%) and only few plasmids have been reported in archaebacterial cytoplasm.

However, National Centre for Biotechnology Information (USA) listed 19 archaebacteria whose genomes had been sequenced by mid-2004. The completely sequenced genome of Methanococcus jannaschii reveals that 56% of its total 1758 genes are uplike those occurring in bacteria and eukaryotes.

RNA Polymerase Structure:

Archaebacteria, like bacteria, possess a single type of RNA polymerases but the latter are complex consisting of upto 14 subunits (3 or 4 large and others small) as against only few subunits in bacteria (c.f. 5 in E. coli). Archaebacteria RNA polymerases are similar to eukaryote RNA polymerase II. However, archaebacterial RNA polymerases are insensitive to drugs rifampin and streptolygidin.

tRNA Nucleotide Sequence:

The archaebacteria lack ribothymine in the common arm (TΨC arm) of transferRNA (tRNA), whereas it is present in most tRNAs in bacteria and eukaryotes; ribothymine is replaced by pseudouridine or L- methylpseudouridine in archaebacteria. Also, they are methionyl-tRNA^met rather than formylmethionyl- tRNA_F^met as indicator-tRNA.

Coenzymes and Cofactors:

The methane production mechanism of methanogenic archaebacteria is unique in the microbial world and involves several novel cofactors and coenzymes not found in any other group of microorganisms.

These coenzymes and cofactors identified so far are:

(i) methanofuran (MP),

(ii) methanopterin (MP),

(iii) coenzyme M (CoM),

(iv) coenzyme F₄₂₀, and

(v) coenzyme F₄₃₀ (Fig. 7.6).

Carbohydrate Metabolism:

(i) CO₂ Assimilation:

Most of the methanogens and extreme thermophiles enjoy autotrophy, and CO₂ fixation takes place in more than one way in them. Thermoproteus and possibly Sulfolobus assimilate carbon dioxide by the reductive tricarboxylic acid cycle (Fig. 7.7A) whereas the methanogens and most of the extreme thermophiles assimilate CO₂ by the reductive acetyl-CoA pathway (Fig. 7.7B).

(ii) Carbohydrate Catabolis:

Bacteria and eukaryotes degrade glucose by way of Embden-Meyerhof pathway (glycolysis) whereas the archaebacteria do not use this pathway due to lack of 6-physphofructokinase enzyme in them. Extreme halophiles and thermophiles degrade glucose using a modified form of the Entner-Doudoroff pathway (Fig. 7.8) in which the initial intermediates are not phosphorylated.

Halophiles and extreme thermophiles (e.g., Thermoplasma) degrade glucose using tricarboxylic acid cycle (TCA cycle); no methanogen has yet been reported using complete TCA cycle. Methanogens do not degrade glucose to any significant extent. They, in contrast with glucose degradation, use gluconeogenesis that proceeds by reversal of the Embden-Meyerhof pathway.

(iii) Oxidation of Pyruvate to Acetyl-CoA:

All known archaebacteria have ability to oxidize pyruvate (pyruvic acid) to acetyl-CoA. But, they use the enzyme pyruvate oxidoreductase for this purpose instead of pyruvate dehydrogenase complex used by respiratory bacteria and eukaryotes.

Protein Synthesis:

It has been studied that deviation in protein synthesis both at transcription and translation levels from eubacteria and eukaryotes undoubtedly exist in archaebacteria.

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Essay # 4. Important Representatives of Archaebacteria:

Keeping the phylogenetic categorization of archaebacteria under the domain Archaea aside, the archaebacterial representatives can be grouped as under on the basis of their strange metabolic and ecological characteristics: methanogens, extreme halophiles, extreme thermophiles, thermoacidophiles and thermophiles.

(i) Methanogens:

Methanogens are the largest group of archaebacteria characterized by their unique energy metabolism in which they convert fermentation products formed by other anaerobic microorganisms notably CO₂, H₂, acetate, formate, methylamine and methanol to either methane (CH₄) or methane and CO₂.

The enzymes used in methanogenesis are very oxygen sensitive, so methanogens are very strict anaerobes (obligate anaerobes) hence produce methane in oxygen-free as well as low redox potential (less than – 333 mv) environment. They are found in all types of anaerobic environments, and are certainly the most prevalent archaebacteria in the ‘moderate’ world.

(a) Representative Genera:

There are many known methanogenic genera, the important ones are Methanobacterium, Methanothermus, Methanococcus, Methanomicrobium, Methanogenium, Methanospirillum, and Methanosarcina. However, a methane producing strain, Methano plasma, has recently been isolated in pure cultures: this strain apparently lacks cell wall.

Methanogens inhabit anaerobic environments rich in organic matter. They have simple nutritional requirements and use large variety of carbon compounds.

Some methanogens can grow as autotrophs and utilize carbon dioxide as a carbon source and hydrogen as an energy source but, they may also utilize formate (a carbon compound) as carbon source. Besides, Methanothrix uses acetate and Methanococcoides utilizes methylamine and methanol. A thermophilic strain of Methanosarcina uses acetate, methylamines, and methanol.

Most known methanogens are mesophilic (requiring optimum temperatures from 21°C to 45°C); some are thermophilic (requiring high temperatures of an optimum between 50°C to 80°C); and so far no psychrophilic (requiring low temperature) methanogens have been isolated.

(b) Methanogenesis (Methane Production):

The methane production mechanism (methanogenesis) is unique in the world of microorganisms and involves several novel group of coenzymes (Coenzyme M, Coenzyme F₄₂₀ and Coenzyme F₄₃₀) and cofactors (methanofuran and tetrahydromethanopterin) which are not found in any other group of eubacteria Methane production is an anaerobic environment process and usually occurs at temperatures ranging from 0°C to 100°C.

There are three different metabolic strategies employed by diverse methanogenic archebacteria. Most methanogenens employ the CO₂-reducing pathway starting with CO₂ or formate.

Others use a Methylotrophic pathway starting with methanol or methylamines (e.g., Methanolobus, Methanoholohium, Methanococcoides). A few methanogens (e.g., Methanosaeta) use an aceticlastic pathway starting with acetate. Methanosarina, however, may use any of the three strategies to produce methane.

CO₂-reducing Pathway to Mathane:

The electrons required for the reduction of carbon dioxide to methane can be supplied form H₂, formate, CO, alcohols, etc.; it is H₂, which is generally used as electron donor during CO₂-reducing pathway.

The reduction of CO₂ by H₂ to produce methane (Fig. 7.9) occurs in the following steps:

(i) CO₂ is activated by a methanofuran (MF) and subsequently reduced to the formyl level,

(ii) The formyl group is transferred from methanofuran to methanopterin (MP) and is subsequently dehydrated and reduced to methylene and methyl levels in two separate steps,

(iii) Methaopterin now transfers the methyl group to coenzyme M (CoM),

(iv) The methyl reductase system reduces methyl-CoM to methane (CH₄) with the involvement of conenzyme F₄₃₀ and coenzyme B (CoB), and during this the coenzyme F₄₃₀ removes the methyl group (CH₃) from methyl-CoM in the form of Ni²⁺-CH₃ complex which is reduced by coenzyme B (CoB) generating methane (CH₄) and a disulfide complex of CoM and CoB (CoM-S-S-CoB), and

(v) Finally, the disulfide complex (CoM-S-S-CoB) is reduced with H₂ to generate free CoM and CoB. It is this reaction during which the energy is conserved in the form of ATP.

(c) Methanogens as Problem-Organisms:

Methanogens can become a problem to ecosystem in future if they are exploited to produce methane. Methane is a greenhouse gas as it absorbs infrared radiation. Evidences are there that the concentrations of methane are continuously rising since many decades and the methane production may significantly aid to the global warming in future.

Recently, it has been found that methanogens oxidize iron into methane and energy. That is, the methanogens growing around buried or submerged iron pipes and other iron objects may bring significant iron corrosion.

Landfill biomass is digested anaerobically to H₂, CO₂, and acetate which in turn are converted into methane by methanogenesis. Landfills have to be carefully vented to prevent very messy methane explosions because houses near older unvented landfills may explode due to the buildup of methane which may seep through the ground into their basements.

(ii) The Halobacteria: Extreme Halophiles:

The halobacteria, e.g., Halobacterium, Halococcus, etc. are aerobic chemoorganotrophs and salt lovers. They thrive in salt-lakes, tidal pools, salt ponds, brines, salted fish and salted hides. It is considered that they require approximately 17 to 23 per cent NaCl for good growth.

Halobacterium’s cell wall is so dependent on the presence of NaCl that it disintegrates if the NaCl concentration drops to or below 8%. Some of them inhabit deep-sea volcanic vents where the water is maintained boiling due to the extreme pressure of the sea-depth and they may flourish even at 104°C temperature.

The halophiles are poorly flagellated rods (Halobacterium) ranging up to 8 µm in length and immotile cocci (Halococcus). The Halobacterium spp are pleomorphic and can undergo morphological changes in response to variation in the salt content of the environment; a very high salt concentration may cause the cells to become round and ultimately lyse.

Light-Mediated ATP Synthesis: The Role of Bacteriorhodopsin:

The Halobacterium carries on unique version of energy synthesis, namely, light- mediated ATP synthesis (Fig. 7.10) which does not involve photosynthesis. The best studied is the Halobacterium salinarium (H. halobium), which usually traps solar energy without the presence of chlorophyll (thus it is not photosynthesis).

When subjected to low oxygen concentrations and high light intensity, it synthesizes a modified cell membrane, namely, purple membrane, which contains a protein pigment called bacteriorhodopsin. Bacteriorhodopsin was so named due to its structural and functional similarity to the visual pigment of the eye called rhodopsin.

Conjugated to bacteriorhodopsin is a molecule of retinal, a carotenoid-like molecule, which has ability to absorb light and catalyse formation of a proton motive force.

Bacteriorhodopsin absorbs light strongly at about 570 nm light-spectrum. The retinal of bacteriorhodopsin, which normally exists in trans-form, becomes exited and converted to its cis-form following the absorption of light. During this conversion, there is translocation of protons to outside surface of the purple membrane.

The retinal molecule then returns to its trans-form in the dark along with the uptake of a proton from the cytoplasm, thus completing the cycle. As protons accumulate on the outer surface of the membrane, the proton motive force increases until the membrane is sufficiently charged to drive ATP synthesis through action of a proton trans locating ATPase.

(iii) Pyrodictium: Extreme Thermophile:

Pyrodictium is the most extreme example of archaebacteria that grow in extreme thermophilic conditions, particularly the submarine volcanic habitats such as thermal springs and deep sea hydrothermal vents. This archaebacterium has been isolated from geothermally heated sea floors and grow at 82-110°C temperature.

Pyrodictium are irregularly disc-shaped and its cell wall is composed of glycoprotein. It is obligately anaerobic growing chemolithotrophically on H₂ with S as electron acceptor or chemoorganotrophically on complex mixture of organic compounds.

How the Pyrodictium, and other extreme thermophiles, tolerate so much heat? In cells of Pyrodictium a heat-shock protein, namely, thermosome, is present. It is considered that this protein functions to keep the other proteins of the cell properly folded and functional and helps cells survive above their maximal growth temperature. For example, the cells of Pyrodictium can survive for one hour at 121°C in the autoclave.

(iv) Sulfolobus, Thermoplasma, Ferroplasma: Thermoacidophiles:

The thermoacidophiles are distinguished by their ability to grow in harsher environments of high temperature and low pH value (acid pH value). They represent a heterogenous group, which can be Sulfolobus, Thermoplasma and Ferroplasma.

Sulfolobus is a gram-negative facultative chemoautotroph. Its cells have an irregular spherical lobed shape. The temperature optimum required is between 70-80°C with a pH optimum of between 2 to 3. Sulfolobus grows in hot acid springs and hot acidic soils all over the world.

The main growth substrate of these is the elemental sulphur. Sulfolobus grows on the surface of droplets or crystals of sulphur and oxidizes it to sulphuric acid which is largely responsible for the acidity of its habitats.

Thermoplasma, like mycoplasmas, lacks cell wall. It is a facultative anaerobe, which utilizes some mono- and disaccharides as source of carbon.

Thermoplasma has been found growing only in the refuse piles from coal mines, which contain residual coal and substantial amounts of iron pyrite (FeS). Oxidation of iron pyrite by some chemoautotrophic bacteria acidifies and heats the pile creating a favourable growth environment for Thermoplasma (temperature 37-65°C; pH 0.5-4.5).

Ferroplasma is a chemolithotrophic relative of Thermoplasma. Like Thermoplasma, it lacks cell wall and enjoys acidophilic life-style, but is not a thermophile as it grows optimally at 35°C in mine tailings containing pyrite (FeS). The latter is used as energy source.

(v) Thermoproteus:

Thermoproteus, a thermophilic archaebacterium, are long thin rods often sharply bent in the middle to produce a V-shaped structure and grow over a temperature range of 78-95°C and a pH range of 2.5-6.5.

Thermoproteus can be identified by the presence of occasional branching of the cells and presence of golf ball-like terminal structures. Their metabolism is strictly respiratory and they use variety of sugars, alcohols, organic acids and carbon monoxide as respiratory substrates.