Archaeabacteria: Characteristics, Types and Phylogeny

In this article we will discuss about:- 1. Taxonomy of Archaebacteria 2. General Characteristics of Archaebacteria 3. Representative Types 4. Phylogeny.

Taxonomy of Archaebacteria:

The domain Archaea has been divided into two Phyla:

1. Crenarchaeota and

2. Euryarchaeota. The first includes the extreme thermophiles, acidophiles and sulfur-metabolizing archaebacteria. They are mostly anaerobic and they occur generally in geo-thermally—heated environment, like sulfur hot springs and sea-floors.

The members of the second phylum, Euryarchaeota, are more diverse and includes anaerobic methanogens, extreme halophiles and extreme thermophiles. The two phyla have been divided mainly on the basis of differences in the 16S r-RNA sequences.

General Characteristics of Archaebacteria:

Archaebacteria may be Gram-positive or Gram-negative. Cells are generally invested with a cell- wall, except those of Thermo plasma, a wall-less mycoplasma-like genus. Archaebacterial cells may be spherical, rod-shaped, spiral, irregularly lobed as in Sulfolobus, or filamentous. Cell diameter ranges between 0.1 μm and 1.5 μm. Cells multiply by several means, like binary fission, budding, fragmentation etc.

The organisms may be aerobic, anaerobic, chemolithotrophic or chemoorganotrophic. They mostly occur in extreme environments, though some are mesophilic. Gram- positive archaebacteria have a thick homogeneous cell wall mainly containing complex polysaccharide. The Gram-negative forms have a thinner wall consisting mainly of protein or glycoprotein.

An outer membrane characteristically present in the Gram-negative true bacteria is absent in archaebacteria. Murein is absent in the cell wall of both Gram-positive and Gram-negative archaebacteria. In some, like Methanobacterium, a peptidoglycan-like polymer, called pseudomurein is present. Due to the absence of murein, the archaebacteria are insensitive to β-lactam antibiotics like penicillins, cephalosporin’s, etc.

A unique feature of archaebacteria is the presence of ether-linked isopranyl lipids in their membranes. The composition of the archaebacterial lipids may change in response to the environment. Under more extreme environmental conditions, like high salinity and high temperature, the composition changes to provide a more rigid and stable membrane to withstand the environmental stress.

Like all other prokaryotes, archaebacteria have a covalently linked closed circular genome, but its size is generally smaller than that of other prokaryotes. The genome size ranges between 0.8 to 1.1 x 10⁹ Daltons. G + C content of DNA varies widely, from 21 to 68 moles%. Ribosomes are of 70S type, but their shape may vary from those of other prokaryotes.

So far as biochemical characteristics are concerned, the archaebacteria do not appear to use the EMP for glucose dissimilation, because of the absence of 6-phosphofructokinase. Tricarboxylic acid cycle has been found to be operative either fully or partly in many halophilic and thermophilic archaebacteria. Mode of metabolism may range from typical organotrophy to strict chemolithotrophy.

Halo bacterium, an extreme halophile, can utilize light energy to produce ATP with the help of a special pigment, called bacteriorhodopsin. The chemolithotrophic members do not use the Calvin cycle for C0₂-fixation, but several other pathways like reductive TCA cycle or reductive acetyl-CoA pathway. At least three members of the group have been reported to be able to fix atmospheric nitrogen.

Some Representative Types of Archaeabacteria:

A. Crenarchaeota:

The Phylum Crenarchaeota is a comparatively small one consisting of a single class.

Thermoprotei divided into three orders:

i. Thermoproteales,

ii. De-sulfurococcales and

iii. Sulfolobales.

Some representative genera are Thermoproteus, Pyrodictium, Sulfolobus etc. Most members are thermophilic to hyperthermophilic, and many are also acidophilic and capable of chemolithotrophic metabolism using H₂, S⁰ and Fe²⁺ as energy source.

Thermoproteus includes members having thin rod-shaped, vibrioid or even branched cells growing under strictly anaerobic conditions at a temperature of 70° to 90°C, where the pH is between 2.5 to 6.5. The organisms are either organotrophic, or facultatively chemolithotrophic using H₂ or S° as oxidisable substrate and CO or CO₂ as carbon source. Thermoproteus neutrophilus has been shown to fix CO₂ by a reductive TCA cycle pathway (Fig. 4.2). By reversal of the TCA cycle, acetyl CoA is produced from citrate with consumption of ATP and coenzyme A.

Acetyl CoA by accepting CO₂ is converted to pyruvate which by reversal of glycolytic pathway produces glucose-6-phosphate:

Pyrodictium is a hyper-thermophile isolated from a geo-thermally heated sea-floor. It is characterized by a disc-shaped cell embedded in a pellicle consisting of a network of fibres. It is an anaerobic obligate chemolithotroph-using H₂ as oxidisable energy source. It can grow between 82°, and 110°C with an optimum temperature of 105°C.

Sulfolobus is acidothermophilic and have members characterized by irregularly lobed spherical cells measuring 0.8 to 1.0 μm in diameter. S. acidocaldarius is an aerobic Gram-negative facultative chemolithotroph having cell walls composed of protein, hexosamine and carbohydrates.

The organism grows in acid hot springs containing sulfur compounds. The organisms thrive at a temperature of 55° to 80°C with an optimum of 75°C and at a pH of 1.55 to 3.5. They oxidize elemental sulfur to sulfuric acid and are capable of chemolithotrophic growth using the oxidizing energy of either sulfur (S°—>S^—) or ferrous iron (Fe²⁺—>Fe³⁺). The bacteria can also grow heterotrophically using sugars and amino acids, e.g. glutamate.

B. Euryarchaeota:

The phylum Euryarchaeota is much larger and more diverse than Crenarchaeota. It includes 7 classes — Methanobacteria, Methanococci, Halo-bacteria, Thermoplasmata, Thermococci, Archaeoglobi and Methanopyri.

There are some 46 genera which can be grouped into four major types:

i. The methanogens,

ii. The extreme halophiles,

iii. The cell wall-less thermophiles and

iv. The thermophilic cocci.

(i) Methanogens:

All methanogenic bacteria belong to Euryarchaeota and they form the largest group of archaebacteria including a variety of morphological forms, like long or short, straight or curved rods, spirilli, cocci or packets of cocci.

All methanogens are strictly anaerobic requiring a low redox potential for optimal growth. They are adapted to a neutral to slightly alkaline pH (6 to 8). Methanogens may be mesophilic or thermophilic. Cell wall is composed of proteins, heteropolysaccharides or sometimes pseudomurein. Some important genera of methanogenic bacteria are Methanobacterium, Methanococcus, Methanomicrobium, Methanospirillum and Methanosarcina.

Some of the characteristic features of these genera are summarized in Table 4.2:

Methanococcus jannaschii was isolated from a hot spot 3 km below the surface of Pacific Ocean where the pressure was over 200 atmospheres. It is an autotroph and is able to grow on CO₂, H₂ and N₂ at a temperature of about 90°C.

It is the first archaebacterium of which the genome has been fully sequenced. More than 50% of its 1,738 genes have been found to differ from those of both prokaryotes and eukaryotes indicating that archaebacteria are genomically distinct from the rest of the living organisms.

Methane (CH₄), the simplest hydrocarbon, is a major component of natural gas and is present ubiquitously in soil, in fresh-water and marine sediments, lakes and oceans, as well as in the atmosphere. Most of the methane, except that of natural gases, is of biological origin.

About 500-800 million tons of methane are produced annually through biological activity. It has a great potential as a pollution-free alternative fuel. But methane, like CO₂, is a ‘green-house’ gas and it poses a threat in global warming. The methanogens synthesise methane by sequential reduction of C0₂ through formyl (-CHO), methenyl (=C-H), methylene (-CH₂-) and methyl (-CH₃) to CH4 with the help of several unique coenzymes.

The pathway of methane formation is shown in Fig. 4.3:

(ii) Halophiles:

The second largest group of the Phylum Euryarchaeota is that of extremely salt-tolerant archaebacteria placed in a single family, — Halo-bacteriaceae. Some of the genera of this group are Halo-bacterium, Halo-coccus, Haloferax, Natronobacter, Natronomonas and Natronococcus.

The most outstanding feature of these archaebacteria is their ability to grow at very high salt concentration. They are irreversibly adapted to conditions where the salinity ranges between 2.0 to 5.5 M, optimal concentration being 3.5 to 5.5 M which means 20 to 29% NaCl. When these bacteria are suspended in salt solutions below 1.5 M concentrations, the cells disintegrate completely.

The cytoplasmic proteins and membrane lipids of extreme halophiles are acidic having net negative charges. The bacteria therefore need a high concentration of positive charges or cations to screen the negative charges to stop repulsion forces from pulling the molecules apart.

Another interesting feature is that although extreme halophiles are tolerant to high NaCl concentration, the salt present inside the cells is mainly KCl and not NaCl. For example, in Halo bacterium the concentration of KCl in cell interior is about 4.0 M compared to 0.7 M concentration of NaCl.

Halo bacteria are normally strict aerobes having a chemoorganotrophic nutrition. A striking feature of some of them, as Halo bacterium salinarium, is to develop under oxygen deficiency a purple membrane. The purple colour of the membrane is due to a proteinaceous pigment called bacteriorhodopsin.

The protein is associated with a prosthetic purple pigment, called retinal. Bacteriorhodopsin forms distinctive hexagonally arranged patches in the cytoplasmic membrane, the retinal moieties occupying the external face of the membrane (Fig. 4.4). The bacteria can produce ATP with the help of light energy trapped by retinal.

The trapped energy is used by the protein part of the pigment to generate a proton gradient across the membrane which is utilized to synthesize ATP from ADP and inorganic phosphate, much in the same way as it occurs in photophosphorylation. However, the process differs from true photosynthesis, because it does not involve CO₂ reduction, or an electron transport system. Some other bacteiorhodopsins found in halo bacteria are involved in other functions, like transport of chloride ions (Cl^–), flagellar activity etc.

(iii) Thermo plasma:

There are two genera of archaebacteria which lack a cell wall. These are Thermo plasma and Picrophilus. Both are moderately thermophilic, growing at a higher temperature limit of 60°C and both are highly acidophilic (pH 1 to 2, or even at pH 0).

Thermo plasma has more or less spherical cells (1 to 1.5 μ) surrounded by a rigid membrane consisting of tetra ethers, lipopolysaccharides and glycoproteins. Their natural habitat is refuse piles of coal mines. At 60°C, the cells tend to be filamentous.

A highly striking feature, unknown in prokaryotic organisms, is that the DNA is associated with histone-like proteins to form particles comparable to the nucleosomes of eukaryotic organisms. Picrophilus has irregularly spherical cells (1 to 1.5 µ). The bacteria are more acidophilic than members of Thermo plasma, having an optimum at about pH 0.7 and having the ability to grow even at pH 0.

(iv) Thermophilic cocci:

Archaebacterial thermophilic cocci belong to 5 genera distributed in three classes, each having a single order and a single family. The genera are Thermococcus, Pyrococcus, Archaeoglobus, Ferro Globus and Methanopyrus.

Thermococcus includes Gram-negative, motile, anaerobic cocci capable of growing optimally between 88° to 100°C. The organisms can reduce S° to S^{– –} (sulfide). G + C content of DNA is 55 moles %.

Pyrococcus was first isolated from geothermally heated marine sediments. The cells are anaerobic, Gram-negative cocci, (0.8 to 2.5 μm), motile, with mono-polar tuft of flagella (about 7 μm long). The bacteria occur often in pairs. They can grow chemoorganotrophically utilizing complex organic substrates at temperatures between 70° to 103°C. G + C content of DNA is 37.1 to 39.8 moles %.

Archaeoglobus is represented by anaerobic, Gram-negative irregularly shaped spherical organisms. They can grow at 83°C, chemolithotrophically reducing sulfate, thiosulfate or sulfite to sulfide, or they can grow chemoorganotrophically. Cell wall is composed of glycoproteins.

Methanopyrus includes Gram-negative, hyper-thermophilic, methanogenic rod-shaped bacteria growing optimally at 98°C. M. kandleri can grow even at 110°C and not below 84°C. These bacteria represent the most ancient branch of the Euryarchaeota.

Phylogeny of Archaebacteria:

Phylogeny of archaebacteria based on 16S r-RNA sequence analysis is shown in Fig. 4-5: