ARCHAEA

The archaea bacteria [Greek; archaios-ancient, and bakterion- small rod] are diverse in
their morphology and physiology. Archaea bacteria are restricted to extreme aquatic and
terrestrial habitats. They are often present in anaerobic, hyper-saline or high temperature
environment. Some times they have also been found in cold environment. They can stain gram
positive as well as gram negative. Morphologically they may be spherical, rod shaped, spiral,
lobed, plate shaped or pleomorphic. A few are single cell and other filamentous or aggregrates.
They range in diameter from 0.1 to 15 µm in length. Physiologicaly either they are aerobic,
facultatively anaerobic or strictly anaerobic. On the basis of ssrRNA analysis, the Archaea
consist of three phylogenetically-distinct groups: Crenarchaeota, Euryarchaeota and
Korarchaeota. However, for the Korarchaeota, only their nucleic acids have been detected, and
no organisms have been isolated or cultured. Based on their physiology, the Archaea can be
organized into three types: methanogens (prokaryotes that produce methane); extreme
halophiles (prokaryotes that live at very high concentrations of salt (NaCl); and extreme (hyper)
thermophiles (prokaryotes that live at very high temperatures). In addition to the unifying
archaeal features that distinguish them from Bacteria (i.e., no murein in cell wall, ester-linked
membrane lipids, etc.), the Archaea exhibit other unique structural or biochemical attributes
which adapt them to their particular habitats. The Crenarchaeota consists mainly of
hyperthermophilic sulfur-dependent prokaryotes and the Euryarchaeota contains the
methanogens and extreme halophiles. ssrRNAs of the Korarchaeota have been obtained from
hyperthermophilic environments similar to those inhabitated by Crenarchaeota. None of the
Korarchaeota has been cultured in the laboratory, although information about them can be
inferred from their genome structure.
Figure 1. Phylogenetic tree of Archaea

CHEMICAL COMPOSITIONAL VARIATIONS IN ARCHAE BACTERIA

Cell wall: The cell wall structure and chemistry of archae bacteria differ from eubacteria. Many
gram positive archae bacteria have a wall with asingle thick homogenous layer like gram positive
eubacteria. Gram negative archae bacteria consists surface layer of protein or glycoprotein
subunits. Archaebacteria cell wall does not have the muramic acid and D-amino acids which is
characteristic feature of eubacterial peptidoglycan. Generally, cell wall is made up of Proteins
and polysaccharides. In archae bacteria two important carbohydrates namely N-
acetylglucosamine and N-acetylosaminuronic acid are found to be attached each other by β,1-3
glycosidic bond. Further they are cross linked by L-aminoacids like Glutamate, alanine and
lysine. This wall structure in archae bacteria is known as Pseudomurein. Some species of the
archae bacteria contain an envelope out side the wall. Gram-negative archae bacteria have a
layer of glycoprotein out side their plasma membrane. The layer may be thick as 20 to 40 nm.
Some times there are two layers. The chemical content of these walls vary considerably species
to species.
Membrane: A most distinctive feature of archae bacteria is the chemical nature of their
membrane lipids. In eubacteria glycerol is attched to fatty acids by ester bond but in archae
bacteria glycerol is attached by ether bond to isoprenoids (with C20-phytanyl). Neutral lipids are
also found in form of free long carbon chain fatty acids or isoprenoid hydrocarbons (C15 to C30).
Usually glycerol attached to isoprenoid of 20 carbons called glycerol diether, while there is chain
of 40 carbons and two glycerol are attached called diglycerol tetraether. Polar lipids
(Phospholipids, sulfolipids and glycolipids) are also present in archaebacterial membrane. These
lipids can be combined in various ways to yield membranes of different rigidity and thickness.

(1) Chirality of glycerol : The basic unit from which cell membranes are built is the phospholipid. There
is a molecule of glycerol which has a phosphate added to one end, and two side chains attached at the
other end. When the cell membrane is put together, the glycerol and phosphate towards end of the
molecules hang out at the surface of the membrane, with the long side chains sandwiched in the middle.
This layering creates an effective chemical barrier around the cell and helps maintain chemical
equilibrium.

While bacteria and eukaryotes have D-glycerol in their membranes, archaeans have L-glycerol in theirs.
This is more than a geometric difference. Chemical components of the cell have to be built by enzymes,
and the "handedness" (chirality) of the molecule is determined by the shape of those enzymes. A cell
that builds one form will not be able to build the other form.

(2) Ether linkage: When side chains are added to the glycerol, most organisms bind them together using
an ester linkage (see diagram above). The side chain that is added has two oxygen atoms attched to one
end. One of these oxygen atoms is used to form the link with the glycerol, and the other protrudes to the
side when the bonding is done. By contrast, archaeal side chains are bound using an ether linkage,
which lacks that additional protruding oxygen atom. This gives the resulting phospholipid different
chemical properties from the membrane lipids of other organisms.
(3) Isoprenoid chains : The side chains in the phospholipids of bacteria and eukaryotes are fatty acids,
chains of usually 16 to 18 carbon atoms. Archaea do not use fatty acids to build their membrane
phospholipids. Instead, they have side chains of 20 carbon atoms built from isoprene. Isoprene is the
simplest member of a class of chemicals called terpenes. By definition, a terpene is any molecule bilt by
connecting isoprene molecules together. Each isoprene unit has a "head" and a "tail" end (like a Lego®
block), but unlike their toy counterparts, isoprene blocks can be joined in many ways. A head can be
attached to a tail or to another head end, and tails can be similarly joined. The immense variety of terpene
compounds that can be built from simple isoprene units include beta-carotene (a vitamin), natural and
synthetic rubbers, plant essential oils (such as spearmint), and steroid hormones (such as estrogen and
testosterone).

(4) Branching of side chains: Not only are the side chains of achaeal membranes built from different
components, but the chains themselves have a different physical structure. Because isoprene is used to
build the side chains, there are side branches off the main chain (see diagram above). The fatty acids of
bacteria and eukaryotes do note have these side branches (the best they can manage is a slight bend in
the middle), and this creates some interesting properties in archaeal membranes. For example, the
isoprene side chains can be joined together. This can mean that the two side chains of a single
phospholipid can join together, or they can be joined to side chains of another phospholipid on the other
side of the membrane. No other group of organisms can form such transmembrane phospholipids.
Another interesting property of the side branches is their ability to form carbon rings. This happens when
one of the side branches curls around and bonds with another atom down the chain to make a ring of five
carbon atoms. Such rings are thought to provide structural stability to the membrane, since they seem to
be more common among species that live at high temperatures.

Coenzymes: Some of the coenzymes and prosthetic groups of archae bacteria are distinct,
although they resemble to eubacteria or eukaryotes. Some examples are F420, a 5-
deazoriboflavin derivative, the nickel tetrapyrol factor F430, tetrahydromethanoprotein, and
coenzyme M. These factors were discovered in methanogenic bacteria.
The DNA dependent RNA polymerase of archaebacteria differ from those of eubacteria in
that they consist of more than four subunits and are resistant to the antibiotics. The nucleotide
sequence of archae bacterial 16S and 5S RNA differ from those of eubacteria.
 PHYSIOLOGICAL VARIATIONS IN ARCHAE BACTERIA
Methanogenic bacteria: Methanogenic bacteria are obligate anaerobes that will not tolerate
even brief exposure to air (O2). Anaerobic environments are plentiful, however, and include
marine and fresh-water sediments, bogs and deep soils, intestinal tracts of animals, and sewage
treatment facilities. Methanogens have an incredible type of metabolism that can use H 2 as an
energy source and CO2 as a carbon source for growth. In the process of making cell material
from H2 and CO2, the methanogens produce methane (CH4) in a unique energy-generating
process. The end product (methane gas) accumulates in their environment. Methanogens’
metabolism created most the natural gas (fossil fuel) reserves that are tapped as energy sources
for domestic or industrial use. Methanogens are normal inhabitants of the rumen (fore-stomach)
of cows and other ruminant animals. A cow belches about 50 liters of methane a day during the
process of eructation (chewing the cud). Methane is a significant greenhouse gas and is
accumulating in the atmosphere at an alarming rate. When rain forests are destroyed and
replaced by cows, it is "double-hit" on the greenhouse: (1) less CO 2 is taken up due to removal of
the autotrophic green plants; (2) additional CO 2 and CH4 are produced as gases by the combined
metabolism of the animal and symbiotic methanogens. Methanogens represent a microbial
system that can be exploited to produce energy from waste materials. Large amounts of
methane are produced during industrial sewage treatment processes, but the gas is usually
wasted rather than trapped for recycling. These bacteria are of almost all shapes known in the
eubacteria like cocci (Methanococcus) rods (Methanobacterium) short rods
(Methanobrevibacter), spirilla (Methanospirillum), filament (Methanothrix), square bacteria
(Methanoplanus) and packets (Methanosarcina).

Halobacteria or Halophiles: These bacteria live in natural environments such as the Dead Sea,
the Great Salt Lake, or evaporating ponds of seawater where the salt concentration is very high
(as high as 5 molar or 25 percent NaCl). The organisms require salt for growth and will not grow
at low salt concentrations (Actually, the cells lyse at low NaCl concentrations). Their cell walls,
ribosomes, and enzymes are stabilized by Na +. Halobacterium halobium, the prevalent species in
the Great Salt Lake, adapts to the high-salt environment by the development of "purple
membrane", formed by patches of light-harvesting pigment in the plasma membrane. The
pigment is a type of rhodopsin called bacteriorhodopsin which reacts with light in a way that
forms a proton gradient on the membrane allowing the synthesis of ATP. This is the only
example in nature of non photosynthetic photophosphorylation. The organisms are heterotrophs
that normally respire by aerobic means. The high concentration of NaCl in their environment
limits the availability of O2 for respiration so they are able to supplement their ATP-producing
capacity by converting light energy into ATP using bacteriorhodopsin. The examples of
halophiles are Halococcus, Halobacterium, Haloferax, Haloarcula, Natromococcus and
Natromobacterium.

Thermo-acidophilic bacteria: These extreme thermophiles or "hyperthermophiles" come from

several distinct phylogenetic lines of Archaea. These organisms require a very high temperature
(80 degrees to 105 degrees) for growth. Their membranes and enzymes are unusually stable at
high temperatures. Most of these Archaea require elemental sulfur for growth. Some are
anaerobes that use sulfur as an electron acceptor for respiration in place of oxygen. Some are
lithotrophs that oxidize sulfur as an energy source. Sulfur-oxidizers grow at low pH (less than pH
2), partly because they acidify their own environment by oxidizing S o (sulfur) to SO4 (sulfuric
acid). Hyperthermophiles are inhabitants of hot, sulfur-rich environments usually associated with
volcanism, such as hot springs, geysers and thermal vents ("smokers") and cracks in the ocean
floor. Sulfolobus was the first hyperthermophilic Archaean discovered by Thomas D. Brock
(1970). Thermus aquaticusis the source of the enzyme taq polymerase used in the polymerase
chain reaction, PCR., The bacterium has an optimum temperature for growth of 70 degrees.
Sulfolobus grows in sulfur-rich, hot acid springs at temperatures as high as 90 degrees and pH
values as low as 1. Thermoplasma, also discovered by Brock, is a unique thermophile that is the
sole representative of a distinct phylogenetic line of Archaea. Thermoplasma resembles the
bacterial mycoplasmas in that it lacks a cell wall. Thermoplasma grows optimally at 55 degrees
and pH 2. Interestingly, it has only been found in self-heating coal refuse piles, which are a man-
made waste. Examples of thermoacidophiles are, Thermoproteus, Pyrodictium, Thermococcus,
Thermodiscus, Desufurococcus, Thermofilum and Archaeoglobus.

Although the Archaea are often inhabitants of unusual or extreme environments, there may be
corresponding species of Bacteria, and even eukaryotes, in these habitats as well. No bacterium
can produce methane, but in many anaerobic environments Bacteria are found in association
with methanogens. With regard to acid tolerance, a bacterium, Thiobacillus, has been observed
growing at pH near 0. A eukaryotic alga, Cyanidium, has also been found growing near pH 0. In
superheated environments (greater than 100 degrees), Archaea may have an exclusive hold,
but Bacteria have been isolated from boiling hot springs in Yellowstone National Park and other
parts of the world. No bacterium grows at the highest salt concentration which supports the
growth of the halobacteria, but osmophilic yeasts and fungi can grow at correspondingly low
water actvities where sugar is the solute in high Concentration.