ARCHAEA

Morphology, Physiology, biochemistry,

diversity & Industrial Applications of domain
Archaea

B.G. Eranga Thilina Jayashantha

B.Sc. (UG) Microbiology (Special)
University of Kelaniya – Sri Lanka
ARCHAEA

Contents

1.) Introduction to Domain Archaea……………………………….02

2.) Fossil records on Archaea………………………………………04
3.) Archaeal Systematics…………………………………………….05
4.) Morphological significances of Archaea……………………...08
5.) Molecular biological significances of Archaea………………15
6.) Viruses of Archaea……………………………………………….17
7.) Significances of Gene Transfer in Archaea…………………...18
8.) Introduction to the Diversity of Archaea………………………20
9.) Euryarchaeota…………………………………………………….24
10.) Thaumarchaeota………………………………………………….32
11.) Nanoarchaeota…………………………………………..32
12.) Korarchaeota……………………………………………………...33
13.) Crenarchaeota…………………………………………………….33
14.) Industrial Applications of Archaea……………………………..35

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1) Introduction to Domain Archaea

Domain Archaea is a Domain in Carl Woese s three domain classification of living organisms. The
domain contains Prokaryotic microorganisms which are adapted for extreme environments. They
show vigorous and stable resistance for extreme and catastrophic environments on Earth. They are
most primitive type of organisms on Earth. According to microbiologists, their formation was
happened nearly 3.5 billion years ago in early young earth with extreme environments (highly
energetic atmosphere, UV, extremely high heat, shock waves due to earthquakes). They have been
being evolved for 3.5 billion years. Therefore they are the oldest members in phylogeny. That is why
they have adapted for extreme conditions.These organisms are living in both aquatic and terrestrial
extreme environments. Majority of aquatic organisms are marine. They are found in hydrothermal
vents in basins of oceans, Hot water springs and highly saline environments. Some terrestrial
organisms are found in volcanos. These examples show the resistance and adaptations of these
organisms to achieve those extreme conditions. There morphological characters are same as other
bacteria but some Archaea show exclusively different characteristics than other bacteria. But their
Molecular biological, Physiological and Biochemical characteristics are entirely different than other
prokaryotes. These different Molecular biological, physiological and Biochemical characteristics serve
them resistance for extreme environments. All Archaea can be divided in to three classical groups.
They are,


Methanogens


Hyper Thermophiles
Extreme Halophiles
The scientific community was understandably shocked in the late 1970s by the discovery of an entirely
new group of organisms the Archaea. Dr. Carl Woese and his colleagues at the University of Illinois
were studying relationships among the prokaryotes using DNA sequences, and found that there were
two distinctly different groups. Those "bacteria" that lived at high temperatures or produced methane
clustered together as a group well away from the usual bacteria and the eukaryotes. Because of this
vast difference in genetic makeup, Woese proposed that life be divided into three domains: Eukaryota,
Eubacteria, and Archaebacteria. He later decided that the term Archaebacteria was a misnomer, and
shortened it to Archaea. The three domains are shown in the illustration bellow, which illustrates also
that each group is very different from the others.

Fig 1: Three Domain Classification system

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Fig 2: The hot springs of Yellowstone National Park, USA, were

among the first places Archaea were discovered.

Archaea include inhabitants of some of the most extreme environments on Earth. Some live near rift
vents in the deep sea at temperatures well over 100 degrees Centigrade. Others live in hot springs
(such as the ones pictured above), or in extremely alkaline or acid waters. They have been found
thriving inside the digestive tracts of cows, termites, and marine life where they produce methane.
They live in the anoxic muds of marshes and at the bottom of the ocean, and even thrive in petroleum
deposits deep underground. Some Archaea can survive the desiccating effects of extremely saline
waters. However, archaea are not restricted to extreme environments; new research is showing that
some archaea are also quite abundant in the plankton of the open sea.
One salt-loving group of archaea includes Halobacterium, a well-studied archaea. The light-sensitive
pigment bacteriorhodopsin gives Halobacterium its natural specific color and provides it with
chemical energy. Bacteriorhodopsin has a lovely purple color and it pumps protons to the outside of
the membrane. When these protons flow back, they are used in the synthesis of ATP, which is the
energy source of the cell. This protein is chemically very similar to the light-detecting
pigment rhodopsin, found in the vertebrate retina.
Fig 3 : Clones of Halobacterium salinarum on an agar plate . These
contain the information for the production of the modified
bacteriorhodopsins.

Fig 4 : Chemiosmotic coupling between the sun

energy, Bacteriorhodopsin and
phosphorylation by ATP synthase(chemical energy)
during metabolism in Halobacterium salinarum.

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2) Fossil records of Archaea

Archaea and Bacteria cells may be of similar sizes and shapes, so the shape of a microbial fossil does not
usually help in determining its origin. Instead of physical features, micro-paleontologists rely on
chemical features. Chemical traces of ancient organisms are called molecular fossils, and include a
wide variety of chemical substances. Ideally, a molecular fossil should be
 A chemical compound that is found in just one group of organisms,
 It is not prone to chemical decay
 Decays into predictable and recognizable secondary chemicals.
In the case of the Archaea, there is a very good candidate to preserve as a molecular fossil from the cell
membrane. Archeal membranes do not contain the same nature of phospholipids that other organisms
have; instead, their membranes are formed from Isoprene chains. Because these particular isoprene
structures are unique to Archaea, In most Archaea they present as Tetra-ether Monolayer. That is why
they are not as prone to decomposition at high temperatures, they make good markers for the
presence of ancient Archaea. So they act as Molecular Fossils during the archeological investigations of
primitive Archaea in order to reveal the mysterious history of Domain Archaea in the Earth.
Molecular fossils of Archaea in the form of isoprenoid residues were first reported from the Messel oil
shale of Germany .These are Miocene deposits whose geologic history is well known. Material from the
shale was dissolved and analyzed using a combination of chromatography and mass spectrometry.
These processes work by separating compounds by weight and other properties, and produce a
"chemical fingerprint". The fingerprint of the Messel shale included isoprene compounds identical to
those found in some Archaea. Based on the geologic history of the Messel area, thermophiles and
halophiles are not likely to have ever lived there, so the most likely culprits to have left these chemical
fingerprints behind are archaeal Methanogens.
Since their discovery in the Messel shales, isoprene compounds indicative of ancient Archaea have
been found in numerous other localities (Hahn & Haug, 1986), including Mesozoic, Paleozoic,
and Precambrian sediments. Their chemical traces have even been found in sediments from the Isua
district of west Greenland, the oldest known sediments on Earth at about 3.8 billion years old

Fig 5 : (a) Gas Chromatographic , (b) Mass spectrometric analysis of samples collected
4|Page from Messel oil shale of Germany to reveal Archaeal molecular fossils.
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3) Archaeal Systematics
The Archaea constitute one of the three domains into which all known life may be divided. There are
two other domains of life. One of these is the Eukaryota, which includes the plants, animals, fungi, and
Protists. Except for the Protists, these organisms have been known and studied since the time
of Aristotle, and are the organisms with which you are most likely familiar. The second domain to be
discovered was the Bacteria, first observed in the 17th century under the microscope by people such
as the Dutch naturalist Antony van Leeuwenhoek. Early classifications depended on the shape, colony
morphology in laboratory cultures, and other physical characteristics.
When biochemistry blossomed as a modern science, chemical characteristics were also used to classify
bacterial species, but even this information was not enough to reliably identify and classify the tiny
microbes. Reliable and repeatable classification of bacteria was not possible until the late 20th century
when molecular biology made it possible to sequence their DNA.
Molecules of DNA are found in the cells of all living things, and store the information cells need to build
proteins and other cell components. One of the most important components of cells are ribosomes, a
large and complex molecule that converts the DNA message into a chemical product (Protein). Most of
the chemical composition of a ribosome is ribosomal RNA, which has its own sequence of building
blocks. With sequencing techniques, a molecular biologist can take apart the building block of RNA one
by one and identify each one. The result is the sequence of those building blocks.
Because ribosomes are so critically important is the functioning of living things, they are not prone to
rapid evolution. A major change in ribosome sequence can render the ribosome unable to fulfill its
duties of building new proteins for the cell. Because of this, we say that the sequence in the ribosomes
is conserved, that it does not change much over time. This slow rate of molecular evolution made
the ribosome sequence a good choice for unlocking the secrets of bacterial evolution. By
comparing the slight differences in ribosome sequence among a wide diversity of bacteria, groups of
similar sequences could be found and recognized as a related group.
In the 1970s, Carl Woese and his colleagues at the University of Illinois at Urbana-Champaign began
investigating the sequences of bacteria with the goal of developing a better picture of bacterial
relationships. Their findings were published in 1977, and included a big surprise. Not all tiny microbes
were closely related. In addition to the bacteria and eukaryote groups in the analysis, there was a third
group of methane-producing microbes. These methanogens were already known to be chemical
oddities in the microbial world, since they were killed by oxygen, produced unusual enzymes, and had
cell walls different from all known bacteria. Carl Woese s Research Papers 977 which included the
first findings of Archaea ;
 An ancient divergence among the bacteria. Balch WE, Magrum LJ, Fox GE, Wolfe RS, Woese CR.J Mol Evol.
1977 Aug 5;9(4):305-11.
 Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Fox GE, Magrum LJ, Balch
WE, Wolfe RS, Woese CR. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4537-4541.
 Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Woese CR, Fox GE. Proc Natl Acad
Sci U S A. 1977 Nov;74(11):5088-90.

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The significance of Woese's work was that he showed these bizarre microbes were different at the
most fundamental level of their biology. Their RNA sequences were no more like those of the bacteria
than like fish or flowers. To recognize this enormous difference, he named the group "Archaebacteria"
to distinguish them from the "Eubacteria" (true bacteria). As the true level of separation between these
organisms became clear, Woese shortened his original name to Archaea to avoid anyone from
thinking that archaea were simply a bacterial group.

Fig 6 : Phylogenic relationships of Domain Archaea according to their molecular biological characteristics ( r-RNA &
DNA Sequencing )

Fig 7 : Evolutionary relationships of Archaea with other two domains

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Archaea have increasingly become the study of scientific investigation. In many ways, archaeal cells
resemble the cells of bacteria, but in a number of important respects, they are more like the cells of
eukaryotes. The question arises whether the Archaea are closer relatives of the Bacteria or the
Eukarya. One novel approach used in addressing the question is to look at sequences of Duplicated
genes in cells. Some DNA sequences occur in more than one copy within each cell, presumably because
an extra copy was made at some point in the past, during the evolutionary timeline There are a very
few genes known to exist in duplicate copies in all living cells, suggesting that the duplication
happened before the separation of the three domains of life.
In comparing the two sets of sequences of Duplicated genes, scientists have found that the
Archaea may actually be more closely related to Eukaryotes than to the Bacteria.

Fig 8 : The technology behind ribosomal RNA gene phylogenies. 1. DNA is extracted from cells. 2. Copies of the gene
encoding rRNA are made by the polymerase chain reaction (PCR). 3, 4. The gene is sequenced and the sequence
aligned with sequences from other organisms. A computer algorithm makes pairwise comparisons at each base and
generates a phylogenetic tree, 5, that depicts evolutionary relationships.

Fig 9 :
Archaea is
more closely
related with
Eukarya than
Bacteis

Fig 10 :
The three domains of cellular organisms are Bacteria, Archaea, and
Eukarya. Archaea and Eukarya diverged long before nucleated cells
with orga elles oder eukaryotes i part a appear i the fossil
record. LUCA, last universal common ancestor.

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4) Morphological significances of Archaea

Even under a high-power light microscope, the largest archaea look like tiny dots. Fortunately,
the electron microscope can magnify even these tiny microbes enough to distinguish their physical
features. You can see archaea images below, made using a variety of micrographic techniques.
Archaeal shapes are quite diverse. Some are spherical, a form known as coccus, and these may be
perfectly round or lobed and lumpy. Some are rod-shaped, a form known as bacillus, and range from
short bar-shaped rods to long slender hair-like forms. Some oddball species have been discovered with
a triangular shape, or even a square shape.

Halococcus salifodinae Sulfolobus Methanosarcina rumen

Methanococcoides burtonii Staphylothermus marinus

Fig 11 : Morphological Diversity of different Archaeal types

Although cell morphology is easily determined, it is a poor predictor of other properties of a cell. For
example, under the microscope many rod-shaped Archaea look identical to rod-shaped Bacteria, yet
we know they are of different phylogenetic domains With very rare exceptions, it is impossible to
predict the physiology, ecology, phylogeny, pathogenic potential, or virtually any other property of a
prokaryotic cell by simply knowing its morphology.

Individual archaea range from 0.1 micrometers μm to over μm in diameter, and occur in various

 Other morphologies in the Crenarchaeota include irregularly shaped lobed cells in Sulfolobus,
shapes, commonly as spheres, rods, spirals or plates.

 Needle-like filaments that are less than half a micrometer in diameter in Thermofilum
 Perfectly rectangular rods in Thermoproteus and Pyrobaculum.
 Haloquadratum walsbyi are flat,
 Square shaped archaea that live in hypersaline pools.

In Thermoplasma and Ferroplasma the lack of a cell wall means that the cells have irregular
shapes, Some species form aggregates or filaments of cells up to 200 μm long.These organisms
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can be prominent in biofilms. Notably, aggregates of Thermococcus coalescens cells fuse

together in culture, forming single giant cells. Archaea in the genus Pyrodictium produce an
elaborate multicellular colony involving arrays of long, thin hollow tubes called cannulae that
stick out from the cells' surfaces and connect them into a dense bush-like agglomeration. The
function of these cannulae is not settled, but they may allow communication or nutrient
exchange with neighbors.Multi-species colonies exist, such as the "string-of-pearls" community
that was discovered in 2001 in a German swamp. Round whitish colonies of a novel
Euryarchaeota species are spaced along thin filaments that can range up to 15 cm long, these
filaments are made of a particular bacteria species.

Specific Characteristics in Archaea cellular membranes

The most striking chemical differences between Archaea and other living things lie in their cell
membrane. There are four fundamental differences between the archaeal membrane and those of all
other cells:
(1) Chirality of glycerol,
(2) Ether linkage,
(3) Isoprenoid chains,
(4) Branching of side chains.

(1) Chirality of glycerol :

The basic unit from which cell membranes are built is the phospholipid. This 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 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.

The glycerol used to make archaeal phospholipids is a stereoisomer of the glycerol used to build
bacterial and eukaryotic membranes. There are two possible forms of the molecule that are mirror
images of each other. It is not possible to turn one into the other simply by rotating it around. While
bacteria and eukaryotes have D-glycerol in their membranes, Archaea 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 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.

Fig 12 : Stereoisomeric difference of glycerol molecules in phospholipids between

(a) Archaea and (b)other organisms ( Bacteria , Eukaryotes )
(a)
This suggests that archaea use entirely different enzymes for
synthesizing phospholipids than do bacteria and eukaryotes. Such
enzymes developed very early in life's history, suggesting an early split
from the other two domains
(b)

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(2) Ether linkage :

When side chains are added to the glycerol, most organisms bind them together using an Ester
linkage. The side chain that is added has two oxygen atoms attached 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. Ether bonds are chemically
more resistant than Ester bonds. This stability might help archaea to survive extreme
temperatures and very acidic or alkaline environments.

(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. Only Archaea use
Isoprenoid chains to make phospholipids in their cell membranes.

(4) Branching of side chains :

Not only are the side chains of Archaeal 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. The fatty acids of bacteria and eukaryotes do
not 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. These branched chains may help
prevent archaeal membranes from leaking at high temperatures.

(5) Arranging phospholipids as Tetra ethers to form Monolayer of cell membrane

In some Archaeal species, isoprene side chains are joined together to form Tetra ether structures.
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. The chemical
nature of these types of molecules can be describe as Bolaamphiphile . No other group of
organisms can form such transmembrane phospholipids. So in this case Lipid bilayer is replaced
by a monolayer. This arrangement may make their membranes more rigid and better able to resist
harsh environments. For example, the lipids in Ferroplasma are of this type, which is thought to
aid this organism's survival in its highly acidic habitat.

(6) Formation of Cyclopropane and Cyclohexane Carbon rings by Isoprenoid side chains

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. They may work in the same way
that cholesterol does in eukaryotic cells to stabilize membranes.

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Fig 13: Membrane structures.

Top, an archaeal phospholipid:

1, isoprene chains;
2, ether linkages;
3, L-glycerol moiety;
4, phosphate group.

Middle, a bacterial or eukaryotic phospholipid:

5, fatty acid chains;
6, ester linkages;
7, D-glycerol moiety;
8, phosphate group.

Bottom:
9, lipid bilayer of bacteria and eukaryotes;
10, lipid monolayer of some archaea

The cytoplasmic membrane of Archaea is formed from either glycerol diethers, which have 20-carbon
side chains (the 20-C unit is called a phytanyl group composed of 5 isoprene units), or diglycerol
tetraethers, which have 40-carbon side chains (Fig 14). In the tetraether lipid, the ends of the phytanyl
side chains that point inward from each glycerol molecule are covalently linked. This forms a lipid
monolayer instead of a lipid bilayer membrane (Fig 14 d, e). In contrast to lipid bilayers, lipid
monolayer membranes are extremely resistant to heat and are therefore widely distributed among
hyperthermophilic Archaea, organisms that grow best at temperatures above 80°C. Membranes with a
mixture of bilayer and monolayer character are also possible, with some of the opposing hydrophobic
groups covalently bonded and others not. Many archaeal lipids contain rings within the hydrocarbon
side chains. For example, crenarchaeol, a lipid widespread among species of Thaumarchaeota, a major
phylum of Archaea, contains four 5-carbon (cyclopentyl) rings and one 6-carbon (cyclohexyl)
ring (Fig 14c). Rings in the hydrocarbon side chains affect the chemical properties of the lipids and
thus overall membrane function. Sugars can also be present in archaeal lipids. For example,
the predominant membrane lipids of many Euryarchaeota, a major group of Archaea that includes the
methanogens and extreme halophiles, are glycerol diether glycolipids. Despite the differences in
chemistry between the cytoplasmic membranes of Archaea and organisms in the other domains, the
fundamental construction of the archaeal cytoplasmic membrane, inner and outer hydrophilic
surfaces and a hydrophobic interior, is the same as that of membranes in Bacteria and Eukarya.
Evolution has selected this design as the best solution to the main function of the cytoplasmic
membrane permeability.

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Fig 14: Major lipids of Archaea and the architecture of archaeal membranes. (a, b) Note that the hydrocarbon of
the lipid is bonded to the glycerol by an ether linkage in both cases. The hydrocarbon is phytanyl (C20) in part and
biphytanyl (C40) in part b. (c) A major lipid of Thaumarchaeota is crenarchaeol, a lipid containing 5- and 6-carbon
rings. (d, e) Membrane structure in Archaea may be bilayer or monolayer (or a mix of both).

Specific Characteristics in Archaea Cell Wall

There are lack of Peptidoglycan present in Archaea cell wall. Instead of Peptidoglycan, There is a
chemical compound called Pseudomurein and it is the major compound in Archaeal Cell wall.
The cell walls of certain methanogenic Archaea contain a molecule that is remarkably similar to
peptidoglycan, a polysaccharide called pseudomurein. The backbone of pseudomurein is formed from
alternating repeats of N-acetylglucosamine (also present in peptidoglycan) and acetyltalosaminuronic
acid; the latter replaces the N-acetylmuramic acid of peptidoglycan. Pseudomurein also differs from
peptidoglycan in that the glycosidic bonds between the sugar derivatives are -1,3 instead of -1,4,
and the amino acids are all of the L-stereoisomer . It is thought that peptidoglycan and pseudomurein
either arose by convergent evolution after Bacteria and Archaea had diverged or, more likely, by
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evolution from a common polysaccharide present in the cell walls of the common ancestor of the
domains Bacteria and Archaea.

Cell walls of some other Archaea lack pseudomurein and instead contain other polysaccharides. For
example, Methanosarcina species have thick polysaccharide walls composed of polymers of
glucose, glucuronic acid, galactosamine uronic acid, and acetate. Extremely halophilic Archaea such as
Halococcus, which are related to Methanosarcina, have similar cell walls that are also highly sulfated.
The negative charges on the sulfate ion (SO4 2-) bind Na+ present in the habitats of Halococcus salt
evaporation ponds and saline seas and lakes at high levels. The sulfate sodium complex helps stabilize
the Halococcus cell wall in such strongly ionic environments.

S-Layers

The most common type of cell wall in Archaea is the paracrystalline surface layer, or S-layer as it is
called. S-layers consist of interlocking molecules of protein or glycoprotein. The paracrystalline
structure of S-layers can form various symmetries, including hexagonal, tetragonal, or trimeric,
depending upon the number and structure of the subunits of which it is composed. S-layers have been
found in representatives of all major lineages of Archaea and also in several species of Bacteria. The
cell walls of some Archaea, for example the methanogen Methanocaldococcus jannaschii, consist only of
an S-layer. Thus, S-layers are sufficiently strong to withstand osmotic pressures without any other wall
components.

Besides serving as protection from osmotic lysis, S-layers may have other functions. For example, as
the interface between the cell and its environment, it is likely that the S-layer functions as a selective
sieve, allowing the passage of low-molecular-weight solutes while excluding large molecules or
structures (such as viruses). The S-layer may also function to retain proteins near the cell surface,
much as the outer membrane does in gram-negative bacteria.

Because they lack peptidoglycan, Archaea are naturally resistant to Lysozyme and the antibiotic
Penicillin, agents that either destroy peptidoglycan or interrupt its biosynthesis.

Fig 15: The S-layer. Transmission electron micrograph of a portion of an

S-layer

 No Archaea have been shown to form Endospores, suggesting that the capacity to produce
endospores evolved sometime after the prokaryotic lineages diverged about 3.5 billion years
ago

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Specific Characteristics in Archaeal Flagella

Motility is important for microorganisms because the ability to move allows cells to explore new
habitats and exploit their resources. In Archaea, Major genera of methanogens, extreme halophiles,
Thermosacidophiles, and Hyperthermophiles are all capable of swimming motility. Archaeal flagella
are roughly half the diameter of bacterial flagella, but impart movement to the cell by rotating, as do
flagella in Bacteria. However, unlike Bacteria, in which a single type of protein makes up the flagella
filament, several different flagellin proteins are known from Archaea, and their amino acid sequences
and genes that encode them bear little relationship to those of bacterial flagellin.

Studies of swimming cells of the extreme halophile Halobacterium show that they swim at speeds only
about one-tenth that of cells of Escherichia coli. Whether this holds for all Archaea is unknown, but the
significantly smaller diameter of the archaeal flagellum compared with the bacterial flagellum would
naturally reduce the torque and power of the flagella motor such that slower swimming speeds are not
surprising. Moreover, from biochemical experiments with Halobacterium it appears that archaeal
flagella are powered directly by ATP rather than by the proton motive force, the source of energy for
the flagella of Bacteria If this holds for the flagella of all motile Archaea, it would mean that the flagella
motors of Archaea and Bacteria employ fundamentally different energy-coupling mechanisms.
Combined with the clear differences in flagellar protein structure between Archaea and Bacteria.
This suggests that, as for endospores, flagellar motility evolved separately as prokaryotes diverged
over 3.5 billion years ago.

Microbiologists recently zeroed in on the movements of swimming Archaea and showed that
Halobacterium was the slowest of all species examined. By contrast, cells of the archaeon
Methanocaldococcus swam nearly 50 times faster than cells of Halobacterium and 10 times faster than
cells of E. coli. Astonishingly, it is the fastest organism on Earth!

 Research report ;
Herzog, B., and R. Wirth. 2012. Swimming behavior of selected species of Archaea. Appl. Environ.
Microbiol. 78: 1670–1674. 25

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5) Molecular Biological significances of Archaea

Molecular biological characters of Archaea is more closely related with Eukarya than Bacteria. But
there are few similarities between Bacteria and Archaea. One similarity is, Genes of Archaea are
located as Operons in the Chromosome as same as in Bacteria.

1.) Transcription factor proteins are similar in Archaea and Eukarya.

2.) During the initiation of Transcription process, TATA-binding protein has bound to the TATA box
and Transcription factor protein B has bound to the B recognition element, then archaeal RNA
polymerase can bind and initiate transcription.

3.) Some archaeal genes have inverted repeats followed by an AT-rich sequence similar to those
found in many bacterial transcription terminators.

4.) One other type of suspected transcription terminator lacks inverted repeats, but contains
repeated runs of Thymine.

5.) No Rho-like proteins are involved for the transcription process in Archaea.

6.) Archaeal RNA Polymerase is complex than bacterial one and it is more similar than Eukaryotic
RNA Polymerases. Archaea contain only a single RNA polymerase that most closely resembles
eukaryotic RNA polymerase II. Both Archaea and Eukarya have RNA polymerase which have 11
or 12 subunits. But Bacterial RNA Polymerase have only 5 subunits ( including sigma factor )

Fig 16: Structure of Bacterial, Archaeal and Eukaryotic RNA Polymerase enzyme complexes.

7.) Structures of Archaeal promoters are resemble to Eukaryotic Promoters.

8.) There are Introns inside the genes in Archaea. But there are no Introns in Bacteria. Archaeal
introns are excised during Transcription by a specific ribonuclease that recognizes exon–intron
junctions. In a few cases, t-RNA s in Archaea are assembled by splicing together segments from
two or three different primary transcripts.

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9.) Normally non sense codons (eg: Stop codons) do not code for any amino acids in genetic code.
Normally there are 20 amino acids are involved to build life. It is a very uncommon thing that
encoding an amino acid from Stop codons. This is very rare incident but it happens in some
higher Eukaryotes as well as in certain Archaea. Pyrrolysine is an amino acid which can only
found in certain Archaea, coded by UAG stop codon. (It is 22nd amino acid that is known as an
uncommon amino acid which is involved to make the life, among 2 uncommon amino acids. 21st
is selenocysteine which can be only found in Higher Eukaryotes). Pyrolysine was first found in
Methanogenic Archaea.

10.) Starting amino acid (which is encoded by the Start codon) in Archaea is Methionine. It is same
as in Eukarya. But in bacteria, Formyl-methionine is the starting amino acid.

11.) Archaea is highly resistant for Chloramphenicol and Streptomycin which are translation
inhibiting antibiotics for Bacteria.

12.) Few repressor or activator proteins from Archaea have yet been characterized in detail, but it is
clear that Archaea have both types of regulatory proteins. Archaeal repressor proteins either
block the binding of RNA polymerase itself or block the binding of TBP (TATA-binding protein)
and TFB (transcription factor B), proteins that are required for RNA polymerase to bind to the
promoter in Archaea .At least some archaeal activator proteins function in just the opposite way,
by recruiting TBP to the promoter, thereby facilitating transcription.

Fig 17:
Repression of genes for nitrogen metabolism in
Archaea.
The NrpR protein of Methanococcus maripaludis
acts as a repressor. It blocks the binding
of the TFB and TBP proteins, which are required for
promoter recognition, to the BRE
site and TATA box, respectively. If there is a
shortage of ammonia, -ketoglutarate
is not converted to glutamate. The -ketoglutarate
accumulates and binds to NrpR,
releasing it from the DNA. Now TBP and TFB can
bind. This in turn allows RNA
polymerase to bind and transcribe the operon.

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6) Viruses of Archaea

Several DNA viruses have been discovered whose hosts are species of Archaea, including
representatives of both the Euryarchaeota and Crenarchaeota phyla. Most viruses that infect species of
Euryarchaeota, including both methanogenic and halophilic Archaea, are of the head and tail type,
resembling phages that infect enteric bacteria, such as phage T4. One novel archaeal virus infects a
halophile and is unusual because it is both enveloped and contains a single-stranded DNA genome.
By contrast, all other characterized archaeal DNA viruses contain double-stranded and typically
circular DNA genomes.

RNA archaeal viruses have been detected in thermal environments inhabited by Crenarchaeota. These
are single-stranded positive sense RNA viruses (positive-strand viruses), but little else is known about
them as they await detailed characterization and laboratory culture. However, as for Bacteria and
Eukarya, it is clear that at least some Archaea are infected by viruses with RNA genomes. The most
distinctive archaeal viruses infect hyperthermophilic Crenarchaeota. For example, the sulfur
chemolithotroph Sulfolobus is host to several structurally unusual viruses. One such virus, called SSV,
forms spindle-shaped virions that often cluster in rosettes. Such viruses are widespread in acidic hot
springs worldwide. Virions of SSV contain a circular DNA genome of about 15 kbp. A second
morphological type of Sulfolobus virus forms a rigid, helical rod-shaped structure. Viruses in this class,
nicknamed SIFV, contain linear DNA genomes about twice the size of that of SSV.

Many variations on the spindle and rod shaped patterns have been seen in archaeal viral isolation
studies. A spindle-shaped virus that infects the hyperthermophile Acidianus displays a novel behavior.
The virion, called ATV, contains A spindle-shaped virus also infects Pyrococcus (Euryarchaeota). This
virus, named PAV1, resembles SSV but is larger and contains a very short tail .PAV1 has a small
circular DNA genome and is released from host cells without cell lysis, probably by a budding
mechanism similar to that of the Escherichia coli bacteriophage M13 Pyrococcus has a growth
temperature optimum of 100°C, meaning that PAV1 virions must be especially heat-stable. Despite
their similar morphologies, genomic comparisons of PAV1 and SSV-type viruses show little sequence
similarity, indicating that the two types of viruses do not have common evolutionary roots.

Replication events in the life cycles of archaeal viruses are not yet clear. However, considering that the
genomes of most of these viruses are double-stranded DNA, it is unlikely that any major novel modes
of replication will be uncovered. However, important molecular details, such as the extent to which
viral rather than host polymerases and other enzymes are used in the replication process, await
further work on these remarkably tough viruses.

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7) Significances of Horizontal Gene Transfer in Archaea

Fig 18: Difference between Horizontal gene

transfer and Vertical gene transfer

Archaea contain a single circular chromosome like most Bacteria and genome analysis indicates that
horizontal transfer of archaeal DNA also occurs in nature, the development of laboratory-based gene
transfer systems lags far behind that for Bacteria. Practical problems here include the fact that
most well-studied Archaea are extremophiles, capable of growth only under extreme conditions of
high salt or high temperature. The temperatures necessary to culture some hyperthermophiles,
for example, will melt agar, and alternative materials are required to form solid media and obtain
colonies. Another problem is that most common antibiotics do not affect Archaea. For example,
penicillins do not affect Archaea because their cell walls lack peptidoglycan. The choice of selectable
markers for genetic crosses is therefore often limited. However, Novobiocin (a DNA gyrase inhibitor)
and Mevinolin (an inhibitor of isoprenoid biosynthesis) are used to inhibit growth of extreme
halophiles, and Puromycin and Neomycin (both protein synthesis inhibitors) inhibit methanogens.
Auxotrophic strains of a few Archaea have also been isolated for genetic selection purposes.

No single species of Archaea has become a model organism for archaeal genetics, although more
genetic work has been done on select species of extreme halophiles (Halobacterium, Haloferax) than
on any other Archaea. Instead, individual mechanisms for gene transfer have been found scattered
among a range of Archaea. In addition, several plasmids have been isolated from Archaea and some
have been used to construct cloning vectors, allowing genetic analysis through cloning and sequencing
rather than traditional genetic crosses. Transposon mutagenesis has been well developed in certain
methanogen species including Methanococcus and Methanosarcina, and other tools such as shuttle
vectors and other in vitro methods of genetic analysis have been developed for study of the highly
unusual biochemistry of the methanogens .

Transformation works reasonably well in several Archaea although details and conditions vary from
organism to organism. One approach requires removal of divalent metal ions, which in turn results in
the disassembly of the glycoprotein cell wall layer surrounding many archaeal cells and hence allows
access by transforming DNA. However, Archaea with rigid cell walls have proven difficult to transform,
although electroporation sometimes works. One exception is in Methanosarcina species, organisms
with a thick cell wall, for which high-efficiency transformation systems have been developed that
employ DNA-loaded lipid
preparations (liposomes) to deliver DNA into the cell. Although viruses that infect Archaea are
plentiful.

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Transduction is extremely rare. Only one archaeal virus, which infects the thermophilic methanogen
Methanothermobacter thermautotrophicus, has been shown to transduce the genes of its host.
Unfortunately the low burst size (about six phages liberated per cell) makes using this system for gene
transfer impractical

When consider about Archaeal Conjugation, Two types of conjugation have been detected in Archaea.
Some strains of Sulfolobus solfataricus contain plasmids that promote conjugation between two cells in
a manner similar to that seen in Bacteria. In this process, cell pairing is independent of pili formation
and DNA transfer is unidirectional. However, most of the genes encoding these functions seem to have
little similarity to those in gram-negative Bacteria. The exception is a gene similar to traG from the F
plasmid, whose protein product participates in stabilizing mating pairs. It thus seems likely that the
actual mechanism of conjugation in Archaea is quite different from that in Bacteria.

Some Halobacteria, in contrast, perform a novel form of conjugation. No fertility plasmids are
required, and DNA transfer is bidirectional. Cytoplasmic bridges form between the mating cells and
probably facilitate inter cell DNA transfer. Neither type of conjugation has been developed to the point
of being used for routine gene transfer or genetic analysis. However, these genetic resources will likely
be useful for developing more routine genetic transfer systems for these organisms in the future.

Fig 19: Molecular features of the three domains

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8) Introduction to the Diversity of Archaea

The domain Archaea consists of seven major phyla, only five of which contain species described on the
basis of cultivated strains. Most described species fall within the phyla Crenarchaeota and
Euryarchaeota, while only a handful of species have been described for the Nanoarchaeota, the
Korarchaeota, and the Thaumarchaeota .

Branching close to the root of the universal tree are Hyperthermophilic species of Crenarchaeota, such
as Pyrolobus , as well as Thermophilic species of Nanoarchaeota and Korarchaeota. These are followed
by the phylum Euryarchaeota, which includes the methanogenic Archaea and the extreme halophiles
and extreme acidophiles, such as Thermoplasma. The phylum Thaumarchaeota was first observed in
the deep ocean in the 1990s but has subsequently been found in soils and marine systems all over the
world. The first species of Thaumarchaeota were shown to be capable of ammonia oxidation. Several
different species have since been isolated and all share this physiological trait. As for Bacteria, many
lineages of Archaea are known only from SSU rRNA genes recovered from the environment and there
remains great opportunity for the discovery of new lineages in the future.

Fig 20: Major Phyla in domain Archaea

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Archaea members are important to conduct bio-geochemical cycles such as Sulphur Cycle, Nitrogen
cycle and etc… They play impotent roles for recycling matter in the enviorenment.

Involvement for Sulphur Cycle 

 Dissimilative Sulfate reduction occurs in Archaeoglobus,


a genus of the archaeal phylum Euryarchaeota.
The sulfur reducing Archaea of which there are many
are all genera of Crenarchaeota (e.g., Acidianus, Sulfolobus,


Pyrodictium, and Thermodiscus).
Sulphur is oxidized by one some members of
Crenarchaeota .

Involvement for Nitrogen Cycle 

 Phylum Euryarchaeota members contain NifH gene which
is responsible for Nitrogenase enzyme. Therefore they


show nitrogen fixing ability.
Ammonia oxidizers are found in archaeal phylum
Thaumarchaeota (Nitrosopumilus, Nitrosocaldus,


Nitrosoarchaeum, Nitrososphaera).
Archaeal ammonia-oxidizers appear to be most common
in habitats where NH3 is present in low concentration.
These organisms are thought to be the dominant
ammonia oxidizers in the oceans where ammonia levels
are very low. Archaeal ammonia-oxidizers are also
common in soils, and in some soils they outnumber
bacterial ammonia-oxidizers by several orders of
magnitude. The availability of NH3 relative to NH4+
declines with pH, and thus acid soils (pH 6 - 6.5), which
are common, may favor organisms able to grow at low


NH3 concentration.
Some members of Archaea do denitrification process.

Involvement for Iron Cycle 

 Dissimillative Iron reduction by Crenarchaeota


(Pyrobaculum)
Two Archaeal phyla involve for Iron Oxidation

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Archaea and Global Warming

Anthropogenic CO2 emissions have significantly affected global climate. However, Archaea and
Bacteria have also profoundly affected our planet, including its climate. One example comes from the
Arctic, where soil is frozen as permafrost. Permafrost can be 100 meters deep and it encompasses 25%
of the terrestrial surface of the Earth. Within permafrost is stored an enormous mass of organic
carbon, most of which has been locked away in ice for more than 20,000 years. But this ice is starting
to thaw, and the result could have global consequences. The Intergovernmental Panel on Climate
Change predicts that Arctic temperatures will increase 7°C by the year 2100. When permafrost melts,
it is converted into wetlands, and these are major habitats for Archaea that produce methane
(methanogens).

Methane is a greenhouse gas with a warming potential 25 times more powerful than CO2. Hence, if
Arctic warming continues at its present pace, much permafrost carbon could be converted into
methane, significantly accelerating global climate change. At Stordalen Mire in northern Sweden,
microbiologists are investigating methanogens in thawed permafrost. Chambers are used to trap and
measure methane produced in the wetlands that have replaced thawed permafrost . The source of
most of the methane was found to be a novel methanogen, Methanoflorens stordalenmirensis, which
grows rapidly in thawed permafrost. M. stordalenmirensis represents a novel order of methanogens
previously called Rice Cluster )). These methanogens are present in wetlands worldwide but M.
stordalenmirensis is the first characterized species of this new taxonomic family, the
Methanoflorentaceae. In addition to human impacts on climate, future control of global climate
change may well depend in a major way on what is discovered about the ecology of methanogenesis by
M. stordalenmirensis.

Archaeal Diversity

A phylogenetic tree of Archaea is shown in. The tree, based on comparative sequences of ribosomal
proteins, reveals several phyla, including the,

 Euryarchaeota,
 Thaumarchaeota
 Nanoarchaeota
 Nanoarchaeota
 Crenarchaeota,

The exact ancestry of these groups remains a contentious issue, and phylogenetic trees constructed
from 16S ribosomal RNA gene sequences often conflict with those made using other genomic loci
The evolutionary history of the Archaea is ancient and complex, involving horizontal gene transfers
within and between phyla. Common traits shared by all Archaea include their ether linked lipids, their
lack of peptidoglycan in cell walls, and their structurally complex RNA polymerases, which resemble
those of Eukarya . But beyond this, Archaea show enormous phenotypic diversity. Archaea include
species that carry out chemoorganotrophic or chemolithotrophic metabolisms, and both aerobic and
anaerobic species are common.

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Chemoorganotrophy is widespread among Archaea, and fermentations and anaerobic respirations are
common. Chemolithotrophy is also well established in the Archaea, with H2 being a common electron
donor, and with ammonia oxidation found among species of Thaumarchaeota.

Anaerobic respiration, especially forms employing elemental sulfur (S) as an electron acceptor, is
prevalent among the Archaea, especially Crenarchaeota.

Aerobic respiration occurs widely in Thaumarchaeota and is common among a few groups of
Euryarchaeota but is characteristic of only a few species of Crenarchaeota.

Euryarchaeota that conserve energy from the production of methane. Methanogenesis is a globally
important process that is uniquely archaeal. Archaea are also well known for containing many species
Of Extremophiles, including species that are Hyperthermophiles, Halophiles and Acidophiles .

However, a great many species in the Euryarchaeota and most Thaumarchaeota are not extremophiles
and are found in soils, sediments, oceans, lakes, in association with animals, and even in the human
gut!

Fig 21: Detailed phylogenetic tree of the Archaea based on comparisons of ribosomal proteins from
sequenced genomes. Each of the five archaeal phyla is indicated in a different color. The Korarchaeota
and Nanoarchaeota are each represented by only a single known species.

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9) Euryarchaeota

Euryarchaeota comprise a large and physiologically diverse group of Archaea. This phylum includes
Methanogens (Strictly Anaerobes ) , many genera of extreme Halophilic Archaea ( mainly obligate
aerobes ), Hyperthermophiles (Thermococcus and Pyrococcus) & Hyperthermophilic methanogen
(Methanopyrus).

 Extreme Halophilic Archaea

Extremely halophilic Archaea, often called the Haloarchaea are a diverse group that inhabits
environments high in salt. These include naturally salty environments, such as solar salt evaporation
ponds and salt lakes, and artificial saline habitats such as the surfaces of heavily salted foods, for
example, certain fish and meats. Such salty habitats are called hypersaline. The term extreme
halophile is used to indicate that these organisms are not only halophilic, but that their requirement
for salt is very high, in some cases at levels near saturation. An organism is considered an extreme
halophile if it requires 1.5 M (about 9%) or more sodium chloride (NaCl) for growth. Most species of
extreme halophiles require 2–4 M NaCl (12–23%) for optimal growth. Virtually all extreme halophiles
can grow at 5.5 M NaCl (32%, the limit of saturation for NaCl), although some species grow very slowly
at this salinity. Some phylogenetic relatives of extremely halophilic Archaea, for example species of
Haloferax and Natronobacterium, are able to grow at much lower salinities, such as at or near that of
seawater (about 2.5% NaCl); nevertheless, these organisms are phylogenetic relatives of other
extreme halophiles.
Eg: Halobacterium , Haloferax ,
Natronobacterium

Fig 22: Some genera of extremely halophilic

Archaea.

Haloarchaea stain gram-negatively,

reproduce by binary fission, and do not
form resting stages or spores. Cells of the
various cultured genera are rod-shaped,
cocci, or cup-shaped, but even cells that
form squares are known. Cells of
Haloquadratum are square in shape and
are only about . μm thick.
Haloquadratum also forms gas vesicles
that allow it to float in its salty
hypersaline habitat, probably as a means
to be in contact with air since most
extreme halophiles are obligate aerobes.

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 Physiological Adaptations of Extremely Halophilic Archaea

Many other extremely halophilic Archaea also produce gas vesicles. Most species of extreme halophiles
lack flagella, but a few strains are weakly motile by flagella that rotate to propel the cell
Forward. The genomes of Halobacterium and Halococcus are unusual in that large plasmids containing
up to 30% of the total cellular DNA are present and the GC base ratio of these plasmids (near 60% GC)
differs significantly from that of chromosomal DNA (66–68% GC). Plasmids from extreme halophiles
are among the largest naturally occurring plasmids known.

Most species of extremely halophilic Archaea are obligate aerobes. Most haloarchaea use amino acids
or organic acids as electron donors and require a number of growth factors such as vitamins for
optimal growth. A few haloarchaea oxidize carbohydrates aerobically, but this capacity is rare; sugar
fermentation does not occur. Electron transport chains containing cytochromes of the a, b, and c types
are present in Halobacterium, and energy is conserved during aerobic growth via a proton motive
force arising from electron transport. Some haloarchaea have been shown to grow anaerobically, as
growth by anaerobic respiration linked to the reduction of nitrate or fumarate has been demonstrated
in certain species.

The Halobacterium cell wall is composed of glycoprotein and is stabilized by Na+. Sodium ions bind to
the outer surface of the Halobacterium wall and are absolutely essential for maintaining cellular
integrity. When insufficient Na+ is present, the cell wall breaks apart and the cell lyses. This is a
consequence of the exceptionally high content of the acidic (negatively charged) amino acids aspartate
and glutamate in the glycoprotein of the Halobacterium cell wall. The negative charge on the carboxyl
Group of these amino acids is bound to Na+; when Na+ is diluted away, the negatively charged parts of
the proteins tend torepel each other, leading to cell lysis.

Fig 24: Electron micrographs of thin sections of the extreme

halophile Halobacterium salinarum.

Natronobacterium, Natronomonas, and their

relatives differ from other extreme halophiles in
being extremely alkaliphilic as well as halophilic.
As befits their soda lake habitat natronobacteria
grow optimally at very low Mg2+ concentrations
and high pH (9–11).

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Water Balance Maintenance 

To maintain the osmotic balance in a high-solute environment

Such as the salt-rich habitats of Halobacterium, organisms must either accumulate or synthesize
solutes intracellularly. These solutes are called compatible solutes. These compounds counteract
the tendency of the cell to become dehydrated under conditions of high osmotic strength by placing
the cell in positive water balance with its surroundings. Cells of Halobacterium, however, do not
synthesize or accumulate organic compounds but instead pump large amounts of K+ from the
environment into the cytoplasm. This ensures that the concentration of K+ inside the cell
Is even greater than the concentration of Na+ outside the cell. This ionic condition maintains positive
water balance.

The Halobacterium cell wall is composed of glycoprotein and is stabilized by Na+. Sodium ions bind
to the outer surface of the Halobacterium wall and are absolutely essential for maintaining cellular
integrity. When insufficient Na+ is present, the cell wall breaks apart and the cell lyses.

This is a consequence of the exceptionally high content of the acidic amino acids aspartate and
glutamate in the glycoprotein of the Halobacterium cell wall. The negative charge on the carboxyl
group of these amino acids is bound to Na+ when Na+ is diluted away, the negatively charged parts of
the proteins tend to repel each other, leading to cell lysis.

Cytoplasmic Compornents of Extreme Halophiles 

Like cell wall proteins, cytoplasmic proteins of Halobacterium are highly acidic, but it is K+, not Na+,
that is required for activity. This makes sense because K+ is the predominant cation in the cytoplasm
of cells of Halobacterium .

Besides having a high acidic amino acid composition, halobacterial cytoplasmic proteins typically
contain lower levels of hydrophobic amino acids and lysine, a positively charged (basic) amino acid,
than proteins of nonhalophiles. This is also to be expected because in a highly ionic cytoplasm, polar
proteins would tend to remain in solution whereas nonpolar proteins would tend to cluster and
perhaps lose activity.
The ribosomes of Halobacterium also require high KCl levels for stability, whereas ribosomes of
nonhalophiles have no KCl requirement.

Extremely halophilic Archaea are thus well adapted, both internally and externally, to life in a highly ionic
environment. Cellular components exposed to the external environment require high Na+ for stability,
whereas internal components require high K+. With the exception of a few extremely halophilic members
of the Bacteria that also use KCl as a compatible solute, in no other group of prokaryotes do we find this
unique requirement for such high amounts of specific cations.

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 Bacteriorhodopsin and Light-Mediated ATP Synthesis in Halobacteria

Certain species of haloarchaea can catalyze a light-driven synthesis of ATP. This occurs without
chlorophyll pigments, so it is not photosynthesis. However, other light-sensitive pigments are present,
including red and orange carotenoids primarily C50 pigments called bacterioruberins and inducible
pigments involved in energy conservation; we discuss these pigments here.
Under conditions of low aeration, Halobacterium salinarum and some other haloarchaea synthesize a
protein called bacteriorhodopsin and insert it into their cytoplasmic membranes. Bacteriorhodopsin
is so named because of its structural and functional similarity to rhodopsin, the visual pigment of the
eye. Conjugated to bacteriorhodopsin is a molecule of retinal, a carotenoid-like molecule that can
absorb light energy and pump a proton across the cytoplasmic membrane. The retinal gives
bacteriorhodopsin a purple hue. Thus cells of Halobacterium that are switched from growth under high
aeration conditions to oxygen limiting growth conditions (a trigger of bacteriorhodopsin synthesis)
gradually change color from orange-red to purple-red as they synthesize bacteriorhodopsin insert it
into their cytoplasmic membranes.

Bacteriorhodopsin absorbs green light around 570 nm. Following absorption, the retinal of
bacteriorhodopsin, which normally exists in a trans configuration (RetT), becomes excited and
converts to the cis (RetC) form. This transformation is coupled to the translocation of a proton across
the cytoplasmic membrane. The retinal molecule then decays to the Trans isomer along with the
uptake of a proton from the cytoplasm, and this completes the cycle. The proton pump is then ready to
repeat the cycle.

As protons accumulate on the outer surface of the membrane, a proton motive force is generated that
is coupled to ATP synthesis through the activity of a proton translocating ATPase. Bacteriorhodopsin-
mediated ATP production in H. salinarum supports slow growth of this organism under anoxic
conditions. The light stimulated proton pump of H. salinarum also functions to pump Na+ out of the cell
by activity of a Na+,H+ antiport system and to drive the uptake of nutrients, including the K+ needed for
osmotic balance. Amino acid uptake by H. salinarum is indirectly driven by light as well, because amino
acids are co transported into the cell with Na+ by an amino acid-Na+ symporter removal of Na+ from
the cell occurs by way of the light-driven Na+-H+ antiporter.

Fig 23: Model for the mechanism of

bacteriorhodopsin.
Light of 570 nm (hν570nm) converts the protonated
retinal of bacteriorhodopsin from the trans form (RetT) to
the cis form (RetC), along with translocation of a proton to
the outer surfaceof the cytoplasmic membrane, thus
establishing a proton motive force. ATPase activity is
driven by the proton motive force.

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 Methanogenic Archaea

Many Euryarchaeota are methanogens, microorganisms that produce methane (CH4) as an integral
part of their energy metabolism. They are strictly anaerobic organisms. Eg: Methanobacterium,
Methanocaldococcus, Methanosarcina. Their taxonomy is based on both phenotypic and phylogenetic
analyses, with several taxonomic orders being recognized. Methanogens show a diversity of cell wall
chemistries. These include the pseudomurein walls of Methanobacterium species and relatives, walls
composed of methanochondroitin (so named because of its structural resemblance to chondroitin, the
connective tissue polymer of vertebrate animals) in Methanosarcina and relatives, the protein or
glycoprotein wallsof Methanocaldococcus and Methanoplanus species, respectively, and the S-layer
walls of Methanospirillum

Fig 25: Characteristics of some methanogenic Archaea

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Methanogens are mesophilic and

nonhalophilic, although speciesthat grow
optimally at very high or very low
temperatures, at very high salt
concentrations, or at extremes of pH,have
also been described. Several substrates
can be converted to CH4by methanogens.
Interestingly, these substrates do not
include such common compounds as
glucose and organic or fatty acids
(other than acetate and pyruvate).
Compounds such as glucose can be
converted to CH4, but only in reactions in
which methanogens and other anaerobes
cooperate. With the right mixture of
organisms, virtually any organic
compound, even hydrocarbons,
can be converted to CH4 plus CO2.
Three classes of compounds make up the
list of methanogenic substrates shown in
Table 16.5. These are CO2-type
substrates, methylated substrates, and
acetate. CO2-type substrates include
CO2 itself, which is reduced to CH4 using
H2 as the electron donor. Other
substrates of this type include formate
and CO, carbon monoxide. Methylated substrates include methanol and many others. Methanol can be
reduced using an external electron donor such as H2, or, alternatively, in the absence of H2, some
CH3OH can be oxidized to CO2 to generate the electrons needed to reduce other molecules of CH3OH to
CH4 . The final methanogenic process is the cleavage of acetate to CO2 plus CH4. Only a few known
methanogens are acetotrophic, although acetate is a major source of CH4 in nature.

Fig 26:

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Fig 27:

Fig 28:

 Thermoplasmatales

A phylogenetically distinct line of Archaea contains Thermophilic and extremely acidophilic

genera: Thermoplasma, Ferroplasma, and Picrophilus. These prokaryotes are among the most
acidophilic of all known microorganisms, with Picrophilus being capable of growth even below

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pH 0. Most are thermophilic as well. These genera also form their own taxonomic order within
the Euryarchaeota, the Thermoplasmatales. Thermoplasma and Ferroplasma lack cell walls, and
in this respect they resemble the mycoplasmas.

 Thermococcales and Methanopyrus

A few euryarchaeotes thrive in thermal environments and some are Hyperthermophiles. We

consider here three hyperthermophilic euryarchaeotes that branch very near the root of the
Euryarchaeota . Two of these, Thermococcus and Pyrococcus, form a distinct taxonomic order:
the Thermococcales. The third organism, Methanopyrus, is a methanogen that closelyresembles
other methanogens in its basic physiology but is unusual in its hyperthermophily, lipids,
and phylogenetic position .
 Archaeoglobales

Hyperthermophilic Crenarchaeota catalyze anaerobic respirations in which elemental sulfur

(S0) is used as an electron acceptor, being reduced to H2S. One hyperthermophilic
euryarchaeote, Archaeoglobus, can reduce sulfate (SO4 −) and forms a phylogenetically distinct
lineage within the Euryarchaeota . Eg: Archaeoglobus, Ferroglobus

Fig 30 : Shadowed preparation of cells of Thermoplasma volcanium

isolated from hot springs.Cells are 1–2 μm in diameter.

Fig 29:

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10) Thaumarchaeota

Early surveys of 16S ribosomal RNA genes from open ocean microbial communities resulted in the
shocking conclusion that Archaea were abundant and widespread in the oceans. At the time, the
archaeal domain was considered to contain only extremophiles and obligate anaerobes, and their
presence in oxygen-rich temperate and even polar oceanic environments was something of a mystery.
Even more remarkable, these novel Archaea were widespread and common in soils all over the world.
Phylogenetic analysis of their 16S ribosomal RNA gene sequences initially suggested that this novel
group of Archaea was a deeply divergent lineage of the Crenarchaeota, a group of hyperthermophilic
Archaea. It was only after genome sequence analysis of the marine nitrifier Nitrosopumilus maritimus
that it became clear that the Thaumarchaeota are a distinct phylum of Archaea. Analyses of genome
sequences confirm that Thaumarchaeota constitute a unique phylum of Archaea and that they
diverged from the primary line of archaeal descent prior to the divergence of Crenarchaeota and
Euryarchaeota. Thaumarchaeota, ubiquitous in soils and found throughout the marine water column
from the equator to the polar seas, are one of the most abundant and widespread phyla on our planet.
In surveys of soil or marine samples, thaumarchaea are often found to be the dominant group of
Archaea. By using fluorescent phylogenetic probes , thaumarchaea have been detected in oxic marine
waters worldwide; they thrive even in waters and sea ice near Antarctica . Marine species are
planktonic.
Nitrosopumilus maritimus grows chemolithotrophically by aerobically oxidizing ammonia (NH3) to
nitrite (NO2–), the first step in nitrification. This organism uses CO2 as its sole carbon
source (autotrophy), as do nitrifying Bacteria . However, unlike ammonia-oxidizing Bacteria such as
Nitrosomonas, N. maritimus is adapted to life under extreme nutrient limitation, as would befit an
organism indigenous to open ocean waters.

11) Nanoarchaeota
The Nanoarchaeota are represented by a
single species, the highly unusual
Nanoarchaeum equitans. N. equitans is one of
the smallest cellular organisms known and
has the smallest genome among species of
Archaea (0.49 Mb). The coccoid cells of N.
equitans are very small, about . μm in
diameter, and have only about 1% of the
volume of an Escherichia coli cell. They
cannot grow in pure culture and replicate
only when attached to the surface of their
host organism, Ignicoccus hospitalis , a Fig 31:
hyperthermophilic species of Crenarchaeota
whose name means the hospitable fireball.
N. equitans grows to 10 or more cells per
Ignicoccus cell and lives an apparently
parasitic lifestyle , making it the only known
archaeal symbiont.
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12) Korarchaeota
Ribosomal RNA sequences of Korarchaeota have been observed in a range of geothermal habitats, both
submarine and terrestrial. However, Korarchaeum cryptofilum, whose name means the cryptic
filament of youth is the only characterized species in the phylum Korarchaeota. First observed as a
16S ribosomal RNA gene phylotype recovered from the hot spring named Obsidian Pool in
Yellowstone National Park, USA, K. cryptofilum has yet to be grown in pure culture, as for N. equitans.
However, its genome sequence has been determined from metagenomic analyses of an enrichment
culture. K. cryptofilum is an obligately anaerobic chemoorganotroph and a hyperthermophile, growing
at 85°C. Cells are long, thin (<0.2-μm diameter) filaments of variable length , with most filaments being
around μm long but some reaching as much as μm. Filaments of K. cryptofilum have a tough
paracrystalline S-layer , which maintains cell integrity in its extremely hot habitat.

13) Crenarchaeota
Crenarchaeota are mostly hyperthermophiles and include species growing optimally above the boiling
point of water. Many hyperthermophiles are chemolithotrophic autotrophs, and because no
phototrophs can survive such temperatures, these organisms are the sole primary producers in these
habitats. Most hyperthermophilic Archaea have been isolated from geothermally heated soils or
waters containing S and H2S, and most species metabolize sulfur in one way or another. In terrestrial
environments, sulfur-rich springs, boiling mud, and soils may have temperatures up to 100°C and are
mildly to extremely acidic owing to the production of sulfuric acid (H2SO4) from the biological
oxidation of H2S and S. Such hot, sulfur-rich environments, called solfataras, are found throughout
the world , including Italy, Iceland, New Zealand, and Yellowstone National Park in Wyoming (USA).
Depending on the surrounding geology, solfataras can be mildly acidic to slightly alkaline (pH 5–8) or
extremely acidic, with pH values below 1. Hyperthermophilic crenarchaeotes have been obtained from
all of these environments, but most inhabit neutral or weakly acidic thermal habitats.
Hyperthermophilic Crenarchaeota also inhabit undersea hot springs called hydrothermal vents.
With a few exceptions, hyperthermophilic Crenarchaeota are obligate anaerobes. Their energy-yielding
metabolism is either chemoorganotrophic or chemolithotrophic or botghand is dependent on diverse
electron donors and acceptors. Fermentation is rare and most bioenergetic strategies involve
anaerobic respirations.

Members of Phylum Crenarchaeota are also found from terrestrial Volcanic Habitats (Eg: Sulfolobus,
Acidianus, Thermoproteus, Pyrobaculum) Terrestrial volcanic habitats can have temperatures as high
as 100°C and are thus suitable for hyperthermophilic Archaea. Two phylogenetically related organisms
isolated from these environments are Sulfolobus and Acidianus. These genera form the heart of an
order called the Sulfolobales. In addition, Sulfolobus has been a model organism for molecular biology
studies of Archaea

Fig 32: Acidophilic hyperthermophilic Archaea, the

Sulfolobales. (a) Sulfolobus acidocaldarius. Electron
micrograph of a thin section. (b) Acidianus infernus.
Electron micrograph of a thin section. Cells of both
organisms vary from 0.8 to 2 μm in diameter.
Sulfolobales typically show temperature optima
below 90°.
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Fig 33:
Fig 34:

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14) Industrial Applications of Archaea

 Extremophiles use as a source of novel enzymes to achieve various industrial
applications
• Extremophilic microorganisms are adapted to survive in ecological niches:
 high temperatures,
 extremes of pH,
 high salt concentrations
 high pressure.
• These microorganisms produce unique biocatalysts which operate under extreme conditions
• Selected extracellular polymer degrading enzymes and other enzymes could be used in food,
chemical and pharmaceutical industries and in environmental biotechnology.
• Examples of enxymes that are produced by using Archaea are Amylases, Pullulanases,
Cyclodextrin glycosyltransferases, Cellulases, Xylanases, Chitinases, Proteinases, Esterases,
Glucose isomerases, Alcohol dehydrogenases and DNA-modifying enzymes )

 Production of Retinal proteins using Halophiles.

With roughly 80 U.S. patents pertaining to bacteriorhodopsin from Halobacterium and commercial
production by several companies, it is one of the most recognized products derived from
halophiles. The ability to convert light to chemical energy in a nonchlorophyll system was first
discovered in the haloarchaea. The apoprotein responsible for this, bacterio-opsin, is combined
with a retinal protein to make bacteriorhodopsin,which is then organized into a two-dimensional
crystalline array in the purple membrane of haloarchaea. Bacteriorhodopsin is the simplest
biological transducer of solar energy and uses light to establish a transmembrane gradient of
proton electrochemical potential.. Bacteriorhodopsin has several qualities that make it useful in an
industrial setting:
 it is very stable over a range of temperatures (0 to 45◦C)
 pH values (1–11)
 its reactions are self-regenerative and can be manipulated chemically, genetically,
& immunologically
Bacteriorhodopsin from Halobacterium species is being marketed for light sensors, nonlinear
optics, and optical data processing . It is also being considered for use as an erasable photochromic
film. A schlieren apparatus using a bacteriorhodopsin film as an adaptive image grid with white
light illumination has been proposed to be used at NASA s Kennedy Space Center for the remote
detection of gas leaks.

 Compatible Solutes.

Halophiles prevent the loss of cellular water in their saline environments either by accumulating
osmotically balanced levels of internal salts or by producing compatible solutes or osmolytes that
can be used to maintain the stability of biomolecules. Most halophilic bacteria and eukaryotes
exclude salts.and instead accumulate high solute concentrations within the cytoplasm. These
osmolytes are usually amino acids (e.g. glycine- betaine, ectoine) or sugars and polyols (e.g.
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sucrose, trehalose, and glycerol) which do not disrupt metabolic processes and have no net charge
at physiological pH. Ectoine and its derivatives have been patented as moisturizers in cosmetics, and
as stabilizers in polymerase chain reactions . Glycine betaine, a common osmolyte, has been
proposed as a feed additive. Its biosynthetic pathway has been characterized and expression of
Ectothiorhodospira halochloris genes has been engineered in Escherichia coli, leading to betaine
accumulation and improved salt tolerance . Halomonas boliviensis is being explored for its use in the
production of ectoine in batch-fed cultures.

 Textile Industry

The textile industry produces a large quantity of polluted wastewater containing azo dyes, phenol,
and toxic anions. The effluent is also highly saline with typical salt concentrations of 15–20%.
Moderate halophiles such as Salinicoccus iranensis and Halomonas species have been isolated from
these wastewaters and are able to decolorize azo dyes and use phenol as a primary source of
carbon and energy .

 Biofuel Production

 Production of Bioplastics

Polyhydroxyalkanoates (PHA) are a heterogeneous group of polyesters which are often employed as
a mode of carbon storage by microbial cells. Halophilic archaea produce large quantities of PHA
which have been utilized for their application as biodegradable plastics. The most common is poly-
beta-hydroxybutyrate (PHB). PHAs can be used as a replacement for thermoplastics and are
biodegradable, biocompatible, and resistant to water. Therefore, they are of interest to the medical
and pharmaceutical community for use in surgical sutures, bone replacement, and delayed release
medications.

 Production of Bio – batteries

 Production of some medicines
 Production of vegetal stem-cells from archeas,
 Using selected archaea forcrop, pest control
 Production of Biofertilizers
 Bioremediation processes in Industries and to clean polluted environments.
 Innovative fermentation processes for the production of archaeal biomass, enzymes
and metabolites.
 Archaeal Enzymes, metabolites and biomass are used in biotechnology.
 The production of biocatalysts and biomolecules from extremophiles.
 Production of Xylanases which are responsible for hydrolyzing Hemicellulose in
paper and pulp industry.
 Methanogenic Archaea are used in Anaerobic digesters and biological reactors to
achieve Methanogenisis.

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References:



http://www.ucmp.berkeley.edu/archaea/archaea.html (5/4/2015)


www.envizont.eu/.../industrial-use-of-archaeas-for-20140421.pptx (5/4/2015)
http://en.wikipedia.org/wiki/Archaea (5/4/2015)

 Madigan,M.T.Martinko,J.M.(2014).Brock Biology of Microorganisms.14th edition.USA.Pearson

educational publishers. pp. 517-542, 125,183,224,273,309,454,517

 Totora,G.J.Fnuke,B.R.etal.(2011).Microbiology An introduction.9th edition.India.Pearson India

Publications.

 Bouzas,T.M.,Velázquez,J.B.,Villa,T.G.(2006). Industrial Applications of Hyperthermophilic Enzymes:

A Review

 Schiraldi,C.,Giuliano,M.,Rosa,M.D.(2002). Perspectives on biotechnological applications of archaea

 Dassarma,P.,Corer,J.A.,etal. HALOPHILES, INDUSTRIAL APPLICATIONS

 Egorova,K.,Antranikian,G.(2005). Industrial relevance of thermophilic Archaea.Current

openion of Microbiology.

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