The Domain Archaea wasn't recognized as a major domain of life until quite

recently. Until the 20th century, most biologists considered all living things to be
classifiable as either a plant or an animal. But in the 1950s and 1960s, most
biologists came to the realization that this system failed to accomodate the fungi,
protists, and bacteria. By the 1970s, a system of Five Kingdoms had come to be
accepted as the model by which all living things could be classified. At a more
fundamental level, a distinction was made between the prokaryotic bacteria and
the four eukaryotic kingdoms (plants, animals, fungi, & protists). The distinction
recognizes the common traits that eukaryotic organisms share, such as nuclei,
cytoskeletons, and internal membranes.

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,
which illustrates also that each group is very different from the others.

It is true that most archaeans don't look that different from bacteria under the
microscope, and that the extreme conditions under which many species live have
made them difficult to culture, so their unique place among living organisms long

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went unrecognized. However, biochemically and genetically, they are as different
from bacteria.

The archaea cells able to live in extreme environments can be classified

depending on their ability to live in specific conditions. Four such classifications
are:

• Tolerance for high temperatures: hyperthermophilic.

• Able to survive acidic environments: acidophilic.
• Can survive in highly alkaline liquids: alkaliphilic.
• Tolerance for high salt content: halophilic.

Some of the most hostile environments on Earth are the deep-sea hydrothermal
vents at the bottom of the Pacific Ocean and hot springs such as those found in
Yellowstone National Park. High temperatures in combination with corrosive
chemicals are usually hostile to life, but archaea such as ignicoccus have no
trouble with those locations.

Ecology

Archaeans include inhabitants of some of the most extreme environments on the

planet. Some live near rift vents in the deep sea at temperatures well over 100
degrees Centigrade. Others live in hot spring 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 archaeans can survive the dessicating effects of extremely saline waters.
One salt-loving group of archaea includes Halobacterium, a well-studied
archaean. The light-sensitive
pigment bacteriorhodopsin gives Halobacterium its 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.

Archaeans may be the only organisms that can live in extreme habitats such as
thermal vents or hypersaline water. They may be extremely abundant in
environments that are hostile to all other life forms. However, archaeans are not

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restricted to extreme environments; new research is showing that archaeans are
also quite abundant in the plankton of the open sea.

Morphology

Archaea are tiny, usually less than one micron long (one one-thousandth of a
millimeter). Even under a high-power light microscope, the largest archaeans
look like tiny dots. Fortunately, the electron microscope can magnify even these
tiny microbes enough to distinguish their physical features. We can see archaean
images below, made using a variety of micrographic techniques.

They 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 like a
postage stamp. Most of them are unicellular, they have 70S sized ribosomes, they
are typically a few micrometers in size, and they reproduce asexually only. They
are known to have many of the same structures that bacteria can have, such as
plasmids, inclusions, flagella, and pili. Capsules and slime layers have been found
but appear to be rare in archaea.

Basic Archaeal Shapes: At far left, Methanococcus janaschii, a coccus form

with numerous flagella attached to one side. At left center, Methanosarcina
barkeri, a lobed coccus form lacking flagella. At right center, Methanothermus
fervidus, a short bacillus form without flagella. At far right, Methanobacterium
thermoautotrophicum, an elongate bacillus form.

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Structural diversity among archaeans is not limited to the overall shape of the
cell. Archaea may have one or more flagella attached to them, or may lack
flagella altogether. The flagella are hair-like appendages used for moving around,
and are attached directly into the outer membrane of the cell. When multiple
flagella are present, they are usually attached all on one side of the cell.

Like bacteria, the cells have a coiled ring of DNA, and the cell cytoplasm
contains ribosomes for the production of cell proteins and other substances the
cell needs. Archaea species share common characteristics such as shape and
metabolism, and they can reproduce via binary fission just like bacteria.
Horizontal gene transfer is common, however, and archaea cells may take up
plasmids containing DNA from their environment or exchange DNA with other
cells. As a result, archaea species can evolve and change rapidly.

Plasma Membrane

There are several characteristics of the plasma membrane that are unique
to Archaea, setting them apart from other domains. One such characteristic is
chirality of the glycerol linkage between the phopholipid head and the side chain.
In archaea it is in the L-isomeric form, while bacteria and eukaryotes have the D-
isomeric form. A second difference is the presence of an ether-linkage between
the glycerol and the side chain, as opposed to the ester-linked lipids found in
bacteria and eukaryotes. The ether-linkage provides more chemical stability to
the membrane. A third and fourth difference are associated with the side chains

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themselves, unbranched fatty acids in bacteria and eukaryotes, while isoprenoid
chains are found in archaea. These isoprenoid chains can have branching side
chains.

Comparison of Plasma Membrane Lipid Between Bacteria and Archaea.

Lastly, the plasma membrane of Archaea can be found as monolayers, where the
isoprene chains of one phospholipid connect with the isoprene chains of a
phospholipid on the opposite side of the membrane. Bacteria and eukaryotes only
have lipid bilayers, where the two sides of the membrane remain separated.

Cell Wall

Like bacteria, the archaeal cell wall is a semi-rigid structure designed to provide
protection to the cell from the environment and from the internal cellular pressure.
While the cell walls of bacteria typically contain peptidoglycan, that particular
chemical is lacking in archaea. Instead, archaea display a wide variety of cell wall
types, adapted for the environment of the organism. Some archaea lack a cell wall
altogether.

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While it is not universal, a large number of Archaea have a proteinaceous S-
layer that is considered to be part of the cell wall itself (unlike in Bacteria, where
an S-layer is a structure in addition to the cell wall). For some Archaea the S-
layer is the only cell wall component, while in others it is joined by additional
ingredients (see below). The archaeal S-layer can be made of either protein or
glycoprotein, often anchored into the plasma membrane of the cell. The proteins
form a two-dimensional crystalline array with a smooth outer surface. A few S-
layers are composed of two different S-layer proteins.

While archaea lack peptidoglycan, a few contain a substance with a similar

chemical structure, known as pseudomurein. Instead of NAM, it contains N-
acetylalosaminuronic acid (NAT) linked to NAG, with peptide interbridges to
increase strength.

Methanochondroitin is a cell wall polymer found in some archaeal cells, similar

in composition to the connective tissue component chondroitin, found in
vertebrates.

Some archaea have a protein sheath composed of a lattice structure similar to an

S-layer.

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Ribosomes

Archaea have ribosomes that are 70S in size, the same as bacteria, it was the
rRNA nucleotide. In addition, archaeal ribosomes have a different shape than
bacterial ribosomes, with proteins that are unique to archaea. This provides them
with resistance to antibiotics that inhibit ribosomal function in bacteria. While
bacterial ribosomes are sensitive to certain chemical inhibiting agents, archaeal
and eukaryotic ribosomes are not sensitive to those agents that archaea deserved
a domain separate from the bacteria. This may suggest a close relationship
between Archaea and eukaryotes.

Genes and its Genetics

Like all living cells, archaea rely on the replication of DNA to ensure that
daughter cells are identical to the parent cell. The DNA structure of archaea is
simpler than that of eukaryotes and similar to the bacterial gene structure. The

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DNA is found in single circular plasmids that are initially coiled and that
straighten out prior to cell division.

While this process and the subsequent binary fission of the cells is like that of
bacteria, the replication and translation of DNA sequences takes place as it does
in eukaryotes.

Once the cell DNA is uncoiled, the RNA polymerase enzyme that is used to
copy the genes is more similar to eukaryote RNA polymerase than it is to the
corresponding bacterial enzyme. Creation of the DNA copy also differs from
the bacterial process.

DNA replication and translation is one of the ways in which archaea are more
like the cells of animals than those of bacteria.

Flagella
As with bacteria, flagella allow the archaea to move. Their structure and
operating mechanism are similar in archaea and bacteria. The flagellum in
archaea is a long stalk with a base that can develop a rotary action in conjunction
with the cell membrane. The rotary action results in a whiplike motion that can
propel the cell forward. In archaea, the stalk is constructed by adding material
at the base, while in bacteria, the hollow stalk is built up by moving material up
the hollow center and depositing it at the top. Flagella are useful in moving cells
toward food and in spreading out after cell division.

Differences and Similarities between Bacteria and Archaea

Structural Characteristic Bacteria Archaea

Cell type Prokaryotic Prokaryotic

Cell morphology Variable Variable

Contains Does not contain

Cell wall
peptidoglycan peptidoglycan

Lipid bilayer or
Cell membrane type Lipid bilayer
lipid monolayer

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 Fatty acids-glycerol Phytanyl-glycerol
Plasma membrane lipids
ester ethers

Chromosome Typically circular Typically circular

Replication origins Single Multiple

RNA polymerase Single Multiple

Initiator tRNA Formyl-methionine Methionine

Resistant
Streptomycin inhibition Sensitive
No
Calvin cycle Yes