The ARCHAEA (/ɑːrˈkiːə/ (_ listen ) or /ɑːrˈkeɪə/
ar-KEE-ə_ or _ar-KAY-ə_ ) constitute a domain and kingdom of
single-celled microorganisms . These microbes (ARCHAEA; singular
ARCHAEON) are prokaryotes , meaning that they have no cell nucleus or
any other membrane-bound organelles in their cells.
Archaea were initially classified as bacteria , receiving the name
ARCHAEBACTERIA (in the Archaebacteria kingdom), but this
classification is outdated. Archaeal cells have unique properties
separating them from the other two domains of life,
Eukaryota . The
Archaea are further divided into multiple recognized
phyla . Classification is difficult because the majority have not been
isolated in the laboratory and have only been detected by analysis of
their nucleic acids in samples from their environment.
Archaea and bacteria are generally similar in size and shape,
although a few archaea have very strange shapes, such as the flat and
square-shaped cells of _
Haloquadratum walsbyi _. Despite this
morphological similarity to bacteria, archaea possess genes and
several metabolic pathways that are more closely related to those of
eukaryotes, notably the enzymes involved in transcription and
translation . Other aspects of archaeal biochemistry are unique, such
as their reliance on ether lipids in their cell membranes , including
Archaea use more energy sources than eukaryotes: these
range from organic compounds , such as sugars, to ammonia , metal ions
or even hydrogen gas . Salt-tolerant archaea (the
Haloarchaea ) use
sunlight as an energy source, and other species of archaea fix carbon
; however, unlike plants and cyanobacteria , no known species of
archaea does both.
Archaea reproduce asexually by binary fission ,
fragmentation , or budding ; unlike bacteria and eukaryotes, no known
species forms spores .
Archaea were initially viewed as extremophiles living in harsh
environments, such as hot springs and salt lakes , but they have since
been found in a broad range of habitats , including soils, oceans, and
marshlands . They are also part of the human microbiota , found in the
colon , oral cavity, and skin.
Archaea are particularly numerous in
the oceans, and the archaea in plankton may be one of the most
abundant groups of organisms on the planet.
Archaea are a major part
of Earth's life and may play roles in both the carbon cycle and the
nitrogen cycle . No clear examples of archaeal pathogens or parasites
are known, but they are often mutualists or commensals . One example
is the methanogens that inhabit human and ruminant guts, where their
vast numbers aid digestion . Methanogens are also used in biogas
production and sewage treatment , and biotechnology exploits enzymes
from extremophile archaea that can endure high temperatures and
organic solvents .
* 1 Classification
* 1.1 New domain
* 1.2 Current classification
* 1.2.1 Concept of species
* 2 Origin and evolution
* 2.1 Comparison to other domains
* 2.2 Relationship to bacteria
* 2.3 Relation to eukaryotes
* 3 Morphology
* 4 Structure, composition development, and operation
Cell wall and flagella
* 4.2 Membranes
* 6 Genetics
Gene transfer and genetic exchange
* 7 Reproduction
* 8 Ecology
* 8.1 Habitats
* 8.2 Role in chemical cycling
* 8.3 Interactions with other organisms
* 8.3.1 Mutualism
* 9 Significance in technology and industry
* 10 See also
* 11 References
* 12 Further reading
* 13 External links
Life timeline view • discuss • edit -4500 — – -4000 —
– -3500 — – -3000 — – -2500 — – -2000 — – -1500 —
– -1000 — – -500 — – 0 — _WATER _ Single-celled
life _PHOTOSYNTHESIS _ EUKARYOTES Multicellular
life LAND LIFE DINOSAURS MAMMALS FLOWERS ←
Earliest Earth (−4540 ) ← Earliest water ← Earliest
life ← LHB meteorites ← Earliest oxygen ←
Atmospheric oxygen ← Oxygen crisis ← Earliest sexual
reproduction ← Ediacara biota ←
← Earliest humans P
n Pongola Huronian
Cryogenian Andean Karoo Quaternary
Axis scale : millions of years .
Orange labels: known _ICE AGES_.
Also see: _
Human timeline _ and _Nature timeline _
Archaea were first found in extreme environments, such as
volcanic hot springs . Pictured here is
Grand Prismatic Spring
Grand Prismatic Spring of
Yellowstone National Park .
For much of the 20th century, prokaryotes were regarded as a single
group of organisms and classified based on their biochemistry ,
morphology and metabolism . For example, microbiologists tried to
classify microorganisms based on the structures of their cell walls ,
their shapes, and the substances they consume. In 1965, Emile
Linus Pauling proposed instead using the sequences
of the genes in different prokaryotes to work out how they are related
to each other. This approach, known as phylogenetics , is the main
method used today.
Archaea were first classified as a separate group of prokaryotes in
Carl Woese and
George E. Fox in phylogenetic trees based on
the sequences of ribosomal RNA (rRNA) genes. These two groups were
originally named the Archaebacteria and Eubacteria and treated as
kingdoms or subkingdoms, which Woese and Fox termed _Urkingdoms_.
Woese argued that this group of prokaryotes is a fundamentally
different sort of life. To emphasize this difference, Woese later
proposed a new natural system of organisms with three separate Domains
Eukarya , the
Bacteria and the Archaea, in what is now known as
"The Woesian Revolution".
The word _archaea_ comes from the
Ancient Greek ἀρχαῖα,
meaning "ancient things", as the first representatives of the domain
Archaea were methanogens and it was assumed that their metabolism
reflected Earth's primitive atmosphere and the organisms' antiquity.
For a long time, archaea were seen as extremophiles that only exist in
extreme habitats such as hot springs and salt lakes . However, as new
habitats were studied, more organisms were discovered. Extreme
halophilic and hyperthermophilic microbes were also included in the
Archaea. By the end of the 20th century, archaea had been identified
in non-extreme environments as well. Today, they are known to be a
large and diverse group of organisms that are widely distributed in
nature and are common in all habitats. This new appreciation of the
importance and ubiquity of archaea came from using polymerase chain
reaction (PCR) to detect prokaryotes from environmental samples (such
as water or soil) by multiplying their ribosomal genes. This allows
the detection and identification of organisms that have not been
cultured in the laboratory.
Biological classification and
ARMAN are a new group of archaea recently discovered in acid mine
The classification of archaea, and of prokaryotes in general, is a
rapidly moving and contentious field. Current classification systems
aim to organize archaea into groups of organisms that share structural
features and common ancestors. These classifications rely heavily on
the use of the sequence of ribosomal RNA genes to reveal relationships
between organisms (molecular phylogenetics ). Most of the culturable
and well-investigated species of archaea are members of two main phyla
Crenarchaeota . Other groups have been
tentatively created. For example, the peculiar species _Nanoarchaeum
equitans _, which was discovered in 2003, has been given its own
Nanoarchaeota . A new phylum
Korarchaeota has also been
proposed. It contains a small group of unusual thermophilic species
that shares features of both of the main phyla, but is most closely
related to the Crenarchaeota. Other recently detected species of
archaea are only distantly related to any of these groups, such as the
Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising
Parvarchaeota ), which were discovered in 2006 and
are some of the smallest organisms known.
A superphylum -
TACK - has been proposed that includes the
Crenarchaeota , and
This superphylum may be related to the origin of eukaryotes. More
recently, the superphylum Asgard has been named and proposed to be
more closely related to the original eukaryote and a sister group to
Concept Of Species
The classification of archaea into species is also controversial.
Biology defines a species as a group of related organisms. The
familiar exclusive breeding criterion (organisms that can breed with
each other but not with others ) is of no help here because archaea
Archaea show high levels of horizontal gene transfer between
lineages. Some researchers suggest that individuals can be grouped
into species-like populations given highly similar genomes and
infrequent gene transfer to/from cells with less-related genomes, as
in the genus _
Ferroplasma _. On the other hand, studies in
Halorubrum _ found significant genetic transfer to/from less-related
populations, limiting the criterion's applicability. A second concern
is to what extent such species designations have practical meaning.
Current knowledge on genetic diversity is fragmentary and the total
number of archaeal species cannot be estimated with any accuracy.
Estimates of the number of phyla range from 18 to 23, of which only 8
have representatives that have been cultured and studied directly.
Many of these hypothesized groups are known from a single rRNA
sequence, indicating that the diversity among these organisms remains
Bacteria also contain many uncultured microbes with
similar implications for characterization.
ORIGIN AND EVOLUTION
Timeline of evolution
The age of the Earth is about 4.54 billion years. Scientific
evidence suggests that life began on Earth at least 3.5 billion years
ago . The earliest evidence for life on Earth is graphite found to
be biogenic in 3.7 billion-year-old metasedimentary rocks discovered
Western Greenland and microbial mat fossils found in 3.48
billion-year-old sandstone discovered in
Western Australia . More
recently, in 2015, "remains of biotic life " were found in 4.1
billion-year-old rocks in Western Australia.
Although probable prokaryotic cell fossils date to almost 3.5 billion
years ago , most prokaryotes do not have distinctive morphologies and
fossil shapes cannot be used to identify them as archaea. Instead,
chemical fossils of unique lipids are more informative because such
compounds do not occur in other organisms. Some publications suggest
that archaeal or eukaryotic lipid remains are present in shales dating
from 2.7 billion years ago; such data have since been questioned.
Such lipids have also been detected in even older rocks from west
Greenland . The oldest such traces come from the Isua district , which
include Earth's oldest known sediments, formed 3.8 billion years ago.
The archaeal lineage may be the most ancient that exists on Earth.
Woese argued that the bacteria, archaea, and eukaryotes represent
separate lines of descent that diverged early on from an ancestral
colony of organisms. One possibility is that this occurred before
the evolution of cells , when the lack of a typical cell membrane
allowed unrestricted lateral gene transfer , and that the common
ancestors of the three domains arose by fixation of specific subsets
of genes. It is possible that the last common ancestor of the
bacteria and archaea was a thermophile , which raises the possibility
that lower temperatures are "extreme environments" in archaeal terms,
and organisms that live in cooler environments appeared only later.
Bacteria are no more related to each other than
they are to eukaryotes, the term _prokaryote'_s only surviving meaning
is "not a eukaryote", limiting its value.
COMPARISON TO OTHER DOMAINS
The following table compares some major characteristics of the three
domains, to illustrate their similarities and differences. Many of
these characteristics are also discussed below.
Ether -linked lipids, pseudopeptidoglycan
Ester -linked lipids, peptidoglycan
Ester-linked lipids, various structures
Circular chromosomes, similar translation and transcription to
Circular chromosomes, unique translation and transcription
Multiple, linear chromosomes, similar translation and transcription
Internal Cell Structure
No membrane-bound organelles or nucleus
No membrane-bound organelles or nucleus
Membrane-bound organelles and nucleus
Various, with methanogenesis unique to Archaea
Various, including photosynthesis, aerobic and anaerobic
respiration, fermentation, and autotrophy
Photosynthesis, cellular respiration and fermentation
Asexual reproduction, horizontal gene transfer
Asexual reproduction, horizontal gene transfer
Sexual and asexual reproduction
Archaea were split off as a third domain because of the large
differences in their ribosomal RNA structure. The particular RNA
molecule sequenced, known as
16s rRNA , is present in all organisms
and always has the same vital function, the production of proteins.
Because this function is so central to life, organisms with mutations
16s rRNA are unlikely to survive, leading to great stability
in the structure of this nucleotide over many generations.
16s rRNA is
also large enough to retain organism-specific information, but small
enough to be sequenced in a manageable amount of time. In 1977, Carl
Woese, a microbiologist studying the genetic sequencing of organisms,
developed a new sequencing method that involved splitting the RNA into
fragments that could be sorted and compared to other fragments from
other organisms. The more similar the patterns between species were,
the more closely related the organisms.
Woese used his new rRNA comparison method to categorize and contrast
different organisms. He sequenced a variety of different species and
happened upon a group of methanogens that had vastly different
patterns than any known prokaryotes or eukaryotes. These methanogens
were much more similar to each other than they were to other organisms
sequenced, leading Woese to propose the new domain of Archaea. One of
the interesting results of his experiments was that the
more similar to eukaryotes than prokaryotes, even though they were
more similar to prokaryotes in structure. This led to the conclusion
Eukarya shared a more recent common ancestor than
Bacteria in general. The development of the nucleus
occurred after the split between
Bacteria and this common ancestor.
Archaea are prokaryotic, they are more closely related to
Eukarya and thus cannot be placed within either the
One property unique to
Archaea is the abundant use of ether-linked
lipids in their cell membranes.
Ether linkages are more chemically
stable than the ester linkages found in
Bacteria and Eukarya, which
may be a contributing factor to the ability of many
Archaea to survive
in extreme environments that place heavy stress on cell membranes,
such as extreme heat and salinity . Comparative analysis of archaeal
genomes has also identified several molecular signatures in the form
of conserved signature indels and signature proteins which are
uniquely present in either all
Archaea or different main groups within
Archaea. Another unique feature of
Archaea is that no other known
organisms are capable of methanogenesis (the metabolic production of
Archaea play a pivotal role in ecosystems with
organisms that derive energy from oxidation of methane, many of which
are Bacteria, as they are often a major source of methane in such
environments and can play a role as primary producers. Methanogens
also play a critical role in the carbon cycle, breaking down organic
carbon into methane, which is also a major greenhouse gas.
RELATIONSHIP TO BACTERIA
Phylogenetic tree showing the relationship
Archaea and other domains of life. Eukaryotes are colored
red, archaea green and bacteria blue. Adapted from Ciccarelli et al.
The relationship between the three domains is of central importance
for understanding the origin of life. Most of the metabolic pathways,
which are the object of the majority of an organism's genes, are
Archaea and Bacteria, while most genes involved in
genome expression are common between
Archaea and Eukarya. Within
prokaryotes, archaeal cell structure is most similar to that of
gram-positive bacteria, largely because both have a single lipid
bilayer and usually contain a thick sacculus (exoskeleton) of varying
chemical composition. In some phylogenetic trees based upon different
gene/protein sequences of prokaryotic homologs, the archaeal homologs
are more closely related to those of gram-positive bacteria. Archaea
and gram-positive bacteria also share conserved indels in a number of
important proteins, such as
Hsp70 and glutamine synthetase I;
however, the phylogeny of these genes was interpreted to reveal
interdomain gene transfer, and might not reflect the organismal
It has been proposed that the archaea evolved from gram-positive
bacteria in response to antibiotic selection pressure . This is
suggested by the observation that archaea are resistant to a wide
variety of antibiotics that are primarily produced by gram-positive
bacteria, and that these antibiotics primarily act on the genes that
distinguish archaea from bacteria. The proposal is that the selective
pressure towards resistance generated by the gram-positive antibiotics
was eventually sufficient to cause extensive changes in many of the
antibiotics' target genes, and that these strains represented the
common ancestors of present-day Archaea. The evolution of
response to antibiotic selection, or any other competitive selective
pressure, could also explain their adaptation to extreme environments
(such as high temperature or acidity) as the result of a search for
unoccupied niches to escape from antibiotic-producing organisms;
Cavalier-Smith has made a similar suggestion. This proposal is also
supported by other work investigating protein structural relationships
and studies that suggest that gram-positive bacteria may constitute
the earliest branching lineages within the prokaryotes.
RELATION TO EUKARYOTES
The evolutionary relationship between archaea and eukaryotes remains
unclear. Aside from the similarities in cell structure and function
that are discussed below, many genetic trees group the two.
Complicating factors include claims that the relationship between
eukaryotes and the archaeal phylum
Crenarchaeota is closer than the
relationship between the
Euryarchaeota and the phylum
and the presence of archaea-like genes in certain bacteria, such as
_Thermotoga maritima _, from horizontal gene transfer . The standard
hypothesis states that the ancestor of the eukaryotes diverged early
from the Archaea, and that eukaryotes arose through fusion of an
archaean and eubacterium, which became the nucleus and cytoplasm ;
this explains various genetic similarities but runs into difficulties
explaining cell structure. An alternative hypothesis, the eocyte
hypothesis , posits that
Eukaryota emerged relatively late from the
A lineage of archaea discovered in 2015, _
Lokiarchaeum _ (of proposed
Lokiarchaeota "), named for a hydrothermal vent called
Loki\'s Castle in the Arctic Ocean, has been found to be most closely
related to eukaryotes known at this time. It has been called a
transitional organism between prokaryotes and eukaryotes.
Until now, several sister phyla of "Lokiarchaeota" have been found
Thorarchaeota ", "
Odinarchaeota ", "
Heimdallarchaeota "), all
together comprising a newly proposed supergroup Asgard, which may
appear as a sister taxon to TACK. Details of the relation of Asgard
members and eukaryotes are still under consideration.
Individual archaea range from 0.1 micrometers (μm) to over 15 μm in
diameter, and occur in various shapes, commonly as spheres, rods,
spirals or plates. Other morphologies in the
irregularly shaped lobed cells in _
Sulfolobus _, needle-like filaments
that are less than half a micrometer in diameter in _
and almost perfectly rectangular rods in _
Thermoproteus _ and
Archaea in the genus _
Haloquadratum _ such as
Haloquadratum walsbyi _ are flat, square archaea that live in
hypersaline pools. These unusual shapes are probably maintained both
by their cell walls and a prokaryotic cytoskeleton . Proteins related
to the cytoskeleton components of other organisms exist in archaea,
and filaments form within their cells, but in contrast to other
organisms, these cellular structures are poorly understood. In
Thermoplasma _ and _
Ferroplasma _ the lack of a cell wall means that
the cells have irregular shapes, and can resemble amoebae .
Some species form aggregates or filaments of cells up to 200 μm
long. These organisms 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 multicell 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
Euryarchaeota species are spaced along thin filaments that can
range up to 15 centimetres (5.9 in) long; these filaments are made of
a particular bacteria species.
STRUCTURE, COMPOSITION DEVELOPMENT, AND OPERATION
_ Diagrammatic view of Methanobrevibacter smithii_, showing the
cell membrane (ochre, with inset) and cell wall (purple).
Archaea and bacteria have generally similar cell structure, but cell
composition and organization set the archaea apart. Like bacteria,
archaea lack interior membranes and organelles . Like bacteria, the
cell membranes of archaea are usually bounded by a cell wall and they
swim using one or more flagella . Structurally, archaea are most
similar to gram-positive bacteria . Most have a single plasma membrane
and cell wall, and lack a periplasmic space ; the exception to this
general rule is _
Ignicoccus _, which possess a particularly large
periplasm that contains membrane-bound vesicles and is enclosed by an
CELL WALL AND FLAGELLA
Cell wall § Archaeal cell walls
Most archaea (but not _
Thermoplasma _ and _
Ferroplasma _) possess a
cell wall. In most archaea the wall is assembled from surface-layer
proteins, which form an
S-layer . An
S-layer is a rigid array of
protein molecules that cover the outside of the cell (like chain mail
). This layer provides both chemical and physical protection, and can
prevent macromolecules from contacting the cell membrane. Unlike
bacteria, archaea lack peptidoglycan in their cell walls.
Methanobacteriales do have cell walls containing pseudopeptidoglycan ,
which resembles eubacterial peptidoglycan in morphology, function, and
physical structure, but pseudopeptidoglycan is distinct in chemical
structure; it lacks
D-amino acids and
N-acetylmuramic acid .
Archaea flagella operate like bacterial flagella—their long stalks
are driven by rotatory motors at the base. These motors are powered by
the proton gradient across the membrane. However, archaeal flagella
are notably different in composition and development. The two types
of flagella evolved from different ancestors. The bacterial flagellum
shares a common ancestor with the type III secretion system , while
archaeal flagella appear to have evolved from bacterial type IV pili .
In contrast to the bacterial flagellum, which is hollow and is
assembled by subunits moving up the central pore to the tip of the
flagella, archaeal flagella are synthesized by adding subunits at the
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
Archaeal membranes are made of molecules that are distinctly
different from those in all other life forms, showing that archaea are
related only distantly to bacteria and eukaryotes. In all organisms,
cell membranes are made of molecules known as phospholipids . These
molecules possess both a polar part that dissolves in water (the
phosphate "head"), and a "greasy" non-polar part that does not (the
lipid tail). These dissimilar parts are connected by a glycerol
moiety. In water, phospholipids cluster, with the heads facing the
water and the tails facing away from it. The major structure in cell
membranes is a double layer of these phospholipids, which is called a
lipid bilayer .
The phospholipids of archaea are unusual in four ways:
* They have membranes composed of glycerol-ether lipids , whereas
bacteria and eukaryotes have membranes composed mainly of
glycerol-ester lipids . The difference is the type of bond that joins
the lipids to the glycerol moiety; the two types are shown in yellow
in the figure at the right. In ester lipids this is an ester bond ,
whereas in ether lipids this is an ether bond .
Ether bonds are
chemically more resistant than ester bonds. This stability might help
archaea to survive extreme temperatures and very acidic or alkaline
Bacteria and eukaryotes do contain some ether lipids,
but in contrast to archaea these lipids are not a major part of their
* The stereochemistry of the archaeal glycerol moiety is the mirror
image of that found in other organisms. The glycerol moiety can occur
in two forms that are mirror images of one another, called
_enantiomers _. Just as a right hand does not fit easily into a
left-handed glove, enantiomers of one type generally cannot be used or
made by enzymes adapted for the other. The archaeal phospholipids are
built on a backbone of _sn_-glycerol-1-phosphate, which is an
enantiomer of _sn_-glycerol-3-phosphate, the phospholipid backbone
found in bacteria and eucaryotes. 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, indicating an early split from the other two domains.
* Archaeal lipid tails differ from those of other organisms in that
they are based upon long isoprenoid chains with multiple
side-branches, sometimes with cyclopropane or cyclohexane rings. By
contrast, the fatty acids in the membranes of other organisms have
straight chains without side branches or rings. Although isoprenoids
play an important role in the biochemistry of many organisms, only the
archaea use them to make phospholipids. These branched chains may help
prevent archaeal membranes from leaking at high temperatures.
* In some archaea, the lipid bilayer is replaced by a monolayer. In
effect, the archaea fuse the tails of two phospholipid molecules into
a single molecule with two polar heads (a bolaamphiphile ); this
fusion 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.
Archaea exhibit a great variety of chemical reactions in their
metabolism and use many sources of energy. These reactions are
classified into nutritional groups , depending on energy and carbon
sources. Some archaea obtain energy from inorganic compounds such as
sulfur or ammonia (they are lithotrophs ). These include nitrifiers ,
methanogens and anaerobic methane oxidisers . In these reactions one
compound passes electrons to another (in a redox reaction), releasing
energy to fuel the cell's activities. One compound acts as an electron
donor and one as an electron acceptor . The energy released is used to
generate adenosine triphosphate (ATP) through chemiosmosis , the same
basic process that happens in the mitochondrion of eukaryotic cells.
Other groups of archaea use sunlight as a source of energy (they are
phototrophs ). However, oxygen–generating photosynthesis does not
occur in any of these organisms. Many basic metabolic pathways are
shared between all forms of life; for example, archaea use a modified
form of glycolysis (the
Entner–Doudoroff pathway ) and either a
complete or partial citric acid cycle . These similarities to other
organisms probably reflect both early origins in the history of life
and their high level of efficiency.
Nutritional types in archaeal metabolism
SOURCE OF ENERGY
SOURCE OF CARBON
Organic compounds or carbon fixation
Ferroglobus _, _
Methanobacteria _ or _
Organic compounds or carbon fixation
Pyrococcus _, _
Sulfolobus _ or _
Euryarchaeota are methanogens (archaea that produce methane as a
result of metabolism) living in anaerobic environments , such as
swamps. This form of metabolism evolved early, and it is even possible
that the first free-living organism was a methanogen. A common
reaction involves the use of carbon dioxide as an electron acceptor to
oxidize hydrogen .
Methanogenesis involves a range of coenzymes that
are unique to these archaea, such as coenzyme M and methanofuran .
Other organic compounds such as alcohols , acetic acid or formic acid
are used as alternative electron acceptors by methanogens. These
reactions are common in gut -dwelling archaea.
Acetic acid is also
broken down into methane and carbon dioxide directly, by
_acetotrophic_ archaea. These acetotrophs are archaea in the order
Methanosarcinales , and are a major part of the communities of
microorganisms that produce biogas . _
Halobacterium salinarum _. The retinol cofactor and residues involved
in proton transfer are shown as ball-and-stick models .
Other archaea use CO
2 in the atmosphere as a source of carbon, in a process called carbon
fixation (they are autotrophs ). This process involves either a highly
modified form of the
Calvin cycle or a recently discovered metabolic
pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle. The
Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota
also use the reductive acetyl-CoA pathway . Carbon–fixation is
powered by inorganic energy sources. No known archaea carry out
photosynthesis . Archaeal energy sources are extremely diverse, and
range from the oxidation of ammonia by the
Nitrosopumilales to the
oxidation of hydrogen sulfide or elemental sulfur by species of
Sulfolobus _, using either oxygen or metal ions as electron
Phototrophic archaea use light to produce chemical energy in the form
of ATP. In the
Halobacteria , light-activated ion pumps like
bacteriorhodopsin and halorhodopsin generate ion gradients by pumping
ions out of the cell across the plasma membrane . The energy stored in
these electrochemical gradients is then converted into ATP by ATP
synthase . This process is a form of photophosphorylation . The
ability of these light-driven pumps to move ions across membranes
depends on light-driven changes in the structure of a retinol cofactor
buried in the center of the protein.
Archaea usually have a single circular chromosome , with as many as
5,751,492 base pairs in _
Methanosarcina acetivorans _, the largest
known archaeal genome. The tiny 490,885 base-pair genome of
Nanoarchaeum equitans _ is one-tenth of this size and the smallest
archaeal genome known; it is estimated to contain only 537
protein-encoding genes. Smaller independent pieces of DNA, called
_plasmids _, are also found in archaea. Plasmids may be transferred
between cells by physical contact, in a process that may be similar to
bacterial conjugation . _
Sulfolobus _ infected with the DNA
virus STSV1 . Bar is 1 micrometer .
Archaea can be infected by double-stranded
DNA viruses that are
unrelated to any other form of virus and have a variety of unusual
shapes, including bottles, hooked rods, or teardrops. These viruses
have been studied in most detail in thermophilics, particularly the
Sulfolobales and Thermoproteales. Two groups of
DNA viruses that infect archaea have been recently
isolated. One group is exemplified by the _
virus 1 _ ("Pleolipoviridae") infecting halophilic archaea and the
other one by the Aeropyrum coil-shaped virus ("Spiraviridae")
infecting a hyperthermophilic (optimal growth at 90–95 °C) host.
Notably, the latter virus has the largest currently reported ssDNA
genome. Defenses against these viruses may involve RNA interference
from repetitive DNA sequences that are related to the genes of the
Archaea are genetically distinct from bacteria and eukaryotes, with
up to 15% of the proteins encoded by any one archaeal genome being
unique to the domain, although most of these unique genes have no
known function. Of the remainder of the unique proteins that have an
identified function, most belong to the Euryarchaea and are involved
in methanogenesis. The proteins that archaea, bacteria and eukaryotes
share form a common core of cell function, relating mostly to
transcription , translation , and nucleotide metabolism . Other
characteristic archaeal features are the organization of genes of
related function—such as enzymes that catalyze steps in the same
metabolic pathway into novel operons , and large differences in tRNA
genes and their aminoacyl tRNA synthetases .
Transcription in archaea more closely resembles eukaryotic than
bacterial transcription, with the archaeal
RNA polymerase being very
close to its equivalent in eukaryotes; while archaeal translation
shows signs of both bacterial and eukaryal equivalents. Although
archaea only have one type of RNA polymerase, its structure and
function in transcription seems to be close to that of the eukaryotic
RNA polymerase II , with similar protein assemblies (the general
transcription factors ) directing the binding of the
RNA polymerase to
a gene's promoter . However, other archaeal transcription factors are
closer to those found in bacteria. Post-transcriptional modification
is simpler than in eukaryotes, since most archaeal genes lack introns
, although there are many introns in their transfer RNA and ribosomal
RNA genes, and introns may occur in a few protein-encoding genes.
GENE TRANSFER AND GENETIC EXCHANGE
Halobacterium volcanii_, an extreme halophilic archaeon, forms
cytoplasmic bridges between cells that appear to be used for transfer
of DNA from one cell to another in either direction.
When the hyperthermophilic archaea _
Sulfolobus solfataricus _ and
Sulfolobus acidocaldarius_ are exposed to the DNA damaging agents UV
irradiation, bleomycin or mitomycin C, species-specific cellular
aggregation is induced. Aggregation in _S. solfataricus_ could not be
induced by other physical stressors, such as pH or temperature shift,
suggesting that aggregation is induced specifically by DNA damage.
Ajon et al. showed that UV-induced cellular aggregation mediates
chromosomal marker exchange with high frequency in _S.
acidocaldarius_. Recombination rates exceeded those of uninduced
cultures by up to three orders of magnitude. Frols et al. and Ajon
et al. hypothesized that cellular aggregation enhances species
specific DNA transfer between _Sulfolobus_ cells in order to provide
increased repair of damaged DNA by means of homologous recombination .
This response may be a primitive form of sexual interaction similar to
the more well-studied bacterial transformation systems that are also
associated with species specific DNA transfer between cells leading to
homologous recombinational repair of DNA damage.
Archaea reproduce asexually by binary or multiple fission ,
fragmentation, or budding ; meiosis does not occur, so if a species of
archaea exists in more than one form, all have the same genetic
Cell division is controlled in a cell cycle ; after the
cell's chromosome is replicated and the two daughter chromosomes
separate, the cell divides. In the genus _
Sulfolobus _, the cycle has
characteristics that are similar to both bacterial and eukaryotic
systems. The chromosomes replicate from multiple starting-points
(origins of replication ) using DNA polymerases that resemble the
equivalent eukaryotic enzymes.
In euryarchaea the cell division protein
FtsZ , which forms a
contracting ring around the cell, and the components of the septum
that is constructed across the center of the cell, are similar to
their bacterial equivalents. In cren- and thaumarchaea, however,
the cell division machinery Cdv fulfills a similar role. This
machinery is related to the eukaryotic ESCRT-III machinery which,
while best known for its role in cell sorting, also has been seen to
fulfill a role in separation between divided cell, suggesting an
ancestral role in cell division.
Both bacteria and eukaryotes, but not archaea, make spores . Some
Haloarchaea undergo phenotypic switching and grow as
several different cell types, including thick-walled structures that
are resistant to osmotic shock and allow the archaea to survive in
water at low salt concentrations, but these are not reproductive
structures and may instead help them reach new habitats.
Archaea that grow in the hot water of the Morning Glory Hot
Yellowstone National Park produce a bright colour
Archaea exist in a broad range of habitats , and as a major part of
global ecosystems , may represent about 20% of microbial cells in the
oceans. The first-discovered archaeans were extremophiles . Indeed,
some archaea survive high temperatures, often above 100 °C (212 °F),
as found in geysers , black smokers , and oil wells. Other common
habitats include very cold habitats and highly saline , acidic , or
alkaline water. However, archaea include mesophiles that grow in mild
conditions, in swamps and marshland , sewage , the oceans , the
intestinal tract of animals, and soils .
Extremophile archaea are members of four main physiological groups.
These are the halophiles , thermophiles , alkaliphiles , and
acidophiles . These groups are not comprehensive or phylum-specific,
nor are they mutually exclusive, since some archaea belong to several
groups. Nonetheless, they are a useful starting point for
Halophiles, including the genus _
Halobacterium _, live in extremely
saline environments such as salt lakes and outnumber their bacterial
counterparts at salinities greater than 20–25%.
best at temperatures above 45 °C (113 °F), in places such as hot
springs; _hyperthermophilic_ archaea grow optimally at temperatures
greater than 80 °C (176 °F). The archaeal _
Methanopyrus kandleri _
Strain 116 can even reproduce at 122 °C (252 °F), the highest
recorded temperature of any organism.
Other archaea exist in very acidic or alkaline conditions. For
example, one of the most extreme archaean acidophiles is _Picrophilus
torridus _, which grows at pH 0, which is equivalent to thriving in
1.2 molar sulfuric acid .
This resistance to extreme environments has made archaea the focus of
speculation about the possible properties of extraterrestrial life .
Some extremophile habitats are not dissimilar to those on
leading to the suggestion that viable microbes could be transferred
between planets in meteorites .
Recently, several studies have shown that archaea exist not only in
mesophilic and thermophilic environments but are also present,
sometimes in high numbers, at low temperatures as well. For example,
archaea are common in cold oceanic environments such as polar seas.
Even more significant are the large numbers of archaea found
throughout the world's oceans in non-extreme habitats among the
plankton community (as part of the picoplankton ). Although these
archaea can be present in extremely high numbers (up to 40% of the
microbial biomass), almost none of these species have been isolated
and studied in pure culture . Consequently, our understanding of the
role of archaea in ocean ecology is rudimentary, so their full
influence on global biogeochemical cycles remains largely unexplored.
Crenarchaeota are capable of nitrification , suggesting
these organisms may affect the oceanic nitrogen cycle , although
Crenarchaeota may also use other sources of energy.
Vast numbers of archaea are also found in the sediments that cover the
sea floor , with these organisms making up the majority of living
cells at depths over 1 meter below the ocean bottom. It has been
demonstrated that in all oceanic surface sediments (from 1000- to
10,000-m water depth), the impact of viral infection is higher on
archaea than on bacteria and virus-induced lysis of archaea accounts
for up to one-third of the total microbial biomass killed, resulting
in the release of ~0.3 to 0.5 gigatons of carbon per year globally.
ROLE IN CHEMICAL CYCLING
Archaea recycle elements such as carbon , nitrogen and sulfur through
their various habitats. Although these activities are vital for normal
ecosystem function, archaea can also contribute to human-made changes,
and even cause pollution .
Archaea carry out many steps in the nitrogen cycle . This includes
both reactions that remove nitrogen from ecosystems (such as nitrate
-based respiration and denitrification ) as well as processes that
introduce nitrogen (such as nitrate assimilation and nitrogen fixation
). Researchers recently discovered archaeal involvement in ammonia
oxidation reactions. These reactions are particularly important in the
oceans. The archaea also appear crucial for ammonia oxidation in
soils. They produce nitrite , which other microbes then oxidize to
nitrate . Plants and other organisms consume the latter.
In the sulfur cycle , archaea that grow by oxidizing sulfur compounds
release this element from rocks, making it available to other
organisms. However, the archaea that do this, such as _Sulfolobus_,
produce sulfuric acid as a waste product, and the growth of these
organisms in abandoned mines can contribute to acid mine drainage and
other environmental damage.
In the carbon cycle , methanogen archaea remove hydrogen and play an
important role in the decay of organic matter by the populations of
microorganisms that act as decomposers in anaerobic ecosystems, such
as sediments, marshes and sewage-treatment works.
Global methane levels in 2011 had increased by a factor of 2.5 since
pre-industrial times: from 722 ppb to 1800 ppb, the highest value in
at least 800,000 years.
Methane has an anthropogenic global warming
potential (AGWP) of 29, which means that it's 29 times stronger in
heat-trapping than carbon dioxide is, over a 100-year time scale.
INTERACTIONS WITH OTHER ORGANISMS
Biological interaction Methanogenic
archaea form a symbiosis with termites .
The well-characterized interactions between archaea and other
organisms are either mutual or commensal . There are no clear examples
of known archaeal pathogens or parasites . However, some species of
methanogens have been suggested to be involved in infections in the
mouth , and _
Nanoarchaeum equitans _ may be a parasite of another
species of archaea, since it only survives and reproduces within the
cells of the Crenarchaeon _
Ignicoccus hospitalis _, and appears to
offer no benefit to its host . In contrast, Archaeal Richmond Mine
Acidophilic Nanoorganisms (ARMAN) occasionally connect with other
archaeal cells in acid mine drainage biofilms. The nature of this
relationship is unknown. However, it is distinct from that of
_Nanarchaeaum–Ignicoccus_ in that the ultrasmall
ARMAN cells are
usually seen independent of the
One well-understood example of mutualism is the interaction between
protozoa and methanogenic archaea in the digestive tracts of animals
that digest cellulose , such as ruminants and termites . In these
anaerobic environments, protozoa break down plant cellulose to obtain
energy. This process releases hydrogen as a waste product, but high
levels of hydrogen reduce energy production. When methanogens convert
hydrogen to methane, protozoa benefit from more energy.
In anaerobic protozoa, such as _Plagiopyla frontata_, archaea reside
inside the protozoa and consume hydrogen produced in their
Archaea also associate with larger organisms. For
example, the marine archaean _
Cenarchaeum symbiosum _ lives within (is
an endosymbiont of) the sponge _
Axinella mexicana _.
Archaea can also be commensals, benefiting from an association
without helping or harming the other organism. For example, the
Methanobrevibacter smithii _ is by far the most common
archaean in the human flora , making up about one in ten of all the
prokaryotes in the human gut. In termites and in humans, these
methanogens may in fact be mutualists, interacting with other microbes
in the gut to aid digestion. Archaean communities also associate with
a range of other organisms, such as on the surface of corals , and in
the region of soil that surrounds plant roots (the rhizosphere ).
SIGNIFICANCE IN TECHNOLOGY AND INDUSTRY
Extremophile archaea, particularly those resistant either to heat or
to extremes of acidity and alkalinity, are a source of enzymes that
function under these harsh conditions. These enzymes have found many
uses. For example, thermostable DNA polymerases , such as the Pfu DNA
polymerase from _
Pyrococcus furiosus _, revolutionized molecular
biology by allowing the polymerase chain reaction to be used in
research as a simple and rapid technique for cloning DNA. In industry,
amylases , galactosidases and pullulanases in other species of
Pyrococcus _ that function at over 100 °C (212 °F) allow food
processing at high temperatures, such as the production of low lactose
milk and whey . Enzymes from these thermophilic archaea also tend to
be very stable in organic solvents, allowing their use in
environmentally friendly processes in green chemistry that synthesize
organic compounds. This stability makes them easier to use in
structural biology . Consequently, the counterparts of bacterial or
eukaryotic enzymes from extremophile archaea are often used in
In contrast to the range of applications of archaean enzymes, the use
of the organisms themselves in biotechnology is less developed.
Methanogenic archaea are a vital part of sewage treatment , since they
are part of the community of microorganisms that carry out anaerobic
digestion and produce biogas . In mineral processing , acidophilic
archaea display promise for the extraction of metals from ores ,
including gold , cobalt and copper .
Archaea host a new class of potentially useful antibiotics . A few of
these archaeocins have been characterized, but hundreds more are
believed to exist, especially within _
Haloarchaea _ and _
These compounds differ in structure from bacterial antibiotics, so
they may have novel modes of action. In addition, they may allow the
creation of new selectable markers for use in archaeal molecular
Aerobic methane production
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