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classification is outdated.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.
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 : the Eukarya
Bacteria and the Archaea, in what is now known as "The Woesian
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
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
Thermofilum , and
almost perfectly rectangular rods in
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
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,
Thermococcus coalescens cells fuse together in culture,
forming single giant cells.
Archaea in the genus
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 novel
are spaced along thin filaments that can range up to 15 centimetres
(5.9 in) long; these filaments are made of a particular bacteria
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
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
Organic compounds or carbon fixation
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 .
. 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 acceptors.
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
Halorubrum pleomorphic 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 viruses.
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
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
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
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
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
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 structural studies.
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
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
Earliest known life forms
Earliest known life forms
List of Archaea genera
List of sequenced archaeal genomes
The Surprising Archaea (book)
* Towards a natural system of organisms: proposal for the domains
Archaea, Bacteria, and Eucarya
Unique properties of hyperthermophilic archaea
* ^ A B C Woese, C.R.; Kandler, O.; Wheelis, M.L. (1990). "Towards
a natural system of organisms: proposal for the domains Archaea,
Bacteria, and Eucarya". Proceedings of the National Academy of
Sciences of the United States of America. 87 (12): 4576–9. Bibcode
:1990PNAS...87.4576W. PMC 54159 . PMID 2112744 . doi
* ^ A B "Taxa above the rank of class". List of Prokaryotic names
with Standing in Nomenclature . Retrieved 8 August 2017.
* ^ Petitjean, C.; Deschamps, P.; López-García, P. & Moreira, D.
(2014). "Rooting the Domain archaea by phylogenomic analysis supports
the foundation of the new kingdom proteoarchaeota" .
Evol. 7 (1): 191–204. PMC 4316627 . PMID 25527841 . doi
* ^ A B "NCBI taxonomy page on Archaea".
* ^ Pace, N.R. (May 18, 2006). "Time for a change". Nature. 441
Bibcode :2006Natur.441..289P. PMID 16710401 . doi
* ^ Stoeckenius, W. (1 October 1981). "Walsby\'s square bacterium:
fine structure of an orthogonal procaryote". J. Bacteriol. 148 (1):
352–60. PMC 216199 . PMID 7287626 .
* ^ Bang, C.; Schmitz, R.A. (2015). "
Archaea associated with human
surfaces: not to be underestimated". FEMS
Microbiology Reviews. 39
(5): 631–48. PMID 25907112 . doi :10.1093/femsre/fuv010 . CS1 maint:
Uses authors parameter (link )
* ^ Staley, J.T. (2006). "The bacterial species dilemma and the
genomic-phylogenetic species concept" . Philosophical Transactions of
the Royal Society B. 361 (1475): 1899–909. PMC 1857736 . PMID
17062409 . doi :10.1098/rstb.2006.1914 .
* ^ Zuckerkandl, E.; Pauling, L. (1965). "Molecules as documents of
evolutionary history". J. Theor. Biol. 8 (2): 357–66. PMID 5876245 .
doi :10.1016/0022-5193(65)90083-4 .
* ^ Woese, C.; Fox, G. (1977). "Phylogenetic structure of the
prokaryotic domain: the primary kingdoms" . Proceedings of the
National Academy of Sciences of the United States of America. 74 (11):
Bibcode :1977PNAS...74.5088W. PMC 432104 . PMID 270744 .
doi :10.1073/pnas.74.11.5088 .
* ^ Archaea. (2008). In Merriam-Webster Online Dictionary.
Retrieved July 1, 2008
* ^ Magrum, L.J.; Luehrsen, K.R.; Woese, C.R. (March 1978). "Are
extreme halophiles actually "bacteria"?". J Mol Evol. 11 (1): 1–10.
PMID 660662 . doi :10.1007/bf01768019 .
* ^ Stetter, K.O. (1996). "Hyperthermophiles in the history of
life.". Ciba Found Symp. 202: 1–10. PMID 9243007 .
* ^ A B C DeLong, E.F. (December 1998). "Everything in moderation:
archaea as 'non-extremophiles'". Current Opinion in Genetics &
Development. 8 (6): 649–54. PMID 9914204 . doi
* ^ Theron, J.; Cloete, T.E. (2000). "Molecular techniques for
determining microbial diversity and community structure in natural
environments". Crit. Rev. Microbiol. 26 (1): 37–57. PMID 10782339 .
doi :10.1080/10408410091154174 .
* ^ Schmidt, T.M. (2006). "The maturing of microbial ecology"
(PDF). Int. Microbiol. 9 (3): 217–23. PMID 17061212 . Archived from
the original (PDF) on 11 September 2008.
* ^ Gevers, D.; Dawyndt, P.; Vandamme, P.; et al. (November 29,
2006). "Stepping stones towards a new prokaryotic taxonomy" .
Philosophical Transactions of the Royal Society B. 361 (1475):
1911–6. PMC 1764938 . PMID 17062410 . doi :10.1098/rstb.2006.1915
* ^ A B Robertson, C.E.; Harris, J.K.; Spear, J.R.; Pace, N.R.
(December 2005). "Phylogenetic diversity and ecology of environmental
Archaea". Current Opinion in Microbiology. 8 (6): 638–42. PMID
16236543 . doi :10.1016/j.mib.2005.10.003 .
* ^ Huber, H.; Hohn, M.J.; Rachel, R.; Fuchs, T.; Wimmer, V.C.;
Stetter, K.O. (2002). "A new phylum of
Archaea represented by a
nanosized hyperthermophilic symbiont". Nature. 417 (6884): 27–8.
Bibcode :2002Natur.417...63H. PMID 11986665 . doi :10.1038/417063a .
* ^ Barns, S.M.; Delwiche, C.F.; Palmer, J.D.; Pace NR (1996).
"Perspectives on archaeal diversity, thermophily and monophyly from
environmental rRNA sequences". Proceedings of the National Academy of
Sciences of the United States of America. 93 (17): 9188–93. Bibcode
:1996PNAS...93.9188B. PMC 38617 . PMID 8799176 . doi
* ^ Elkins, J.G.; et al. (June 2008). "A korarchaeal genome reveals
insights into the evolution of the Archaea". Proceedings of the
National Academy of Sciences of the United States of America. 105
Bibcode :2008PNAS..105.8102E. PMC 2430366 . PMID
18535141 . doi :10.1073/pnas.0801980105 .
* ^ Baker, B.J.; Tyson, G.W.; Webb, R.I.; Flanagan, J.; Hugenholtz,
P. & Banfield, J.F. (2006). "Lineages of acidophilic
by community genomic analysis. Science". Science. 314 (6884):
Bibcode :2006Sci...314.1933B. PMID 17185602 . doi
* ^ Baker, B.J.; et al. (May 2010). "Enigmatic, ultrasmall,
uncultivated Archaea" . Proceedings of the National Academy of
Sciences of the United States of America. 107 (19): 8806–11. Bibcode
:2010PNAS..107.8806B. PMC 2889320 . PMID 20421484 . doi
* ^ Guy, L.; Ettema, T.J. (19 December 2011). "The archaeal 'TACK'
superphylum and the origin of eukaryotes.".
Trends Microbiol. 19 (12):
580–587. PMID 22018741 . doi :10.1016/j.tim.2011.09.002 .
* ^ A B Zaremba-Niedzwiedzka, K; et al. (2017). "Asgard archaea
illuminate the origin of eukaryotic cellular complexity". Nature. 541:
353–358. doi :10.1038/nature21031 . CS1 maint: Explicit use of et
al. (link )
* ^ de Queiroz, K. (2005). "Ernst Mayr and the modern concept of
species". Proceedings of the National Academy of Sciences of the
United States of America. 102 (Suppl 1): 6600–7. Bibcode
:2005PNAS..102.6600D. PMC 1131873 . PMID 15851674 . doi
* ^ Eppley, J.M.; Tyson, G.W.; Getz, W.M.; Banfield, J.F. (2007).
"Genetic exchange across a species boundary in the archaeal genus
ferroplasma". Genetics. 177 (1): 407–16. PMC 2013692 . PMID
17603112 . doi :10.1534/genetics.107.072892 .
* ^ Papke, R.T.; Zhaxybayeva, O.; Feil, E.J.; Sommerfeld, K.;
Muise, D.; Doolittle, W.F. (2007). "Searching for species in
haloarchaea". Proceedings of the National Academy of Sciences of the
United States of America. 104 (35): 14092–7. Bibcode
:2007PNAS..10414092P. PMC 1955782 . PMID 17715057 . doi
* ^ Kunin, V.; Goldovsky, L.; Darzentas, N.; Ouzounis, C.A. (2005).
"The net of life: reconstructing the microbial phylogenetic network".
Genome Res. 15 (7): 954–9. PMC 1172039 . PMID 15965028 . doi
* ^ Hugenholtz, P. (2002). "Exploring prokaryotic diversity in the
genomic era" .
Genome Biol. 3 (2): REVIEWS0003. PMC 139013 . PMID
11864374 . doi :10.1186/gb-2002-3-2-reviews0003 .
* ^ Rappé, M.S.; Giovannoni, S.J. (2003). "The uncultured
microbial majority". Annu. Rev. Microbiol. 57: 369–94. PMID 14527284
. doi :10.1146/annurev.micro.57.030502.090759 .
* ^ "Age of the Earth". U.S. Geological Survey. 1997. Archived from
the original on 23 December 2005. Retrieved 2006-01-10.
* ^ Dalrymple, G. Brent (2001). "The age of the Earth in the
twentieth century: a problem (mostly) solved".
Geological Society of London. 190 (1): 205–221. Bibcode
:2001GSLSP.190..205D. doi :10.1144/GSL.SP.2001.190.01.14 .
* ^ Manhesa, Gérard; Allègre, Claude J.; Dupréa, Bernard &
Hamelin, Bruno (1980). "Lead isotope study of basic-ultrabasic layered
complexes: Speculations about the age of the earth and primitive
Earth and Planetary Science Letters . 47 (3):
Bibcode :1980E&PSL..47..370M. doi
* ^ de Duve, Christian (October 1995). "The Beginnings of
American Scientist . Retrieved 15 January 2014.
* ^ Timmer, John (4 September 2012). "3.5 billion year old organic
deposits show signs of life".
Ars Technica . Retrieved 15 January
* ^ Ohtomo, Y.; Kakegawa, T.; Ishida, A.; Nagase, T.; Rosingm M.T.
(8 December 2013). "Evidence for biogenic graphite in early Archaean
Isua metasedimentary rocks". Nature Geoscience.
Nature Geoscience . 7:
Bibcode :2014NatGe...7...25O. doi :10.1038/ngeo2025 . Retrieved 9
* ^ Borenstein, Seth (13 November 2013). "Oldest fossil found: Meet
your microbial mom". Associated Press. Retrieved 15 November 2013.
* ^ Noffke, Nora; Christian, Daniel; Wacey, David; Hazen, Robert M.
(8 November 2013). "Microbially Induced Sedimentary Structures
Recording an Ancient
Ecosystem in the ca. 3.48 Billion-Year-Old
Dresser Formation, Pilbara, Western Australia". Astrobiology (journal)
. 13 (12): 1103–24.
Bibcode :2013AsBio..13.1103N. PMC 3870916 .
PMID 24205812 . doi :10.1089/ast.2013.1030 . Retrieved 15 November
* ^ Borenstein, Seth (19 October 2015). "Hints of life on what was
thought to be desolate early Earth".
Excite . Yonkers, NY: Mindspark
Interactive Network .
Associated Press . Retrieved 2015-10-20.
* ^ Bell, Elizabeth A.; Boehnike, Patrick; Harrison, T. Mark; et
al. (19 October 2015). "Potentially biogenic carbon preserved in a 4.1
billion-year-old zircon" (PDF). Proc. Natl. Acad. Sci. U.S.A.
Washington, D.C.: National Academy of Sciences. 112 (47): 14518–21.
Bibcode :2015PNAS..11214518B. ISSN 1091-6490 . PMC 4664351 . PMID
26483481 . doi :10.1073/pnas.1517557112 . Retrieved 2015-10-20.
* ^ Schopf J (2006). "Fossil evidence of Archaean life" (PDF).
Philosophical Transactions of the Royal Society B. 361 (1470):
869–85. PMC 1578735 . PMID 16754604 . doi :10.1098/rstb.2006.1834
* ^ Chappe B; Albrecht P; Michaelis W (July 1982). "Polar Lipids of
Archaebacteria in Sediments and Petroleums". Science. 217 (4554):
Bibcode :1982Sci...217...65C. PMID 17739984 . doi
* ^ Brocks JJ; Logan GA; Buick R; Summons RE (1999). "Archean
molecular fossils and the early rise of eukaryotes". Science. 285
(5430): 1033–6. PMID 10446042 . doi :10.1126/science.285.5430.1033 .
* ^ Rasmussen B; Fletcher IR; Brocks JJ; Kilburn MR (October 2008).
"Reassessing the first appearance of eukaryotes and cyanobacteria".
Nature. 455 (7216): 1101–4.
Bibcode :2008Natur.455.1101R. PMID
18948954 . doi :10.1038/nature07381 .
* ^ Hahn, Jürgen; Pat Haug (1986). "Traces of Archaebacteria in
ancient sediments". System Applied Microbiology. 7 (Archaebacteria '85
Proceedings): 178–83. doi :10.1016/S0723-2020(86)80002-9 .
* ^ Wang M; Yafremava LS; Caetano-Anollés D; Mittenthal JE;
Caetano-Anollés G (2007). "Reductive evolution of architectural
repertoires in proteomes and the birth of the tripartite world" .
Genome Res. 17 (11): 1572–85. PMC 2045140 . PMID 17908824 . doi
* ^ Woese CR; Gupta R (1981). "Are archaebacteria merely derived
'prokaryotes'?". Nature. 289 (5793): 95–6. Bibcode
:1981Natur.289...95W. PMID 6161309 . doi :10.1038/289095a0 .
* ^ A B C Woese C (1998). "The universal ancestor". Proceedings of
the National Academy of Sciences of the United States of America. 95
Bibcode :1998PNAS...95.6854W. PMC 22660 . PMID
9618502 . doi :10.1073/pnas.95.12.6854 .
* ^ A B Kandler O. The early diversification of life and the origin
of the three domains: A proposal. In: Wiegel J, Adams WW, editors.
Thermophiles: The keys to molecular evolution and the origin of life?
Athens: Taylor and Francis, 1998: 19-31.
* ^ Gribaldo S; Brochier-Armanet C (2006). "The origin and
evolution of Archaea: a state of the art" . Philosophical Transactions
of the Royal Society B. 361 (1470): 1007–22. PMC 1578729 . PMID
16754611 . doi :10.1098/rstb.2006.1841 .
* ^ A B Woese CR (1 March 1994). "There must be a prokaryote
somewhere: microbiology\'s search for itself". Microbiol. Rev. 58 (1):
1–9. PMC 372949 . PMID 8177167 .
* ^ Information is from Willey JM, Sherwood LM, Woolverton CJ.
Microbiology 7th ed. (2008), Ch. 19 pp. 474–475, except where noted.
* ^ Jurtshuk, Peter (1996). Medical
Microbiology (4th ed.).
Galveston (TX): University of Texas Medical Branch at Galveston.
Retrieved 5 November 2014.
* ^ A B C Woese C; Fox G (1977). "Phylogenetic structure of the
prokaryotic domain: the primary kingdoms" . Proceedings of the
National Academy of Sciences of the United States of America. 74 (11):
Bibcode :1977PNAS...74.5088W. PMC 432104 . PMID 270744 .
doi :10.1073/pnas.74.11.5088 .
* ^ Howland, John L. (2000). The Surprising Archaea: Discovering
Another Domain of Life. Oxford: Oxford University Press. pp. 25–30.
ISBN 0-19-511183-4 .
* ^ A B C Cavicchioli, Ricardo (January 2011). "Archaea- timeline
of the third domain". Nature Reviews Microbiology. 9 (1): 51–61.
PMID 21132019 . doi :10.1038/nrmicro2482 . Retrieved 5 November 2014.
* ^ Gupta R. S., Shami A. (2011). "Molecular signatures for the
Crenarchaeota and the Thaumarchaeota". Antonie van Leeuwenhoek. 99:
133–157. PMID 20711675 . doi :10.1007/s10482-010-9488-3 .
* ^ Gao B., Gupta R. S. (2007). "Phylogenomic analysis of proteins
that are distinctive of
Archaea and its main subgroups and the origin
of methanogenesis" . BMC Genomics. 8: 86. PMC 1852104 . PMID
17394648 . doi :10.1186/1471-2164-8-86 .
* ^ Gupta R.S., Naushad S., Baker S. (Mar 2015). "Phylogenomic
analyses and molecular signatures for the class
Halobacteria and its
two major clades: a proposal for division of the class Halobacteria
into an emended order
Halobacteriales and two new orders,
Haloferacales ord. nov. and Natrialbales ord. nov., containing the
novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov".
Int J Syst Evol Microbiol. 65 (3): 1050–69. PMID 25428416 . doi
:10.1099/ijs.0.070136-0 . CS1 maint: Multiple names: authors list
* ^ Deppenmeier, U. (2002). "The unique biochemistry of
methanogenesis". Prog Nucleic
Acid Res Mol Biol. Progress in Nucleic
Acid Research and Molecular Biology. 71: 223–283. ISBN 9780125400718
. PMID 12102556 . doi :10.1016/s0079-6603(02)71045-3 .
* ^ Ciccarelli, F.D.; Doerks, T.; von Mering, C.; Creevey, C.J.;
Snel, B.; Bork, P. (2006). "Toward automatic reconstruction of a
highly resolved tree of life". Science. 311 (5765): 1283–7. Bibcode
:2006Sci...311.1283C. PMID 16513982 . doi :10.1126/science.1123061 .
* ^ Koonin, E.V.; Mushegian, A.R.; Galperin, M.Y.; Walker, D.R.
(1997). "Comparison of archaeal and bacterial genomes: computer
analysis of protein sequences predicts novel functions and suggests a
chimeric origin for the archaea". Mol Microbiol. 25 (4): 619–637.
PMID 9379893 . doi :10.1046/j.1365-2958.1997.4821861.x .
* ^ A B C D E Gupta R. S. (1998). "Protein phylogenies and
signature sequences: A reappraisal of evolutionary relationships among
archaebacteria, eubacteria, and eukaryotes" . Microbiol. Mol. Biol.
Rev. 62 (4): 1435–1491. PMC 98952 . PMID 9841678 .
* ^ Koch AL (2003). "Were
Gram-positive rods the first bacteria?".
Trends Microbiol. 11 (4): 166–170. PMID 12706994 . doi
* ^ A B C Gupta, R.S. (1998). "What are archaebacteria: life's
third domain or monoderm prokaryotes related to gram-positive
bacteria? A new proposal for the classification of prokaryotic
organisms". Mol. Microbiol. 29 (3): 695–708. PMID 9723910 . doi
* ^ Gogarten, Johann Peter (1994). "Which is the Most Conserved
Group of Proteins? Homology - Orthology, Paralogy, Xenology and the
Fusion of Independent Lineages.". Journal of Molecular Evolution. 39
(5): 541–543. PMID 7807544 . doi :10.1007/bf00173425 .
* ^ Brown, J.R.; Masuchi, Y.; Robb, F.T.; Doolittle, W.F. (1994).
"Evolutionary relationships of bacterial and archaeal glutamine
synthetase genes". J Mol Evol. 38 (6): 566–576. PMID 7916055 . doi
* ^ A B C Gupta R.S. (2000). "The natural evolutionary
relationships among prokaryotes". Crit. Rev. Microbiol. 26 (2):
111–131. PMID 10890353 . doi :10.1080/10408410091154219 .
* ^ Gupta RS. Molecular Sequences and the Early History of Life.
In: Sapp J, editor. Microbial Phylogeny and Evolution: Concepts and
Controversies. New York: Oxford University Press, 2005: 160-183.
* ^ Cavalier-Smith T (2002). "The neomuran origin of
archaebacteria, the negibacterial root of the universal tree and
bacterial megaclassification". Int J Syst Evol Microbiol. 52 (1):
7–76. PMID 11837318 . doi :10.1099/00207713-52-1-7 .
* ^ Valas, R.E.; Bourne, P.E. (2011). "The origin of a derived
superkingdom: how a
Gram-positive bacterium crossed the desert to
become an archaeon" . Biol Direct. 6: 16. PMC 3056875 . PMID
21356104 . doi :10.1186/1745-6150-6-16 .
* ^ Skophammer, R.G.; Herbold, C.W.; Rivera, M.C.; Servin, J.A.;
Lake, J.A. (2006). "Evidence that the root of the tree of life is not
within the Archaea". Mol Biol Evol. 23 (9): 1648–1651. PMID 16801395
. doi :10.1093/molbev/msl046 .
* ^ Lake JA (January 1988). "Origin of the eukaryotic nucleus
determined by rate-invariant analysis of rRNA sequences". Nature. 331
Bibcode :1988Natur.331..184L. PMID 3340165 . doi
* ^ Nelson, K.E.; et al. (1999). "Evidence for lateral gene
Archaea and bacteria from genome sequence of
Thermotoga maritima". Nature. 399 (6734): 323–9. Bibcode
:1999Natur.399..323N. PMID 10360571 . doi :10.1038/20601 .
* ^ Gouy M; Li WH (May 1989). "Phylogenetic analysis based on rRNA
sequences supports the archaebacterial rather than the eocyte tree".
Nature. 339 (6220): 145–7.
Bibcode :1989Natur.339..145G. PMID
2497353 . doi :10.1038/339145a0 .
* ^ Yutin, N.; Makarova, K.S.; Mekhedov, S.L.; Wolf, Y.I.; Koonin,
E.V. (May 2008). "The deep archaeal roots of eukaryotes". Mol. Biol.
Evol. 25 (8): 1619–30. PMC 2464739 . PMID 18463089 . doi
* ^ Lake JA. (1988). "Origin of the eukaryotic nucleus determined
by rate-invariant analysis of rRNA sequences". Nature. 331 (6152):
Bibcode :1988Natur.331..184L. PMID 3340165 . doi
* ^ Williams, Tom A.; Foster, Peter G.; Cox, Cymon J.; Embley, T.
Martin (December 2013). "An archaeal origin of eukaryotes supports
only two primary domains of life". Nature. 504 (7479): 231–236.
Bibcode :2013Natur.504..231W. PMID 24336283 . doi :10.1038/nature12779
* ^ Zimmer, Carl (May 6, 2015). "Under the Sea, a Missing Link in
the Evolution of Complex Cells".
New York Times
New York Times . Retrieved May 6,
* ^ Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L.;
Zaremba-Niedzwiedzka, Katarzyna; Martijn, Joran; Lind, Anders E.;
Eijk, Roel van; Schleper, Christa; Guy, Lionel (2015). "Complex
archaea that bridge the gap between prokaryotes and eukaryotes".
Nature. 521 (7551): 173–179.
Bibcode :2015Natur.521..173S. PMC
4444528 . PMID 25945739 . doi :10.1038/nature14447 .
* ^ K. W. Seitz et al.: Genomic reconstruction of a novel, deeply
branched sediment archaeal phylum with pathways for acetogenesis and
sulfur reduction, in: ISME J. 2016 Jul 10(7) 1696-705, doi:
* ^ A B C D Krieg, Noel (2005). Bergey's Manual of Systematic
Bacteriology. US: Springer. pp. 21–6. ISBN 978-0-387-24143-2 .
* ^ Barns, Sue and Burggraf, Siegfried. (1997) Crenarchaeota.
Version 1 January 1997. in The Tree of
Life Web Project
* ^ Walsby, A.E. (1980). "A square bacterium". Nature. 283 (5742):
Bibcode :1980Natur.283...69W. doi :10.1038/283069a0 .
* ^ Hara, F.; Yamashiro, K.; Nemoto, N.; et al. (2007). "An actin
homolog of the archaeon
Thermoplasma acidophilum that retains the
ancient characteristics of eukaryotic actin". J. Bacteriol. 189 (5):
2039–45. PMC 1855749 . PMID 17189356 . doi :10.1128/JB.01454-06 .
* ^ Trent JD; Kagawa HK; Yaoi T; Olle E; Zaluzec NJ (1997).
"Chaperonin filaments: the archaeal cytoskeleton?". Proceedings of the
National Academy of Sciences of the United States of America. 94 (10):
Bibcode :1997PNAS...94.5383T. PMC 24687 . PMID 9144246 .
doi :10.1073/pnas.94.10.5383 .
* ^ Hixon, W.G.; Searcy, D.G. (1993). "Cytoskeleton in the
Thermoplasma acidophilum? Viscosity increase in
soluble extracts". BioSystems. 29 (2–3): 151–60. PMID 8374067 .
doi :10.1016/0303-2647(93)90091-P .
* ^ A B Golyshina OV; Pivovarova TA; Karavaiko GI; et al. (1 May
Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic,
autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic
member of the Ferroplasmaceae fam. nov., comprising a distinct lineage
of the Archaea". Int. J. Syst. Evol. Microbiol. 50 (3): 997–1006.
PMID 10843038 . doi :10.1099/00207713-50-3-997 .
* ^ Hall-Stoodley, L.; Costerton, J.W.; Stoodley, P. (2004).
"Bacterial biofilms: from the natural environment to infectious
diseases". Nature Reviews Microbiology. 2 (2): 95–108. PMID 15040259
. doi :10.1038/nrmicro821 .
* ^ Kuwabara, T.; Minaba, M.; Iwayama, Y.; et al. (November 2005).
Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic
archaeon from Suiyo Seamount". Int. J. Syst. Evol. Microbiol. 55 (Pt
6): 2507–14. PMID 16280518 . doi :10.1099/ijs.0.63432-0 .
* ^ Nickell, S.; Hegerl, R.; Baumeister, W.; Rachel, R. (2003).
Pyrodictium cannulae enter the periplasmic space but do not enter the
cytoplasm, as revealed by cryo-electron tomography". J. Struct. Biol.
141 (1): 34–42. PMID 12576018 . doi :10.1016/S1047-8477(02)00581-6 .
* ^ Horn, C.; Paulmann, B.; Kerlen, G.; Junker, N.; Huber, H. (15
August 1999). "In vivo observation of cell division of anaerobic
hyperthermophiles by using a high-intensity dark-field microscope". J.
Bacteriol. 181 (16): 5114–8. PMC 94007 . PMID 10438790 .
* ^ Rudolph C; Wanner G; Huber R (May 2001). "Natural communities
of novel archaea and bacteria growing in cold sulfurous springs with a
string-of-pearls-like morphology" . Appl. Environ. Microbiol. 67 (5):
2336–44. PMC 92875 . PMID 11319120 . doi
* ^ A B Thomas NA; Bardy SL; Jarrell KF (2001). "The archaeal
flagellum: a different kind of prokaryotic motility structure". FEMS
Microbiol. Rev. 25 (2): 147–74. PMID 11250034 . doi
* ^ Rachel R; Wyschkony I; Riehl S; Huber H (March 2002). "The
ultrastructure of Ignicoccus: evidence for a novel outer membrane and
for intracellular vesicle budding in an archaeon" . Archaea. 1 (1):
9–18. PMC 2685547 . PMID 15803654 . doi :10.1155/2002/307480 .
* ^ Sára M; Sleytr UB (2000). "S-Layer proteins". J. Bacteriol.
182 (4): 859–68. PMC 94357 . PMID 10648507 . doi
* ^ Engelhardt H; Peters J (1998). "Structural research on surface
layers: a focus on stability, surface layer homology domains, and
surface layer-cell wall interactions". J Struct Biol. 124 (2–3):
276–302. PMID 10049812 . doi :10.1006/jsbi.1998.4070 .
* ^ A B Kandler, O; König, H (1998). "
Cell wall polymers in
Archaea (Archaebacteria)" (PDF). Cellular and Molecular
(CMLS). 54 (4): 305–308. doi :10.1007/s000180050156 .
* ^ Howland, John L. (2000). The Surprising Archaea: Discovering
Another Domain of Life. Oxford: Oxford University Press. p. 32. ISBN
* ^ Gophna U; Ron EZ; Graur D (July 2003). "Bacterial type III
secretion systems are ancient and evolved by multiple
horizontal-transfer events". Gene. 312: 151–63. PMID 12909351 . doi
* ^ Nguyen L; Paulsen IT; Tchieu J; Hueck CJ; Saier MH (April
2000). "Phylogenetic analyses of the constituents of Type III protein
secretion systems". J. Mol. Microbiol. Biotechnol. 2 (2): 125–44.
PMID 10939240 .
* ^ Ng SY; Chaban B; Jarrell KF (2006). "Archaeal flagella,
bacterial flagella and type IV pili: a comparison of genes and
posttranslational modifications". J. Mol. Microbiol. Biotechnol. 11
(3–5): 167–91. PMID 16983194 . doi :10.1159/000094053 .
* ^ Bardy SL; Ng SY; Jarrell KF (February 2003). "Prokaryotic
Microbiology (Reading, Engl.). 149 (Pt 2):
295–304. PMID 12624192 . doi :10.1099/mic.0.25948-0 .
* ^ A B Koga Y; Morii H (2007). "Biosynthesis of ether-type polar
lipids in archaea and evolutionary considerations". Microbiol. Mol.
Biol. Rev. 71 (1): 97–120. PMC 1847378 . PMID 17347520 . doi
* ^ De Rosa M; Gambacorta A; Gliozzi A (1 March 1986). "Structure,
biosynthesis, and physicochemical properties of archaebacterial
lipids". Microbiol. Rev. 50 (1): 70–80. PMC 373054 . PMID 3083222
* ^ Albers, S.V.; van de Vossenberg, J.L.; Driessen, A.J.; Konings,
W.N. (September 2000). "Adaptations of the archaeal cell membrane to
heat stress". Front. Biosci. 5: D813–20. PMID 10966867 . doi
* ^ Damsté JS; Schouten S; Hopmans EC; van Duin AC; Geenevasen JA
(October 2002). "Crenarchaeol: the characteristic core glycerol
dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan
pelagic crenarchaeota". J.
Lipid Res. 43 (10): 1641–51. PMID
12364548 . doi :10.1194/jlr.M200148-JLR200 .
* ^ Koga Y; Morii H (November 2005). "Recent advances in structural
research on ether lipids from archaea including comparative and
physiological aspects". Biosci. Biotechnol. Biochem. 69 (11):
2019–34. PMID 16306681 . doi :10.1271/bbb.69.2019 .
* ^ Hanford MJ; Peeples TL (January 2002). "Archaeal tetraether
lipids: unique structures and applications". Appl. Biochem.
Biotechnol. 97 (1): 45–62. PMID 11900115 . doi :10.1385/ABAB:97:1:45
* ^ Macalady JL; Vestling MM; Baumler D; Boekelheide N; Kaspar CW;
Banfield JF (October 2004). "Tetraether-linked membrane monolayers in
Ferroplasma spp: a key to survival in acid". Extremophiles. 8 (5):
411–9. PMID 15258835 . doi :10.1007/s00792-004-0404-5 .
* ^ A B C Valentine DL (2007). "Adaptations to energy stress
dictate the ecology and evolution of the Archaea". Nature Reviews
Microbiology. 5 (4): 316–23. PMID 17334387 . doi
* ^ A B C Schäfer G; Engelhard M; Müller V (1 September 1999).
"Bioenergetics of the Archaea". Microbiol. Mol. Biol. Rev. 63 (3):
570–620. PMC 103747 . PMID 10477309 .
* ^ Zillig W (December 1991). "Comparative biochemistry of Archaea
and Bacteria". Current Opinion in Genetics & Development. 1 (4):
544–51. PMID 1822288 . doi :10.1016/S0959-437X(05)80206-0 .
* ^ Romano A; Conway T (1996). "Evolution of carbohydrate metabolic
pathways". Res Microbiol. 147 (6–7): 448–55. PMID 9084754 . doi
* ^ Koch A (1998). "How did bacteria come to be?". Adv Microb
Physiol. Advances in Microbial Physiology. 40: 353–99. ISBN
978-0-12-027740-7 . PMID 9889982 . doi :10.1016/S0065-2911(08)60135-6
* ^ DiMarco AA; Bobik TA; Wolfe RS (1990). "Unusual coenzymes of
methanogenesis". Annu. Rev. Biochem. 59: 355–94. PMID 2115763 . doi
* ^ Klocke M; Nettmann E; Bergmann I; et al. (May 2008).
"Characterization of the methanogenic
Archaea within two-phase biogas
reactor systems operated with plant biomass". Syst. Appl. Microbiol.
31 (3): 190–205. PMID 18501543 . doi :10.1016/j.syapm.2008.02.003 .
* ^ Based on PDB 1FBB. Data published in Subramaniam S; Henderson R
(August 2000). "Molecular mechanism of vectorial proton translocation
by bacteriorhodopsin". Nature. 406 (6796): 653–7. PMID 10949309 .
doi :10.1038/35020614 .
* ^ Mueller-Cajar O; Badger MR (August 2007). "New roads lead to
Rubisco in archaebacteria". BioEssays. 29 (8): 722–4. PMID 17621634
. doi :10.1002/bies.20616 .
* ^ Berg IA; Kockelkorn D; Buckel W; Fuchs G (December 2007). "A
3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide
assimilation pathway in Archaea". Science. 318 (5857): 1782–6.
Bibcode :2007Sci...318.1782B. PMID 18079405 . doi
* ^ Thauer RK (December 2007). "Microbiology. A fifth pathway of
carbon fixation". Science. 318 (5857): 1732–3. PMID 18079388 . doi
* ^ Bryant DA; Frigaard NU (November 2006). "Prokaryotic
photosynthesis and phototrophy illuminated".
Trends Microbiol. 14
(11): 488–96. PMID 16997562 . doi :10.1016/j.tim.2006.09.001 .
* ^ Könneke M; Bernhard AE; de la Torre JR; Walker CB; Waterbury
JB; Stahl DA (September 2005). "Isolation of an autotrophic
ammonia-oxidizing marine archaeon". Nature. 437 (7058): 543–6.
Bibcode :2005Natur.437..543K. PMID 16177789 . doi :10.1038/nature03911
* ^ A B Francis CA; Beman JM; Kuypers MM (May 2007). "New processes
and players in the nitrogen cycle: the microbial ecology of anaerobic
and archaeal ammonia oxidation". ISME J. 1 (1): 19–27. PMID 18043610
. doi :10.1038/ismej.2007.8 .
* ^ Lanyi JK (2004). "Bacteriorhodopsin". Annu. Rev. Physiol. 66:
665–88. PMID 14977418 . doi
* ^ A B Allers T; Mevarech M (2005). "Archaeal genetics — the
third way". Nature Reviews Genetics. 6 (1): 58–73. PMID 15630422 .
doi :10.1038/nrg1504 .
* ^ Galagan JE; Nusbaum C; Roy A; et al. (April 2002). "The genome
of M. acetivorans reveals extensive metabolic and physiological
Genome Res. 12 (4): 532–42. PMC 187521 . PMID
11932238 . doi :10.1101/gr.223902 .
* ^ Waters E; et al. (2003). "The genome of
insights into early archaeal evolution and derived parasitism".
Proceedings of the National Academy of Sciences of the United States
of America. 100 (22): 12984–8.
Bibcode :2003PNAS..10012984W. PMC
240731 . PMID 14566062 . doi :10.1073/pnas.1735403100 .
* ^ Schleper C; Holz I; Janekovic D; Murphy J; Zillig W (1 August
1995). "A multicopy plasmid of the extremely thermophilic archaeon
Sulfolobus effects its transfer to recipients by mating". J.
Bacteriol. 177 (15): 4417–26. PMC 177192 . PMID 7635827 .
* ^ Sota M; Top EM (2008). "Horizontal
Gene Transfer Mediated by
Plasmids". Plasmids: Current Research and Future Trends. Caister
Academic Press. ISBN 978-1-904455-35-6 .
* ^ Xiang, X.; Chen, L.; Huang, X.; Luo, Y.; She, Q.; Huang, L.
Sulfolobus tengchongensis spindle-shaped virus STSV1:
virus-host interactions and genomic features". J. Virol. 79 (14):
8677–86. PMC 1168784 . PMID 15994761 . doi
* ^ Prangishvili D; Forterre P; Garrett RA (2006). "Viruses of the
Archaea: a unifying view". Nature Reviews Microbiology. 4 (11):
837–48. PMID 17041631 . doi :10.1038/nrmicro1527 .
* ^ Prangishvili D; Garrett RA (2004). "Exceptionally diverse
morphotypes and genomes of crenarchaeal hyperthermophilic viruses".
Biochem. Soc. Trans. 32 (Pt 2): 204–8. PMID 15046572 . doi
* ^ Pietilä MK; Roine E; Paulin L; Kalkkinen N; Bamford DH (March
2009). "An ssDNA virus infecting archaea; A new lineage of viruses
with a membrane envelope". Mol. Microbiol. 72 (2): 307–19. PMID
19298373 . doi :10.1111/j.1365-2958.2009.06642.x .
* ^ Mochizuki T; Krupovic M; Pehau-Arnaudet G; Sako Y; Forterre P;
Prangishvili D (2012). "Archaeal virus with exceptional virion
architecture and the largest single-stranded DNA genome" . Proceedings
of the National Academy of Sciences of the United States of America.
109 (33): 13386–13391.
Bibcode :2012PNAS..10913386M. PMC 3421227
. PMID 22826255 . doi :10.1073/pnas.1203668109 .
* ^ Mojica FJ; Díez-Villaseñor C; García-Martínez J; Soria E
(2005). "Intervening sequences of regularly spaced prokaryotic repeats
derive from foreign genetic elements". J. Mol. Evol. 60 (2): 174–82.
PMID 15791728 . doi :10.1007/s00239-004-0046-3 .
* ^ Makarova KS; Grishin NV; Shabalina SA; Wolf YI; Koonin EV
(2006). "A putative RNA-interference-based immune system in
prokaryotes: computational analysis of the predicted enzymatic
machinery, functional analogies with eukaryotic RNAi, and hypothetical
mechanisms of action" . Biol. Direct. 1: 7. PMC 1462988 . PMID
16545108 . doi :10.1186/1745-6150-1-7 .
* ^ Graham DE; Overbeek R; Olsen GJ; Woese CR (2000). "An archaeal
genomic signature". Proceedings of the National Academy of Sciences of
the United States of America. 97 (7): 3304–8. Bibcode
:2000PNAS...97.3304G. PMC 16234 . PMID 10716711 . doi
* ^ A B Gaasterland T (1999). "Archaeal genomics". Current Opinion
in Microbiology. 2 (5): 542–7. PMID 10508726 . doi
* ^ Dennis PP (1997). "Ancient Ciphers: Translation in Archaea".
Cell. 89 (7): 1007–10. PMID 9215623 . doi
* ^ Werner F (September 2007). "Structure and function of archaeal
RNA polymerases". Mol. Microbiol. 65 (6): 1395–404. PMID 17697097 .
doi :10.1111/j.1365-2958.2007.05876.x .
* ^ Aravind L; Koonin EV (1999). "DNA-binding proteins and
evolution of transcription regulation in the archaea". Nucleic Acids
Res. 27 (23): 4658–70. PMC 148756 . PMID 10556324 . doi
* ^ Lykke-Andersen J; Aagaard C; Semionenkov M; Garrett RA
(September 1997). "Archaeal introns: splicing, intercellular mobility
and evolution". Trends Biochem. Sci. 22 (9): 326–31. PMID 9301331 .
doi :10.1016/S0968-0004(97)01113-4 .
* ^ Watanabe Y; Yokobori S; Inaba T; et al. (January 2002).
"Introns in protein-coding genes in Archaea". FEBS Lett. 510 (1–2):
27–30. PMID 11755525 . doi :10.1016/S0014-5793(01)03219-7 .
* ^ Yoshinari S; Itoh T; Hallam SJ; et al. (August 2006). "Archaeal
pre-mRNA splicing: a connection to hetero-oligomeric splicing
endonuclease". Biochem. Biophys. Res. Commun. 346 (3): 1024–32. PMID
16781672 . doi :10.1016/j.bbrc.2006.06.011 .
* ^ Rosenshine, I; Tchelet, R; Mevarech, M. (1989). "The mechanism
of DNA transfer in the mating system of an archaebacterium". Science.
245 (4924): 1387–1389.
Bibcode :1989Sci...245.1387R. PMID 2818746 .
doi :10.1126/science.2818746 .
* ^ A B C Fröls, S; Ajon, M; Wagner, M; Teichmann, D; Zolghadr, B;
Folea, M; Boekema, EJ; Driessen, AJ; Schleper, C; et al. (2008).
"UV-inducible cellular aggregation of the hyperthermophilic archaeon
Sulfolobus solfataricus is mediated by pili formation". Mol Microbiol.
70 (4): 938–52. PMID 18990182 . doi
* ^ A B C Ajon, M; Fröls, S; van Wolferen, M; Stoecker, K;
Teichmann, D; Driessen, AJ; Grogan, DW; Albers, SV; Schleper, C.; et
al. (2011). "UV-inducible DNA exchange in hyperthermophilic archaea
mediated by type IV pili". Mol Microbiol. 82 (4): 807–17. PMID
21999488 . doi :10.1111/j.1365-2958.2011.07861.x .
* ^ Fröls, S; White, MF; Schleper, C. (2009). "Reactions to UV
damage in the model archaeon
Sulfolobus solfataricus". Biochem Soc
Trans. 37 (1): 36–41. PMID 19143598 . doi :10.1042/BST0370036 .
* ^ Bernstein, H; Bernstein, C (2013). Bernstein, Carol, ed.
Evolutionary Origin and Adaptive Function of Meiosis, Meiosis. InTech.
ISBN 978-953-51-1197-9 .
* ^ A B Bernander R (1998). "
Archaea and the cell cycle". Mol.
Microbiol. 29 (4): 955–61. PMID 9767564 . doi
* ^ Kelman LM; Kelman Z (2004). "Multiple origins of replication in
Trends Microbiol. 12 (9): 399–401. PMID 15337158 . doi
* ^ Lindås AC; Karlsson EA; Lindgren MT; Ettema TJ; Bernander R.
(2008). "A unique cell division machinery in the Archaea" . Proc Natl
Acad Sci U S A. 105 (48): 18942–6.
Bibcode :2008PNAS..10518942L. PMC
2596248 . PMID 18987308 . doi :10.1073/pnas.0809467105 .
* ^ Samson RY; Obita T; Freund SM; Williams RL; Bell SD. (2008). "A
role for the ESCRT system in cell division in archaea" . Science. 322:
Bibcode :2008Sci...322.1710S. PMC 4121953 . PMID 19008417
. doi :10.1126/science.1165322 .
* ^ Pelve EA; Lindås AC; Martens-Habbena W; de la Torre JR; Stahl
DA; Bernander R (2011). "Cdv-based cell division and cell cycle
organization in the thaumarchaeon Nitrosopumilus maritimus.". Mol
Microbiol. 82 (3): 555–566. PMID 21923770 . doi
* ^ Onyenwoke RU; Brill JA; Farahi K; Wiegel J (2004). "Sporulation
genes in members of the low G+C Gram-type-positive phylogenetic branch
( Firmicutes)". Arch. Microbiol. 182 (2–3): 182–92. PMID 15340788
. doi :10.1007/s00203-004-0696-y .
* ^ Kostrikina NA; Zvyagintseva IS; Duda VI (1991). "Cytological
peculiarities of some extremely halophilic soil archaeobacteria".
Arch. Microbiol. 156 (5): 344–49. doi :10.1007/BF00248708 .
* ^ DeLong EF; Pace NR (2001). "Environmental diversity of bacteria
and archaea". Syst. Biol. 50 (4): 470–8. PMID 12116647 . doi
* ^ A B Pikuta EV; Hoover RB; Tang J (2007). "Microbial
extremophiles at the limits of life". Crit. Rev. Microbiol. 33 (3):
183–209. PMID 17653987 . doi :10.1080/10408410701451948 .
* ^ Madigan MT; Martino JM (2006). Brock Biology of Microorganisms
(11th ed.). Pearson. p. 136. ISBN 0-13-196893-9 .
* ^ Takai K; Nakamura K; Toki T; Tsunogai U; Miyazaki M; Miyazaki
J; Hirayama H; Nakagawa S; Nunoura T; Horikoshi K (2008). "Cell
proliferation at 122°C and isotopically heavy CH4 production by a
hyperthermophilic methanogen under high-pressure cultivation" .
Proceedings of the National Academy of Sciences of the United States
of America. 105 (31): 10949–54.
Bibcode :2008PNAS..10510949T. PMC
2490668 . PMID 18664583 . doi :10.1073/pnas.0712334105 .
* ^ Ciaramella M; Napoli A; Rossi M (February 2005). "Another
extreme genome: how to live at pH 0".
Trends Microbiol. 13 (2):
49–51. PMID 15680761 . doi :10.1016/j.tim.2004.12.001 .
* ^ Javaux EJ (2006). "Extreme life on Earth—past, present and
possibly beyond". Res. Microbiol. 157 (1): 37–48. PMID 16376523 .
doi :10.1016/j.resmic.2005.07.008 .
* ^ Nealson KH (January 1999). "Post-Viking microbiology: new
approaches, new data, new insights" (PDF). Origins of
Evolution of Biospheres. 29 (1): 73–93. PMID 11536899 . doi
* ^ Davies PC (1996). "The transfer of viable microorganisms
between planets". Ciba Found. Symp. 202: 304–14; discussion 314–7.
PMID 9243022 .
* ^ López-García P; López-López A; Moreira D; Rodríguez-Valera
F (July 2001). "Diversity of free-living prokaryotes from a deep-sea
site at the Antarctic Polar Front". FEMS Microbiol. Ecol. 36 (2–3):
193–202. PMID 11451524 . doi :10.1016/s0168-6496(01)00133-7 .
* ^ Karner MB; DeLong EF; Karl DM (2001). "Archaeal dominance in
the mesopelagic zone of the Pacific Ocean". Nature. 409 (6819):
Bibcode :2001Natur.409..507K. PMID 11206545 . doi
* ^ Giovannoni SJ; Stingl U (2005). "Molecular diversity and
ecology of microbial plankton". Nature. 437 (7057): 343–8. Bibcode
:2005Natur.437..343G. PMID 16163344 . doi :10.1038/nature04158 .
* ^ DeLong EF; Karl DM (September 2005). "Genomic perspectives in
microbial oceanography". Nature. 437 (7057): 336–42. Bibcode
:2005Natur.437..336D. PMID 16163343 . doi :10.1038/nature04157 .
* ^ Konneke M; Bernhard AE; de la Torre JR; Walker CB; Waterbury
JB; Stahl DA (2005). "Isolation of an autotrophic ammonia-oxidizing
marine archaeon". Nature. 437 (7057): 543–6. Bibcode
:2005Natur.437..543K. PMID 16177789 . doi :10.1038/nature03911 .
* ^ Agogué, H; Brink, M; Dinasquet, J; Herndl, GJ (2008). "Major
gradients in putatively nitrifying and non-nitrifying
Archaea in the
deep North Atlantic". Nature. 456 (7223): 788–791. Bibcode
:2008Natur.456..788A. PMID 19037244 . doi :10.1038/nature07535 .
* ^ Teske A; Sørensen KB (January 2008). "Uncultured archaea in
deep marine subsurface sediments: have we caught them all?". ISME J. 2
(1): 3–18. PMID 18180743 . doi :10.1038/ismej.2007.90 .
* ^ Lipp JS; Morono Y; Inagaki F; Hinrichs KU (July 2008).
"Significant contribution of
Archaea to extant biomass in marine
subsurface sediments". Nature. 454 (7207): 991–4. Bibcode
:2008Natur.454..991L. PMID 18641632 . doi :10.1038/nature07174 .
* ^ Danovaro R, Dell'Anno A, Corinaldesi C, Rastelli E, Cavicchioli
R, Krupovic M, Noble RT, Nunoura T, Prangishvili D (2016).
"Virus-mediated archaeal hecatomb in the deep seafloor" . Science
Advances. 2 (10): e1600492. PMC 5061471 . PMID 27757416 . doi
* ^ Cabello P; Roldán MD; Moreno-Vivián C (November 2004).
Nitrate reduction and the nitrogen cycle in archaea". Microbiology
(Reading, Engl.). 150 (Pt 11): 3527–46. PMID 15528644 . doi
* ^ Mehta MP; Baross JA (December 2006). "
Nitrogen fixation at 92
degrees C by a hydrothermal vent archaeon". Science. 314 (5806):
Bibcode :2006Sci...314.1783M. PMID 17170307 . doi
* ^ Coolen MJ; Abbas B; van Bleijswijk J; et al. (April 2007).
Crenarchaeota in suboxic waters of the
Black Sea: a basin-wide ecological study using 16S ribosomal and
functional genes and membrane lipids". Environ. Microbiol. 9 (4):
1001–16. PMID 17359272 . doi :10.1111/j.1462-2920.2006.01227.x .
* ^ Leininger, S.; Urich, T.; Schloter, M.; Schwark, L.; Qi, J.;
Nicol, G. W.; Prosser, J. I. ; Schuster, S. C.; Schleper, C. (2006).
Archaea predominate among ammonia-oxidizing prokaryotes in soils".
Nature . 442 (7104): 806–809.
Bibcode :2006Natur.442..806L. PMID
16915287 . doi :10.1038/nature04983 .
* ^ Baker, B. J; Banfield, J. F (2003). "Microbial communities in
acid mine drainage". FEMS
Microbiology Ecology. 44 (2): 139–152.
PMID 19719632 . doi :10.1016/S0168-6496(03)00028-X .
* ^ Schimel J (August 2004). "Playing scales in the methane cycle:
from microbial ecology to the globe". Proceedings of the National
Academy of Sciences of the United States of America. 101 (34):
Bibcode :2004PNAS..10112400S. PMC 515073 . PMID 15314221
. doi :10.1073/pnas.0405075101 .
* ^ Ipcc ar5 wg1 (2013). "Climate Change 2013: The Physical Science
Basis - Summary for Policymakers" (PDF). Cambridge University Press.
* ^ Ipcc ar5 wg1 (2013). "Climate Change 2013: The Physical Science
Basis - Anthropogenic and Natural Radiative Forcing Supplementary
Material" (PDF). Cambridge University Press.
* ^ Eckburg P; Lepp P; Relman D (2003). "
Archaea and their
potential role in human disease" . Infect Immun. 71 (2): 591–6. PMC
145348 . PMID 12540534 . doi :10.1128/IAI.71.2.591-596.2003 .
* ^ Cavicchioli R; Curmi P; Saunders N; Thomas T (2003).
"Pathogenic archaea: do they exist?". BioEssays. 25 (11): 1119–28.
PMID 14579252 . doi :10.1002/bies.10354 .
* ^ Lepp P; Brinig M; Ouverney C; Palm K; Armitage G; Relman D
Archaea and human periodontal disease" .
Proceedings of the National Academy of Sciences of the United States
of America. 101 (16): 6176–81.
Bibcode :2004PNAS..101.6176L. PMC
395942 . PMID 15067114 . doi :10.1073/pnas.0308766101 .
* ^ Vianna ME; Conrads G; Gomes BP; Horz HP (April 2006).
"Identification and quantification of archaea involved in primary
endodontic infections". J. Clin. Microbiol. 44 (4): 1274–82. PMC
1448633 . PMID 16597851 . doi :10.1128/JCM.44.4.1274-1282.2006 .
* ^ Waters E; et al. (October 2003). "The genome of Nanoarchaeum
equitans: insights into early archaeal evolution and derived
parasitism". Proceedings of the National Academy of Sciences of the
United States of America. 100 (22): 12984–8. Bibcode
:2003PNAS..10012984W. PMC 240731 . PMID 14566062 . doi
* ^ Jahn U; Gallenberger M; Paper W; et al. (March 2008).
Nanoarchaeum equitans and
Ignicoccus hospitalis: new insights into a
unique, intimate association of two archaea". J. Bacteriol. 190 (5):
1743–50. PMC 2258681 . PMID 18165302 . doi :10.1128/JB.01731-07 .
* ^ Baker BJ; Comolli LR; Dick GJ; Hauser LJ; Hyatt D; Dill BD;
Land ML; VerBerkmoes NC; Hettich RL; Banfield JF (May 2010).
"Enigmatic, ultrasmall, uncultivated Archaeaa". Proceedings of the
National Academy of Sciences of the United States of America. 107
Bibcode :2010PNAS..107.8806B. PMC 2889320 . PMID
20421484 . doi :10.1073/pnas.0914470107 .
* ^ Chaban B; Ng SY; Jarrell KF (February 2006). "Archaeal
habitats—from the extreme to the ordinary". Can. J. Microbiol. 52
(2): 73–116. PMID 16541146 . doi :10.1139/w05-147 .
* ^ Schink B (June 1997). "Energetics of syntrophic cooperation in
methanogenic degradation" . Microbiol. Mol. Biol. Rev. 61 (2):
262–80. PMC 232610 . PMID 9184013 .
* ^ Lange, M; Westermann, P; Ahring, BK (2005). "
protozoa and metazoa". Applied
Microbiology and Biotechnology. 66 (5):
465–474. PMID 15630514 . doi :10.1007/s00253-004-1790-4 .
* ^ van Hoek AH; van Alen TA; Sprakel VS; et al. (1 February 2000).
"Multiple acquisition of methanogenic archaeal symbionts by anaerobic
ciliates". Mol. Biol. Evol. 17 (2): 251–8. PMID 10677847 . doi
* ^ Preston, C.M; Wu, K.Y; Molinski, T.F; Delong, E.F (1996). "A
psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum
symbiosum gen. nov., sp. nov" . Proceedings of the National Academy of
Sciences of the United States of America. 93 (13): 6241–6. Bibcode
:1996PNAS...93.6241P. PMC 39006 . PMID 8692799 . doi
* ^ Eckburg PB; et al. (June 2005). "Diversity of the human
intestinal microbial flora" . Science. 308 (5728): 1635–8. Bibcode
:2005Sci...308.1635E. PMC 1395357 . PMID 15831718 . doi
* ^ Samuel BS; Gordon JI (June 2006). "A humanized gnotobiotic
mouse model of host-archaeal-bacterial mutualism" . Proceedings of the
National Academy of Sciences of the United States of America. 103
Bibcode :2006PNAS..10310011S. PMC 1479766 . PMID
16782812 . doi :10.1073/pnas.0602187103 .
* ^ Wegley, L; Yu, Y; Breitbart, M; Casas, V; Kline, D.I; Rohwer, F
(2004). "Coral-associated Archaea" (PDF). Marine Ecology Progress
Series. 273: 89–96. doi :10.3354/meps273089 . Archived from the
original (PDF) on 11 September 2008.
* ^ Chelius MK; Triplett EW (April 2001). "The Diversity of Archaea
Bacteria in Association with the Roots of Zea mays L". Microb.
Ecol. 41 (3): 252–63.
JSTOR 4251818 . PMID 11391463 . doi
* ^ Simon HM; Dodsworth JA; Goodman RM (October 2000).
Crenarchaeota colonize terrestrial plant roots". Environ. Microbiol.
2 (5): 495–505. PMID 11233158 . doi
* ^ Breithaupt H (2001). "The hunt for living gold. The search for
organisms in extreme environments yields useful enzymes for industry"
. EMBO Rep. 2 (11): 968–71. PMC 1084137 . PMID 11713183 . doi
* ^ A B Egorova, K.; Antranikian, G. (December 2005). "Industrial
relevance of thermophilic Archaea". Current Opinion in Microbiology. 8
(6): 649–55. PMID 16257257 . doi :10.1016/j.mib.2005.10.015 .
* ^ Synowiecki J; Grzybowska B; Zdziebło A (2006). "Sources,
properties and suitability of new thermostable enzymes in food
processing". Crit Rev Food Sci Nutr. 46 (3): 197–205. PMID 16527752
. doi :10.1080/10408690590957296 .
* ^ Jenney FE; Adams MW (January 2008). "The impact of
extremophiles on structural genomics (and vice versa)". Extremophiles.
12 (1): 39–50. PMID 17563834 . doi :10.1007/s00792-007-0087-9 .
* ^ Schiraldi C; Giuliano M; De Rosa M (2002). "Perspectives on
biotechnological applications of archaea" . Archaea. 1 (2): 75–86.
PMC 2685559 . PMID 15803645 . doi :10.1155/2002/436561 .
* ^ Norris, P.R.; Burton, N.P.; Foulis, N.A. (April 2000).
"Acidophiles in bioreactor mineral processing". Extremophiles. 4 (2):
71–6. PMID 10805560 . doi :10.1007/s007920050139 .
* ^ Shand RF; Leyva KJ (2008). "Archaeal Antimicrobials: An
Undiscovered Country". In Blum P. Archaea: New Models for Prokaryotic
Biology. Caister Academic Press. ISBN 978-1-904455-27-1 .
* Howland, John L. (2000). The Surprising Archaea: Discovering
Another Domain of Life. Oxford University. ISBN 978-0-19-511183-5 .
* Martinko JM; Madigan MT (2005). Brock Biology of Microorganisms
(11th ed.). Englewood Cliffs, N.J: Prentice Hall. ISBN 0-13-144329-1 .
* Garrett RA; Klenk H (2005). Archaea: Evolution, Physiology and
Molecular Biology. WileyBlackwell. ISBN 1-4051-4404-1 .
* Cavicchioli R (2007). Archaea: Molecular and Cellular Biology.
American Society for Microbiology. ISBN 1-55581-391-7 .
* Blum P, ed. (2008). Archaea: New Models for Prokaryotic Biology.
Caister Academic Press. ISBN 978-1-904455-27-1 .
* Lipps G (2008). "Archaeal Plasmids". Plasmids: Current Research
and Future Trends. Caister Academic Press. ISBN 978-1-904455-35-6 .
* Sapp, Jan (2009). The New Foundations of Evolution: On the Tree of
Life. New York: Oxford University Press. ISBN 0-19-538850-X .
* Schaechter, M (2009).
Archaea (Overview) in The Desk Encyclopedia
Microbiology (2nd ed.). San Diego and London: Elsevier Academic
Press. ISBN 978-0-12-374980-2 .
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* Introduction to the Archaea, ecology, systematics and morphology
* Oceans of
Archaea – E.F. DeLong, ASM News, 2003
* NCBI taxonomy page on Archaea
* Genera of the domain
Archaea – list of Prokaryotic names with
Standing in Nomenclature
* Shotgun sequencing finds nanoorganisms – discovery of the