Where in this photo can I find archaea?

Where in this photo can I find archaea?

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This photo is from Guide to the Six Kingdoms of Life under Archaebacteria:

It's not obvious to me where I can find archaea in this photo, although the website seems to indicate it's clear.

Question: Where in this photo can I find archaea?

It's probably the yellow bacterial mats, which are rich in life. The mats are a stratified ecology which varies with distance from the surface, so they are rich in many species of algea, procarote and eukariote. In Yellowstone, the bacterial mats can range in color including brown, green, yellow and orange. They are different to precipitated minerals.

You can say "The photographer contains archaea"! So, no need to search very far.

Here is a pic of an bacterial mat habitat:

You can see in some videos. Ideally we would have a a biology video demonstrating the stuff at Yellowstone to show if it's squishy, slimy, spongey, has growth rings, colord layers, cross sections… although it's only tourist videos for the moment.

Carl Woese

In 1977, Carl Woese overturned one of the major dogmas of biology. Until that time, biologists had taken for granted that all life on Earth belonged to one of two primary lineages, the eukaryotes (which include animals, plants, fungi and certain unicellular organisms such as paramecium) and the prokaryotes (all remaining microscopic organisms). Woese discovered that there were actually three primary lineages. Within what had previously been called prokaryotes, there exist two distinct groups of organisms no more related to one another than they were to eukaryotes. Because of Woese’s work, it is now widely agreed that there are three primary divisions of living systems – the Eukarya, Bacteria, and Archaea, a classification scheme that Woese proposed in 1990.

The new group of organisms – the Archaea – was initially thought to exist only in extreme environments, niches devoid of oxygen and whose temperatures can be near or above the normal boiling point of water. Microbiologists later realized that Archaea are a large and diverse group of organisms that are widely distributed in nature and are common in much less extreme habitats, such as soils and oceans. As such, they are significant contributors to the global carbon and nitrogen cycles.

The method Woese used to identify this “third form of life,” which involved comparing the sequences of a particular molecule central to cellular function, called ribosomal RNA, has become the standard approach used to identify and classify all organisms. These techniques have also revolutionized ecology, because it is now possible to survey an ecosystem by collecting ribosomal DNA from the environment, thus sidestepping the often impossible task of culturing the organisms that are there. These microorganisms and the revolutionary methods that Woese introduced into science can offer insights into the nature and evolution of cells.

In 1996, Woese and colleagues (University of Illinois professor Gary Olsen and researchers from the Institute for Genomic Research) published in the journal Science the first complete genome structure of an archaeon, Methanococcus jannaschii. Based on this work, they concluded that the Archaea are more closely related to humans than to bacteria. “The Archaea are related to us, to the eukaryotes they are descendants of the microorganisms that gave rise to the eukaryotic cell billions of years ago,” Woese said at the time.

Woese’s experimental discoveries were made in the context of his search for a deep understanding of the process of evolution. As early as the 1970’s Woese was thinking about what sort of theory of evolution one would need in the era before genes as we know them had emerged. At such a time, the standard population genetics theory of evolution would not be applicable. Woese articulated early clear proposals about the nature of what has come to be known as the last universal common ancestor, concluding for a variety of reasons that the universal ancestor was not a single organism, but rather groupings of loosely structured cells that existed together during a time when genetic mutation rates were high and the transfer of genes between cells occurred more frequently than in the present day. The most detailed version of these proposals was put forward on the basis of Woese’s work here at IGB (with University of Illinois professor Nigel Goldenfeld). These groups of primitive cells, called progenotes, evolved together and eventually formed the three ancestral lineages.

“Carl's work, in my view, ranks along with the theory of superconductivity as the most important scientific work ever done on this campus – or indeed anywhere else,” says Dr. Nigel Goldenfeld, leader of the IGB Biocomplexity research theme and long-time colleague of Dr. Woese. “It remains one of the 20th century's landmark achievements in biology, and a rock solid foundation for our growing understanding of the evolution of life.”

Woese passed away in December of 2012 at the age of 84.

Publications and Resources

Read the groundbreaking 1977 publication “Phylogenetic structure of the prokaryotic domain: The primary kingdoms,” by Carl R. Woese and George E. Fox, in which Archaea, the third domain of life, is identified.

Commentaries on the 1977 publication include “Woese and Fox: Life, rearranged,” by Prashant Nair, and “Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life,” by Norman R. Pace, Jan Sapp, and Nigel Goldenfeld.

The 30 th anniversary of the first report of the discovery of Archaea was celebrated in 2007 at the IGB, with a symposium covering the historical aspects of the discovery and how this knowledge has transformed microbial ecology. The program, including videos of the presentations, is available at

Carl R. Woese Memorial

On January 26, 2013, a memorial was held with a number of speakers sharing their remembrances of their interaction with Carl.

The speakers included IGB Director Gene Robinson, President Robert Easter, University of Illinois (at the 4:20 mark), Professor Larry Gold, University of Colorado (at the 9:15 mark), Professor Nigel Goldenfeld (at the 16:20 mark), Professor Richard Herman (at the 24:10 mark), Professor Gary Olsen (at the 31:15 mark), Professor Norman Pace, University of Colorado (at the 36:10 mark), Professor Emeritus Karl Stetter, Universität Regensburg (at the 37:46 mark), LAS Dean Ruth Watkins (at the 41:08 mark), Chancellor Phyllis Wise (at the 47:05 mark), and Professor Emeritus Ralph Wolfe (at the 49:32 mark). The open mike comments begin at the 54:14 mark.

Memories shared via the online guest book can also be viewed here.

Carl R. Woese Research Fund

Donations may be made to the Carl R. Woese Research Fund. Dr. Woese approved this fund to support research on evolution, systems biology and ecosystem dynamics at the Carl R. Woese Institute for Genomic Biology. Gifts may be sent to the “University of Illinois Foundation” in care of the Carl R. Woese Institute for Genomic Biology, 1206 W. Gregory Drive, Urbana, IL 61801 or via the secure website At the bottom of the page is a section "I would like my donation allocated to the following specific fund(s):" Specify your donation amount, and in the field "Other - Indicate where to direct donation here" please type “Carl R. Woese Research Fund” in the box. Click the continue button on the bottom of the page, and you will be directed to a secure page for contact and credit card information. You will have the chance to review this information before submission.

About Dr. Woese

Carl Woese was a professor of microbiology at the University of Illinois at Urbana-Champaign and a faculty member of the Carl R. Woese Institute for Genomic Biology. He was awarded the John D. and Catherine T. MacArthur Foundation “genius” award in 1984, and the National Academy of Sciences elected him to membership in 1988. In 1992 the Dutch Royal Academy of Science gave him the highest honor bestowed upon any microbiologist, the Leeuwenhoek Medal, awarded only once every 10 years. He was given the National Medal of Science in 2000 “for his brilliant and original insights, through molecular studies of RNA sequences, to explore the history of life on Earth.” In 2003 the Royal Swedish Academy of Sciences awarded Woese the Crafoord Prize in Biosciences for his discovery of the third domain of life. The Crafoord award honors scientists whose work does not fall into any of the categories covered by Nobel Prizes. The Royal Society, the world’s oldest continuously active scientific organization, elected Woese as a foreign member in 2006. He held the Stanley O. Ikenberry Endowed Chair and served as Center for Advanced Study Professor of Microbiology.

Newly-Discovered Microbe Turns Oil into Methane

Methanoliparia, a species of archaea from deep-sea oil seeps of the Gulf of Mexico, splits long-chain hydrocarbons into methane and carbon dioxide, according to a new paper published in the journal mBio.

Methanoliparia is an important methanogenic alkane degrader in subsurface environments, producing methane by alkane disproportionation as a single organism. This image shows Methanoliparia cells attached to a droplet of oil. Scale bar – 10 μm. Image credit: Max Planck Institute for Marine Microbiology.

“Methanoliparia transforms hydrocarbons by a process called alkane disproportionation. It splits the oil into methane and carbon dioxide,” said lead author Dr. Rafael Laso-Pérez, a researcher at the Max-Planck Institute for Marine Microbiology and MARUM, and his colleagues.

“Previously, this transformation was thought to require a complex partnership between two kinds of organisms: archaea and bacteria.”

The scientists collected sediment samples from the Chapopote Knoll, an oil seep (about 10,000 feet, or 3,000 m, depth) in the Gulf of Mexico.

They carried out genomic analyses that revealed that Methanoliparia is equipped with novel enzymes to use the quite unreactive oil without having oxygen at hand.

“This is the first time we get to see a microbe that has the potential to degrade oil to methane all by itself,” Dr. Laso-Pérez said.

“The new organism, Methanoliparia, is kind of a composite being. Some of its relatives are multi-carbon hydrocarbon-degrading archaea, others are the long-known own methanogens that form methane as metabolic product,” added senior author Dr. Gunter Wegener, also from the Max-Planck Institute for Marine Microbiology and MARUM.

With the combined enzymatic tools of both relatives, Methanoliparia activates and degrades the oil but forms methane as final product.

“Microscopy shows that Methanoliparia cells attach to oil droplets. We did not find any hints that it requires bacteria or other archaea as partners,” Dr. Wegener said.

“We scanned DNA-libraries and found that Methanoliparia is frequently detected in oil reservoirs — and only in oil reservoirs — all over the oceans,” Dr. Laso-Pérez said.

“Thus, this organism could be a key agent in the transformation of long-chain hydrocarbons to methane.”

The team now plans to dig deeper into the secret life of this microbe.

“Now we have the genomic evidence and pictures about the wide distribution and surprising potential of Methanoliparia. But we can’t yet grow them in the lab. That will be the next step to take. It will enable us to investigate many more exciting details,” Dr. Wegener said.

“For example, whether it is possible to reverse the process, which would ultimately allow us to transform a greenhouse gas into fuel.”

Rafael Laso-Pérez et al. 2019. Anaerobic Degradation of Non-Methane Alkanes by “Candidatus Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico. mBio 10: e01814-19 doi: 10.1128/mBio.01814-19

Glimpsing grandmother

But what kind of cell was that ancestor archaeon? And how did it meet, and merge with, its bacterial partners?

Biologist Lynn Margulis was the first to propose, in 1967, that eukaryotes arose when one cell swallowed others 7 . Most researchers agree that some engulfment went on, but they have different ideas about when that happened, and how the internal compartments in eukaryotes came about. “Several dozen models that were tested have died along the way because they’re no longer plausible,” says Sven Gould, an evolutionary cell biologist at Heinrich Heine University in Düsseldorf, Germany. Other theories might rise or fall as cell biologists add to their understanding of archaea.

Many models assume that the cells that eventually became eukaryotic were already quite complex, with flexible membranes and internal compartments, before they ever met the bacterium that was to become the mitochondrion. These theories require cells to have developed a way of gobbling up external material, known as phagocytosis, so they could snap up the passing bacterium in a fateful bite (see ‘Two ways to make complex cells’). By contrast, Gould and others think that mitochondria were acquired early on, and that they then helped to fuel a larger, more complex cell.

The Baums’ model is one of few to explain how mitochondria could arise without phagocytosis. David Baum first came up with the idea as an undergraduate at the University of Oxford, UK, in 1984. His process starts with archaea and bacteria hanging out, sharing resources. The archaeon might start to stretch and bulge its exterior membranes to boost the surface area for nutrient exchange. With time, those bulges might spread and grow around the bacteria until the bacteria were, more or less, inside the archaeon. At the same time, the archaeon’s original exterior membrane, now dwarfed by the long tentacles surrounding it, would evolve into the boundary of the new nucleus, while the cell’s new exterior membrane would form when some particularly long tentacles grew right around the edge, greatly enlarging the cell compared to its archaeal precursor. This process differs from phagocytosis, in that it starts with a community of organisms and takes place over long timescales, rather than in a single bite.

Nik Spencer/Nature Source: B. Baum & D. A. Baum BMC Biol. 18, 72 (2020).

David Baum’s tutor told him the idea was creative, but lacking in evidence. He set it aside. But he’d already shared his enthusiasm for life science with his cousin Buzz, a child then, at regular family dinners in Oxford. “That’s partly why I went into biology,” recalls Buzz.

In 2013, David decided to write up his theory. He sent a note to Buzz, by now running his own lab, who helped develop the theory further. The duo defined several aspects of biology that support their idea, such as the fact that archaea and bacteria have been found living side by side and trading nutrients. The Baums struggled to publish their proposal, but it finally found a home at BMC Biology 2 in 2014.

The idea received an enthusiastic response, Buzz recalls, especially from cell biologists. But back in 2014, David still thought they had just a 50–50 chance of being right.

And then, five years later, the spaghetti-and-meatball images appeared. Both Baums were thrilled.

Archaea and the origins of eukaryotes

The species was the first to be cultured from a group called the Asgard archaea. These organisms, described in 2015, have genes encoding proteins that many scientists consider remarkably similar to those of eukaryotes 8 . Researchers quickly came to suspect that the archaeal ancestor of eukaryotes was something akin to an Asgard archaeon. By pointing to a potential grandmother, the discovery supported the Baums’ hypothesis.

The Asgard representative — which doesn’t yet have a finalized name, and is currently known as Candidatus ‘Prometheoarchaeum syntrophicum’ — grew in a bioreactor alongside either of a pair of microbial hangers-on with which it shared nutrients. Notably, it lacked any complex internal membranes or signs that it could ever hope to phagocytose those associates. It had three systems that could be associated with cell division: proteins that are equivalent to FtsZ ESCRTs and the muscle-contraction protein actin, which also contributes to division in eukaryotes. The culturers haven’t yet worked out which it uses to split itself, says team member Masaru Nobu, a microbiologist at the National Institute of Advanced Industrial Science and Technology in Tokyo.

The big surprise came when the cells stopped dividing and sprouted tentacles. It’s possible, the Baums suggest, that these might amplify nutrient exchange with the microbes that the archaeon was co-cultured with, as their model predicted for the grandmother cell.

On the basis of their observations, Nobu and his colleagues developed a theory about how eukaryotes evolved that shares much with the Baums’ idea. It involves one microbe extending filaments that eventually engulf its partner 1 . “I like our hypothesis because it allows for these complexities that are unique to eukaryotes” — nuclei and mitochondria — “happening at the same time”, says Nobu.

Archaebacteria Examples

Archaebacteria are known to survive in conditions where life can't be even imagined. They are the extreme survivors of the Universe. Take a look at the examples of archaebacteria in this article.

Archaebacteria are known to survive in conditions where life can’t be even imagined. They are the extreme survivors of the Universe. Take a look at the examples of archaebacteria in this article.

Archaebacteria are single-celled organisms that can survive in extreme conditions. They are believed to be the oldest form of organisms, being about 3.5 billion years old. In the past, they were placed under the Kingdom Monera along with bacteria. However, this classification is no longer followed. Since archaebacteria are biochemically and genetically different from bacteria and possess unique evolutionary history, they have a separate domain in the three-domain system of biological classification. In fact, archaebacteria are no longer called so, they are instead known as archaea.

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Archaebacteria belong to a group of primitive prokaryotes that are able to live in an environment that is not suitable for any other living organism. They are found in extreme conditions of acidic, alkaline, salt marshes, and hot sulfur springs. Therefore, they are also called extremophiles, i.e., lover of extreme conditions. They are of different shapes, like spherical, spiral, and rodlike. They are different from bacteria as they have a different cell structure and cell membrane. Unlike bacteria, whose cell walls contain peptidoglycan, the cell walls of archaea do not contain peptidoglycan. Another difference between them is the fact that archaea can survive in conditions where most bacteria cannot. Archaebacteria are divided into three main subgroups, based on the extreme habitats they are found in. These are:

Methanogens are organisms that live in swamps and marshes under anaerobic conditions. They are also found in the gut of some herbivores and humans. They are present in dead and decaying matter too. They are strictly anaerobic organisms and are killed when exposed to oxygen. They reduce carbon dioxide using H2 and release methane in swamps and marshes that is called marsh gas. They are thus added to biogas reactors for production of methane gas for cooking and sewage treatment plants.

» Examples of Methanogens
Methanosphaera stadtmanae
Methanothermus fervidus
Methanolinea mesophila
Methanocaldococcus jannaschii
Methanotorris igneus
Methanomicrobium mobile
Methanoculleus chikugoensis
Methanofollis aquaemaris
Methanogenium marisnigri
Methanolacinia paynteri
Methanoplanus petrolearius
Methanocorpusculum labreanurn
Methanospirillum hungatei
Methanosarcina barkeri
Methanococcoides burtonii
Methanohalobium evestigatum
Methanohalophilus mahii
Methanolobus zinderi
Methanosalsum zhilinae
Methanosaeta thermoacetophila
Methanocaldococcus jannaschii
Methanocella paludicola
Methanopyrus kandleri
Methanofollis formosanus
Methanococcus aeolicus
Methanocalculus taiwanensis
Methanimicrococcus blatticola
Methanocalculus chunghsingensis
Methanomethylovorans hollandica
Methanothermococcus okinawensis
Methanothermobacter thermautotrophicus
Methanobacterium thermoautotrophicum

Halophiles are organisms that survive in an environment with high salt concentration. They are found in the Great Salt Lake, Dead Sea, and highly saline waters. Many species of halophiles contain a pink/red pigment known as carotenoids. They form colonies of bacteria, which can be as much as 100 million bacteria per millimeter!

» Examples of Halophiles

Thermoacidophiles or thermophiles are organisms that live in hot and acidic conditions. They can survive in sulfur-rich environment, like hot springs and geysers that have temperatures of over 50 °C. Thermoacidophiles have both aerobic and anaerobic species, and they are often recognized from their color, which forms due to photosynthetic pigmentation. This archaea can be seen in the Yellowstone National Park.

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» Examples of Thermoacidophiles

Thermoplasma acidophilum
Thermoproteus tenax
Chaetomium thermophilum
Humicola insolens
Thermomyces lanuginosus
Thermoascus aurantiacus
Brevibacillus levickii
Sulfolobus yangmingensis
Archaebacteria are a diverse group of organisms, and recent research has recognized this group as a major part of the Earth’s life. There are many species of Archaea found, and the above were just some examples of this group.

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Early concept Edit

For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry, morphology and metabolism. Microbiologists tried to classify microorganisms based on the structures of their cell walls, their shapes, and the substances they consume. [9] In 1965, Emile Zuckerkandl and Linus Pauling [10] instead proposed using the sequences of the genes in different prokaryotes to work out how they are related to each other. This phylogenetic approach is the main method used today. [11]

Archaea – at that time only the methanogens were known – were first classified separately from bacteria in 1977 by Carl Woese and George E. Fox based on their ribosomal RNA (rRNA) genes. [12] They called these groups the Urkingdoms of Archaebacteria and Eubacteria, though other researchers treated them as kingdoms or subkingdoms. Woese and Fox gave the first evidence for Archaebacteria as a separate "line of descent": 1. lack of peptidoglycan in their cell walls, 2. two unusual coenzymes, 3. results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed reclassifying organisms into three natural domains known as the three-domain system: the Eukarya, the Bacteria and the Archaea, [1] in what is now known as "The Woesian Revolution". [13]

The word archaea comes from the Ancient Greek ἀρχαῖα , meaning "ancient things", [14] 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, but as new habitats were studied, more organisms were discovered. Extreme halophilic [15] and hyperthermophilic microbes [16] were also included in Archaea. For a long time, archaea were seen as extremophiles that exist only in extreme habitats such as hot springs and salt lakes, but 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 abundantly distributed throughout nature. [17] This new appreciation of the importance and ubiquity of archaea came from using polymerase chain reaction (PCR) to detect prokaryotes from environmental samples (such as water or soil) by multiplying their ribosomal genes. This allows the detection and identification of organisms that have not been cultured in the laboratory. [18] [19]

Classification Edit

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. [20] These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships among organisms (molecular phylogenetics). [21] Most of the culturable and well-investigated species of archaea are members of two main phyla, the Euryarchaeota and Crenarchaeota. Other groups have been tentatively created, like the peculiar species Nanoarchaeum equitans, which was discovered in 2003 and has been given its own phylum, the Nanoarchaeota. [22] 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. [23] [24] 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 Micrarchaeota and Parvarchaeota), which were discovered in 2006 [25] and are some of the smallest organisms known. [26]

A superphylum – TACK – which includes the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota was proposed in 2011 to be related to the origin of eukaryotes. [27] In 2017, the newly discovered and newly named Asgard superphylum was proposed to be more closely related to the original eukaryote and a sister group to TACK. [28]

Cladogram Edit

According to Tom A. Williams et al. (2017) [29] and Castelle & Banfield (2018) [30] (DPANN):

Taxonomy Edit

  • "Euryarchaeida" Luketa 2012
    • "Hydrothermarchaeota" Jungbluth, Amend & Rappe 2016
      • "Hydrothermarchaeia" Chuvochina et al. 2019
      • ?"Persephonarchaea" Mwirichia et al. 2016
      • "Hadarchaeia" Chuvochina et al. 2019
        Zillig & Reysenbach 2002Garrity & Holt 2002Boone 2002BBoone 2002
    • "Izemarchaea" Adam et al. 2017
    • "Poseidoniia" Rinke et al. 2019Reysenbach 2002
    • "Methanonatronarchaeia" Sorokin et al. 2017
    • "Methanoliparia" Borrel et al. 2019
    • "Syntropharchaeia" Garrity, Bell & Lilburn 2003Garrity & Holt 2002Grant et al. 2002
      • "Altarchaeota" corrig. Probst et al. 2018
        • "Altarchaeia" corrig. Probst et al. 2014
        • "Iainarchaeia" Rinke et al. 2020
        • "Micrarchaeia"
        • "Undinarchaeia" Dombrowski et al. 2020
        • "Aenigmatarchaeia" corrig. Rinke et al. 2020
        • "Huberarchaeia" corrig. Probst et al. 2019
        • ?"Nanohalobia" La Cono et al. 2020
        • ?"Nanohalarchaeia" corrig. Narasingarao et al. 2012
        • "Nanosalinia" Rinke et al. 2020
        • "Nanoarchaeia"
        • "Filarchaeota" Cavalier-Smith, T. 2014[34] (TACK)
          • ?"Brockarchaeota" De Anda et al. 2018
          • "Korarchaeota" Barns et al. 1996
            • "Korarchaeia" Rinke et al. 2020
              Stieglmeier et al. 2014
            • "Methanomethylia" Vanwonterghem et al. 2016
            • "Thermoproteia" (Thermoprotei)
            • "Borrarchaeota" Liu et al. 2020
            • ?"Baldrarchaeota" Liu et al. 2020
            • "Odinarchaeota" Katarzyna Zaremba-Niedzwiedzka et al. 2017
            • "Helarchaeota" Seitz et al. 2019
            • "Lokiarchaeota" Spang et al. 2015
            • "Thorarchaeota" Seitz et al. 2016
            • ?"Hermodarchaeota" Liu et al. 2020
            • ?"Sifarchaeota" Farag et al. 2020
            • ?"Wukongarchaeota" Liu et al. 2020
            • ?"Hodarchaeota" Liu et al. 2020
            • ?"Gerdarchaeota" ai et al. 2020
            • ?"Kariarchaeota" Liu et al. 2020
            • "Heimdallarchaeota" Katarzyna Zaremba-Niedzwiedzka et al. 2017

            Concept of species Edit

            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 since archaea only reproduce asexually. [35]

            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. [36] On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. [37] Some researchers question whether such species designations have practical meaning. [38]

            Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any accuracy. [21] 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 obscure. [39] The Bacteria also include many uncultured microbes with similar implications for characterization. [40]

            The age of the Earth is about 4.54 billion years. [41] [42] [43] Scientific evidence suggests that life began on Earth at least 3.5 billion years ago. [44] [45] The earliest evidence for life on Earth is graphite found to be biogenic in 3.7-billion-year-old metasedimentary rocks discovered in Western Greenland [46] and microbial mat fossils found in 3.48-billion-year-old sandstone discovered in Western Australia. [47] [48] In 2015, possible remains of biotic matter were found in 4.1-billion-year-old rocks in Western Australia. [49] [50]

            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. [51] Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms. [52] Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago, [53] though such data have since been questioned. [54] These lipids have also been detected in even older rocks from west Greenland. The oldest such traces come from the Isua district, which includes Earth's oldest known sediments, formed 3.8 billion years ago. [55] The archaeal lineage may be the most ancient that exists on Earth. [56]

            Woese argued that the Bacteria, Archaea, and Eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. [57] [58] One possibility [58] [59] 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. [58] [59] It is possible that the last common ancestor of bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" for archaea, and organisms that live in cooler environments appeared only later. [60] Since archaea and bacteria are no more related to each other than they are to eukaryotes, the term prokaryote may suggest a false similarity between them. [61] However, structural and functional similarities between lineages often occur because of shared ancestral traits or evolutionary convergence. These similarities are known as a grade, and prokaryotes are best thought of as a grade of life, characterized by such features as an absence of membrane-bound organelles.

            Comparison with other domains Edit

            The following table compares some major characteristics of the three domains, to illustrate their similarities and differences. [62]

            Property Archaea Bacteria Eukarya
            Cell membrane Ether-linked lipids Ester-linked lipids Ester-linked lipids
            Cell wall Pseudopeptidoglycan, glycoprotein, or S-layer Peptidoglycan, S-layer, or no cell wall Various structures
            Gene structure Circular chromosomes, similar translation and transcription to Eukarya Circular chromosomes, unique translation and transcription Multiple, linear chromosomes, but translation and transcription similar to Archaea
            Internal cell structure No membrane-bound organelles (? [63] ) or nucleus No membrane-bound organelles or nucleus Membrane-bound organelles and nucleus
            Metabolism [64] Various, including diazotrophy, with methanogenesis unique to Archaea Various, including photosynthesis, aerobic and anaerobic respiration, fermentation, diazotrophy, and autotrophy Photosynthesis, cellular respiration, and fermentation no diazotrophy
            Reproduction Asexual reproduction, horizontal gene transfer Asexual reproduction, horizontal gene transfer Sexual and asexual reproduction
            Protein synthesis initiation Methionine Formylmethionine Methionine
            RNA polymerase Many One Many
            EF-2/EF-G Sensitive to diphtheria toxin Resistant to diphtheria toxin Sensitive to diphtheria toxin

            Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular molecule 16S rRNA is key to the production of proteins in all organisms. Because this function is so central to life, organisms with mutations in their 16S rRNA are unlikely to survive, leading to great (but not absolute) stability in the structure of this polynucleotide over generations. 16S rRNA is large enough to show organism-specific variations, but still small enough to be compared quickly. In 1977, Carl Woese, a microbiologist studying the genetic sequences of organisms, developed a new comparison method that involved splitting the RNA into fragments that could be sorted and compared with other fragments from other organisms. [12] The more similar the patterns between species, the more closely they are related. [65]

            Woese used his new rRNA comparison method to categorize and contrast different organisms. He compared a variety of species and happened upon a group of methanogens with rRNA vastly different from any known prokaryotes or eukaryotes. [12] These methanogens were much more similar to each other than to other organisms, leading Woese to propose the new domain of Archaea. [12] His experiments showed that the archaea were genetically more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure. [66] This led to the conclusion that Archaea and Eukarya shared a common ancestor more recent than Eukarya and Bacteria. [66] The development of the nucleus occurred after the split between Bacteria and this common ancestor. [66] [1]

            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 conserved signature indels and signature proteins uniquely present in either all archaea or different main groups within archaea. [67] [68] [69] Another unique feature of archaea, found in no other organisms, is methanogenesis (the metabolic production of methane). Methanogenic 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. [70]

            Relationship to bacteria Edit

            The relationships among the three domains are 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 common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya. [72] Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayer [73] and usually contain a thick sacculus (exoskeleton) of varying chemical composition. [74] 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. [73] Archaea and gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase I [73] [75] but the phylogeny of these genes was interpreted to reveal interdomain gene transfer, [76] [77] and might not reflect the organismal relationship(s). [78]

            It has been proposed that the archaea evolved from gram-positive bacteria in response to antibiotic selection pressure. [73] [75] [79] This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are produced primarily by gram-positive bacteria, [73] [75] and that these antibiotics act primarily 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. [79] The evolution of Archaea in 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 [79] [80] Cavalier-Smith has made a similar suggestion. [81] This proposal is also supported by other work investigating protein structural relationships [82] and studies that suggest that gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes. [83]

            Relation to eukaryotes Edit

            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. [84]

            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 Crenarchaeota [85] and the presence of archaea-like genes in certain bacteria, such as Thermotoga maritima, from horizontal gene transfer. [86] The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea, [87] [88] and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm this hypothesis explains various genetic similarities but runs into difficulties explaining cell structure. [85] An alternative hypothesis, the eocyte hypothesis, posits that Eukaryota emerged relatively late from the Archaea. [89]

            A lineage of archaea discovered in 2015, Lokiarchaeum (of proposed new Phylum "Lokiarchaeota"), named for a hydrothermal vent called Loki's Castle in the Arctic Ocean, was found to be the most closely related to eukaryotes known at that time. It has been called a transitional organism between prokaryotes and eukaryotes. [90] [91]

            Several sister phyla of "Lokiarchaeota" have since been found ("Thorarchaeota", "Odinarchaeota", "Heimdallarchaeota"), all together comprising a newly proposed supergroup Asgard, which may appear as a sister taxon to Proteoarchaeota. [28] [3] [92]

            Details of the relation of Asgard members and eukaryotes are still under consideration, [93] although, in January 2020, scientists reported that Candidatus Prometheoarchaeum syntrophicum, a type of Asgard archaea, may be a possible link between simple prokaryotic and complex eukaryotic microorganisms about two billion years ago. [94] [95]

            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. [96] Other morphologies in the Crenarchaeota include 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 Thermoproteus and Pyrobaculum. [97] Archaea in the genus Haloquadratum such as Haloquadratum walsbyi are flat, square specimens that live in hypersaline pools. [98] These unusual shapes are probably maintained by both their cell walls and a prokaryotic cytoskeleton. Proteins related to the cytoskeleton components of other organisms exist in archaea, [99] and filaments form within their cells, [100] but in contrast with other organisms, these cellular structures are poorly understood. [101] In Thermoplasma and Ferroplasma the lack of a cell wall means that the cells have irregular shapes, and can resemble amoebae. [102]

            Some species form aggregates or filaments of cells up to 200 μm long. [96] These organisms can be prominent in biofilms. [103] Notably, aggregates of Thermococcus coalescens cells fuse together in culture, forming single giant cells. [104] Archaea in the genus Pyrodictium produce an elaborate multicell colony involving arrays of long, thin hollow tubes called cannulae that stick out from the cells' surfaces and connect them into a dense bush-like agglomeration. [105] The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors. [106] Multi-species colonies exist, such as the "string-of-pearls" community that was discovered in 2001 in a German swamp. Round whitish colonies of a novel Euryarchaeota species are spaced along thin filaments that can range up to 15 centimetres (5.9 in) long these filaments are made of a particular bacteria species. [107]

            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. [61] Like bacteria, the cell membranes of archaea are usually bounded by a cell wall and they swim using one or more flagella. [108] 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 outer membrane. [109]

            Cell wall and flagella Edit

            Most archaea (but not Thermoplasma and Ferroplasma) possess a cell wall. [102] In most archaea the wall is assembled from surface-layer proteins, which form an S-layer. [110] An S-layer is a rigid array of protein molecules that cover the outside of the cell (like chain mail). [111] This layer provides both chemical and physical protection, and can prevent macromolecules from contacting the cell membrane. [112] Unlike bacteria, archaea lack peptidoglycan in their cell walls. [113] 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, substituting the latter with N-Acetyltalosaminuronic acid. [112]

            Archaeal flagella are known as archaella, that operate like bacterial flagella – their long stalks are driven by rotatory motors at the base. These motors are powered by a proton gradient across the membrane, but archaella are notably different in composition and development. [108] The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system, [114] [115] while archaeal flagella appear to have evolved from bacterial type IV pili. [116] In contrast with the bacterial flagellum, which is hollow and assembled by subunits moving up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits at the base. [117]

            Membranes Edit

            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. [118] 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. [119]

            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-esterlipids. [120] 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. [121]
            • 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 eukaryotes. This suggests that archaea use entirely different enzymes for synthesizing phospholipids as compared to bacteria and eukaryotes. Such enzymes developed very early in life's history, indicating an early split from the other two domains. [118]
            • 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. [122] 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. [123]
            • 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. [124] For example, the lipids in Ferroplasma are of this type, which is thought to aid this organism's survival in its highly acidic habitat. [125]

            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 chemotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers. [126] 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. [127]

            Other groups of archaea use sunlight as a source of energy (they are phototrophs), but oxygen–generating photosynthesis does not occur in any of these organisms. [127] Many basic metabolic pathways are shared among 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. [128] These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency. [129]

            Nutritional types in archaeal metabolism
            Nutritional type Source of energy Source of carbon Examples
            Phototrophs Sunlight Organic compounds Halobacterium
            Lithotrophs Inorganic compounds Organic compounds or carbon fixation Ferroglobus, Methanobacteria or Pyrolobus
            Organotrophs Organic compounds Organic compounds or carbon fixation Pyrococcus, Sulfolobus or Methanosarcinales

            Some 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. [130] 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. [131] 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. [132]

            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 [134] or another metabolic pathway called the 3-hydroxypropionate/ 4-hydroxybutyrate cycle. [135] The Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota also use the reductive acetyl-CoA pathway. [136] Carbon fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis [137] (Halobacterium is the only known phototroph archeon but it uses an alternative process to photosynthesis). Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales [138] [139] to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors. [127]

            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 and into the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase. [96] 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. [140]

            Archaea usually have a single circular chromosome, [141] with as many as 5,751,492 base pairs in Methanosarcina acetivorans, [142] 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. [143] 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. [144] [145]

            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. [147] Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaeota 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. [148] 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. [148]

            Transcription in archaea more closely resembles eukaryotic than bacterial transcription, with the archaeal RNA polymerase being very close to its equivalent in eukaryotes, [141] while archaeal translation shows signs of both bacterial and eukaryotic equivalents. [149] Although archaea have only 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, [150] but other archaeal transcription factors are closer to those found in bacteria. [151] 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, [152] and introns may occur in a few protein-encoding genes. [153] [154]

            Gene transfer and genetic exchange Edit

            Haloferax 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. [155]

            When the hyperthermophilic archaea Sulfolobus solfataricus [156] and Sulfolobus acidocaldarius [157] are exposed to DNA-damaging UV irradiation or to the agents 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, [156] suggesting that aggregation is induced specifically by DNA damage. Ajon et al. [157] 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. [156] [158] and Ajon et al. [157] hypothesized that cellular aggregation enhances species-specific DNA transfer between Sulfolobus cells in order to provide increased repair of damaged DNA by means of homologous recombination. This response may be a primitive form of sexual interaction similar to the more well-studied bacterial transformation systems that are also associated with species-specific DNA transfer between cells leading to homologous recombinational repair of DNA damage. [159]

            Archaeal viruses Edit

            Archaea are the target of a number of viruses in a diverse virosphere distinct from bacterial and eukaryotic viruses. They have been organized into 15-18 DNA-based families so far, but multiple species remain un-isolated and await classification. [160] [161] [162] These families can be informally divided into two groups: archaea-specific and cosmopolitan. Archaeal-specific viruses target only archaean species and currently include 12 families. Numerous unique, previously unidentified viral structures have been observed in this group, including: bottle-shaped, spindle-shaped, coil-shaped, and droplet-shaped viruses. [161] While the reproductive cycles and genomic mechanisms of archaea-specific species may be similar to other viruses, they bear unique characteristics that were specifically developed due to the morphology of host cells they infect. [160] Their virus release mechanisms differ from that of other phages. Bacteriophages generally undergo either lytic pathways, lysogenic pathways, or (rarely) a mix of the two. [163] Most archaea-specific viral strains maintain a stable, somewhat lysogenic, relationship with their hosts – appearing as a chronic infection. This involves the gradual, and continuous, production and release of virions without killing the host cell. [164] Prangishyili (2013) noted that it has been hypothesized that tailed archaeal phages originated from bacteriophages capable of infecting haloarchaeal species. If the hypothesis is correct, it can be concluded that other double-stranded DNA viruses that make up the rest of the archaea-specific group are their own unique group in the global viral community. Krupovic et al. (2018) states that the high levels of horizontal gene transfer, rapid mutation rates in viral genomes, and lack of universal gene sequences have led researchers to perceive the evolutionary pathway of archaeal viruses as a network. The lack of similarities among phylogenetic markers in this network and the global virosphere, as well as external linkages to non-viral elements, may suggest that some species of archaea specific viruses evolved from non-viral mobile genetic elements (MGE). [161]

            These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales. [165] Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the Halorubrum pleomorphic virus 1 (Pleolipoviridae) infecting halophilic archaea, [166] and the other one by the Aeropyrum coil-shaped virus (Spiraviridae) infecting a hyperthermophilic (optimal growth at 90–95 °C) host. [167] 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. [168] [169]

            Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding mitosis and meiosis do not occur, so if a species of archaea exists in more than one form, all have the same genetic material. [96] Cell division is controlled in a cell cycle after the cell's chromosome is replicated and the two daughter chromosomes separate, the cell divides. [170] 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. [171]

            In Euryarchaeota 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. [170] In cren- [172] [173] and thaumarchaea, [174] 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. [175]

            Both bacteria and eukaryotes, but not archaea, make spores. [176] Some species of 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. [177]

            Communication Edit

            Quorum sensing was originally thought to not exist in Archaea, but recent studies have shown evidence of some species being able to perform cross-talk through quorum sensing. Other studies have shown syntrophic interactions between archaea and bacteria during biofilm growth. Although research is limited in archaeal quorum sensing, some studies have uncovered LuxR proteins in archaeal species, displaying similarities with bacteria LuxR, and ultimately allowing for the detection of small molecules that are used in high density communication. Similarly to bacteria, Archaea LuxR solos have shown to bind to AHLs (lactones) and non-AHLs ligans, which is a large part in performing intraspecies, interspecies, and interkingdom communication through quorum sensing. [178]

            Habitats Edit

            Archaea exist in a broad range of habitats, and are now recognized as a major part of global ecosystems, [17] and may represent about 20% of microbial cells in the oceans. [179] However, the first-discovered archaeans were extremophiles. [126] 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, but archaea include mesophiles that grow in mild conditions, in swamps and marshland, sewage, the oceans, the intestinal tract of animals, and soils. [17]

            Extremophile archaea are members of four main physiological groups. These are the halophiles, thermophiles, alkaliphiles, and acidophiles. [180] 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 classification. [181]

            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%. [126] Thermophiles grow 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). [182] The archaeal Methanopyrus kandleri Strain 116 can even reproduce at 122 °C (252 °F), the highest recorded temperature of any organism. [183]

            Other archaea exist in very acidic or alkaline conditions. [180] 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. [184]

            This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life. [185] Some extremophile habitats are not dissimilar to those on Mars, [186] leading to the suggestion that viable microbes could be transferred between planets in meteorites. [187]

            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. [188] 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). [189] 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. [190] Consequently, our understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on global biogeochemical cycles remains largely unexplored. [191] Some marine Crenarchaeota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle, [138] although these oceanic Crenarchaeota may also use other sources of energy. [192]

            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. [193] [194] 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. [195]

            Role in chemical cycling Edit

            Archaea recycle elements such as carbon, nitrogen, and sulfur through their various habitats. [196] 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). [197] [198] Researchers recently discovered archaeal involvement in ammonia oxidation reactions. These reactions are particularly important in the oceans. [139] [199] 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. [200]

            In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from rocks, making it available to other organisms, but 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. [201]

            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. [202]

            Interactions with other organisms Edit

            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, [203] [204] but some species of methanogens have been suggested to be involved in infections in the mouth, [205] [206] 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, [143] and appears to offer no benefit to its host. [207]

            Mutualism Edit

            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. [208] 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. [209]

            In anaerobic protozoa, such as Plagiopyla frontata, archaea reside inside the protozoa and consume hydrogen produced in their hydrogenosomes. [210] [211] Archaea also associate with larger organisms. For example, the marine archaean Cenarchaeum symbiosum lives within (is an endosymbiont of) the sponge Axinella mexicana. [212]

            Commensalism Edit

            Archaea can also be commensals, benefiting from an association without helping or harming the other organism. For example, the methanogen 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. [213] In termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the gut to aid digestion. [214] Archaean communities also associate with a range of other organisms, such as on the surface of corals, [215] and in the region of soil that surrounds plant roots (the rhizosphere). [216] [217]

            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. [218] [219] These enzymes have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, revolutionized molecular biology by allowing the polymerase chain reaction to be used in research as a simple and rapid technique for cloning DNA. In industry, amylases, galactosidases and pullulanases in other species of Pyrococcus that function at over 100 °C (212 °F) allow food processing at high temperatures, such as the production of low lactose milk and whey. [220] 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. [219] 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. [221]

            In contrast with 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. [222] In mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper. [223]

            Archaea host a new class of potentially useful antibiotics. A few of these archaeocins have been characterized, but hundreds more are believed to exist, especially within Haloarchaea and Sulfolobus. 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 biology. [224]


            The canonical MutL-MutS pathway

            MMR is the process by which bases incorporated in error by the DNA replication machinery are detected and corrected. The MutL-MutS MMR pathway first characterised in Escherichia coli is present in most bacteria (with the notable exception of the Actinobacteria) and in the eukarya, but is the exception rather than the rule in the archaea (Kelman and White 2005). Most archaea lack plausible MutS and MutL homologues, and those that have them tend to be temperature mesophiles such as halophiles and methanogens that most likely captured these genes by lateral gene transfer from bacteria (Fig. 2). The mode of inheritance of a bacterial-type MMR pathway from bacteria to the eukarya is a matter of conjecture. One possibility is that endosymbiotic event that led to the evolution of the mitochondrion from an Alpha-proteobacterium allowed the bacterial genes for MMR to become established in the early eukaryal genome. An alternative possibility is that the eukarya inherited the bacterial MMR machinery via their archaeal lineage. It is notable that the ASGARD archaea including Lokiarchaeum and Thorarchaeum, which have been proposed as the most closely related extant archaea to the progenitor of the eukarya (Eme et al. 2017), possess clear MutS and MutL homologues.

            The emerging role of EndoMS

            The lack of canonical MMR in most archaea is not reflected in high mutation rates (Grogan 2004), and deletion of MutS-MutL in Halobacterium salinarum did not give rise to a hypermutation phenotype (Busch and DiRuggiero 2010). These observations suggest that alternative pathways exist to detect and remove mismatches post DNA replication.

            To search for this pathway, Ishino et al. ( 2016) devised a functional screen for enzymes capable of cleaving DNA mismatches in Pyrococcus furiosus. This resulted in the identification of an enzyme, which was named EndoMS for endonuclease mismatch specific, capable of cleaving a range of mismatched DNAs by the introduction of staggered cleavages in both strands of the DNA, leaving 5 nt 5 ΄ -overhangs (Ishino et al. 2016). EndoMS had originally been identified in the Myllykallio lab and named NucS, based on its activity against single-stranded DNA (Ren et al. 2009). The structure of NucS revealed a dimeric, two-domain organisation, and the enzyme was shown to form a physical interaction with the sliding clamp PCNA (proliferating cell nuclear antigen) (Ren et al. 2009). As the enzyme has a much higher specificity for mismatches than for branched or ssDNA, the nomenclature ‘EndoMS’ will be used henceforth. The recent DNA:protein co-crystal structure reveals that EndoMS wraps around mismatched DNA substrates, flipping out two bases and cleaving the DNA backbone in a manner reminiscent of type II restriction enzymes (Nakae et al. 2016) (Fig. 3). The enzyme is active against G-T, G-G, T-T, T-C and A-G mismatches, but not against C-C, A-C or A-A mismatches in vitro (Ishino et al. 2016), which is consistent with higher binding affinities for substrates with a mismatched G or T (Nakae et al. 2016).

            Structure of the EndoMS dimer bound to DNA (Nakae et al. 2016). EndoMS subunits are shown in cyan and green, with the N-terminal dimerisation domain at the top and the C-terminal nuclease domains at the bottom. The two catalytic sites are indicated by the green spheres that denote the active site magnesium ions. The DNA duplex (blue) is distorted by EndoMS binding and two bases are flipped out.

            Structure of the EndoMS dimer bound to DNA (Nakae et al. 2016). EndoMS subunits are shown in cyan and green, with the N-terminal dimerisation domain at the top and the C-terminal nuclease domains at the bottom. The two catalytic sites are indicated by the green spheres that denote the active site magnesium ions. The DNA duplex (blue) is distorted by EndoMS binding and two bases are flipped out.

            EndoMS has a complex distribution in the archaea (Fig. 2), with examples in the halophiles, various thermophiles from the crenarchaeal and euryarchaeal phyla, and Thorarchaeum from the ASGARD phylum. EndoMS is also present in some bacterial genomes, particularly the phylum Actinobacteria where MutS-MutL is generally absent. A screen for mutation avoidance genes showed that deletion of the gene encoding EndoMS in Mycobacterium smegmatis resulted in a hypermutation phenotype, increasing background mutation rate by about 100-fold (Castaneda-Garcia et al. 2017). The higher rates of mutation were due to elevated levels of transitions (A:T to G:C or G:C to A:T), which is a hallmark of an MMR defect, and similar effects were observed when EndoMS was deleted in Streptomyces coelicolor. Mycobacterial EndoMS has no nuclease activity when presented with mismatched DNA substrates in vitro, suggesting that further components in this non-canonical MMR pathway remain to be identified (Castaneda-Garcia et al. 2017).

            Taken together, the studies in archaea and bacteria make a compelling case that EndoMS participates in an MMR pathway. However, many important aspects of this pathway remain to be elucidated. The generation of double-strand breaks (DSB) by P. furiosus EndoMS is suggestive of an MMR process that functions via HR/DSBR (Ishino et al. 2016). This has the advantage that there is no need to identify nascent DNA strands to pinpoint the mismatched base, as both will be resected during DSBR. The observation that EndoMS is sometimes found in an operon with the RadA recombinase lends further support to this hypothesis (Ren et al. 2009). However, generation of a DSB each time a mismatch is detected seems a risky strategy, unless HR is very efficient. This is probably the case in many of the Euryarchaea, which are highly polyploid. It is much less obvious for the Crenarchaea, which have a eukaryal-like cell cycle with monoploid and diploid stages (Lundgren and Bernander 2007). Clearly, dissection and reconstitution of the pathway using genetic and biochemical techniques is a pressing priority. The interaction of archaeal EndoMS with the sliding clamp PCNA may provide a means to locate EndoMS at the replication fork to interrogate newly synthesised DNA, and could give the opportunity for co-location of a variety of DNA manipulation enzymes on the PCNA toolbelt (Beattie and Bell 2011). In this regard, it will be interesting to see whether the bacterial EndoMS protein requires an interaction with the bacterial sliding clamp for activity.

            Archaebacteria Characteristics

            Archaebacteria have a number of characteristics not seen in more “modern” cell types. These include:

            Archaebacteria have cell membranes made of ether-linked phospholipids, while bacteria and eukaryotes both make their cell membranes out of ester-linked phospholipids

            Archaebacteria use a sugar that is similar to, but not not the same as, the peptidoglycan sugar used in bacteria cell membranes.

            Archaebacteria have a single, round chromosome like bacteria, but their gene transcription is similar to that which occurs in the nuclei of eukaryotic cells.

            This leads to the strange situation that most genes involving most life functions, such as production of the cell membrane, are more closely shared by Eukarya and Bacteria – but genes involved in the process of gene transcription are most closely shared by Eukarya and Archaea.

            This has led some scientists to propose that eukaryotic cells arose from a fusion of archaebacteria with bacteria, possibly when an archaebacteria began living endosymbiotically inside a bacterial cell.

            Other scientists believe that eukaryotes descended directly from archaebacteria, based on the findings of archaebacteria species, Lokiarcheota, which contains some found only in eukaryotes, which in eukaryotes code for genes with uniquely eukaryotic abilities.

            It is thought that Lokiarcheota may be a transitional form between Archaea and Eukaryota.

            3. Only archaebacteria are capable of methanogenesis – a form of anaerobic respiration that produces methane.

            Archaebacteria who use other forms of cellular respiration also exist, but methane-producing cells are not found in Bacteria or Eukarya.

            4. Differences in ribosomal RNA that suggest they diverged from both Bacteria and Eukarya at a point in the distant past

            Archaea: Systematics

            The Archaea constitute one of the three domains into which all known life may be divided. There are two other domains of life. One of these is the Eukaryota, which includes the plants, animals, fungi, and protists. Except for the protists, these organisms have been known and studied since the time of Aristotle, and are the organisms with which you are most likely familiar. The second domain to be discovered was the Bacteria, first observed in the 17th century under the microscope by people such as the Dutch naturalist Antony van Leeuwenhoek.

            The tiny size of bacteria made them difficult to study. Early classifications depended on the shape of individuals, the appearance of colonies in laboratory cultures, and other physical characteristics. When biochemistry blossomed as a modern science, chemical characteristics were also used to classify bacterial species, but even this information was not enough to reliably identify and classify the tiny microbes. Reliable and repeatable classification of bacteria was not possible until the late 20th century when molecular biology made it possible to sequence their DNA.

            Molecules of DNA are found in the cells of all living things, and store the information cells need to build proteins and other cell components. One of the most important components of cells is the ribosome, a large and complex molecule that converts the DNA message into a chemical product. Most of the chemical composition of a ribosome is RNA, a molecule very similar to DNA, and which has its own sequence of building blocks. With sequencing techniques, a molecular biologist can take apart the building block of RNA one by one and identify each one. The result is the sequence of those building blocks.

            Because ribosomes are so critically important is the functioning of living things, they are not prone to rapid evolution. A major change in ribosome sequence can render the ribosome unable to fulfill its duties of building new proteins for the cell. Because of this, we say that the sequence in the ribosomes is conserved -- that it does not change much over time. This slow rate of molecular evolution made the ribosome sequence a good choice for unlocking the secrets of bacterial evolution. By comparing the slight differences in ribosome sequence among a wide diversity of bacteria, groups of similar sequences could be found and recognized as a related group.

            In the 1970s, Carl Woese and his colleagues at the University of Illinois at Urbana-Champaign began investigating the sequences of bacteria with the goal of developing a better picture of bacterial relationships. Their findings were published in 1977, and included a big surprise. Not all tiny microbes were closely related. In addition to the bacteria and eukaryote groups in the analysis, there was a third group of methane-producing microbes. These methanogens were already known to be chemical oddities in the microbial world, since they were killed by oxygen, produced unusual enzymes, and had cell walls different from all known bacteria.

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

            Since the discovery that methanogens belong to the Archaea and not to the Bacteria, a number of other archaeal groups have been discovered. These include some truly weird microbes that thrive in extremely salty water, as well as microbes that live at temperatures close to boiling. Even more recently, scientists have begun finding archaea in an increasing array of habitats, such as the ocean surface, deep ocean muds, salt marshes, the guts of animals, and even in oil reserves deep below the surface of the Earth. Archaea have gone from obscurity to being nearly ubiquitous in only 25 years!

            Archaeans have increasingly become the study of scientific investigation. In many ways, archaeal cells resemble the cells of bacteria, but in a number of important respects, they are more like the cells of eukaryotes. The question arises whether the Archaea are closer relatives of the bacteria or our our group, the eukaryotes. This is a very difficult question to answer, because we are talking about the deepest branches of the tree of life itself we do not have any early ancestors of life around today for comparison. One novel approach used in addressing the question is to look at sequences of duplicated genes. Some DNA sequences occur in more than one copy within each cell, presumably because an extra copy was made at some point in the past. There are a very few genes known to exist in duplicate copies in all living cells, suggesting that the duplication happened before the separation of the three domains of life. In comparing the two sets of sequences, scientists have found that the Archaea may actually be more closely related to us (and the other eukaryotes) than to the bacteria.

            Looking for LUCA, the Last Universal Common Ancestor

            Around 4 billion years ago there lived a microbe called LUCA — the Last Universal Common Ancestor. There is evidence that it could have lived a somewhat ‘alien’ lifestyle, hidden away deep underground in iron-sulfur rich hydrothermal vents. Anaerobic and autotrophic, it didn’t breath air and made its own food from the dark, metal-rich environment around it. Its metabolism depended upon hydrogen, carbon dioxide and nitrogen, turning them into organic compounds such as ammonia. Most remarkable of all, this little microbe was the beginning of a long lineage that encapsulates all life on Earth.

            If we trace the tree of life far enough back in time, we come to find that we’re all related to LUCA . If the war cry for our exploration of Mars is ‘follow the water’, then in the search for LUCA it’s ‘follow the genes’. The study of the genetic tree of life, which reveals the genetic relationships and evolutionary history of organisms, is called phylogenetics. Over the last 20 years our technological ability to fully sequence genomes and build up vast genetic libraries has enabled phylogenetics to truly come of age and has taught us some profound lessons about life’s early history.

            For a long time it was thought that the tree of life formed three main branches, or domains, with LUCA at the base —eukarya, bacteria and archaea. The latter two— the prokaryotes— share similarities in being unicellular and lack a nucleus, and are differentiated from one another by subtle chemical and metabolic differences. Eukarya, on the other hand, are the complex, multicellular life forms comprised of membrane-encased cells, each incorporating a nucleus containing the genetic code as well as the mitochondria ‘organelles’ powering the cell’s metabolism. The eukarya are considered so radically different from the other two branches as to necessarily occupy its own domain.

            However, a new picture has emerged that places eukarya as an offshoot of bacteria and archaea. This “two-domain tree” was first hypothesized by evolutionary biologist Jim Lake at UCLA in 1984, but only got a foothold in the last decade, in particular due to the work of evolutionary molecular biologist Martin Embley and his lab at the University of Newcastle, UK, as well as evolutionary biologist William Martin at the Heinrich Heine University in Düsseldorf, Germany.

            Bill Martin and six of his Düsseldorf colleagues (Madeline Weiss, Filipa Sousa, Natalia Mrnjavac, Sinje Neukirchen, Mayo Roettger and Shijulal Nelson-Sathi) published a 2016 paper in the journal Nature Microbiology describing this new perspective on LUCA and the two-domain tree with phylogenetics.

            Ancient genes

            Previous studies of LUCA looked for common, universal genes that are found in all genomes, based on the assumption that if all life has these genes, then these genes must have come from LUCA . This approach has identified about 30 genes that belonged to LUCA , but they’re not enough to tell us how or where it lived. Another tactic involves searching for genes that are present in at least one member of each of the two prokaryote domains, archaea and bacteria. This method has identified 11,000 common genes that could potentially have belonged to LUCA , but it seems far-fetched that they all did: with so many genes LUCA would have been able to do more than any modern cell can.

            Bill Martin and his team realized that a phenomenon known as lateral gene transfer ( LGT ) was muddying the waters by being responsible for the presence of most of these 11,000 genes. LGT involves the transfer of genes between species and even across domains via a variety of processes such as the spreading of viruses or homologous recombination that can take place when a cell is placed under some kind of stress.

            A growing bacteria or archaea can take in genes from the environment around them by ‘recombining’ new genes into their DNA strand. Often this newly-adopted DNA is closely related to the DNA already there, but sometimes the new DNA can originate from a more distant relation. Over the course of 4 billion years, genes can move around quite a bit, overwriting much of LUCA’s original genetic signal. Genes found in both archaea and bacteria could have been shared through LGT and hence would not necessarily have originated in LUCA .

            Knowing this, Martin’s team searched for ‘ancient’ genes that have exceptionally long lineages but do not seem to have been shared around by LGT , on the assumption that these ancient genes should therefore come from LUCA . They laid out conditions for a gene to be considered as originating in LUCA . To make the cut, the ancient gene could not have been moved around by LGT and it had to be present in at least two groups of archaea and two groups of bacteria.

            “While we were going through the data, we had goosebumps because it was all pointing in one very specific direction,” says Martin.

            Once they had finished their analysis, Bill Martin’s team was left with just 355 genes from the original 11,000, and they argue that these 355 definitely belonged to LUCA and can tell us something about how LUCA lived.

            Such a small number of genes, of course, would not support life as we know it, and critics immediately latched onto this apparent gene shortage, pointing out that essential components capable of nucleotide and amino acid biosynthesis, for example, were missing. “We didn’t even have a complete ribosome,” admits Martin.

            However, their methodology required that they omit all genes that have undergone LTG , so had a ribosomal protein undergone LGT , it wouldn’t be included in the list of LUCA’s genes. They also speculated that LUCA could have gotten by using molecules in the environment to fill the functions of lacking genes, for example molecules that can synthesize amino acids. After all, says Martin, biochemistry at this early stage in life’s evolution was still primitive and all the theories about the origin of life and the first cells incorporate chemical synthesis from their environment.

            What those 355 genes do tell us is that LUCA lived in hydrothermal vents. The Düsseldorf team’s analysis indicates that LUCA used molecular hydrogen as an energy source. Serpentinization within hydrothermal vents can produce copious amounts of molecular hydrogen. Plus, LUCA contained a gene for making an enzyme called ‘reverse gyrase’, which is found today in extremophiles existing in high-temperature environments including hydrothermal vents.

            Two-domain tree

            Martin Embley, who specializes in the study eukaryotic evolution, says the realization of the two-domain tree over the past decade, including William Martin’s work to advance the theory, has been a “breakthrough” and has far-reaching implications on how we view the evolution of early life. “The two-domain tree of life, where the basal split is between the archaea and the bacteria, is now the best supported hypothesis,” he says.

            It is widely accepted that the first archaea and bacteria were likely clostridia (anaerobes intolerant of oxygen) and methanogens, because today’s modern versions share many of the same properties as LUCA . These properties include a similar core physiology and a dependence on hydrogen, carbon dioxide, nitrogen and transition metals (the metals provide catalysis by hybridizing their unfilled electron shells with carbon and nitrogen). Yet, a major question remains: What were the first eukaryotes like and where do they fit into the tree of life?

            Phylogenetics suggests that eukaryotes evolved through the process of endosymbiosis, wherein an archaeal host merged with a symbiont, in this case a bacteria belonging to the alphaproteobacteria group. In the particular symbiosis that spawned the development of eukarya, the bacteria somehow came to thrive within their archaeal host rather than be destroyed. Hence, bacteria came to not only exist within archaea but empowered their hosts to grow bigger and contain increasingly large amounts of DNA . After aeons of evolution, the symbiont bacteria evolved into what we know today as mitochondria, which are little battery-like organelles that provide energy for the vastly more complex eukaryotic cells. Consequently, eukaryotes are not one of the main branches of the tree-of-life, but merely a large offshoot.

            A paper that appeared recently in Nature, written by a team led by Thijs Ettema at Uppsala University in Sweden, has shed more light on the evolution of eukaryotes. In hydrothermal vents located in the North Atlantic Ocean — centered between Greenland, Iceland and Norway, known collectively as Loki’s Castle— they found a new phylum of archaea that they fittingly named the ‘Asgard’ super-phylum after the realm of the Norse gods. The individual microbial species within the super-phylum were then named after Norse gods: Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota. This super-phylum represents the closest living relatives to eukaryotes, and Ettema’s hypothesis is that eukaryotes evolved from one of these archaea, or a currently undiscovered sibling to them, around 2 billion years ago.

            Closing in on LUCA

            If it’s possible to date the advent of eukaryotes, and even pinpoint the species of archaea and bacteria they evolved from, can phylogenetics also date LUCA’s beginning and its split into the two domains?

            It must be noted that LUCA is not the origin of life. The earliest evidence of life dates to 3.7 billion years ago in the form of stromatolites, which are layers of sediment laid down by microbes. Presumably, life may have existed even before that. Yet, LUCA ’s arrival and its evolution into archaea and bacteria could have occurred at any point between 2 to 4 billion years ago.

            Phylogenetics help narrow this down, but Martin Embley isn’t sure our analytical tools are yet capable of such a feat. “The problem with phylogenetics is that the tools commonly used to do phylogenetic analysis are not really sophisticated enough to deal with the complexities of molecular evolution over such vast spans of evolutionary time,” he says. Embley believes this is why the three-domain tree hypothesis lasted so long – we just didn’t have the tools required to disprove it. However, the realization of the two-domain tree suggests that better techniques are now being developed to handle these challenges.

            These techniques include examining the ways biochemistry, as performed in origin-of-life experiments in the lab, can coincide with the realities of what actually happens in biology. This is a concern for Nick Lane, an evolutionary biochemist at University College of London, UK. “What I think has been missing from the equation is a biological point of view,” he says. “It seems trivially easy to make organic [compounds] but much more difficult to get them to spontaneously self-organize, so there are questions of structure that have largely been missing from the chemist’s perspective.”

            For example, Lane highlights how lab experiments routinely construct the building blocks of life from chemicals like cyanide, or how ultraviolet light is utilized as an ad hoc energy source, yet no known life uses these things. Although Lane sees this as a disconnect between lab biochemistry and the realities of biology, he points out that William (Bill) Martin’s work is helping to fill the void by corresponding to real-world biology and conditions found in real-life hydrothermal vents. “That’s why Bill’s reconstruction of LUCA is so exciting, because it produces this beautiful, independent link-up with real world biology,” Lane says.

            The biochemistry results in part from the geology and the materials that are available within it to build life, says Martin Embley. He sees phylogenetics as the correct tool to find the answer, citing the Wood–Ljungdahl carbon-fixing pathway as evidence for this.

            Carbon-fixing involves taking non-organic carbon and turning it into organic carbon compounds that can be used by life. There are six known carbon-fixing pathways and work conducted over many decades by microbiologist Georg Fuchs at the University of Freiburg has shown that the Wood–Ljungdahl pathway is the most ancient of all the pathways and, therefore, the one most likely to have been used by LUCA . Indeed, this is corroborated by the findings of Bill Martin’s team.

            In simple terms the Wood–Ljundahl pathway, which is adopted by bacteria and archaea, starts with hydrogen and carbon dioxide and sees the latter reduced to carbon monoxide and formic acid that can be used by life. “The Wood–Ljungdahl pathway points to an alkaline hydrothermal environment, which provides all the things necessary for it — structure, natural proton gradients, hydrogen and carbon dioxide,” says Martin. “It’s marrying up a geological context with a biological scenario, and it has only been recently that phylogenetics has been able to support this.”

            Astrobiological implications

            Understanding the origin of life and the identity of LUCA is vital not only to explaining the presence of life on Earth, but possibly that on other worlds, too. Hydrothermal vents that were home to LUCA turn out to be remarkably common within our solar system. All that’s needed is rock, water and geochemical heat. “I think that if we find life elsewhere it’s going to look, at least chemically, very much like modern life,” says Martin.

            Moons with cores of rock surrounded by vast global oceans of water, topped by a thick crust of water-ice, populate the Outer Solar System. Jupiter’s moon Europa and Saturn’s moon Enceladus are perhaps the most famous, but there is evidence that hints at subterranean oceans on Saturn’s moons Titan and Rhea, as well as the dwarf planet Pluto and many other Solar System bodies. It’s not difficult to imagine hydrothermal vents on the floors of some of these underground seas, with energy coming from gravitational tidal interactions with their parent planets. The fact that the Sun does not penetrate through the ice ceiling does not matter — the kind of LUCA that Martin describes had no need for sunlight either.

            “Among the astrobiological implications of our LUCA paper is the fact that you do not need light,” says Martin. “It’s chemical energy that ran the origin of life, chemical energy that ran the first cells and chemical energy that is present today on bodies like Enceladus.”

            As such, the discoveries that are developing our picture of the origin of life and the existence of LUCA raise hopes that life could just as easily exist in a virtually identical environment on a distant locale such as Europa or Enceladus. Now that we know how LUCA lived, we know the signs of life to look out for during future missions to these icy moons.

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