Archaea

• 1. Introduction

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  Archaea live at pH 0, the equivalent of thriving in 1.2 molar sulfuric acid, and one of them reproduces at 122 degrees Celsius, the highest temperature recorded for any organism. For much of the 20th century, no one knew these creatures formed their own branch of life. They were filed away as bacteria, even named archaebacteria, a label that has since fallen out of use. Then a microbiologist found a handful of methane-producing cells whose genetic fingerprint matched nothing else alive. The word archaea comes from the Ancient Greek for ancient things, a nod to the assumption that these organisms echoed Earth's primitive atmosphere. So what makes a cell archaeal rather than bacterial when, under a microscope, the two often look identical? Why does an organism that resembles a bacterium share its most vital machinery with you? And how did a group once dismissed as fringe extremists turn out to be among the most abundant living things in the ocean? The answers reach from the deepest sea vents to the human gut.

• 2. The Third Branch

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  In 1977, Carl Woese and George E. Fox split archaea away from bacteria using ribosomal RNA, and at that time only the methanogens were known. Woese had built a new comparison method that broke RNA into fragments, sorted them, and matched the patterns across species. The more alike the patterns, the closer the kinship. He came upon a group of methanogens whose RNA was unlike any known prokaryote or eukaryote, yet strikingly similar to one another. That oddity led him to propose an entirely new domain.

  The particular molecule at the heart of the discovery is 16S ribosomal RNA, central to protein production in every organism. Because that function is so essential, mutations in 16S rRNA rarely survive, which keeps its structure stable across generations. It is large enough to carry organism-specific variation, yet small enough to compare quickly. Woese and Fox offered three lines of evidence for a separate line of descent: a lack of peptidoglycan in the cell walls, two unusual coenzymes, and the results of that 16S sequencing.

  Woese, Otto Kandler, and Mark Wheelis then proposed reorganizing life into three domains: the Eukarya, the Bacteria, and the Archaea. This restructuring is now called the Woesian Revolution. The idea did not arrive in a vacuum. Back in 1965, Emile Zuckerkandl and Linus Pauling had suggested using gene sequences, rather than shape or diet, to work out how prokaryotes relate to each other. That phylogenetic approach remains the main method used today, and it would soon reveal that the prokaryote label hid a false similarity between two profoundly different forms of life.

• 3. An Alien Membrane

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  Every cell membrane in nature is built from phospholipids, molecules with a water-loving phosphate head and a greasy tail, joined by a glycerol moiety. Archaea break the rules of this universal design in four ways. Their lipids attach to glycerol through ether bonds rather than the ester bonds found in bacteria and eukaryotes, and ether linkages are more chemically stable. That stability may help many archaea endure the heat and salinity that punish ordinary membranes.

  The stereochemistry of the archaeal glycerol is the mirror image of everyone else's. Just as a right hand will not slip into a left-handed glove, the enzymes built for one form cannot generally make or use the other. Archaea build their membranes on sn-glycerol-1-phosphate, the enantiomer of the sn-glycerol-3-phosphate that bacteria and eukaryotes use. This implies they rely on entirely different enzymes, ones that emerged very early in life's history.

  Archaeal lipid tails are long isoprenoid chains carrying side branches, sometimes capped with cyclopentane or cyclohexane rings, where other organisms use straight fatty acids. Only archaea use isoprenoids to build phospholipids, and those branches may keep their membranes from leaking at high temperatures. In some species the bilayer collapses into a monolayer. The cell fuses two phospholipid tails into a single molecule with two heads, a bolaamphiphile, stiffening the membrane. The lipids in Ferroplasma take this form, which is thought to help it survive its highly acidic home.

• 4. Closer To Us Than To Bacteria

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  Woese's experiments revealed a paradox: archaea look like prokaryotes but read like eukaryotes. Their genes were genetically more similar to eukaryotes than to bacteria, even as their structure stayed prokaryotic. The conclusion was that Archaea and Eukarya share a more recent common ancestor than either shares with Bacteria, and that the nucleus developed only after that split. Most of an organism's genes run metabolic pathways, and there archaea and bacteria overlap. But the genes that govern gene expression are shared between archaea and eukaryotes.

  Transcription in archaea sits much closer to the eukaryotic version. Archaeal RNA polymerase resembles eukaryotic RNA polymerase II, and similar general transcription factors guide it to a gene's promoter. Yet some archaeal transcription factors lean bacterial instead, and translation carries traces of both worlds. Most archaeal genes lack introns, making post-transcriptional modification simpler than in eukaryotes, though introns crowd their transfer RNA and ribosomal RNA genes.

  A lineage discovered in 2015 sharpened the picture. Lokiarchaeum, named for the hydrothermal vent Loki's Castle in the Arctic Ocean, was the closest known relative of eukaryotes at the time, described as a transitional organism between prokaryotes and eukaryotes. Sister groups soon followed, named Thorarchaeota, Odinarchaeota, and Heimdallarchaeota, gathered under a proposed supergroup called Asgard. In January 2020, scientists reported that Promethearchaeum syntrophicum, an Asgard archaeon, may mark a link between simple and complex microbial life around two billion years ago.

• 5. Strange Bodies

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  Haloquadratum walsbyi grows as flat, perfectly square cells that live in hypersaline pools, a shape unlike almost anything else in biology. Individual archaea span from 0.1 micrometers to over 15 micrometers across, taking the form of spheres, rods, spirals, or plates. Within the Thermoproteota the variety widens: lobed cells in Sulfolobus, needle-thin filaments under half a micrometer wide in Thermofilum, and near-rectangular rods in Thermoproteus and Pyrobaculum. In Thermoplasma and Ferroplasma the absence of a cell wall leaves the cells shapeless, resembling amoebae.

  Some archaea band together into structures far larger than a single cell. Aggregates of Thermococcus coalescens fuse in culture into single giant cells. Pyrodictium builds elaborate colonies threaded with long, thin, hollow tubes called cannulae that link cells into a dense bush-like mass, perhaps for communication or nutrient exchange. In 2001, a string-of-pearls community was found in a German swamp, with round whitish colonies of a novel Methanobacteriati species strung along filaments up to 15 centimeters long, the filaments themselves made of a particular bacteria.

  Most archaea wear a cell wall, but not the peptidoglycan of bacteria. Instead they build an S-layer, a rigid array of protein molecules that covers the cell like chain mail and shields it chemically and physically. Methanobacteriales carry pseudopeptidoglycan, which mimics bacterial peptidoglycan in form and function but differs in chemistry, lacking D-amino acids and N-acetylmuramic acid. To swim, archaea spin an archaellum, a stalk turned by a rotary motor powered by a proton gradient. Unlike the hollow bacterial flagellum assembled at its tip, the archaellum likely evolved from bacterial type IV pili and grows by adding subunits at its base.

• 6. Living On Anything

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  Picrophilus torridus grows at pH 0, and across the domain archaea draw energy from a startling spread of sources, from sugars to ammonia, metal ions, and even hydrogen gas. They fall into nutritional groups by how they gather energy and carbon. Chemotrophs pull energy from inorganic compounds like sulfur or ammonia, passing electrons from a donor to an acceptor in redox reactions and banking the released energy as ATP through chemiosmosis, the same process running in a eukaryotic mitochondrion.

  Methanogenesis is the one metabolism found in no other organisms, the production of methane. Some Methanobacteriati live as methanogens in anaerobic places such as swamps, often using carbon dioxide as an electron acceptor to oxidize hydrogen. The reactions lean on coenzymes unique to these archaea, including coenzyme M and methanofuran. Acetotrophic archaea in the order Methanosarcinales break acetic acid directly into methane and carbon dioxide, and they form a major part of the communities that generate biogas.

  Phototrophic archaea use light without ever producing oxygen. In the Halobacteria, light-driven ion pumps such as bacteriorhodopsin and halorhodopsin push ions across the plasma membrane, building gradients that ATP synthase converts into ATP. The trick depends on light-driven changes in a retinol cofactor buried at the protein's center. Other archaea fix carbon through a modified Calvin cycle or the 3-hydroxypropionate / 4-hydroxybutyrate cycle, but no known archaea both fix carbon and harvest light the way cyanobacteria do.

• 7. From Sea Vents To The Gut

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  Archaea may make up about 20 percent of microbial cells in the oceans, and the archaea drifting in plankton may rank among the most abundant groups of organisms on the planet. The first ones found were extremophiles, isolated in hot springs and salt lakes where nothing else lived. Halophiles like Halobacterium outnumber bacteria where salinity passes 20 to 25 percent. Hyperthermophiles thrive above 80 degrees Celsius, and Methanopyrus kandleri Strain 116 reproduces at 122 degrees. Yet they also crowd cold polar seas, soils, sewage, and the guts of animals.

  In the human microbiome, archaea matter in the gut, the mouth, and on the skin. Methanobrevibacter smithii is by far the most common archaean in human flora, about one in ten of the prokaryotes in the human gut. Methanogens partner with protozoa in the digestive tracts of cellulose-eaters like ruminants and termites, consuming the hydrogen those protozoa release so energy production can continue. In Plagiopyla frontata and other anaerobic protozoa, archaea live inside the host and feed on hydrogen from its hydrogenosomes. The marine archaean Cenarchaeum symbiosum lives as an endosymbiont of the sponge Axinella mexicana.

  Through these habitats archaea drive the cycling of carbon, nitrogen, and sulfur. They run many steps of the nitrogen cycle, oxidizing ammonia in oceans and soils to produce nitrite that other microbes turn to nitrate for plants. Sulfur-oxidizing archaea like Sulfolobus free the element from rock but excrete sulfuric acid, and their growth in abandoned mines can feed acid mine drainage. As of 2024, only one species of non-eukaryotic archaea has been found to be parasitic, while many serve as mutualists or commensals.

• 8. Tools From Extremes

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  Pfu DNA polymerase from Pyrococcus furiosus changed molecular biology by making the polymerase chain reaction a fast, simple way to clone DNA. The same PCR technique that detects archaea in water and soil grew out of the heat-tolerant enzymes archaea carry. Other species of Pyrococcus supply amylases, galactosidases, and pullulanases that work above 100 degrees Celsius, enabling high-temperature food processing such as low-lactose milk and whey. These enzymes also hold up in organic solvents, making them useful in green chemistry and in structural biology.

  Methanogenic archaea anchor sewage treatment, carrying out anaerobic digestion and producing biogas. In mineral processing, acidophilic archaea show promise for pulling gold, cobalt, and copper from ores. Archaea also host their own antibiotics, the archaeocins; only a few have been characterized, but hundreds more are believed to wait, especially within Halobacteria and Sulfolobus. Because their structures differ from bacterial antibiotics, they may act in new ways.

  Much of this remains barely mapped. Estimates of archaeal phyla range from 18 to 23, yet only 8 have representatives that have been cultured and studied directly, and many groups are known from a single rRNA sequence. In ocean surface sediments from 1,000 to 10,000 meters deep, viral infection strikes archaea harder than bacteria, with virus-induced lysis releasing an estimated 0.3 to 0.5 gigatons of carbon each year. The archaeal lineage may be the most ancient on Earth, and the rocks of Greenland's Isua district, formed 3.8 billion years ago, still hold its earliest chemical traces.