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A prokaryote () is a
single-celled organism A unicellular organism, also known as a single-celled organism, is an organism that consists of a single cell, unlike a multicellular organism that consists of multiple cells. Organisms fall into two general categories: prokaryotic organisms an ...
that lacks a
nucleus Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom * Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucl ...
and other
membrane-bound organelle In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as Organ (anatomy), organs are to the ...
s. The word ''prokaryote'' comes from the
Greek Greek may refer to: Greece Anything of, from, or related to Greece, a country in Southern Europe: *Greeks, an ethnic group. *Greek language, a branch of the Indo-European language family. **Proto-Greek language, the assumed last common ancestor ...
πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connections". Pearson Education. San Francisco: 2003. In the
two-empire system The two-empire system (two-superkingdom system) was the top-level biological classification system in general use before the establishment of the three-domain system. It classified cellular life into Prokaryota and Eukaryota as either "empires" or ...
arising from the work of
Édouard Chatton Édouard Chatton (; 11 October 1883 – 23 April 1947) was a French biologist who first characterized the distinction between the prokaryotic and eukaryotic cellular types. Chatton coined the terms and published them first in his 1937 paper ' ...
, prokaryotes were classified within the empire Prokaryota. But in the
three-domain system The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryota or Eukarya. The key difference fr ...
, based upon molecular analysis, prokaryotes are divided into two domains: ''
Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
'' (formerly Eubacteria) and ''
Archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
'' (formerly Archaebacteria). Organisms with nuclei are placed in a third domain,
Eukaryota Eukaryotes () are organisms whose Cell (biology), cells have a cell nucleus, nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the ...
. In the study of the origins of life, prokaryotes are thought to have arisen before eukaryotes. Besides the absence of a nucleus, prokaryotes also lack
mitochondria A mitochondrion (; ) is an organelle found in the Cell (biology), cells of most Eukaryotes, such as animals, plants and Fungus, fungi. Mitochondria have a double lipid bilayer, membrane structure and use aerobic respiration to generate adenosi ...
, or most of the other membrane-bound organelles that characterize the eukaryotic cell. It was once thought that prokaryotic cellular components within the
cytoplasm In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The ...
were unenclosed, except for an outer
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment ( ...
, but
bacterial microcompartment Bacterial microcompartments (BMCs) are organelle-like structures found in bacteria. They consist of a protein shell that encloses enzymes and other proteins. BMCs are typically about 40–200 nanometers in diameter and are made entirely of prote ...
s, which are thought to be simple organelles enclosed in protein shells, have been discovered, along with other
prokaryotic organelles A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...
. While being
unicellular A unicellular organism, also known as a single-celled organism, is an organism that consists of a single cell, unlike a multicellular organism that consists of multiple cells. Organisms fall into two general categories: prokaryotic organisms and ...
, some prokaryotes, such as
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blu ...
, may form large
colonies In modern parlance, a colony is a territory subject to a form of foreign rule. Though dominated by the foreign colonizers, colonies remain separate from the administration of the original country of the colonizers, the '' metropolitan state'' ...
. Others, such as
myxobacteria The myxobacteria ("slime bacteria") are a group of bacteria that predominantly live in the soil and feed on insoluble organic substances. The myxobacteria have very large genomes relative to other bacteria, e.g. 9–10 million nucleotides except ...
, have multicellular stages in their life cycles. Prokaryotes are asexual, reproducing without fusion of
gametes A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce ...
, although
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...
also takes place. Molecular studies have provided insight into the evolution and interrelationships of the three domains of life. The division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization; only eukaryotic cells have an enveloped nucleus that contains its chromosomal DNA, and other characteristic membrane-bound organelles including mitochondria. Distinctive types of prokaryotes include
extremophile An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism that is able to live (or in some cases thrive) in extreme environments, i.e. environments that make survival challenging such as due to extreme temper ...
s and
methanogen Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain Archaea. All known methanogens are members of the archaeal phylum Euryarchaeota. Methanogens are com ...
s; these are common in some extreme environments.


History

The distinction between prokaryotes and eukaryotes was firmly established by the microbiologists
Roger Stanier Roger Yate Stanier (22 October 1916 – 29 January 1982) was a Canadian microbiologist who was influential in the development of modern microbiology. As a member of the Delft School and former student of C. B. van Niel, he made important contribu ...
and
C. B. van Niel Cornelis Bernardus van Niel (also known as Kees van Niel) (November 4, 1897 – March 10, 1985) was a Dutch-American microbiologist. He introduced the study of general microbiology to the United States and made key discoveries explaining t ...
in their 1962 paper ''The concept of a bacterium'' (though spelled procaryote and eucaryote there). That paper cites
Édouard Chatton Édouard Chatton (; 11 October 1883 – 23 April 1947) was a French biologist who first characterized the distinction between the prokaryotic and eukaryotic cellular types. Chatton coined the terms and published them first in his 1937 paper ' ...
's 1937 book ''Titres et Travaux Scientifiques'' for using those terms and recognizing the distinction. One reason for this classification was so that what was then often called blue-green algae (now called
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blu ...
) would not be classified as plants but grouped with bacteria.


Structure

Prokaryotes have a
prokaryotic cytoskeleton The prokaryotic cytoskeleton is the collective name for all structural filaments in prokaryotes. It was once thought that prokaryotic cells did not possess cytoskeletons, but advances in visualization technology and structure determination led t ...
that is more primitive than that of the eukaryotes. Besides homologues of actin and tubulin (
MreB MreB is a protein found in bacteria that has been identified as a homologue of actin, as indicated by similarities in tertiary structure and conservation of active site peptide sequence. The conservation of protein structure suggests the common a ...
and
FtsZ FtsZ is a protein encoded by the ''ftsZ'' gene that assembles into a ring at the future site of bacterial cell division (also called the Z ring). FtsZ is a prokaryotic homologue of the eukaryotic protein tubulin. The initials FtsZ mean "Filamen ...
), the helically arranged building-block of the
flagellum A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have f ...
,
flagellin Flagellin is a globular protein that arranges itself in a hollow cylinder to form the filament in a bacterial flagellum. It has a mass of about 30,000 to 60,000 daltons. Flagellin is the principal component of bacterial flagella, and is present ...
, is one of the most significant cytoskeletal proteins of bacteria, as it provides structural backgrounds of
chemotaxis Chemotaxis (from '' chemo-'' + ''taxis'') is the movement of an organism or entity in response to a chemical stimulus. Somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemica ...
, the basic cell physiological response of bacteria. At least some prokaryotes also contain intracellular structures that can be seen as primitive organelles. Membranous organelles (or intracellular membranes) are known in some groups of prokaryotes, such as vacuoles or membrane systems devoted to special metabolic properties, such as
photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...
or
chemolithotrophy Lithotrophs are a diverse group of organisms using an inorganic substrate (usually of mineral origin) to obtain reducing equivalents for use in biosynthesis (e.g., carbon dioxide fixation) or energy conservation (i.e., ATP production) via aerobic ...
. In addition, some species also contain carbohydrate-enclosed microcompartments, which have distinct physiological roles (e.g.
carboxysome Carboxysomes are bacterial microcompartments (BMCs) consisting of polyhedral protein shells filled with the enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)—the predominant enzyme in carbon fixation and the rate limiting e ...
s or gas vacuoles). Most prokaryotes are between 1 µm and 10 µm, but they can vary in size from 0.2 µm (''
Mycoplasma genitalium ''Mycoplasma genitalium'' (''MG'', commonly known as Mgen) is a sexually transmitted, small and pathogenic bacterium that lives on the mucous epithelial cells of the urinary and genital tracts in humans. Medical reports published in 2007 and 2 ...
'') to 750 µm (''
Thiomargarita namibiensis ''Thiomargarita namibiensis'' is a Gram-negative coccoid bacterium, found in the ocean sediments of the continental shelf of Namibia. It is the second largest bacterium ever discovered, as a rule in diameter, but sometimes attaining . Cells of ...
'').


Morphology

Prokaryotic cells have various shapes; the four basic shapes of bacteria are: *
Cocci A coccus (plural cocci) is any bacterium or archaeon that has a spherical, ovoid, or generally round shape. Bacteria are categorized based on their shapes into three classes: cocci (spherical-shaped), bacillus (rod-shaped) and spiral ( of whi ...
– A bacterium that is spherical or ovoid is called a coccus (Plural, cocci). e.g. ''Streptococcus, Staphylococcus.'' *
Bacilli Bacilli is a taxonomic class of bacteria that includes two orders, Bacillales and Lactobacillales, which contain several well-known pathogens such as ''Bacillus anthracis'' (the cause of anthrax). ''Bacilli'' are almost exclusively gram-positi ...
– A bacterium with cylindrical shape called rod or a bacillus (Plural, bacilli). *
Spiral bacteria Spiral bacteria, bacteria of spiral ( helical) shape, form the third major morphological category of prokaryotes along with the rod-shaped bacilli and round cocci. Spiral bacteria can be subclassified by the number of twists per cell, cell thick ...
– Some rods twist into spiral shapes and are called spirilla (singular, spirillum). *
Vibrio ''Vibrio'' is a genus of Gram-negative bacteria, possessing a curved-rod (comma) shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Being highly salt tolerant and unable to survive ...
– comma-shaped The archaeon
Haloquadratum ''Haloquadratum'' (common abbreviation: ''Hqr.'') is a genus of archaean, belonging to the family Haloferacaceae. The first species to be identified in this group, ''Haloquadratum walsbyi'', is unusual in that its cells are shaped like square, ...
has flat square-shaped cells.


Reproduction

Bacteria and archaea reproduce through asexual reproduction, usually by
binary fission Binary may refer to: Science and technology Mathematics * Binary number, a representation of numbers using only two digits (0 and 1) * Binary function, a function that takes two arguments * Binary operation, a mathematical operation that t ...
. Genetic exchange and recombination still occur, but this is a form of
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...
and is not a replicative process, simply involving the transference of DNA between two cells, as in bacterial conjugation.


DNA transfer

DNA transfer between prokaryotic cells occurs in bacteria and archaea, although it has been mainly studied in bacteria. In bacteria, gene transfer occurs by three processes. These are (1) bacterial virus (
bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacteri ...
)-mediated transduction, (2)
plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...
-mediated
conjugation Conjugation or conjugate may refer to: Linguistics * Grammatical conjugation, the modification of a verb from its basic form * Emotive conjugation or Russell's conjugation, the use of loaded language Mathematics * Complex conjugation, the chang ...
, and (3)
natural transformation In category theory, a branch of mathematics, a natural transformation provides a way of transforming one functor into another while respecting the internal structure (i.e., the composition of morphisms) of the categories involved. Hence, a natur ...
. Transduction of bacterial genes by bacteriophage appears to reflect an occasional error during intracellular assembly of
virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...
particles, rather than an
adaptation In biology, adaptation has three related meanings. Firstly, it is the dynamic evolutionary process of natural selection that fits organisms to their environment, enhancing their evolutionary fitness. Secondly, it is a state reached by the po ...
of the host bacteria. The transfer of bacterial DNA is under the control of the bacteriophage's genes rather than bacterial genes. Conjugation in the well-studied '' E. coli'' system is controlled by plasmid genes, and is an adaptation for distributing copies of a plasmid from one bacterial host to another. Infrequently during this process, a plasmid may integrate into the host bacterial chromosome, and subsequently transfer part of the host bacterial DNA to another bacterium. Plasmid mediated transfer of host bacterial DNA (conjugation) also appears to be an accidental process rather than a bacterial adaptation. Natural bacterial
transformation Transformation may refer to: Science and mathematics In biology and medicine * Metamorphosis, the biological process of changing physical form after birth or hatching * Malignant transformation, the process of cells becoming cancerous * Trans ...
involves the transfer of DNA from one bacterium to another through the intervening medium. Unlike transduction and conjugation, transformation is clearly a bacterial
adaptation In biology, adaptation has three related meanings. Firstly, it is the dynamic evolutionary process of natural selection that fits organisms to their environment, enhancing their evolutionary fitness. Secondly, it is a state reached by the po ...
for DNA transfer, because it depends on numerous bacterial gene products that specifically interact to perform this complex process. For a bacterium to bind, take up and recombine donor DNA into its own chromosome, it must first enter a special physiological state called competence. About 40 genes are required in ''Bacillus subtilis'' for the development of competence. The length of DNA transferred during ''B. subtilis'' transformation can be as much as a third to the whole chromosome. Transformation is a common mode of DNA transfer, and 67 prokaryotic species are thus far known to be naturally competent for transformation. Among archaea, '' Halobacterium volcanii'' forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another. Another archaeon, ''
Sulfolobus solfataricus ''Saccharolobus solfataricus'' is a species of thermophilic archaeon. It was transferred from the genus ''Sulfolobus'' to the new genus ''Saccharolobus'' with the description of Saccharolobus caldissimus in 2018. It was first isolated and disco ...
'', transfers DNA between cells by direct contact. Frols et al. found that exposure of ''S. solfataricus'' to DNA damaging agents induces cellular aggregation, and suggested that cellular aggregation may enhance DNA transfer among cells to provide increased repair of damaged DNA via homologous recombination.


Sociality

While prokaryotes are considered strictly unicellular, most can form stable aggregate communities. When such communities are encased in a stabilizing polymer matrix ("slime"), they may be called "
biofilms A biofilm comprises any syntrophic consortium of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular po ...
". Cells in biofilms often show distinct patterns of
gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. The ...
(phenotypic differentiation) in time and space. Also, as with multicellular eukaryotes, these changes in expression often appear to result from
cell-to-cell signaling In biology, cell signaling (cell signalling in British English) or cell communication is the ability of a cell to receive, process, and transmit signals with its environment and with itself. Cell signaling is a fundamental property of all cellula ...
, a phenomenon known as
quorum sensing In biology, quorum sensing or quorum signalling (QS) is the ability to detect and respond to cell population density by gene regulation. As one example, QS enables bacteria to restrict the expression of specific genes to the high cell densities at ...
. Biofilms may be highly heterogeneous and structurally complex and may attach to solid surfaces, or exist at liquid-air interfaces, or potentially even liquid-liquid interfaces. Bacterial biofilms are often made up of microcolonies (approximately dome-shaped masses of bacteria and matrix) separated by "voids" through which the medium (e.g., water) may flow easily. The microcolonies may join together above the substratum to form a continuous layer, closing the network of channels separating microcolonies. This structural complexity—combined with observations that oxygen limitation (a ubiquitous challenge for anything growing in size beyond the scale of diffusion) is at least partially eased by movement of medium throughout the biofilm—has led some to speculate that this may constitute a
circulatory system The blood circulatory system is a system of organs that includes the heart, blood vessels, and blood which is circulated throughout the entire body of a human or other vertebrate. It includes the cardiovascular system, or vascular system, tha ...
and many researchers have started calling prokaryotic communities multicellular (for example ). Differential cell expression, collective behavior, signaling,
programmed cell death Programmed cell death (PCD; sometimes referred to as cellular suicide) is the death of a cell (biology), cell as a result of events inside of a cell, such as apoptosis or autophagy. PCD is carried out in a biological process, which usually confers ...
, and (in some cases) discrete
biological dispersal Biological dispersal refers to both the movement of individuals (animals, plants, fungi, bacteria, etc.) from their birth site to their breeding site ('natal dispersal'), as well as the movement from one breeding site to another ('breeding dis ...
events all seem to point in this direction. However, these colonies are seldom if ever founded by a single founder (in the way that animals and plants are founded by single cells), which presents a number of theoretical issues. Most explanations of
co-operation Cooperation (written as co-operation in British English) is the process of groups of organisms working or acting together for common, mutual, or some underlying benefit, as opposed to working in competition for selfish benefit. Many animal a ...
and the
evolution of multicellularity A multicellular organism is an organism that consists of more than one cell, in contrast to unicellular organism. All species of animals, land plants and most fungi are multicellular, as are many algae, whereas a few organisms are partially uni ...
have focused on high relatedness between members of a group (or colony, or whole organism). If a copy of a gene is present in all members of a group, behaviors that promote cooperation between members may permit those members to have (on average) greater fitness than a similar group of selfish individuals (see
inclusive fitness In evolutionary biology, inclusive fitness is one of two metrics of evolutionary success as defined by W. D. Hamilton in 1964: * Personal fitness is the number of offspring that an individual begets (regardless of who rescues/rears/supports them ...
and
Hamilton's rule Kin selection is the evolutionary strategy that favours the reproductive success of an organism's relatives, even when at a cost to the organism's own survival and reproduction. Kin altruism can look like altruistic behaviour whose evolution ...
). Should these instances of prokaryotic sociality prove to be the rule rather than the exception, it would have serious implications for the way we view prokaryotes in general, and the way we deal with them in medicine. Bacterial biofilms may be 100 times more resistant to antibiotics than free-living unicells and may be nearly impossible to remove from surfaces once they have colonized them. Other aspects of bacterial cooperation—such as bacterial conjugation and quorum-sensing-mediated
pathogenicity In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a ge ...
, present additional challenges to researchers and medical professionals seeking to treat the associated diseases.


Environment

Prokaryotes have diversified greatly throughout their long existence. The metabolism of prokaryotes is far more varied than that of eukaryotes, leading to many highly distinct prokaryotic types. For example, in addition to using
photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...
or
organic compound In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen or carbon-carbon bonds. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. The ...
s for energy, as eukaryotes do, prokaryotes may obtain energy from
inorganic compound In chemistry, an inorganic compound is typically a chemical compound that lacks carbon–hydrogen bonds, that is, a compound that is not an organic compound. The study of inorganic compounds is a subfield of chemistry known as '' inorganic chemist ...
s such as
hydrogen sulfide Hydrogen sulfide is a chemical compound with the formula . It is a colorless chalcogen-hydride gas, and is poisonous, corrosive, and flammable, with trace amounts in ambient atmosphere having a characteristic foul odor of rotten eggs. The unde ...
. This enables prokaryotes to thrive in harsh environments as cold as the snow surface of
Antarctica Antarctica () is Earth's southernmost and least-populated continent. Situated almost entirely south of the Antarctic Circle and surrounded by the Southern Ocean, it contains the geographic South Pole. Antarctica is the fifth-largest contine ...
, studied in
cryobiology Cryobiology is the branch of biology that studies the effects of low temperatures on living things within Earth's cryosphere or in science. The word cryobiology is derived from the Greek words κρῧος ryos "cold", βίος ios "life", and λό ...
, or as hot as undersea
hydrothermal vent A hydrothermal vent is a fissure on the seabed from which geothermally heated water discharges. They are commonly found near volcanically active places, areas where tectonic plates are moving apart at mid-ocean ridges, ocean basins, and hotspot ...
s and land-based
hot spring A hot spring, hydrothermal spring, or geothermal spring is a spring produced by the emergence of geothermally heated groundwater onto the surface of the Earth. The groundwater is heated either by shallow bodies of magma (molten rock) or by circ ...
s. Prokaryotes live in nearly all environments on Earth. Some archaea and bacteria are
extremophile An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism that is able to live (or in some cases thrive) in extreme environments, i.e. environments that make survival challenging such as due to extreme temper ...
s, thriving in harsh conditions, such as high temperatures (
thermophile A thermophile is an organism—a type of extremophile—that thrives at relatively high temperatures, between . Many thermophiles are archaea, though they can be bacteria or fungi. Thermophilic eubacteria are suggested to have been among the earl ...
s) or high salinity (
halophile The halophiles, named after the Greek word for "salt-loving", are extremophiles that thrive in high salt concentrations. While most halophiles are classified into the domain Archaea, there are also bacterial halophiles and some eukaryotic species, ...
s). Many archaea grow as
plankton Plankton are the diverse collection of organisms found in Hydrosphere, water (or atmosphere, air) that are unable to propel themselves against a Ocean current, current (or wind). The individual organisms constituting plankton are called plankt ...
in the oceans.
Symbiotic Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasit ...
prokaryotes live in or on the bodies of other organisms, including humans. Prokaryote have high populations in the
soil Soil, also commonly referred to as earth or dirt, is a mixture of organic matter, minerals, gases, liquids, and organisms that together support life. Some scientific definitions distinguish ''dirt'' from ''soil'' by restricting the former te ...
- including the
rhizosphere The rhizosphere is the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. Soil pores in the rhizosphere can contain many bacteria and other microor ...
and rhizosheath. Soil prokaryotes are still heavily undercharacterized despite their easy proximity to humans and their tremendous economic importance to agriculture.


Classification

In 1977,
Carl Woese Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. Woese is famous for defining the Archaea (a new domain of life) in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, ...
proposed dividing prokaryotes into the
Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
and
Archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
(originally Eubacteria and Archaebacteria) because of the major differences in the structure and genetics between the two groups of organisms. Archaea were originally thought to be extremophiles, living only in inhospitable conditions such as extremes of
temperature Temperature is a physical quantity that expresses quantitatively the perceptions of hotness and coldness. Temperature is measured with a thermometer. Thermometers are calibrated in various temperature scales that historically have relied o ...
, pH, and
radiation In physics, radiation is the emission or transmission of energy in the form of waves or particles through space or through a material medium. This includes: * ''electromagnetic radiation'', such as radio waves, microwaves, infrared, visi ...
but have since been found in all types of
habitat In ecology, the term habitat summarises the array of resources, physical and biotic factors that are present in an area, such as to support the survival and reproduction of a particular species. A species habitat can be seen as the physical ...
s. The resulting arrangement of Eukaryota (also called "Eucarya"), Bacteria, and Archaea is called the
three-domain system The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryota or Eukarya. The key difference fr ...
, replacing the traditional
two-empire system The two-empire system (two-superkingdom system) was the top-level biological classification system in general use before the establishment of the three-domain system. It classified cellular life into Prokaryota and Eukaryota as either "empires" or ...
.


Phylogenetic tree

According to the phylogenetic analysis of Zhu (2019), the relationships could be the following:


Evolution

A widespread current model of the evolution of the first living organisms is that these were some form of prokaryotes, which may have evolved out of
protocell A protocell (or protobiont) is a self-organized, endogenously ordered, spherical collection of lipids proposed as a stepping-stone toward the origin of life. A central question in evolution is how simple protocells first arose and how they could ...
s, while the eukaryotes evolved later in the history of life. Some authors have questioned this conclusion, arguing that the current set of prokaryotic species may have evolved from more complex eukaryotic ancestors through a process of simplification. Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single gene pool. This controversy was summarized in 2005:
There is no consensus among biologists concerning the position of the eukaryotes in the overall scheme of cell evolution. Current opinions on the origin and position of eukaryotes span a broad spectrum including the views that eukaryotes arose first in evolution and that prokaryotes descend from them, that eukaryotes arose contemporaneously with eubacteria and archaebacteria and hence represent a primary line of descent of equal age and rank as the prokaryotes, that eukaryotes arose through a symbiotic event entailing an endosymbiotic origin of the nucleus, that eukaryotes arose without endosymbiosis, and that eukaryotes arose through a symbiotic event entailing a simultaneous endosymbiotic origin of the flagellum and the nucleus, in addition to many other models, which have been reviewed and summarized elsewhere.
The oldest known
fossil A fossil (from Classical Latin , ) is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, shells, exoskeletons, stone imprints of animals or microbes, objects preserved ...
ized prokaryotes were laid down approximately 3.5 billion years ago, only about 1 billion years after the formation of the Earth's crust. Eukaryotes only appear in the fossil record later, and may have formed from
endosymbiosis An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within" ...
of multiple prokaryote ancestors. The oldest known fossil eukaryotes are about 1.7 billion years old. However, some genetic evidence suggests eukaryotes appeared as early as 3 billion years ago. While Earth is the only place in the universe where life is known to exist, some have suggested that there is evidence on Mars of fossil or living prokaryotes. However, this possibility remains the subject of considerable debate and skepticism.


Relationship to eukaryotes

The division between prokaryotes and eukaryotes is usually considered the most important distinction or difference among organisms. The distinction is that eukaryotic cells have a "true"
nucleus Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom * Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucl ...
containing their DNA, whereas prokaryotic cells do not have a nucleus. Both eukaryotes and prokaryotes contain large
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
/
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
structures called
ribosome Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to ...
s, which produce protein, but the
ribosomes Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to f ...
of prokaryotes are smaller than those of eukaryotes.
Mitochondria A mitochondrion (; ) is an organelle found in the Cell (biology), cells of most Eukaryotes, such as animals, plants and Fungus, fungi. Mitochondria have a double lipid bilayer, membrane structure and use aerobic respiration to generate adenosi ...
and
chloroplast A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in ...
s, two organelles found in many eukaryotic cells, contain ribosomes similar in size and makeup to those found in prokaryotes. This is one of many pieces of evidence that mitochondria and chloroplasts are descended from free-living bacteria. The
endosymbiotic theory Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory,) is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibl ...
holds that early eukaryotic cells took in primitive prokaryotic cells by
phagocytosis Phagocytosis () is the process by which a cell uses its plasma membrane to engulf a large particle (≥ 0.5 μm), giving rise to an internal compartment called the phagosome. It is one type of endocytosis. A cell that performs phagocytosis is ...
and adapted themselves to incorporate their structures, leading to the mitochondria and chloroplasts. The
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
in a prokaryote is held within a DNA/protein complex in the
cytosol The cytosol, also known as cytoplasmic matrix or groundplasm, is one of the liquids found inside cells (intracellular fluid (ICF)). It is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondri ...
called the nucleoid, which lacks a nuclear envelope. The complex contains a single, cyclic, double-stranded molecule of stable chromosomal DNA, in contrast to the multiple linear, compact, highly organized
chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
s found in eukaryotic cells. In addition, many important genes of prokaryotes are stored in separate circular DNA structures called
plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...
s. Like Eukaryotes, prokaryotes may partially duplicate genetic material, and can have a
haploid Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Sets of chromosomes refer to the number of maternal and paternal chromosome copies, respectively ...
chromosomal composition that is partially replicated, a condition known as
merodiploid A merodiploid is a partially diploid bacterium, which has its own chromosome complement and a chromosome fragment introduced by conjugation, transformation or transduction. It can also be defined as an essentially haploid organism In ...
y. Prokaryotes lack
mitochondria A mitochondrion (; ) is an organelle found in the Cell (biology), cells of most Eukaryotes, such as animals, plants and Fungus, fungi. Mitochondria have a double lipid bilayer, membrane structure and use aerobic respiration to generate adenosi ...
and
chloroplast A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in ...
s. Instead, processes such as
oxidative phosphorylation Oxidative phosphorylation (UK , US ) or electron transport-linked phosphorylation or terminal oxidation is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine tri ...
and
photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...
take place across the prokaryotic
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment ( ...
. However, prokaryotes do possess some internal structures, such as
prokaryotic cytoskeleton The prokaryotic cytoskeleton is the collective name for all structural filaments in prokaryotes. It was once thought that prokaryotic cells did not possess cytoskeletons, but advances in visualization technology and structure determination led t ...
s. It has been suggested that the bacterial phylum
Planctomycetota The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammoniu ...
has a membrane around the nucleoid and contains other membrane-bound cellular structures. However, further investigation revealed that Planctomycetota cells are not compartmentalized or nucleated and, like other bacterial membrane systems, are interconnected. Prokaryotic cells are usually much smaller than eukaryotic cells. Therefore, prokaryotes have a larger
surface-area-to-volume ratio The surface-area-to-volume ratio, also called the surface-to-volume ratio and variously denoted sa/vol or SA:V, is the amount of surface area per unit volume of an object or collection of objects. SA:V is an important concept in science and engin ...
, giving them a higher
metabolic rate Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...
, a higher growth rate, and as a consequence, a shorter generation time than eukaryotes. There is increasing evidence that the roots of the eukaryotes are to be found in (or at least next to) the archaean
asgard In Nordic mythology, Asgard (Old Norse: ''Ásgarðr'' ; "enclosure of the Æsir") is a location associated with the gods. It appears in a multitude of Old Norse sagas and mythological texts. It is described as the fortified home of the Æsir ...
group, perhaps
Heimdallarchaeota Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of archaea that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota, and Heimdallarchaeota. It appears the eukaryotes emerged within the Asgard, in a branch containin ...
(an idea which is a modern version of the 1984
eocyte hypothesis The eocyte hypothesis in evolutionary biology proposes the origin of eukaryotes from a group of prokaryotes called eocytes (later classified as Thermoproteota, a group of archaea). After his team at the University of California, Los Angeles disc ...
, ''eocytes'' being an old synonym for ''
Thermoproteota The Thermoproteota (also known as crenarchaea) are archaea that have been classified as a phylum of the Archaea domain. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteris ...
'', a
taxon In biology, a taxon (back-formation from ''taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular nam ...
to be found nearby the then-unknown Asgard group) For example,
histones In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn ar ...
which usually package DNA in eukaryotic nuclei, have also been found in several archaean groups, giving evidence for
homology Homology may refer to: Sciences Biology *Homology (biology), any characteristic of biological organisms that is derived from a common ancestor * Sequence homology, biological homology between DNA, RNA, or protein sequences *Homologous chrom ...
. This idea might clarify the mysterious predecessor of eukaryotic cells ( eucytes) which engulfed an
alphaproteobacterium Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (formerly Proteobacteria). The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria. The Alphaproteobacteria are highly diverse a ...
forming the first eucyte ( LECA, last eukaryotic common ancestor) according to
endosymbiotic theory Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory,) is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibl ...
. There might have been some additional support by viruses, called viral eukaryogenesis. The non-bacterial group comprising archaea and eukaryota was called
Neomura Neomura is a possible clade composed of the two domains of life of Archaea and Eukaryota. The group was named by Thomas Cavalier-Smith in 2002. Its name means "new walls", reflecting his hypothesis that it evolved from Bacteria, and one of t ...
by
Thomas Cavalier-Smith Thomas (Tom) Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow (21 October 1942 – 19 March 2021), was a professor of evolutionary biology in the Department of Zoology, at the University of Oxford. His research has led to discov ...
in 2002. However, in a
cladistic Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived char ...
view, eukaryota ''are'' archaea in the same sense as
birds Birds are a group of warm-blooded vertebrates constituting the class Aves (), characterised by feathers, toothless beaked jaws, the laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart, and a strong yet lightweigh ...
''are''
dinosaurs Dinosaurs are a diverse group of reptiles of the clade Dinosauria. They first appeared during the Triassic period, between 243 and 233.23 million years ago (mya), although the exact origin and timing of the evolution of dinosaurs is t ...
because they evolved from the
maniraptora Maniraptora is a clade of coelurosaurian dinosaurs which includes the birds and the non-avian dinosaurs that were more closely related to them than to ''Ornithomimus velox''. It contains the major subgroups Avialae, Deinonychosauria, Oviraptoros ...
dinosaur group. In contrast, archaea ''without'' eukaryota appear to be a
paraphyletic In taxonomy (general), taxonomy, a group is paraphyletic if it consists of the group's most recent common ancestor, last common ancestor and most of its descendants, excluding a few Monophyly, monophyletic subgroups. The group is said to be pa ...
group, just like dinosaurs without birds.


Prokaryotes may be split into two groups

Unlike the above assumption of a fundamental split between prokaryotes and eukaryotes, the most important difference between biota may be the division between bacteria and the rest (archaea and eukaryota). For instance,
DNA replication In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
differs fundamentally between bacteria and archaea (including that in eukaryotic nuclei), and it may not be homologous between these two groups. Moreover,
ATP synthase ATP synthase is a protein that catalyzes the formation of the energy storage molecule adenosine triphosphate (ATP) using adenosine diphosphate (ADP) and inorganic phosphate (Pi). It is classified under ligases as it changes ADP by the formation ...
, though common (homologous) in all organisms, differs greatly between bacteria (including eukaryotic
organelle In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' the ...
s such as
mitochondria A mitochondrion (; ) is an organelle found in the Cell (biology), cells of most Eukaryotes, such as animals, plants and Fungus, fungi. Mitochondria have a double lipid bilayer, membrane structure and use aerobic respiration to generate adenosi ...
and
chloroplast A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in ...
s) and the archaea/eukaryote nucleus group. The last common antecessor of all life (called
LUCA The last universal common ancestor (LUCA) is the most recent population from which all organisms now living on Earth share common descent—the most recent common ancestor of all current life on Earth. This includes all cellular organisms; th ...
, last universal common ancestor) should have possessed an early version of this protein complex. As ATP synthase is obligate membrane bound, this supports the assumption that LUCA was a cellular organism. The
RNA world hypothesis The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence ...
might clarify this scenario, as LUCA might have been a ribocyte (also called ribocell) lacking DNA, but with an
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
genome built by
ribosome Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to ...
s as primordial self-replicating entities. A
Peptide-RNA world The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existenc ...
(also called RNP world) hypothesis has been proposed based on the idea that
oligopeptide An oligopeptide, often just called peptide ('' oligo-'', "a few"), consists of two to twenty amino acids and can include dipeptides, tripeptides, tetrapeptides, and pentapeptides. Some of the major classes of naturally occurring oligopeptides incl ...
s may have been built together with primordial nucleic acids at the same time, which also supports the concept of a ribocyte as LUCA. The feature of DNA as the material base of the genome might have then been adopted separately in bacteria and in archaea (and later eukaryote nuclei), presumably by help of some viruses (possibly retroviruses as they could reverse transcribe RNA to DNA). As a result, prokaryota comprising bacteria and archaea may also be
polyphyletic A polyphyletic group is an assemblage of organisms or other evolving elements that is of mixed evolutionary origin. The term is often applied to groups that share similar features known as homoplasies, which are explained as a result of converg ...
.


See also


References


External links


Prokaryote versus eukaryote, BioMineWiki

The Taxonomic Outline of Bacteria and Archaea

The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology



TOLWEB page on Eukaryote-Prokaryote phylogeny
{{Authority control Bacteriology Biochemistry Paraphyletic groups Articles containing video clips