Three-domain system in the context of "Marine bacteria"

A prokaryote (/proʊˈkærioʊt, -ət/; less commonly spelled procaryote) is a microorganism whose usually single cell lacks a nucleus or other membrane-bound organelles. The word prokaryote comes from the Ancient Greek πρό (pró), meaning 'before', and κάρυον (káruon), meaning 'nut' or 'kernel'. In the earlier two-empire system, prokaryotes formed the empire Prokaryota. In the three-domain system, based upon molecular phylogenetics, prokaryotes are divided into two domains: Bacteria and Archaea. A third domain, Eukaryota, consists of organisms with nuclei.

Prokaryotes evolved before eukaryotes, and lack nuclei, mitochondria, and most of the other distinct organelles that characterize the eukaryotic cell. Some unicellular prokaryotes, such as cyanobacteria, form colonies held together by biofilms, and large colonies can create multilayered microbial mats. Prokaryotes are asexual, reproducing via binary fission. Horizontal gene transfer is common as well.

The two-empire system (two-superkingdom system) was the top-level biological classification system in general use from the early 20th century until the establishment of the three-domain system (which itself is currently being challenged by the two-domain system). It classified cellular life into Prokaryota and Eukaryota as either "empires" or "superkingdoms". When the three-domain system was introduced, some biologists preferred the two-superkingdom system, claiming that the three-domain system overemphasized the division between Archaea and Bacteria. However, given the current state of knowledge and the rapid progress in biological scientific advancement, especially due to genetic analyses, that view has all but vanished.

Some prominent scientists, such as the late Thomas Cavalier-Smith, still hold and held to the two-empire system. The late Ernst Mayr, one of the 20th century's leading evolutionary biologists, wrote dismissively of the three-domain system, "I cannot see any merit at all in a three empire cladification." Additionally, the scientist Radhey Gupta argues for a return to the two-empire system, claiming that the primary division within prokaryotes should be among those surrounded by a single membrane (monoderm), including gram-positive bacteria and archaebacteria, and those with an inner and outer cell membrane (diderm), including gram-negative bacteria.

In biological taxonomy, a domain (/dəˈmeɪn/ or /doʊˈmeɪn/) (Latin: regio or dominium), also dominion, superkingdom, realm, or empire, is the highest taxonomic rank of all organisms taken together. It was introduced in the three-domain system of taxonomy devised by Carl Woese, Otto Kandler and Mark Wheelis in 1990.

According to the domain system, the tree of life consists of either three domains, Archaea, Bacteria, and Eukarya, or two domains, Archaea and Bacteria, with Eukarya included in Archaea. In the three-domain model, the first two are prokaryotes, single-celled microorganisms without a membrane-bound nucleus. All organisms that have a cell nucleus and other membrane-bound organelles are included in Eukarya and called eukaryotes.

Asgard archaea (previously known as superphylum "Asgard" or phylum "Asgardarchaeota") are a kingdom belonging to the domain Archaea that contain eukaryotic signature proteins.

After including the kingdom category into ICNP, the only validly published names of this group are kingdom Promethearchaeati and phylum Promethearchaeota. All formerly proposed "phyla" would be de-ranked to classes in this framework. It appears that the eukaryotes, the domain that contains the animals, plants, fungi and protists, emerged within the Promethearchaeati, in a branch containing the "Heimdallarchaeia" [de; es]. This supports the two-domain system of classification over the three-domain system.

The two-domain system is a biological classification of all organisms in the tree of life into two domains: Archaea, which includes eukaryotes in this classification, and Bacteria. It emerged from development of knowledge of archaea diversity and challenges the widely accepted three-domain system that classifies life into Bacteria, Archaea, and Eukarya. It was preceded by the eocyte hypothesis of James A. Lake in the 1980s, which was largely superseded by the three-domain system, due to evidence at the time. Better understanding of archaea, especially of their roles in the origin of eukaryotes through symbiogenesis with bacteria, led to the revival of the eocyte hypothesis in the 2000s. The two-domain system became more widely accepted after the discovery of a large kingdom of archaea called Promethearchaeati in 2017, which evidence suggests to be the evolutionary root of eukaryotes, thereby making eukaryotes members of the domain Archaea.

While the features of promethearchaea do not completely rule out the three-domain system, the notion that eukaryotes originated within Archaea has been strengthened by genetic and proteomic studies. Under the three-domain system, Eukarya is mainly distinguished by the presence of "eukaryotic signature proteins" that are not found in Archaea and Bacteria. However, promethearchaea contain genes that code for multiple such proteins.