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| title | chunk | source | category | tags | date_saved | instance |
|---|---|---|---|---|---|---|
| Archaea | 2/9 | https://en.wikipedia.org/wiki/Archaea | reference | science, encyclopedia | 2026-05-05T07:15:06.056512+00:00 | kb-cron |
The classification of archaea, and of prokaryotes in general, is a rapidly moving and contentious field. Current classification systems aim to organize archaea into groups of organisms that share structural features and common ancestors. These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships among organisms (molecular phylogenetics). Most of the culturable and well-investigated species of archaea are members of two main kingdoms, the Methanobacteriati and the Thermoproteati (formerly TACK). Other groups have been tentatively created, such as the peculiar species Nanoarchaeum equitans – discovered in 2003 and assigned its own phylum, the Nanoarchaeota (reassigned to Nanobdellota in 2023). A new phylum "Korarchaeota" (now Thermoproteota) has also been proposed, containing a small group of unusual thermophilic species sharing features of both the main phyla. Other 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 and are some of the smallest organisms known. A superphylum – "TACK" (now kingdom Thermoproteati) – which includes the Thaumarchaeota (now Nitrososphaerota), "Augarchaeota", Crenarchaeota (now Thermoproteota), and "Korarchaeota" (now Thermoproteota) was proposed in 2011 to be related to the origin of eukaryotes. In 2017, the newly discovered and newly named "Asgard" (now kingdom Promethearchaeati) superphylum was proposed to be more closely related to the original eukaryote and a sister group to Thermoproteati / "TACK". In 2013, the superphylum "DPANN" (now kingdom Nanobdellati) was proposed to group "Nanoarchaeota", "Nanohaloarchaeota", Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising "Micrarchaeota" and "Parvarchaeota"), and other similar archaea. This archaeal superphylum encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, Nanobdellati/"DPANN" may include members obligately dependent on symbiotic interactions, and may even include novel parasites. However, other phylogenetic analyses found that Nanobdellati/"DPANN" does not form a monophyletic group, and that the apparent grouping is caused by long branch attraction (LBA), suggesting that all these lineages belong to Methanobacteriati.
=== Phylogeny === According to Tom A. Williams et al. 2017, Castelle & Banfield (2018) and GTDB release 10-RS226 (16th April 2025).
=== Concept of species === The classification of archaea into species is also controversial. Ernst Mayr's species definition – a reproductively isolated group of interbreeding organisms - does not apply, as archaea reproduce only asexually. Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus Ferroplasma. On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. Some researchers question whether such species designations have practical meaning. Current knowledge on genetic diversity in archaeans is fragmentary, so the total number of species cannot be estimated with any accuracy. Estimates of the number of phyla range from 18 to 23, of which only 8 have representatives that have been cultured and studied directly. Many of these hypothesized groups are known from a single rRNA sequence, so the level of diversity remains obscure. This situation is also seen in the Bacteria; many uncultured microbes present similar issues with characterization.
== Prokaryotic phyla ==
=== Valid phyla === The following phyla have been validly published according to the Prokaryotic Code; belonging to the four kingdoms of archaea:
Methanobacteriota Microcaldota Nanobdellota Promethearchaeota Thermoproteota
=== Candidate phyla === The following phyla have been proposed, but have not been validly published according to the Prokaryotic Code; phyla that do not belong to any kingdom are shown in bold:
== Origin and evolution ==
The age of the Earth is about 4.54 billion years. Scientific evidence suggests that life began on Earth at least 3.5 billion years ago. The earliest evidence for life on Earth is graphite found to be biogenic in 3.7-billion-year-old metasedimentary rocks discovered in Western Greenland and microbial mat fossils found in 3.48-billion-year-old sandstone discovered in Western Australia. In 2015, possible remains of biotic matter were found in 4.1-billion-year-old rocks in Western Australia. Although probable prokaryotic cell fossils date to almost 3.5 billion years ago, most prokaryotes do not have distinctive morphologies, and fossil shapes cannot be used to identify them as archaea. Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms. Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago, though such data have since been questioned. 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. The archaeal lineage may be the most ancient that exists on Earth. Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. One possibility is that this occurred before the evolution of cells, when the lack of a typical cell membrane allowed unrestricted lateral gene transfer, and that the common ancestors of the three domains arose by fixation of specific subsets of genes. It is possible that the last common ancestor of 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. 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. 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 === The following table compares some major characteristics of the three domains, to illustrate their similarities and differences.