Temporal range: Neoproterozoic–Recent
Lühe, 1913 emend. Cavalier-Smith, 1998
|Subphyla and Infraphyla|
Amoebozoa is a major taxonomic group containing about 2,400 described species of amoeboid protists, often possessing blunt, fingerlike, lobose pseudopods and tubular mitochondrial cristae. In most classification schemes, Amoebozoa is ranked as a phylum within either the kingdom Protista or the kingdom Protozoa. In the classification favored by the International Society of Protistologists, it is retained as an unranked "supergroup" within Eukaryota. Molecular genetic analysis supports Amoebozoa as a monophyletic clade. Most phylogenetic trees identify it as the sister group to Opisthokonta, another major clade which contains both Fungi and Animals as well as some 300 species of unicellular protists. Amoebozoa and Opisthokonta are sometimes grouped together in a high-level taxon, variously named Unikonta, Amorphea or Opimoda.
Amoebozoa includes many of the best-known amoeboid organisms, such as Chaos, Entamoeba, Pelomyxa and the genus Amoeba itself. Species of Amoebozoa may be either shelled (testate), or naked, and cells may possess flagella. Free-living species are common in both salt and freshwater, as well as soil, moss and leaf litter. Some live as parasites or symbiotes of other organisms, and some are known to cause disease in humans and other organisms.
While the majority of amoebozoan species are unicellular, the group also includes several varieties of slime molds, which have a macroscopic, multicellular stage of life during which individual amoeboid cells aggregate to produce spores.
Amoebozoa vary greatly in size. Some are only 10–20 μm in diameter, while others are among the largest protozoa. The well-known species Amoeba proteus, which may reach 800 μm in length, is often studied in schools and laboratories as a representative cell or model organism, partly because of its convenient size. Multinucleate amoebae like Chaos and Pelomyxa (the so-called "giant amoebae") may be several millimetres in length, and some multicellular amoebozoa, such as the "dog vomit" slime mold Fuligo septica, can cover an area of several square meters.
Amoebozoa is a large and diverse group, but certain features are common to many of its members. The amoebozoan cell is typically divided into a granular central mass, called endoplasm, and a clear outer layer, called ectoplasm. During locomotion, the endoplasm flows forwards and the ectoplasm runs backwards along the outside of the cell. In motion, many amoebozoans have a clearly defined anterior and posterior and may assume a "monopodial" form, with the entire cell functioning as a single pseudopod. Large pseudopods may produce numerous clear projections called subpseudopodia (or determinate pseudopodia), which are extended to a certain length and then retracted, either for the purposed of locomotion or food intake. A cell may also form multiple indeterminate pseudopodia, through which the entire contents of the cell flow in the direction of locomotion. These are more or less tubular and are mostly filled with granular endoplasm. The cell mass flows into a leading pseudopod, and the others ultimately retract, unless the organism changes direction.
While most amoebozoans are "naked," like the familiar Amoeba and Chaos, or covered with a loose coat of minute scales, like Cochliopodium and Korotnevella, members of the order Arcellinida form rigid shells, or tests, equipped with a single aperture through which the pseudopods emerge. Arcellinid tests may be secreted from organic materials, as in Arcella, or built up from collected particles cemented together, as in Difflugia.
In all amoebozoa, the primary mode of nutrition is phagocytosis, in which the cell surrounds potential food particles with its pseudopods, sealing them into vacuoles within which they may be digested and absorbed. Some amoebozoans have a posterior bulb called a uroid, which may serve to accumulate waste, periodically detaching from the rest of the cell. When food is scarce, most species can form cysts, which may be carried aerially and introduce them to new environments. In slime moulds, these structures are called spores, and form on stalked structures called fruiting bodies or sporangia.
The majority of Amoebozoa lack flagella and more generally do not form microtubule-supported structures except during mitosis. However, flagella do occur among the Archamoebae, and many slime moulds produce biflagellate gametes. The flagellum is generally anchored by a cone of microtubules, suggesting a close relationship to the opisthokonts. The mitochondria in amoebozoan cells characteristically have branching tubular cristae. However, among the Archamoebae, which are adapted to anoxic or microaerophilic habitats, mitochondria have been lost.
Place of Amoebozoa in the Eukaryote Tree
It appears (based on molecular genetics) that the members of Amoebozoa form a sister group to animals and fungi, diverging from this lineage after it had split from the other groups, as illustrated below:
Strong similarities between Amoebozoa and Opisthokonts lead to the hypothesis that they form a distinct clade. Thomas Cavalier-Smith proposed the name "unikonts" (formally, Unikonta) for this branch, whose members were believed to have been descended from a common ancestor possessing a single emergent flagellum rooted in one basal body. However, while the close relationship between Amoebozoa and Opisthokonta is robustly supported, recent work has shown that the hypothesis of a uniciliate ancestor is probably false. In their Revised Classification of Eukaryotes (2012), Adl et al. proposed Amorphea as a more suitable name for a clade of approximately the same composition, a sister group to the Diaphoretickes. More recent work places the members of Amorphea together with the malawimonids and collodictyonids in a proposed clade called Opimoda, which comprises one of two major lineages diverging at the root of the eukaryote tree of life.
Subphyla within Amoebozoa: Lobosa and Conosa
Traditionally all amoebozoa with lobose pseudopods were grouped together in the class Lobosea, placed with other amoeboids in the phylum Sarcodina or Rhizopoda, but these were considered to be unnatural groups. Structural and genetic studies identified the percolozoans and several archamoebae as independent groups. In phylogenies based on rRNA their representatives were separate from other amoebae, and appeared to diverge near the base of eukaryotic evolution, as did most slime molds.
However, revised trees by Cavalier-Smith and Chao in 1996 suggested that the remaining lobosans do form a monophyletic group, to which the Archamoebae and Mycetozoa were closely related, although the percolozoans were not. Subsequently they emended the phylum Amoebozoa to include both the subphylum Lobosa and a new subphylum Conosa, comprising the Archamoebae and the Mycetozoa.
Recent molecular genetic data appear to support this primary division of the Amoebozoa into Lobosa and Conosa. The former, as defined by Cavalier-Smith and his collaborators, consists largely of the classic Lobosea: non-flagellated amoebae with blunt, lobose pseudopods (Amoeba, Acanthamoeba, Arcella, Difflugia etc.). The latter is made up of both amoeboid and flagellated cells, characteristically with more pointed or slightly branching subpseudopodia (Archamoebae and the Mycetozoan slime molds).
Phylogeny within Amoebozoa
From a recent study by Cavalier-Smith, Chao & Lewis 2016. 
Vase-shaped microfossils (VSMs) discovered around the world show that amoebozoans have existed since the Neoproterozoic Era. The fossil species Melanocyrillium hexodiadema, Palaeoarcella athanata, and Hemisphaeriella ornata come from rocks 750 million years old. All three VSMs share a hemispherical shape, invaginated aperture, and regular indentations, that strongly resemble modern arcellinids, which are shell-bearing amoeboids. P. athanata in particular looks the same as the extant genus Arcella.
List of amoebozoan protozoa pathogenic to humans
The recently available Acanthamoeba genome sequence revealed several orthologs of genes employed in meiosis of sexual eukaryotes. These genes included Spo11, Mre11, Rad50, Rad51, Rad52, Mnd1, Dmc1, Msh and Mlh. This finding suggests that Acanthamoeba is capable of some form of meiosis and may be able to undergo sexual reproduction.
In sexually reproducing eukaryotes, homologous recombination (HR) ordinarily occurs during meiosis. The meiosis-specific recombinase, Dmc1, is required for efficient meiotic HR, and Dmc1 is expressed in Entamoeba histolytica. The purified Dmc1 from E. histolytica forms presynaptic filaments and catalyzes ATP-dependent homologous DNA pairing and DNA strand exchange over at least several thousand base pairs. The DNA pairing and strand exchange reactions are enhanced by the eukaryotic meiosis-specific recombination accessory factor (heterodimer) Hop2-Mnd1. These processes are central to meiotic recombination, suggesting that E. histolytica undergoes meiosis.
Studies of Entamoeba invadens found that, during the conversion from the tetraploid uninucleate trophozoite to the tetranucleate cyst, homologous recombination is enhanced. Expression of genes with functions related to the major steps of meiotic recombination also increased during encystations. These findings in E. invadens, combined with evidence from studies of E. histolytica indicate the presence of meiosis in the Entamoeba.
Since Amoebozoa diverged early from the eukaryotic family tree, these results also suggest that meiosis was present early in eukaryotic evolution.
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