Sarcodina

An amoeba (; less commonly spelled ameba or amœba; : amoebas (less commonly, amebas) or amoebae (amebae) ), often called an amoeboid, is a type of cell or unicellular organism with the ability to alter its shape, primarily by extending and retracting pseudopods. Amoebae do not form a single taxonomic group; instead, they are found in every major lineage of eukaryotic organisms. Amoeboid cells occur not only among the protozoa, but also in fungi, algae, and animals.

Microbiologists often use the terms "amoeboid" and "amoeba" interchangeably for any organism that exhibits amoeboid movement.

In older classification systems, most amoebae were placed in the class or subphylum Sarcodina, a grouping of single-celled organisms that possess pseudopods or move by protoplasmic flow. However, molecular phylogenetic studies have shown that Sarcodina is not a monophyletic group whose members share common descent. Consequently, amoeboid organisms are no longer classified together in one group.

The best known amoeboid protists are ''Chaos carolinense'' and ''Amoeba proteus'', both of which have been widely cultivated and studied in classrooms and laboratories. Other well known species include the so-called "brain-eating amoeba" ''Naegleria fowleri'', the intestinal parasite ''Entamoeba histolytica'', which causes amoebic dysentery, and the multicellular "social amoeba" or slime mould ''Dictyostelium discoideum''.

Biology

Pseudopods and movement

Amoebae do not have cell walls, which allows for free movement. Amoebae move and feed by using pseudopods, which are bulges of cytoplasm formed by the coordinated action of actin microfilaments pushing out the plasma membrane that surrounds the cell. The appearance and internal structure of pseudopods are used to distinguish groups of amoebae from one another. Amoebozoan species, such as those in the genus ''Amoeba'', typically have bulbous (lobose) pseudopods, rounded at the ends and roughly tubular in cross-section. Cercozoan amoeboids, such as ''Euglypha'' and ''Gromia'', have slender, thread-like (filose) pseudopods. Foraminifera emit fine, branching pseudopods that merge with one another to form net-like (reticulose) structures. Some groups, such as the Radiolaria and Heliozoa, have stiff, needle-like, radiating axopodia (actinopoda) supported from within by bundles of microtubules.

Free-living amoebae may be "testate" (enclosed within a hard shell), or "naked" (also known as gymnamoebae, lacking any hard covering). The shells of testate amoebae may be composed of various substances, including calcium, silica, chitin, or agglutinations of found materials like small grains of sand and the frustules of diatoms.

To regulate osmotic pressure, most freshwater amoebae have a contractile vacuole which expels excess water from the cell. This organelle is necessary because freshwater has a lower concentration of solutes (such as salt) than the amoeba's own internal fluids (cytosol). Because the surrounding water is hypotonic with respect to the contents of the cell, water is transferred across the amoeba's cell membrane by osmosis. Without a contractile vacuole, the cell would fill with excess water and, eventually, burst. Marine amoebae do not usually possess a contractile vacuole because the concentration of solutes within the cell are in balance with the tonicity of the surrounding water.

Nutrition

The food sources of amoebae vary. Some amoebae are predatory and live by consuming bacteria and other protists. Some are detritivores and eat dead organic material.

Amoebae typically ingest their food by phagocytosis, extending pseudopods to encircle and engulf live prey or particles of scavenged material. Amoeboid cells do not have a mouth or cytostome, and there is no fixed place on the cell at which phagocytosis normally occurs.

Some amoebae also feed by pinocytosis, imbibing dissolved nutrients through vesicles formed within the cell membrane.

Size range

The size of amoeboid cells and species is extremely variable. The marine amoeboid '' Massisteria voersi'' is just 2.3 to 3 micrometres in diameter, within the size range of many bacteria. At the other extreme, the shells of deep-sea xenophyophores can attain 20 cm in diameter. Most of the free-living freshwater amoebae commonly found in pond water, ditches, and lakes are microscopic, but some species, such as the so-called "giant amoebae" ''Pelomyxa palustris'' and ''Chaos carolinense'', can be large enough to see with the naked eye.

Sexual reproduction

Recent evidence indicates that several Amoebozoa lineages undergo meiosis.

Orthologs of genes employed in meiosis of sexual eukaryotes have recently been identified in the ''Acanthamoeba'' genome. These genes included ''Spo11, Mre11, Rad50, Rad51, Rad52, Mnd1, Dmc1, Msh'' and '' Mlh''. This finding suggests that the ‘'Acanthamoeba'’ are capable of some form of meiosis and may be able to undergo sexual reproduction.

The meiosis-specific recombinase, Dmc1, is required for efficient meiotic homologous recombination, and ''Dmc1'' is expressed in ''Entamoeba histolytica''. The purified Dmc1 from ''E. histolytica'' forms presynaptic filaments and catalyses 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 increase during encystations. These findings in ''E. invadens'', combined with evidence from studies of ''E. histolytica'' indicate the presence of meiosis in the ''Entamoeba''.

''Dictyostelium discoideum'' in the supergroup Amoebozoa can undergo mating and sexual reproduction including meiosis when food is scarce.

Since the Amoebozoa diverged early from the eukaryotic family tree, these results suggest that meiosis was present early in eukaryotic evolution. Furthermore, these findings are consistent with the proposal of Lahr et al. that the majority of amoeboid lineages are anciently sexual.

Ecology

Pathogenic amoebae

Some amoebae can infect other organisms pathogenically, causing disease:

*''Entamoeba histolytica'' is the cause of amoebiasis, or amoebic dysentery.
*''Naegleria fowleri'' (the "brain-eating amoeba") is a fresh-water-native species that can be fatal to humans if introduced through the nose.
*''Acanthamoeba'' can cause amoebic keratitis and encephalitis in humans.
*'' Balamuthia mandrillaris'' is the cause of (often fatal) granulomatous amoebic meningoencephalitis.

Amoebae have been found to harvest and grow the bacteria implicated in plague. Amoebae can likewise play host to microscopic organisms that are pathogenic to people and help in spreading such microbes. Bacterial pathogens (for example, ''Legionella'') can oppose absorption of food when devoured by amoebae.
The currently generally utilized and best-explored amoebae that host other organisms are Acanthamoeba castellanii and Dictyostelium discoideum.
Microorganisms that can overcome the defenses of one-celled organisms can shelter and multiply inside them, where they are shielded from unfriendly outside conditions by their hosts.

History of knowledge and classification

Conceptual origins

The earliest record of an amoeboid organism was produced in 1755 by August Johann Rösel von Rosenhof, who named his discovery "Der Kleine Proteus" ("the Little Proteus"). Rösel's illustrations show an unidentifiable freshwater amoeba, similar in appearance to the common species now known as ''Amoeba proteus''. The term "Proteus animalcule" remained in use throughout the 18th and 19th centuries, as an informal name for any large, free-living amoeboid.

In 1822, the genus ''Amiba'' (from the Greek ἀμοιβή ''amoibe'', meaning "change") was erected by the French naturalist Bory de Saint-Vincent. Bory's contemporary, C. G. Ehrenberg, adopted the genus in his own classification of microscopic creatures, but changed the spelling to ''Amoeba''.

In 1841, Félix Dujardin coined the term "''sarcode''" (from Greek σάρξ ''sarx'', "flesh", and εἶδος ''eidos'', "form") for the "thick, glutinous, homogeneous substance" which fills protozoan cell bodies. Although the term originally referred to the protoplasm of any protozoan, it soon came to be used in a restricted sense to designate the gelatinous contents of amoeboid cells. Thirty years later, the Austrian zoologist Ludwig Karl Schmarda used "sarcode" as the conceptual basis for his division Sarcodea, a phylum-level group made up of "unstable, changeable" organisms with bodies largely composed of "sarcode". Later workers, including the influential taxonomist Otto Bütschli, amended this group to create the class Sarcodina, a taxon that remained in wide use throughout most of the 20th century.

Traditional classification

For convenience, all amoebae were grouped as Sarcodina and generally divided into morphological categories, on the basis of the form and structure of their pseudopods. Amoebae with pseudopods supported by regular arrays of microtubules (such as the freshwater Heliozoa and marine Radiolaria) were classified as Actinopoda, whereas those with unsupported pseudopods were classified as Rhizopoda. The Rhizopods were further subdivided into lobose, filose, plasmodial and reticulose, according to the morphology of their pseudopods. During the 1980s, taxonomists reached the following classification, based exclusively on morphological comparisons:

* Sarcodina : all amoebae.

:*Rhizopoda : amorphous amoebae that lack axopodia and move through pseudopodia.

::* Heterolobosea : amoebae with eruptive pseudopodia, similar to the lobose ones but with a distinct movement, and usually with flagellate life stages. It was traditionally divided into those which aggregate to form fruiting bodies ( Acrasida) and those that do not ( Schizopyrenida).

::* Lobosea : amoebae with lobose pseudopodia. This paraphyletic group is now represented by a big portion of the current phylum Amoebozoa, in particular the classes Tubulinea, Discosea and Cutosea.

:::*Gymnamoebia : lobose naked amoebae. This polyphyletic group included the classic amorphous amoebae with big, blunt pseudopodia, such as Euamoebida, Leptomyxida, Acanthopodida, Echinamoebida, Entamoebida, etc.

:::*Testacealobosia : lobose testate amoebae. This polyphyletic group included three unrelated lineages of amoebozoans enclosed by tests or other complex coverings: Arcellinida, Himatismenida and Trichosida.

::* Caryoblastea : amoebae with sparse, non-motile flagella on the surface. This group only includes the order Pelobiontida, which now belongs to the amoebozoan group Archamoebae together with some naked amoebae.

::* Eumycetozoea : plasmodial amoebae with filiform subpseudopodia that produce fruiting bodies.

::* Plasmodiophorea : endoparasitic plasmodial amoebae with minute pseudopodia. This group is now an order within Rhizaria, closely related to the endoparasites Phagomyxida.

::* Filosea : amoebae with filose pseudopodia.

:::*Aconchulinia : filose naked amoebae, sometimes covered in scales. This group included two unrelated taxa: the nucleariid amoebae, closely related to fungi; and most of the Vampyrellida, found in Rhizaria.

:::*Testaceafilosia : filose testate amoebae. This group included taxa now found throughout Rhizaria, such as Gromiida and Euglyphida.

::*Granuloreticulosea : amoebae with delicate granular pseudopodia. This group included both the Foraminifera (now in Rhizaria) and some members of Vampyrellida.

::*Xenophyophorea : plasmodial amoebae enclosed in a branched-tube system composed of a transparent organic substance. This group is now fully integrated into the Foraminifera.

:*Actinopoda : spherical amoebae that float in the water column. This group included those organisms that have a heliozoan-type appearance, with radially positioned filopodia, reticulopodia or axopodia surrounding the cell body. These were the Radiolaria, Phaeodaria, Proteomyxidea (all three now in Rhizaria), Centroplasthelida (now in Haptista), and Actinophryida (now in Stramenopiles).

Transitional period

In the final decades of the 20th century, a series of molecular phylogenetic analyses confirmed that Sarcodina was not a monophyletic group, and that amoebae evolved from flagellate ancestors. The protozoologist Thomas Cavalier-Smith proposed that the ancestor of most eukaryotes was an amoeboflagellate much like modern heteroloboseans, which in turn gave rise to a paraphyletic Sarcodina from which other groups (e.g., alveolates, animals, plants) evolved by a secondary loss of the amoeboid phase. In his scheme, the Sarcodina were divided into the more primitive Eosarcodina (with the phyla Reticulosa and Mycetozoa) and the more derived Neosarcodina (with the phyla Amoebozoa for lobose amoebae and Rhizopoda for filose amoebae).

Shortly after, phylogenetic analyses disproved this hypothesis, as non-amoeboid zooflagellates and amoeboflagellates were found to be completely intermingled with amoebae. With the addition of many flagellates to Rhizopoda and the removal of some amoebae, the name was rejected in favour of a new name Cercozoa. As such, both names Rhizopoda and Sarcodina were finally abandoned as formal taxa, but they remained useful as descriptive terms for amoebae. The phylum Amoebozoa was conserved, as it still primarily included amoeboid organisms, and now included the Mycetozoa.

Current classification

Today, amoebae are dispersed among many high-level taxonomic groups. The majority of traditional sarcodines are placed in two eukaryote supergroups: Amoebozoa and Rhizaria. The rest have been distributed among the excavates, opisthokonts, stramenopiles and minor clades.

* Amoebozoa : includes all naked and testate lobose amoebae (traditional Lobosea) as well as the pelobionts and eumycetozoans, and a few flagellates.
* Rhizaria : includes amoebae bearing reticulose or filose pseudopodia, the majority of which were traditionally classified as Filosea, Granuloreticulosea and Actinopoda, such as Euglyphida, Gromiida, Radiolaria, Proteomyxidea, Phaeodarea and Foraminifera (including Xenophyophorea). It also houses a large diversity of free-living flagellates, amoeboflagellates and parasites like the Plasmodiophorida.
* Heterolobosea : amoebae with lobose pseudopodia but eruptive flow of cytoplasm. Currently it includes the aggregative Acrasida, as well as several other amoeboflagellates. They are a class of excavates closely related to Euglenozoa, with whom they share their characteristic discoidal mitochondrial cristae.
* Stramenopiles : although primarily composed by flagellates, it contains a few groups of amoebae. For example: the Actinophryida, an order with typical heliozoan morphology; the amoeboid '' Rhizochromulina'', a genus of chrysophytes; or '' Synchroma'', a genus of amoeboid algae with reticulate axopodia.
* Rotosphaerida : also known as nucleariids, includes a few filose amoebae traditionally classified within the Filosea, positioned as the sister group of Fungi.
* Centroplasthelida : heliozoans with a centroplast from which axopodia arise. They are closely related to the haptophyte algae inside the supergroup Haptista.
* Rigifilida : a small order of filose amoebae previously interpreted as nucleariids. Together with the flagellate orders Mantamonadida and Diphylleida, it composes the CRuMs clade, positioned closest to Amorphea.
* Breviatea : includes enigmatic free-living amoeboflagellates related to opisthokonts.

The following cladogram shows the sparse positions of amoeboid groups (in bold), based on molecular phylogenetic analyses:

Amoeboid cells in other organisms

Amoeboid cell types in multicellular organisms

Some multicellular organisms have amoeboid cells only in certain phases of life, or use amoeboid movements for specialized functions. In the immune system of humans and other animals, amoeboid white blood cells pursue invading organisms, such as bacteria and pathogenic protists, and engulf them by phagocytosis. Sponges exhibit a totipotent cell type known as archaeocytes, capable of transforming into the feeding cells or choanocytes.

Amoeboid dispersal stages

Amoeboid stages also occur in the multicellular fungus-like protists, the so-called slime moulds. Both the plasmodial slime moulds, currently classified in the class Myxogastria, and the cellular slime moulds of the groups Acrasida and Dictyosteliida, live as amoebae during their feeding stage. The amoeboid cells of the former combine to form a giant multinucleate organism, while the cells of the latter live separately until food runs out, at which time the amoebae aggregate to form a multicellular migrating "slug" which functions as a single organism.

Other organisms may also present amoeboid cells during certain life-cycle stages, e.g., the gametes of some green algae ( Zygnematophyceae) and pennate diatoms, the spores (or dispersal phases) of some Mesomycetozoea, and the sporoplasm stage of Myxozoa and of Ascetosporea.

References

Further reading

*Walochnik, J. & Aspöck, H. (2007)
Amöben: Paradebeispiele für Probleme der Phylogenetik, Klassifikation und Nomenklatur
''Denisia'' 20: 323–350. (In German)

External links

Amoebae: Protists Which Move and Feed Using Pseudopodia
at the Tree of Life web project
* Siemensma, F
Microworld: world of amoeboid organisms

* Völcker, E. & Clauß, S
Visual key to amoeboid morphotypes
Penard Labs.

website of Maciver Lab of the University of Edinburgh, brings together information from published sources.

– informative amoeba videos.

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Cell biology
Motile cells
Microbiology
Microorganisms
Eukaryote morphology
Protists