Nucleariids
Nuclearia thermophila
Scientific classification
Domain:	Eukaryota
Clade:	Amorphea
Clade:	Obazoa
Clade:	Opisthokonta
Clade:	Holomycota
Order:	Rotosphaerida Rainer 1968[2][3]
Family:	Nucleariidae Cann & Page 1979[1]
Genera
See text
Diversity
Around 50 species[4]
Synonyms[3]
CristidiscoididaPage 1987[5] CristidiscoidiaCavalier-Smith 1993[6] PompholyxophryidaePage 1987 NucleariaeTedersoo et al. 2018[7] NuclearidaTedersoo et al. 2018 NuclearideaTedersoo et al. 2018 NucleariidaCavalier-Smith 1993 FonticulidaTedersoo et al. 2018 FonticuleaTedersoo et al. 2018 FonticulidaCavalier-Smith 1993 FonticulaceaeWorley, Raper & Hohl 1979[8]

Thenucleariids, ornucleariid amoebae, are a group ofamoebae that comprise thesister clade of thefungi. Together, they form the cladeHolomycota. They are aquatic organisms found infreshwater and marine habitats, as well as in faeces. They are free-livingphagotrophic predators that mostly consumealgae andbacteria.

Nucleariids are characterized by simple, spherical or flattened single-celled bodies with filopodia (fine, thread-likepseudopods), covered by a mucous coat. They lackflagella andmicrotubules. Inside thecytoplasm of some species areendosymbioticproteobacteria. Some species are naked, with only the mucous coat as cover, while others (known as 'scaled' nucleariids) have silica-based or exogenous particles of various shapes.

An exceptional nucleariid,Fonticula alba, developsmulticellular fruiting bodies (sorocarps) for spore dispersal. It is one of several cases of independently evolved multicellularity withinOpisthokonta, the clade that houses bothHolozoa (which includesanimals) and Holomycota.

Initially, nucleariids were grouped with other filose amoebae (i.e., with filopodia) based on their superficial similarity. Silica-scaled and naked nucleariids were classified into separatefamilies from one another,Pompholyxophryidae andNucleariidae, respectively. Due to its nature as aslime mold, the genusFonticula has also been classified separatedly, particularly withacrasids and other slime molds. With advancements inelectron microscopy andmolecular phylogenetics, the three groups were revealed to belong to the sameclade as sister to the fungi. Due to lack of molecular data, the three groups are treated as onefamily, under the name of Nucleariidae.

Various conflicting systems of above-family classification exist for nucleariids, with older systems grouping them as aclassCristidiscoidea composed of twoorders: one forFonticula and another for the remaining species.Mycologists regard them as an independentkingdom of life,Nucleariae, with twophyla that mirror those two orders. They are generally accepted byprotistologists as a single orderRotosphaerida, which is the oldest taxonomic name for these organisms.

Nucleariids aresingle-celledamoebae that lackflagella and have radiatingfilopodia (i.e., thread-likepseudopodia). They have a spherical or sometimes flattened cell bodies^[9] with one or few conspicuousnuclei, each with a prominent centralnucleolus except forFonticula andParvularia:Parvularia can also have peripheral nucleoral material instead,^[10] andFonticula has an indistinct nucleolus. Thecytoplasm contains multiplevacuoles, including food vesicles,contractile vacuoles in freshwater species, andlipid globules. They have relatively simple cells in comparison to otherprotists: they lackflagella,cytoplasmicmicrotubules,^[a]extrusomes, and specialorganelles.^[4] Exceptionally, some species containendosymbioticproteobacteria (most frequently members of the genusRickettsia).^[11]

Most nucleariids have some kind of mucous coat, with or without coverings. The coverings can be made withendogenoussilica-based particles (known as idiosomes) or withexogenous particles (known as xenosomes).^[4] These particles are developed into hollow siliceous scales or spines.^[12] The mucous coat itself—sometimes calledglycocalyx—is enigmatic, as it can be present or absent in the same organism depending on the conditions. It appears to be made of one or two layers fibrous material running parallel to the cell membrane, and it often houses bacterial ectosymbionts. Surrounding the cell periphery, the characteristic hyaline (i.e., transparent) filopodia are found, originating from any point of the cell surface, sometimes branching or tapering but are never stiff oranastomosing (fusing with one another). UnlikeHeliozoa, these filopodia are not supported by microtubules and do not contain extrusomes.^[4]

Most species develop aresting cyst during theirlife cycle consisting of a smooth spherical cell covered by one or more thick layers of a translucent material.^[4]

Nucleariids thrive in water bodies worldwide. Most live in a variety offreshwater environments, including hot spring waters of around 30 °C.^[13] Others are found in marine environments (e.g.,Lithocolla), and others inhabit faeces (Fonticula).^[4]

Nucleariids are free-livingphagotrophs, and preferably consumecyanobacteria and other algae.^[9] Small-celled species like those ofParvularia andFonticula feed on smallbacteria, while larger cells such asNuclearia,Pompholyxophrys andLithocolla can also feed on detritus and unicellular eukaryoticalgae (e.g.,diatoms). All of them are slow-paced grazers^[14] that probably grow in response to the availability of their food sources, such as afteralgal blooms.^[4]

Nucleariids are among the closest relatives offungi,^[15] together forming thecladeHolomycota.^{[16][17][7][4]} This clade is, in turn, closely related toHolozoa, the clade containinganimals and their closestprotist relatives. Together, they form the cladeOpisthokonta. After animals and fungi, nucleariids include the third known occurrence ofmulticellularity among opisthokonts:^[b] the speciesFonticula alba, a type ofslime mold, capable of aggregative multicellular fruiting that developssorocarps (stalks with masses of spores) fordispersal. The existence ofFonticula alba suggests that opisthokonts have a great propensity toward multicellularity.^[16]

Nucleariids are unique within their greater evolutionary context.Apusomonads (relatives of opisthokonts), holozoans and fungi all evolved from ancestors that were single-celledphagotrophicflagellates. Opisthokonts, in particular, are characterized by a singleposteriorflagellum. Even the mostbasal-branching fungi (aphelids,rozellids andmicrosporidia)^[c] are single-celled flagellates that prey on other eukaryotes.^[18] The last common ancestor of nucleariids, however, had lost the opisthokont flagellum and its cell polarity, and had gained the characteristic mucous coat.^[4] The presence offilopodia is more common among opisthokonts, shared with aphelids^[18] and most holozoans.^[20]

The history of the classification of nucleariids is full of incongruence betweenmorphology andmolecular phylogeny. Toward the end of the 19th century, most nucleariid species had already been described, and were classified with other naked or scaled filose amoebae.^[21][4] During the second half of the 20th century, naturalist Heinrich Rainer described a subgroup ofheliozoans,Rotosphaeridia, to accommodate non-flagellated, scaled, filose amoebae withoutaxopodia (the nucleariidsPompholyxophrys,Pinaciophora,Lithocolla andRhabdiophrys).^[2]

Protozoologists John P. Cann and Frederick C. Page established the familyNucleariidae to include the naked generaNuclearia,Gobiella andNucleosphaerium^[1] (later synonymized withNuclearia).^[22] Through studies of their fine cellularultrastructure viatransmission electron microscopy, the orderCristidiscoidida was established within the class Filosea, to accommodate both families Nucleariidae and the silica-scaledPompholyxophryidae (e.g.,Pompholyxophrys,Pinaciophora andRhabdiophrys), because they all shared disc-shapedmitochondrial cristae as acommon characteristic (i.e., they were discicristate).^[5][23][4]

The genusFonticula was continually excluded, as it was considered anacrasid^[8] or aslime mold,^[24] until 1993, when protozoologistThomas Cavalier-Smith created the subclassCristidiscoidia to house two orders:Nucleariida (with Nucleariidae and Pompholyxophryidae) andFonticulida (with Fonticulidae).^[6][4] However, he later considered scaled nucleariids (Pompholyxophryidae) as members of theCercozoa, completely separate from naked ones,^[25] but this is no longer accepted.^[11] In a 1999 taxonomic revision by Kirill A. Mikrjukov, Cristidiscoidida was regarded as ajunior synonym of Rotosphaerida, which finally united all discicristate filose amoebae. He also includedBelonocystis^[26] andMicronuclearia in this order,^[27] which now are known to belong toAmoebozoa andCRuMs, respectively.^[4]

At present, different conflicting classifications for nucleariids remain in use depending on the authors. Cavalier-Smith maintained his system through the years, using the nameCristidiscoidea as a class of hisparaphyletic phylumChoanozoa, which included all protists most closely related toanimals andfungi.^[28]Mycologists have proposed a separatekingdomNucleariae with lower ranks for Cavalier-Smith's two orders (phylaNuclearida andFonticulida, classesNuclearidea andFonticulidea), but without specifying their taxonomic composition.^[7] Generally, protistologists prefer using the order Rotosphaerida instead, as it has priority over more recent names.^[26][3][11] Most studies using the name Cristidiscoidea have only includedNuclearia or environmental sequences, while those using Rotosphaerida have been used when studying the scale-bearing amoebae and, more recently, the naked ones as well.^[4]

At the family-level rank, although historically both Nucleariidae and Pompholyxophryidae have been used separately for naked and scale-bearing nucleariids respectively,^[26] and Fonticulidae solely forFonticula,^[6] protistologists tend to use only Nucleariidae now,^[23][4] as there is no clear evolutionary separation between the three families.^[11]

Of all nucleariids, only a few have been isolated andmolecularly analyzed.^[11] Many genera remain asincertae sedis due to the lack of molecular data,^[29] as it is difficult to confirm their evolutionary position other than by morphological similarity. The following is a list of nucleariid genera with definite placement:^[23][4]

• FonticulaWorley, Raper & Hohl 1979^[8]
• LithocollaSchulze 1874
• NucleariaCienkowski 1865 (=NuclearellaFrenzel 1897;NuclearinaFrenzel 1897;NucleosphaeriumCann & Page 1979)
• ParvulariaLópez-Escardó 2017^[10]
• PompholyxophrysArcher 1869 (=HyalolampeGreeff 1869^[26]

The following are genera regarded as possibly belonging to this order:^[23][4]

• ElaeorhanisGreef, 1873 (=LithosphaerellaFrenzel 1897;EstrellaFrenzel 1897) – may also be related toDiplophrys, a member of thelabyrinthulomycete orderAmphitremida.^[30]
• PinaciophoraGreeff 1869 (=PinacocystisHertwig & Lesser 1874;PinaciocystisRoskin 1929;PotamodiscusGerloff 1968)^[26]
• RabdiasterMikrjukov 1999^[26]
• RabdiophrysRainer 1968^[2]
• ThomseniophoraNicholls 2012^[31]
• VampyrellidiumZopf 1885

• Holomycota
• Nucleariids

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