Abstract
Using morphological traits and molecular-genetic research methods, the authors have identified 24 species of naked amoeba from natural biotopes. The 18S rRNA gene sequences were obtained for the following species of naked amoeba: Amoeba proteus isolate AP07 (ON907618), Saccamoeba limax isolate SLU_22 (OP894078), Saccamoeba limax isolate SL_Uk19 (OQ520144), Saccamoeba sp. strain IDL777 (MZ079370), Thecamoeba striata isolate THS19 (OQ134482), Thecamoeba striata isolate THS20 (OQ134483), Thecamoeba similis isolate Prut river (OL604177), Thecamoeba similis isolate Baggersee Innsbruck (Baggersee Rossau) (OL604178), Thecamoeba quadrilineata isolate THQD2 (ON398269), Thecamoeba quadrilineata isolate THQA1 (ON398268), Thecamoeba sp. strain THS203 (MZ079371), Stenamoeba stenopodia isolate UKSS7 (OP375108), Stenamoeba stenopodia isolate POLSS7 (OP419588), Korotnevella stella isolate KSD2 (ON398267), Korotnevella stella isolate KSA1 (ON398266), Vexillifera bacillipedes isolate river Dnepr (OK649262), Vannella lata isolate Kamenka river (OL305063), Vannella lata isolate Varta river (OL305064), Vannella sp. strain VLS303 (MZ079372), Vannella simplex isolate Black Sea (OM403052), Vannella simplex isolate Mediterranean Sea (OM403053), Ripella sp. strain RPL100 (MZ079369), Mayorella vespertilioides isolate MV_7 (OP739500), Mayorella sp. isolate MY_7 (OP729930), Acanthamoeba sp. strain ATM123 (MZ079366), Acanthamoeba sp. isolate river Elbe (OK649261), Acanthamoeba polyphaga isolate AcPoly01 (ON908497), Acanthamoeba polyphaga isolate AcPoly15 (ON908496), Acanthamoeba griffini isolate Black sea (OM522832), Acanthamoeba griffini isolate Mediterranean Sea (OM522833), Cochliopodium actinophorum strain COP101 (MZ079367), Cochliopodium minus isolate river Stokhid (OK649264), Cochliopodium sp. strain COP102 (MZ079368), Vahlkampfia avara isolate VA7 (OP179657), Willaertia magna isolate river Teterev (OK649263). All of the naked amoebae species on the phylogenetic tree constructed based on the 18S rRNA gene are located within Amoebozoa and grouped with Tubulinea and Discosea. There are separate groups of freshwater, marine, and terrestrial biotopes; these groups are sister species relative to one another with low results of bootstrap analysis, which shows a low accuracy in the distances of particular amoeba species isolated from different natural biotopes.
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REFERENCES
Amaral Zettler, L.A., Nerad, T.A., O’Kelly, C.J., Peglar, M.T., Gillevet, pp.M., Silberman, J.D., and Sogin, M.L., A Molecular reassessment of the leptomyxid amoebae, Protist, 2000, vol. 151, pp. 275–282. https://doi.org/10.1078/1434-4610-00025
Anderson, O.R., A Half-century of research on free-living amoebae (1965–2017): Review of biogeographic, ecological and physiological studies, Acta Protozool., 2018, vol. 57, no. 1, pp. 1–28. https://doi.org/10.4467/16890027AP.18.001.8395
Bass, D., Silberman, J.D., Brown, M.W., Tice, A.K., Jousset, A., Geisen, S., and Hartikainen, H., Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists, Environ. Microbiol., 2016, vol. 18, pp. 1604–1619. https://doi.org/10.1111/1462-2920.13235
Bolivar, I., Fahrni, J.F., Smirnov, A., and Pawlowski, J., SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): the origin of gymnamoebae revisited, Mol. Biol. Evol., 2001, vol. 18, pp. 2306–2314. https://doi.org/10.1093/oxfordjournals.molbev.a003777
Brown, S. and Jonckheere, J.F., A reevaluation of the amoeba genus Vahlkampfia based on SSUrDNA sequences, Eur. J. Protistol., 1999, vol. 35, no. 1, pp. 49–54. https://doi.org/10.1016/S0932-4739(99)80021-2
Brown, M.W., Spiegel, F.W., and Silberman, J.D., Amoeba at attention: phylogenetic affinity of Sappinia pedata, J. Eukaryotic Microbiol., 2007, vol. 54, pp. 511–519. https://doi.org/10.1111/j.1550-7408.2007.00292.x
Bütschli, O., Protozoa mit einem beitrag: Palaeontologische entwicklung der Rhizopoda, in Die Klassen und Ordnungen des Thierreichs, Wissenschaftlich Dargestellt in Wort und Bild, vol. 1: Abtheilung: Sarkodina und Sporozoa, Schwager, C. and Bronn, H.G., Eds., Leipzig: Winter’sche Verlagshandlung, 1880–1882, pp. I–XVIII.
Calkins, G.N., The Protozoa, New York: Columbia Press/Macmillan, 1901.
Cavalier-Smith, T., A revised six-kingdom system of life, Biol. Rev., 1998, vol. 73, pp. 203–266. https://doi.org/10.1017/s0006323198005167
Cavalier-Smith, T., Chao, E.E.-Y., and Oates, B., Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium, Eur. J. Protistol., 2004, vol. 40, pp. 21–48. https://doi.org/10.1016/j.ejop.2003.10.001
Cavalier-Smith, T., Megaphylogeny, cell body plans, adaptive zones: causes and timing of eukaryote basal radiations, J. Eukaryotic Microbiol., 2009, vol. 56, pp. 26–33. https://doi.org/10.1111/j.1550-7408.2008.00373.x
Cavalier-Smith, T., Chao, E.E., and Lewis, R., 187-gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution, Mol. Phylogenet. Evol., 2016, vol. 99, pp. 275–296. https://doi.org/10.1016/j.ympev.2016.03.023
Cole, J., Anderson, O.R., Tekle, Y.I., Grant, J., Katz, L.A., and Nerad, T., A description of a new “Amoebozoan” isolated from the American lobster, Homarus americanus, J. Eukaryotic Microbiol., 2010, vol. 57, pp. 40–47.
Corsaro, D. and Venditti, D., Molecular phylogenetics evidence for a novel lineage of amoebae within discosea (Amoebozoa: Lobosa), Acta Protozool., 2013, vol. 52, pp. 309–316.
Corsaro, D., Michel, R., Walochnikc, J., Muller, K.-D., and Greuba, G., Saccamoeba lacustris, sp. nov. (Amoebozoa: Lobosea: Hartmannellidae), a new lobose amoeba, parasitized by the novel chlamydia “Candidatus Metachlamydia lacustris” (Chlamydiae: Parachlamydiaceae), Eur. J. Protistol., 2010, vol. 46, pp. 86–95.
Delage, Y. and Hérouard, E., Traité de Zoologie Concrète, vol. 1: La Cellule et les Protozoaires, Paris: Schleicher Frères, 1896.
Dykova, I., Bohacova, L., Fiala, I., Machackova, B., Peckova, H., and Dvorakova, H., Amoebae of the genera Vannella Bovee, 1965 and Platyamoeba Page, 1969 isolated from fish and their phylogeny inferred from SSU rRNA gene and ITS sequences, Eur. J. Protistol., 2005, vol. 41, pp. 219–230.
Dykova, I., Kostka, M., and Peckova, H., Morphology and SSU rDNA-based phylogeny of a new strain of Saccamoeba sp. (Saccamoeba Frenzel, 1892, Amoebozoa), Acta Protozool., 2008, vol. 47, no. 4, pp. 397–405.
Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K., MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms, Mol. Biol. Evol., 2018, vol. 35, no. 6, pp. 1547–1549. https://doi.org/10.1093/molbev/msy096
Lahr, D.J.G., Grant, J.R., and Katz, L.A., Multigene phylogenetic reconstruction of the Tubulinea (Amoebozoa) corroborates four of the six major lineages, while additionally revealing that shell composition does not predict phylogeny in the Arcellinida, Protist, 2013, vol. 164, no. 3, pp. 323–339. https://doi.org/10.1016/j.protis.2013.02.003
Lahr, D.J., Grant, J., Molestina, R., Katz, L.A., and Anderson, O.R., Sapocribrum chincoteaguense n. gen. n. sp.: A small, scale-bearing amoebozoan with flabellinid affinities, J. Eukaryotic Microbiol., 2015, vol. 4, pp. 444–453. https://doi.org/10.1111/jeu.12199
Leidy, J., Freshwater rhizopods of North America. United States Geological Survey of the Territories Report, 1879, vol. 12, pp. 1–324.
Maniatis, T., Fritsch, E.F., and Sambrook, J., Molecular Cloning, a Laboratory Manual, New York: Cold Spring Harbor, 1982.
Medlin, L., Elwood, H.J., Stickel, S., and Sogin, M.L., The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions, Gene, 1988, vol. 71, pp. 491–499.
Mrva, M., Morphological studies on two rare soil amoebae Deuteramoeba algonquinensis and D. mycophaga (Gymnamoebia, Amoebidae), Protist, 2010, vol. 6, pp. 284–289.
Page, F.C., Marine Gymnamoebae, Cambridge: Institute Terrestrial Ecology, 1983.
Page, F.C., A New Key to Freshwater and Soil Gymnamoebea, Ambleside: Freshwater Biological Association, 1988.
Page, F.C. and Robson, E.A., Fine structure and taxonomic position of Hydramoeba hydroxena (Entz, 1912), Protistologica, 1983, vol. 19, pp. 41–50.
Page, F.C. and Siemensma, F.J., Nackte Rhizopoda und Heliozoea, in Protozoenfauna, Stuttgart: Gustav Fischer Verlag, 1991, pp. 3–170.
Pawlowski, J. and Burki, F., Untangling the phylogeny of amoeboid protists, J. Eukaryotic Microbiol., 2009, vol. 56, pp. 16–25. https://doi.org/10.1111/j.1550-7408.2008.00379.x
Peglar, M.T., Amaral Zettler, L.A., Anderson, O.R., Nerad, T.A., Gillevet, P.M., Mullen, T.E., Frasca, Jr.S., Silberman, J.D., O’Kelly, C.J., and Sogin, M.L., Two new small subunit ribosomal RNA gene lineages with in the subclass Gymnamoebia, J. Eukaryotic Microbiol., 2003, vol. 50, pp. 224–232. https://doi.org/10.1111/j.1550-7408.2003.tb00122.x
Penard, E., Faune Rhizopodique du Bassin du Leman, Geneve: Henry Kundig, 1902.
Sims, G.P., Rogerson, A., and Aitken, R., Primary and secondary structure of the small-subunit ribosomal RNA of the naked, marine amoeba Vannella anglica: Phylogenetic implications, J. Mol. Evol., 2018, vol. 48, pp. 740–749. https://doi.org/10.1007/pl00006518
Tekle, Y.I., Grant, J., Anderson, O.R., Nerad, T.A., Cole, J.C., Patterson, D.J., and Katz, L.A., Phylogenetic placement of diverse amoebae inferred from multigene analyses and assessment of clade stability within “Amoebozoa” upon removal of varying rate classes of SSU-rDNA, Mol. Phylogenet. Evol., 2008, vol. 47, pp. 339–352. https://doi.org/10.1016/j.ympev.2007.11.015
Willumsen, N.B.S., Chaos zoochlorellae sp. nov. (Gymnamoebia, Amoebidae) from a Danis freshwater pond, J. Nat. Hist., 1982, vol. 16, pp. 803–813.
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Patsyuk, M. Phylogenetic Relationships among Naked Amoebae Found in Natural Biotopes. Cytol. Genet. 57, 567–578 (2023). https://doi.org/10.3103/S0095452723060063
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DOI: https://doi.org/10.3103/S0095452723060063