Squamamoeba japonica n. g. n. sp. (Amoebozoa): A Deep-sea Amoeba from the Sea of Japan with a Novel Cell Coat Structure

Protist

Volumn 164, Issue 1, 2013, Pages 13-23

  Kudryavtsev, Alexander ^a,b,c   Pawlowski, Jan ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

^c FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Amoebae; Cell coat; Deep sea protists; Phylogeny; SSU rRNA; Taxonomy; Ultrastructure.

Indexed keywords

PROTOZOAL DNA; PROTOZOAL RNA; RIBOSOME DNA; RNA 18S; SEA WATER;

AMOEBOZOA; ARTICLE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; CYTOLOGY; DNA SEQUENCE; GENETICS; GLYCOCALYX; ISOLATION AND PURIFICATION; JAPAN; MICROSCOPY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PARASITOLOGY; PHYLOGENY; RNA GENE; SEDIMENT; ULTRASTRUCTURE;

AMOEBOZOA; CLUSTER ANALYSIS; DNA, PROTOZOAN; DNA, RIBOSOMAL; GENES, RRNA; GEOLOGIC SEDIMENTS; GLYCOCALYX; JAPAN; MICROSCOPY; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, PROTOZOAN; RNA, RIBOSOMAL, 18S; SEAWATER; SEQUENCE ANALYSIS, DNA;

AMOEBA (GENUS); AMOEBOZOA; DERMAMOEBA; HIMATISMENIDA; JAPONICA; PROTISTA; TRICHOSIDA;

EID: 84872263069     PISSN: 14344610     EISSN: 16180941     Source Type: Journal    
DOI: 10.1016/j.protis.2012.07.003     Document Type: Article

References (43)

1. Altekar G., Dwarkadas S., Huelsenbeck J.P., Ronquist F. Parallel metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 2004, 20:407-415.
2. Angell R.W. Structure of Trichosphaerium micrum sp. n. J Eukaryot Microbiol 1975, 22:18-22.
3. Angell R.W. Observations on Trichosphaerium platyxyrum sp. n. J Eukaryot Microbiol 1976, 23:357-364.
4. Arndt H., Hausmann K., Wolf M. Deep-sea heterotrophic nanoflagellates of the Eastern Mediterranean Sea: qualitative and quantitative aspects of their pelagic and benthic occurrence. Mar Ecol Prog Ser 2003, 256:45-56.
5. Atkins M.S., Anderson O.R., Wirsen C.O. Effect of hydrostatic pressure on the growth rates and encystment of flagellated protozoa isolated from a deep-sea hydrothermal vent and a deep shelf region. Mar Ecol Prog Ser 1998, 171:85-95.
6. Atkins M.S., Teske A.P., Anderson O.R. A survey of flagellate diversity at four deep-sea hydrothermal vents in the eastern Pacific Ocean using structural and molecular approaches. J Eukaryot Microbiol 2000, 47:400-411.
7. Atkins M.S., Hanna M.A., Kupetsky E.A., Saito M.A., Taylor C.D., Wirsen C.O. Tolerance of flagellated protists to high sulfide and metal concentrations potentially encountered at deep-sea hydrothermal vents. Mar Ecol Prog Ser 2002, 226:63-75.
8. Furtado J.S., Olive L.S. Ultrastructure of the protostelid Ceratiomyxella tahitiensis including scale formation. Nova Hedwigia 1971, 21:537-576.
9. Furtado J.S., Olive L.S. Scale formation in a primitive mycetozoan. Trans Am Microsc Soc 1972, 91:594-596.
10. Gouy M., Guindon S., Gascuel O., Galtier N., Gouy M., Gautier C. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 2010, 27:221-224.
11. Gooday A.J. The biology of deep-sea foraminifera: a review of some advances and their applications in paleoceanography. Palaios 1994, 9:14-31.
12. Gooday A.J. Organic-walled allogromiids: aspects of their occurrence, diversity and ecology in marine habitats. J Foram Res 2002, 32:384-399.
13. Gooday A.J., Bowser S.S. The second species of Gromia (Protista) from the deep sea: its natural history and association with the Pakistan margin oxygen minimum zone. Protist 2005, 156:113-126.
14. Gooday A.J., Kamenskaya O.E., Cedhagen T. New and little-known Komokiacea (Foraminifera) from the bathyal and abyssal Weddell Sea and adjacent areas. Zool J Linn Soc 2007, 151:219-251.
15. Hausmann K., Weitere M., Wolf M., Arndt H. Meteora sporadica gen. nov. et sp. nov. (Protista incertae sedis) - an extraordinary free-living protist from the Mediterranean deep sea. Eur J Protistol 2002, 38:171-177.
16. Hausmann K., Hülsmann N., Polianski I., Schade S., Weitere M. Composition of benthic protozoan communities along a depth transect in the eastern Mediterranean Sea. Deep-Sea Res I 2002, 49:1959-1970.
17. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755.
18. Kudryavtsev A. Microscopic evidence for inclusion of Parvamoeba Rogerson, 1993 into the order Himatismenida (Amoebozoa). Eur J Protistol 2012, 47:85-88.
19. Kudryavtsev A., Smirnov A. Cochliopodium gallicum n. sp. (Himatismenida), an amoeba bearing unique scales, from cyanobacterial mats in the Camargue (France). Eur J Protistol 2006, 42:3-7.
20. Kudryavtsev A., Pawlowski J., Hausmann K. Description of Paramoeba atlantica n. sp. (Amoebozoa, Dactylopodida) - a marine amoeba from the Eastern Atlantic, with emendation of the dactylopodid families. Acta Protozool 2011, 50:239-253.
21. Kudryavtsev A., Wylezich C., Pawlowski J. Ovalopodium desertum n. sp. and the phylogenetic relationships of Cochliopodiidae (Amoebozoa). Protist 2011, 162:571-589.
22. Lahr D.J.G., Grant J., Nguyen T., Lin J.H., Katz L.A. Comprehensive phylogenetic reconstruction of Amoebozoa based on concatenated analyses of SSUrDNA and actin Genes. PLoS ONE 2011, 6:e22780.
23. Lanave C., Preparata G., Saccone C., Serio G. A new method for calculating evolutionary substitution rates. J Mol Evol 1984, 20:86-93.
24. Moran D.M., Anderson O.R., Dennett M.R., Caron D.A., Gast R.J. A description of seven Antarctic marine gymnamoebae including a new subspecies, two new species and a new genus: Neoparamoeba aestuarina antarctica n. subsp., Platyamoeba oblongata n. sp., Platyamoeba contorta n. sp. and Vermistella antarctica n. gen. n. sp. J Eukaryot Microbiol 2007, 54:169-183.
25. Nassonova E., Smirnov A., Fahrni J., Pawlowski J. Barcoding amoebae: comparison of SSU, ITS and COI genes as tools for molecular identification of naked lobose amoebae. Protist 2010, 161:102-115.
26. Nylander JAA (2004) MrModeltest v2. Program Dstributed by the Author. Evolutionary Biology Centre, Uppsala University.
27. Nylander JAA (2006) Mailfit script, Distributed by the Author. Evolutionary Biology Centre, Uppsala University.
28. Pawlowski J., Christen R., Lecroq B., Bachar D., Shahbazkia H.R., Amaral-Zettler L., Guillou L. Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS ONE 2011, 6:e18169.
29. Posada D., Crandall K.A. Selecting the best-fit model of nucleotide substitution. Syst Biol 2001, 50:580-601.
30. Pussard M. Description d'une amibe de type flabellulien: Pessonella marginata n. g. n. sp. (Mayorellidae, Amoebaea). Protistologica 1973, 9:175-185.
31. Rogerson A., Hannah F.J., Anderson O.R. A rdedscription of Rhabdamoeba marina, an inconspicuous marine amoeba from benthic sediments. Invertebr Biol 1998, 117:261-270.
32. Ronquist F., Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
33. Scheckenbach F., Wylezich C., Weitere M., Hausmann K., Arndt H. Molecular identity of strains of heterotrophic flagellates isolated from surface waters and deep-sea sediments of the South Atlantic based on SSU rDNA. Aquat Microb Ecol 2005, 38:239-247.
34. Schuster F.L. Fine Structure of the schizont stage of the testate marine ameba, Trichosphaerium sp. J Eukaryot Microbiol 1976, 23:86-93.
35. Sheehan R., Banner F.T. Trichosphaerium-an extraordinary testate Rhizopod from coastal waters. Estuar Coast Mar Sci 1973, 1:245-250.
36. Smirnov A.V. Korotnevella diskophora n.sp. (Gymnamoebia, Paramoebidae) - small freshwater amoeba with peculiar scales. Protistology 1999, 1:30-33.
37. Smirnov A.V., Kudryavtsev A.A. Pellitidae n. fam. (Lobosea, Gymnamoebia) - a new family, accommodating two amoebae with an unusual cell coat and an original mode of locomotion, Pellita catalonica n. g., n. sp. and Pellita digitata comb. nov. Eur J Protistol 2005, 41:257-267.
38. Smirnov A.V., Bedjagina O.M., Goodkov A.V. Dermamoeba algensis n. sp. (Amoebozoa, Dermamoebidae) - an algivorous lobose amoeba with complex cell coat and unusual feeding mode. Eur J Protistol 2011, 47:67-78.
39. Smirnov A.V., Chao E., Nassonova E.S., Cavalier-Smith T. A revised classification of naked lobose amoebae (Amoebozoa: Lobosa). Protist 2011, 162:545-570.
40. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
41. Tekle Y., Grant J., Anderson O.R., Nerad T.A., Cole J.C., Patterson D.J., 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, 47:339-352.
42. Wuyts J., Van de Peer Y., De Wachter R. Distribution of substitution rates and location of insertion sites on the tertiary structure of ribosomal RNA. Nucleic Acids Res 2001, 29:5017-5028.
43. Wuyts J., De Rijk P., Van de Peer Y., Pison G., Rousseeuw P., De Wachter R. Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res 2000, 28:4698-4708.