Identification and phylogenetic analysis of morphologically similar naked amoebae using small subunit ribosomal RNA

Journal of Eukaryotic Microbiology

Volumn 49, Issue 6, 2002, Pages 478-484

  Sims, Gary P ^a,b,c   Aitken, Robert ^b   Rogerson, Andrew ^a,d  

^a UNIVERSITY MARINE BIOLOGICAL STATION   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d Oceanog Ctr of Nova SE Univ ^*  (United States)

Author keywords

Amoeba; Cell surface structure; Glycocalyx; Gymnamoebae; Molecular phylogeny; Platyamoeba; Protozoa; SsrRNA, taxonomy; Vannella

Indexed keywords

DETECTION METHOD; IDENTIFICATION METHOD; MICROORGANISM; PHYLOGENETICS;

AMOEBA; ANIMALS; BASE SEQUENCE; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RIBOTYPING; RNA, PROTOZOAN; RNA, RIBOSOMAL, 18S; SEQUENCE ANALYSIS, DNA;

PLATYAMOEBA; PROTOZOA; VANNELLA;

EID: 0036865860     PISSN: 10665234     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1550-7408.2002.tb00232.x     Document Type: Article

References (44)

1. Amaral Zettler, L. A., Nerad, T. A., O'Kelly, C. J., Peglar, T., Gillevet, J. D., Silberman, J. D. & Sogin, M. L. 2000. A molecular reassessment of the leptomyxid amoebae. Protistologica, 151:275-282.
2. Anderson, O. R. & Rogerson, A. 1995. Annual abundances and growth-potential of gymnamoebae in the Hudson Estuary with comparative data from the Firth of Clyde. Eur. J. of Protist., 31:223-233.
3. Anderson, O. R., Rogerson, A. & Hannah, F. 1997. Three new limax amoebae isolated from marine surface sediments: Vahlkampfia caledonica n. sp., Saccamoeba marina n. sp., and Hartmannella vacuolata n. sp. J. Enkaryot. Microbiol., 44:33-42.
4. Armstrong, E., Rogerson, A. & Leftley, J. 2000. The abundance of heterotrophic protists associated with intertidal seaweeds. Estuarine Coastal Shelf Sci., 50:415-424.
5. Arndt, H. 1993. A critical review of the importance of rhizopods (naked and testate amoeba) and actinopods (heliozoa) in lake plankton. Mar. Micro. Food Webs, 7:3-29.
6. Bolivar, I., Fahrni, J. F., Smirnov, A. & Pawlowski, J. 2002. SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnaoebia): The origin of gymnamoebae revisited. Mol. Biol. Evol., 18:2306-2314.
7. Brown, S. & De Jonckheere, J. F. 1994. Identification and phylogenetic relationships of Vahlkampfia spp. (Free-Living Amoebae) by Riboprinting. FEMS Micro. Letters, 115:241-246.
8. Butler, H. & Rogerson, A. 1995. Temporal and spatial abundance of naked amebas (Gymnamoebae) in marine benthic sediments of the Clyde-Sea area, Scotland. J. Eukaryot. Microbiol., 42:724-730.
9. Butler, H. G. & Rogerson, A. 2000. Naked amoebae from benthic sediments in the Clyde Sea area, Scotland. Ophelia, 53:37-54.
10. Clark, C. G. 1997. Riboprinting: A tool for the study of genetic diversity in microorganisms. J. Eukaryot. Microbiol., 44:277-283.
11. Clark, C. G. & Diamond, L. S. 1991. The Laredo strain and other Entamoeba histolytica-like amebae are Entamoeba-moshkovskii. Mol. Biochem. Parasit., 46:11-18.
12. Clark, C. G. & Diamond, L. S. 1997. Intraspecific variation and phylogenetic relationships in the genus Entamoeba as revealed by riboprinting. J. Eukaryot. Microbiol., 44:142-154.
13. Coleman, D. C. 1994. The microbial loop concept as used in terrestrial soil ecology studies. Micro. Ecol., 28:245-250.
14. De Jonckheere, J. F. 1994. Comparison of partial ssurDNA sequences suggests revisions of species names in the genus Naegleria. Euro. J. Protist., 30:333-341.
15. De Jonckheere, J. F. 1995. Willaertia-Minor is a species of Naegleria - Evidence that Naegleria flagellates can divide. Euro. J. Protist., 31: 58-62.
16. Dowling, T. E., Moritz, C., Palmer, J. D. & Riesberg, L. H. 1996. Nucleic Acids III: Analysis of fragments and restriction sites. In: Hillis, D. M, Moritz, C. & Mable, B. K (ed.), Molecular Systematics. Sinauer Associates Inc., Sunderland, Massachusettes.
17. Ekelund, F. & Ronn, R. 1994. Notes on protozoa in agricultural soil with emphasis on heterotrophic flagellates and naked amebas and their ecology. FEMS Micro. Rev., 15:321-353.
18. Felsenstein, J. 1985. Confidence limits on phylogenies - An approach using the Bootstrap. Evolution, 39:783-791.
19. Finlay, B. J., Clarke, K. J., Cowling, A. J., Hindle, R. M., Rogerson, A. & Berninger, U. G. 1988. On the abundance and distribution of protozoa and their food in a productive fresh-water pond. Euro. J. Protist., 23:205-217.
20. Finlay, B. J., Black, H. I. J., Brown, S., Clarke, K. J., Esteban, G. F., Hindle, R. M., Olmo, J. L., Rollett, A. & Vickerman, K. 2000. Estimating the growth potential of the soil protozoan community. Protist, 151:69-80.
21. Foissner, W. 1999. Protist diversity: Estimates of the near-imponderable. Protist, 150:363-368.
22. Johnson, A. M., Fielke, R., Christy, P. E., Robinson, B. & Baverstock, P. R. 1990. Small subunit ribosomal-RNA evolution in the genus Acanthamoeba. J. Gen. Micro., 136:1689-1698.
23. Laybourn-Parry, J. & Rogerson, A. 1993. Seasonal patterns of protozooplankton in Lake Windermere, England. Arch. Fur Hydrobiol., 129:25-43.
24. Maidak, B. L., Cole, J. R., Lilburn, T. G., Parker, C. T., Saxman, P. R., Farris, R. J., Garrity, G. M., Olsen, G. J., Schmidt, M. & Tiedje, J. M. 2001. The RDP-II (Ribosomal Database Project). Nucl. Acids Res., 29:173-174.
25. Olsen, G. J., Matsuda, H., Hagstrom, R. & Overbeek, R. 1994. Fastdnaml - A tool for construction of phylogenetic trees of DNA sequences using Maximum-Likelihood. Comp. App. Biosci., 10:41-48.
26. Page, F. C. 1971. A comparative study of five freshwater and marine species of Thecamoebidae. Trans. Amer. Microscopy Soc., 90:157-173.
27. Page, F. C. 1979a. Two genera of marine amoebae (Gymnamoebia) with distinct surface structures: Vannella Bovee, 1965, and Pseudoparamoeba n. gen., with two new species of Vannella. Protistologica, 15:245-247.
28. Page, F. C. 1979b. Vexillifera armata n. sp (Gymnamoebia, Paramoebidae), an eustuarine amoeba with distinctive surface structures and trichocyst-like bodies. Protistologica, 15:111-122.
29. Page, F. C. 1980a. Fine-structure of some marine strains of Platyamoeba (Gymnamoebia, Thecamoebidae). Protistologica, 16:605-612.
30. Page, F. C. 1980b. A light-microscopical and electron-microscopical comparison of limax and flabellate marine amebae belonging to 4 genera. Protistologica, 16:57-78.
31. Page, F. C. 1983. Marine Gymnamoebae. Institute of Freshwater Ecology, CCAP, NERC, Cambridge.
32. Page, F. C. 1987. The classification of naked amoebae (Phylum-Rhizopoda). Arch. Fur Protist., 133:199-217.
33. Page, F. C. 1988. A New Key to Freshwater and Soil Gymnamoebae. Freshwater Biological Association, Ambleside, Cumbria, UK.
34. Page, F. C. & Blakey, S. M. 1979. Cell surface structure as a taxonomic character in the Thecamoebidae (Protozoa: Gymnamoebia). Zoo. J. Linn. Soc., 66:113-135.
35. Rogerson, A. & Gwaltney, C. 2000. High numbers of naked amoebae in the planktonic waters of a mangrove stand in southern Florida, USA. J. Eukaryot. Microbiol., 47:235-241.
36. Rogerson, A. & Laybourn-Parry, J. 1992. Bacterioplankton abundance and production in the Clyde Estuary, Scotland. Arch. Fur Hydrobiol., 126:1-14.
37. Sawyer, T. K. 1975. Clydonella n. g. (Amoebidae: Thecamoebidae), proposed to provide an appropriate generic home for Schaeffer's marine species of Rugipes, C. vivax (Schaeffer, 1926) n. comb. Trans. Amer. Microscopy Soc., 94:395-400.
38. Sawyer, T. K. 1980. Marine amoebae from clean and stressed bottom sediments of the Atlantic Ocean and Gulf of Mexico. J. Protozoology, 27:13-32.
39. Sims, G. P., Rogerson, A. & Aitken, R. 1999. Primary and secondary structure of the small-subunit ribosomal RNA of the naked, marine amoeba Vannella anglica: Phylogenetic implications. J. Mol. Evol., 48:740-749.
40. Smirnov, A. V. 2001. Diversity of Gymnamoebae (rhizopoda) in artificial cyanobacterial mats after four years in the laboratory. Ophelia, 54:223-227.
41. Stothard, D. R., Schroeder-Diedrich, J. M., Awwad, M. H., Gast, R. J., Ledee, D. R., Rodriguez-Zaragoza, S., Dean, C. L., Fuerst, P. A. & Byers, T. J. 1998. The evolutionary history of the genus Acanthamoeba and the identification of eight new 18S rRNA gene sequence types. J. Eukaryot. Microbiol., 45:45-54.
42. Swofford, D. L. 1993. PAUP: Phylogenetic analysis using parsimony. Natural History Survey, Champaign, Illinois.
43. Vargas, R. & Hattori, T. 1990. The distribution of protozoa among soil aggregates. FEMS Micro. Ecol., 74:73-77.
44. Weekers, P. H. H., Gast, R. J., Fuerst, P. A. & Byers, T. J. 1994. Sequence variations in small-subunit ribosomal-RNAs of Hartmannella vermiformis and their phylogenetic implications. Mol. Biol. Evol., 11:684-690.