Composition of groundwater nanoprotist communities in different aquifers based on aliquot cultivation and genotype assessment of cercomonads

Fundamental and Applied Limnology

Volumn 174, Issue 3, 2009, Pages 261-269

  Loquay, Nina ^a   Wylezich, Claudia ^a,b   Arndt, Hartmut ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

^b LEIBNIZ INSTITUTE FOR BALTIC SEA RESEARCH   (Germany)

Author keywords

Cercomonas; D3 d5 domain of lsu rrna; Diversity; Groundwater; Heterotrophic flagellates; Nanofauna; Pollution; Protozoa

Indexed keywords

ABUNDANCE; AQUIFER; CHLORIDE; CILIATE; CONCENTRATION (COMPOSITION); CULTIVATION; FLAGELLATE; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GENOTYPE; GROUNDWATER POLLUTION; HABITAT TYPE; NITRATE; PARAMETERIZATION; TAXONOMY;

ALPS; COLOGNE; EIFEL; GERMANY; NORTH RHINE-WESTPHALIA; RHINELAND-PALATINATE;

AMOEBA (GENUS); BICOSOECIDA; CENTROHELIOZOA; CERCOMONADIDA; CERCOMONAS; CILIOPHORA; EUGLENIDA; HELIOZOA; MASTIGOPHORA (FLAGELLATES); PROTISTA; PROTOZOA;

EID: 77954601792     PISSN: 18639135     EISSN: None     Source Type: Journal    
DOI: 10.1127/1863-9135/2009/0174-0261     Document Type: Article

References (34)

1. Altschul, S. F., Madden, T. L., Schaeffer, A. A., Zhang, J., Zhang, Z., Miller, M. & Lipman, D. J., 1997: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. - Nucleic Acids Res. 25: 3389-3402.
2. Arndt, H., Dietrich, D., Auer, B., Cleven, E.-J., Gräfenhahn, T., Weitere, M., & Mylnikov, A. P., 2000: Functional diversity of heterotrophic flagellates in aquatic ecosystems. - In: Leadbeater, B. S. C. & Green, J. C. (eds): The Flagellates. -Taylor & Francis, London.
3. Atkins, M., Teske, A. & Anderson, O., 2000: A survey of flagellate diversity at four deep-sea hydrothermal vents in the Eastern Pacific Ocean using structural and molecular approaches. - J. Eukaryot. Microbiol. 47: 400-411.
4. Azam, F., Fenchel, T., Field, J. G., Meyer-Reil, L.-A. & Thingtad, F., 1983: The ecological role of water-column microbes in the sea. - Mar. Ecol. Prog. Ser. 10: 257-263.
5. Bass, D. & Cavalier-Smith, T., 2004: Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). - Internat. J. Syst. Evol. Microbiol. 54: 2393-2404.
6. Boenigk, J., Pfandl, K., Stadler, P. & Chatzinotas, A., 2005: High diversity of the 'Spumella-like' flagellates: an investigation based on the SSU rRNA gene sequences of isolates from habitats located in six different geographic regions. Environ. Microbiol. 7: 685-697.
7. Butler, H. & Rogerson, M., 1995: Temporal and spatial abundance of naked amoebae (Gymnamoebae) in marine benthic sediments of the Clyde Sea area, Scotland. - J. Eukaryot. Microbiol. 42: 724-730. (Pubitemid 3017815)
8. Cavalier-Smith, T., 1998: A revised six-kingdom system of life. - Biol. Rev. Philos. Soc. 73: 203-266.
9. Cavalier-Smith, T. & Chao, E. E.-Y., 2003: Phylogeny and classification of phylum Cercozoa (Protozoa). - Protistology 154: 341-358. (Pubitemid 37425136)
10. Clark, C. G., 1992: DNA purification from polysaccharide rich cells. - In: Lee, J. J. & Soldo, A. T. (eds): Protocols in protozoology, Vol. 1. - Allen Press, Lawrence, Kansas, pp. D-3.1-2.
11. Ekelund, F., Daugbjerg, N. & Fredslund, L., 2004: Phylogeny of Heteromita, Cercomonas, Thaumatomonas based on SSU rDNA sequences, including the description of Neocercomonas jutlandica sp. nov., gen. nov. - Eur. J. Protistol. 40: 119-135.
12. Felsenstein, J., 1985: Confidence limits on phytogenies: an approach using the bootstrap. - Evolution 39: 783-791.
13. - 1989: PHYLIP - Phylogeny Inference Package (Version 3.2). -Cladistics 5: 164-166.
14. Fenchel, T., 1987: Ecology of Protozoa. The Biology of Freeliving Phagotrophic Protists. - Springer-Verlag, Berlin.
15. Finlay, B. J., 2002: Global dispersal of free living microbial eukaryote species. - Science 296: 1061-1063.
16. Garstecki, T. & Arndt, H., 2000: Seasonal abundances and community structure of benthic rhizopods in shallow lagoons of the southern Baltic Sea. - Eur. J. Protistol. 36: 103-115.
17. Gibert, J., Stanford, J. A., Dole-Olivier, M. J. & Ward, J. V., 1994: Basic attributes of groundwater ecosystems and prospects for research. - In: Gibert, J., Danielopol, D. L. & Stanford, J. A. (eds): Groundwater ecology. - Academic Press, San Diego, pp. 8-42.
18. Griebler, C. & Mößlacher, F. 2003: Grundwasserö kologie. UTB-Facultas Verlag, Wien.
19. Guillard, R. & Lorenzen, C., 1972: Yellow-green algae with chlorophyllide. - C. J. Phycol. 8: 10-14.
20. Hasegawa, M., Kishino, H. & Yano, T., 1985: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. - J. Mol. Evol. 22: 160-174.
21. Karpov, S. A., Bass, D., Mylnikov, A. P. & Cavalier-Smith, T., 2006: Molecular phytogeny of Cercomonadidae and kinetid patterns of Cercomonas and Eocercomonas gen. nov, (Cercomonadida, Cercozoa). - Protistology 157: 125-158.
22. Kimura, M., 1980: A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. - J. Mol. Evol. 16: 111-120.
23. Markmann, M. & Tautz, D., 2005: An approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. - Philos. Trans. R. Soc. Lond. B.360: 1917-1924.
24. Massana, R., Terrado, R., Forn, I., Lovejoy, C. & Pedrós-Alió, C., 2006: Distribution and abundance of uncultured heterotrophic flagellates in the world oceans. - Environ. Microbiol. 8: 1515-1522.
25. Novarino, G., Warren, A., Buttler, H., Lambourne, G., Boxshall, A., Batemen, J., Kinner, N. E., Harvey, R. W., Mosse, R. A. & Teltsch, B., 1997: Protistan communities in aquifers: a review. - FEMS Microbiol. Rev. 20: 261-275.
26. Patterson, D. J., 1993: The current status of the free-living heterotrophic flagellates. - J. Eukaryot. Microbiol. 40: 606-609.
27. Scheckenbach, F., Wylezich, C., Weitere, M., Hausmann, K. & Arndt, H., 2005: Molecular identity of strains heterotrophic flagellates isolated from surface waters and deep-sea sediment of the South Atlantic based on SSU rDNA. - Aquat. Microb. Ecol. 38: 239-247.
28. Scheckenbach, F., Wylezich, C., Weitere, M., Mylnikov, A. P. & Arndt, H., 2006: Molecular comparisons of freshwater and marine isolates of the same morphospecies of heterotrophic flagellates. -Appl. Environ. Microbiol. 72: 6638-6643.
29. Schmidt, H. A., Strimmer, K., Vingron, M. & von Haeseler, A., 2002: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. - Bioinformatics 18: 502-504. (Pubitemid 34284960)
30. th ed. - Prentice Hall, New Jersey.
31. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G., 1997: The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. - Nucleic Acids Res. 24: 4876-4882. (Pubitemid 28022245)
32. Vejdovsky, F., 1882: Tierische Organismen der Brunnengewässer von Prag - Selbstverlag, Prague.
33. Wylezich, C., Mylnikov, A. F., Weitere, M. & Arndt, H., 2007: Distribution and phylogenetic relationships of freshwater thaumatomonads with a description of the new species Thaumatomonas coloniensis n. sp. - J. Eukaryot. Microbiol. 54: 347-357.
34. Zarda, B., Mattison, G., Hess, A., Hahn, D., Höhener, P. & Zeyer, J., 1998: Analyses of bacterial and protozoan communities in an aquifer contaminated with monoaromatic hydrocarbons. - FEMS Microbiol. Ecol. 27: 141-152.