Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

Molecular Ecology

Volumn 19, Issue 14, 2010, Pages 2908-2915

  Nolte, Viola ^a   Pandey, Ram Vinay ^a   Jost, Steffen ^b   Medinger, Ralph ^b,c   Ottenwälder, Birgit ^d   Boenigk, Jens ^b   Schlötterer, Christian ^a  

^a UNIVERSITY OF VETERINARY MEDICINE   (Austria)

^b ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

^c UNIVERSITY OF INNSBRUCK   (Austria)

^d Eurofins Medinet Inc   (Germany)

Author keywords

2nd generation sequencing; 454 protist diversity; species turnover; temporal sampling

Indexed keywords

FRESH WATER;

ARTICLE; AUSTRIA; BIODIVERSITY; BIOLOGY; DNA SEQUENCE; ECOSYSTEM; EUKARYOTE; GENETICS; SEASON;

AUSTRIA; BIODIVERSITY; COMPUTATIONAL BIOLOGY; ECOSYSTEM; EUKARYOTA; FRESH WATER; SEASONS; SEQUENCE ANALYSIS, DNA;

PROTISTA;

EID: 77954557093     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04669.x     Document Type: Article

References (40)

1. Adl SM, Simpson AG, Farmer MA et al. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology, 52, 399 451.
2. Aguilera A, Zettler E, Gomez F et al. (2007) Distribution and seasonal variability in the benthic eukaryotic community of Rio Tinto (SW, Spain), an acidic, high metal extreme environment. Systematic and Applied Microbiology, 30, 531 546.
3. Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM (2009) A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE, 4, e6372.
4. Andersen RA, Van de Peer Y, Potter D et al. (1999) Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae. Protist, 150, 71 84.
5. Araújo MFF, Godinho MJL (2008) Spatial and seasonal variations of planktonic protists (Mastigophora, Sarcodina and Ciliophora) in a river-lacustrine system in northeast Brazil. Acta Limnologica Brasiliensia, 20, 235 244.
6. Auinger BM, Pfandl K, Boenigk J (2008) Improved methodology for identification of protists and microalgae from plankton samples preserved in Lugol's iodine solution: combining microscopic analysis with single-cell PCR. Applied and Environmental Microbiology, 74, 2505 2510.
7. Baas-Becking LGM (1934) Geobiologie of inleiding tot de milieukunde. W.P. Van Stockum & Zoon
8. Beijerinck MW (1913) De infusies en de ontdekking der bakteriën. In : Jaarboek van de Koninklijke Aakademie voor Weten-schappen, pp. 1 28.
9. 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. Environmental Microbiology, 7, 685 697.
10. Boenigk J, Pfandl K, Garstecki T, Novarino G, Chatzinotas A (2006) Evidence for geographic isolation and signs of endemism within a protistan morphospecies. Applied Environmental Microbiology, 72, 5159 5164.
11. Boenigk J, Jost S, Stoeck T, Garstecki T (2007) Differential thermal adaptation of clonal strains of a protist morphospecies originating from different climatic zones. Environmental Microbiology, 9, 593 602.
12. Burki F, Inagaki Y, Bråte J et al. (2009) Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Genome Biology and Evolution, 2009, 231 238.
13. Cavalier-Smith T (1998) A revised six-kingdom system of life. Biological Reviews of Cambridge Philosophical Society, 73, 203 266.
14. Cermeno P, Falkowski PG (2009) Controls on diatom biogeography in the ocean. Science, 325, 1539 1541.
15. Corliss JO (1999) Biodiversity, classification, and numbers of species of protists. In : Nature and Human Society: The Quest for a Sustainable Worl (eds Raven PH, Williams T). pp. 130 155, National Academy Press
16. Darling KF, Wade CM, Stewart IA et al. (2000) Molecular evidence for genetic mixing of Arctic and Antarctic subpolar populations of planktonic foraminifers. Nature, 405, 43 47.
17. Diez B, Pedros-Alio C, Massana R (2001) Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Applied and Environmental Microbiology, 67, 2932 2941.
18. Finlay BJ (2001) Protozoa. In : Encyclopedia of Biodiversit (ed Levin SA). pp. 901 915, Academic Press
19. Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science, 296, 1061 1063.
20. Finlay BJ, Clarke KJ (1999) Apparent global ubiquity of species in the protist genus Paraphysomonas. Protist, 150, 419 430.
21. Foissner W (2007) Protist diversity and distribution: some basic considerations. Biodiversity and Conservation, 17, 235 242.
22. Green JL, Holmes AJ, Westoby M et al. (2004) Spatial scaling of microbial eukaryote diversity. Nature, 432, 747 750.
23. Lefranc M, Thenot A, Lepere C, Debroas D (2005) Genetic diversity of small eukaryotes in lakes differing by their trophic status. Applied and Environmental Microbiology, 71, 5935 5942.
24. Lopez-Garcia P, Rodriguez-Valera F, Pedros-Alio C, Moreira D (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature, 409, 603 607.
25. Massana R, Balague V, Guillou L, Pedros-Alio C (2004) Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches. FEMS Microbiology and Ecology, 50, 231 243.
26. Medinger R, Nolte V, Pandey RV, Jost S, Ottenwälder B, Schlötterer C, Boenigk J (2010) Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Molecular Ecology, 19, s1, 32 40.
27. Moon-van der Staay SY, De Wachter R, Vaulot D (2001) Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature, 409, 607 610.
28. Pandey RV, Nolte V, Schlötterer C (2010) CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. BMC Research Notes, 3, 3.
29. Pither J (2007) Comment on "Dispersal limitations matter for microbial morphospecies". Science, 316, 1124. Author reply 1124.
30. Preisig HR, Vørs N, Hällfors G (1991) Diversity of heterotrophic heterokont flagellates. In : The Biology of Free-Living Heterotrophic Flagellate (eds Patterson DJ, Larsen J). pp. 361 399, Clarendon Press
31. Qiu X, Wu L, Huang H et al. (2001) Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Applied and Environmental Microbiology, 67, 880 887.
32. Rynearson TA, Armbrust EV (2005) Maintenance of clonal diversity during a spring bloom of the centric diatom Ditylum brightwellii. Molecular Ecology, 14, 1631 1640.
33. Rynearson TA, Newton JA, Armbrust VE (2006) Spring bloom development, genetic variation, and population succession in the planktonic diatom Ditylum brightwellii. Limnology and Oceanography, 51, 1249 1261.
34. Slapeta J, Moreira D, Lopez-Garcia P (2005) The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes. Proceedings of the Royal Society of London, Series B: Biological Sciences, 272, 2073 2081.
35. Sogin ML, Morrison HG, Huber JA et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences, USA, 103, 12115 12120.
36. Stoeck T, Hayward B, Taylor GT, Varela R, Epstein SS (2006) A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist, 157, 31 43.
37. Stoeck T, Bruemmer F, Foissner W (2007) Evidence for local ciliate endemism in an alpine anoxic lake. Microbial Ecology, 54, 478 486.
38. Stoeck T, Behnke A, Christen R et al. (2009) Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biology, 7, 72.
39. Tamigneaux E, Mingelbier M, Klein B, Legendre L (1997) Grazing by protists and seasonal changes in the size structure of protozooplankton and phytoplankton in a temperate nearshore environment (western Gulf of St. Lawrence, Canada). Marine Ecology Progress Series, 146, 231 247.
40. Telford RJ, Vandvik V, Birks HJ (2006) Dispersal limitations matter for microbial morphospecies. Science, 312, 1015.