An SSU rDNA barcoding approach to the diversity of marine interstitial cercozoans, including descriptions of four novel genera and nine novel species Free

Abstract

Environmental DNA surveys have revealed a great deal of hidden diversity within the Cercozoa. An investigation into the biodiversity of heterotrophic flagellates in marine benthic habitats of British Columbia, Canada, demonstrated the presence of several undescribed taxa with morphological features that resemble the cercozoan genera and . Nine novel species of marine interstitial cercozoans are described that are distributed into five genera, four of which are new. Phylogenetic analyses of small subunit rDNA sequences derived from two uncultured isolates of and nine novel cercozoan species (within four novel genera) provided organismal anchors that helped establish the cellular identities of several different environmental sequence clades. These data, however, also showed that the rarity of distinctive morphological features in cryomonads, and other groups of cercozoans, makes the identification and systematics of the group very difficult. Therefore, a DNA barcoding approach was applied as a diagnostic tool for species delimitation that used a 618 bp region at the 5′ end of the SSU rDNA sequence. Nucleotide sequence analysis of this region showed high intergeneric sequence divergences of about 7 % and very low intraspecific sequence divergences of 0–0.5 %; phylogenetic analyses inferred from this barcoding region showed very similar tree topologies to those inferred from the full-length sequence of the gene. Overall, this study indicated that the 618 bp barcoding region of SSU rDNA sequences is a useful molecular signature for understanding the biodiversity and interrelationships of marine benthic cercozoans.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.013888-0
2010-08-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/8/1962.html?itemId=/content/journal/ijsem/10.1099/ijs.0.013888-0&mimeType=html&fmt=ahah

References

  1. Al Qassab S., Lee W. J., Murray S., Patterson D. J. 2002; Flagellates from stromatolites and surrounding sediments in Shark Bay, Western Australia. Acta Protozool 41:91–144
    [Google Scholar]
  2. Auer B., Arndt H. 2001; Taxonomic composition and biomass of heterotrophic flagellates in relation to lake trophy and season. Freshw Biol 46:959–972 [CrossRef]
    [Google Scholar]
  3. Barth D., Krenek S., Fokin S. I., Berendonk T. U. 2006; Intraspecific genetic variation in Paramecium revealed by mitochondrial cytochrome c oxidase I sequences. J Eukaryot Microbiol 53:20–25 [CrossRef]
    [Google Scholar]
  4. Bass D., Cavalier-Smith T. 2004; Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). Int J Syst Evol Microbiol 54:2393–2404 [CrossRef]
    [Google Scholar]
  5. Berney C., Fahrni J., Pawlowski J. 2004; How many novel eukaryotic ‘kingdoms’? Pitfalls and limitations of environmental DNA surveys. BMC Biol 2: 13 [CrossRef]
    [Google Scholar]
  6. Cavalier-Smith T. 1998a; A revised six-kingdom system of life. Biol Rev Camb Philos Soc 73:203–266 [CrossRef]
    [Google Scholar]
  7. Cavalier-Smith T. 1998b; Neomonada and the origin of animals and fungi . In Evolutionary Relationships Among Protozoa pp 375–407 Edited by Coombs G. H., Vickerman K., Sleigh M. A., Warren A. London: Kluwer Academic Publishers;
    [Google Scholar]
  8. Cavalier-Smith T., Chao E. E. 2003; Phylogeny and classification of Phylum Cercozoa (Protozoa). Protist 154:341–358 [CrossRef]
    [Google Scholar]
  9. Chantangsi C., Lynn D. H., Brandl M. T., Cole J. C., Hetrick N., Ikonomi P. 2007; Barcoding ciliates: a comprehensive study of 75 isolates of genus Tetrahymena . Int J Syst Evol Microbiol 57:2412–2425 [CrossRef]
    [Google Scholar]
  10. Chantangsi C., Esson H. J., Leander B. S. 2008; Morphology and molecular phylogeny of a marine interstitial tetraflagellate with putative endosymbionts: Auranticordis quadriverberis n. gen. et sp. (Cercozoa). BMC Microbiol 8: 123 [CrossRef]
    [Google Scholar]
  11. Cummings D. J. 1992; Mitochondrial genomes of the ciliates. Int Rev Cytol 141:1–64
    [Google Scholar]
  12. Drebes G., Kühn S. F., Gmelch A., Schnepf E. 1996; Cryothecomonas aestivalis sp. nov., a colourless nanoflagellate feeding on the marine centric diatom Guinardia delicatula (Cleve) Hasle. Helgol Meeresunters 50:497–515 [CrossRef]
    [Google Scholar]
  13. Ekelund F., Patterson D. J. 1997; Some heterotrophic flagellates from a cultivated garden soil in Australia. Arch Protistenkd 148:461–478 [CrossRef]
    [Google Scholar]
  14. Fenchel T. 1987 Ecology of Protozoa: the Biology of Free-Living Phagotrophic Protists Berlin: Springer-Verlag;
    [Google Scholar]
  15. Godfray H. C. J. 2002; Challenges for taxonomy. Nature 417:17–19 [CrossRef]
    [Google Scholar]
  16. Guindon S., Gascuel O. 2003; PhyML - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704 [CrossRef]
    [Google Scholar]
  17. Hargraves P. E. 2002; The ebridian flagellates Ebria and Hermesinum . Plankton Biol Ecol 49:9–16
    [Google Scholar]
  18. Hebert P. D. N., Ratnasingham S., deWaard J. R. 2003a; Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci 270 (Suppl. 1):S96–S99 [CrossRef]
    [Google Scholar]
  19. Hebert P. D. N., Cywinska A., Ball S. L., deWaard J. R. 2003b; Biological identifications through DNA barcodes. Proc Biol Sci 270:313–322 [CrossRef]
    [Google Scholar]
  20. Hondeveld B. J. M., Bak R. P. M., van Duyl F. C. 1992; Bacterivory by heterotrophic nanoflagellates in marine sediments measured by uptake of fluorescently labeled bacteria. Mar Ecol Prog Ser 89:63–71 [CrossRef]
    [Google Scholar]
  21. Hoppenrath M., Leander B. S. 2006a; Dinoflagellate, euglenid or cercomonad? The ultrastructure and molecular phylogenetic position of Protaspis grandis n. sp. J Eukaryot Microbiol 53:327–342 [CrossRef]
    [Google Scholar]
  22. Hoppenrath M., Leander B. S. 2006b; Ebriid phylogeny and the expansion of the Cercozoa. Protist 157:279–290 [CrossRef]
    [Google Scholar]
  23. Huelsenbeck J. P., Ronquist F. 2001; mrbayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755 [CrossRef]
    [Google Scholar]
  24. Kimura M. 1980; A simple method of estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [CrossRef]
    [Google Scholar]
  25. Kühn S. F., Lange M., Medlin L. K. 2000; Phylogenetic position of Cryothecomonas inferred from nuclear-encoded small subunit ribosomal RNA. Protist 151:337–345 [CrossRef]
    [Google Scholar]
  26. Larsen J., Patterson D. J. 1990; Some flagellates (Protista) from tropical marine sediments. J Nat Hist 24:801–937 [CrossRef]
    [Google Scholar]
  27. Lee W. J. 2008; Free-living heterotrophic euglenids from marine sediments of the Gippsland Basin, southeastern Australia. Mar Biol Res 4:333–349 [CrossRef]
    [Google Scholar]
  28. Lee W. J., Patterson D. J. 2000; Heterotrophic flagellates (Protista) from marine sediments of Botany Bay, Australia. J Nat Hist 34:483–562 [CrossRef]
    [Google Scholar]
  29. Lee W. J., Brandt S. M., Vørs N., Patterson D. J. 2003; Darwin's heterotrophic flagellates. Ophelia 57:63–98 [CrossRef]
    [Google Scholar]
  30. Lee W. J., Simpson A. G. B., Patterson D. J. 2005; Free-living heterotrophic flagellates from freshwater sites in Tasmania (Australia), a field survey. Acta Protozool 44:321–350
    [Google Scholar]
  31. Long E. O., David I. B. 1980; Repeated genes in eukaryotes. Annu Rev Biochem 49:727–764 [CrossRef]
    [Google Scholar]
  32. Lynn D. H., Strüder-Kypke M. C. 2006; Species of Tetrahymena identical by small subunit rRNA gene sequences are discriminated by mitochondrial cytochrome c oxidase I gene sequences. J Eukaryot Microbiol 53:385–387 [CrossRef]
    [Google Scholar]
  33. Marande W., Burger G. 2007; Mitochondrial DNA as a genomic jigsaw puzzle. Science 318: 415 [CrossRef]
    [Google Scholar]
  34. Massana R., Pedrós-Alió C. 2008; Unveiling new microbial eukaryotes in the surface ocean. Curr Opin Microbiol 11:213–218 [CrossRef]
    [Google Scholar]
  35. Minelli A. 1993 Biological Systematics: The State of the Art London: Chapman & Hall;
    [Google Scholar]
  36. Myl'nikov A. P., Karpov S. A. 2004; Review of diversity and taxonomy of cercomonads. Protistology 3:201–217
    [Google Scholar]
  37. Norman J. E., Gray M. W. 1997; The cytochrome oxidase subunit 1 gene ( cox1 ) from the dinoflagellate, Crypthecodinium cohnii . FEBS Lett 413:333–338 [CrossRef]
    [Google Scholar]
  38. Park S. J., Park B. J., Pham V. H., Yoon D. N., Kim S. K., Rhee S. K. 2008; Microeukaryotic diversity in marine environments, an analysis of surface layer sediments from the East Sea. J Microbiol 46:244–249 [CrossRef]
    [Google Scholar]
  39. Ronquist F., Huelsenbeck J. P. 2003; mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574 [CrossRef]
    [Google Scholar]
  40. Saunders G. W. 2005; Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philos Trans R Soc Lond B Biol Sci 360:1879–1888 [CrossRef]
    [Google Scholar]
  41. Schnepf E., Kühn S. F. 2000; Food uptake and fine structure of Cryothecomonas longipes sp. nov., a marine nanoflagellate incertae sedis feeding phagotrophically on large diatoms. Helgol Mar Res 54:18–32 [CrossRef]
    [Google Scholar]
  42. Scicluna S. M., Tawari B., Clark C. G. 2006; DNA barcoding of Blastocystis . Protist 157:77–85 [CrossRef]
    [Google Scholar]
  43. Skuja H. 1939; Beitrag zur Algenflora Lettlands II. Acta Horti Bot Univ Latviensis 11/12:41–169
    [Google Scholar]
  44. Šlapeta J., Moreira D., López-García P. 2005; The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes. Proc Biol Sci 272:2073–2081 [CrossRef]
    [Google Scholar]
  45. Sogin M. L., Swanton M. T., Gunderson J. H., Elwood H. J. 1986; Sequence of the small subunit ribosomal RNA gene from the hypotrichous ciliate Euplotes aediculatus . J Protozool 33:26–29 [CrossRef]
    [Google Scholar]
  46. Stoeck T., Epstein S. 2003; Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl Environ Microbiol 69:2657–2663 [CrossRef]
    [Google Scholar]
  47. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [CrossRef]
    [Google Scholar]
  48. Tautz D., Arctander P., Minelli A., Thomas R. H., Vogler A. P. 2002; DNA points the way ahead in taxonomy. Nature 418: 479
    [Google Scholar]
  49. Tautz D., Arctander P., Minelli A., Thomas R. H., Vogler A. P. 2003; A plea for DNA taxonomy. Trends Ecol Evol 18:70–74 [CrossRef]
    [Google Scholar]
  50. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
  51. Thomsen H. A., Buck K. R., Bolt P. A., Garrison D. L. 1991; Fine structure and biology of Cryothecomonas gen. nov. (Protista incertae sedis ) from the ice biota. Can J Zool 69:1048–1070 [CrossRef]
    [Google Scholar]
  52. Uhlig G. 1964; Eine einfache methode zur extraktion der vagilen, mesopsammalen Mikrofauna. Helgol Wiss Meeresunters 11:178–185 [CrossRef]
    [Google Scholar]
  53. Vørs N. 1993; Heterotrophic amoebae, flagellates and heliozoa, from Arctic marine waters (North West Territories. Canada and West Greenland). Polar Biol 13:113–126
    [Google Scholar]
  54. Weisse T. 2008; Distribution and diversity of aquatic protists: an evolutionary and ecological perspective. Biodivers Conserv 17:243–259 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.013888-0
Loading
/content/journal/ijsem/10.1099/ijs.0.013888-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed