1887

Abstract

The majority of environmental micro-organisms identified with the rRNA approach have never been visualized. Thus, their reliable classification and taxonomic assignment is often difficult or even impossible. In our preliminary 18S rRNA gene sequencing work from the world’s largest anoxic marine environment, the Cariaco Basin (Caribbean Sea, Venezuela), we detected a ciliate clade, designated previously as CAR_H [Stoeck, S., Taylor, G. T. & Epstein, S. S. (2003). , 5656–5663]. Here, we combine the traditional rRNA detection method of fluorescent hybridization (FISH) with scanning electron microscopy (SEM) and confirm the phylogenetic separation of the CAR_H sequences from all other ciliate classes by showing an outstanding morphological feature of this group: a unique, archway-shaped kinety surrounding the oral apparatus and extending to the posterior body end in CAR_H cells. Based on this specific feature and the molecular phylogenies, we propose a novel ciliate class, Cariacotrichea nov. cl.

Funding
This study was supported by the:
  • NSF (Award OCE 03-26175, MCB-0348407, DEB-0816840 and MCB-0348341)
  • Austrian Science Foundation (Award P-20360-B17)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.034710-0
2012-06-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/6/1425.html?itemId=/content/journal/ijsem/10.1099/ijs.0.034710-0&mimeType=html&fmt=ahah

References

  1. Abramoff M. D., Magelhaes P. J., Ram S. J. 2004; Image processing with ImageJ. Biophotonics International 11:36–42
    [Google Scholar]
  2. Alexander E., Stock A., Breiner H. W., Behnke A., Bunge J., Yakimov M. M., Stoeck T. 2009; Microbial eukaryotes in the hypersaline anoxic L’Atalante deep-sea basin. Environ Microbiol 11:360–381 [View Article][PubMed]
    [Google Scholar]
  3. Behrens S., Rühland C., Inácio J., Huber H., Fonseca A., Spencer-Martins I., Fuchs B. M., Amann R. 2003; In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl Environ Microbiol 69:1748–1758 [View Article][PubMed]
    [Google Scholar]
  4. Edgcomb V. P., Kysela D. T., Teske A., de Vera Gomez A., Sogin M. L. 2002; Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc Natl Acad Sci U S A 99:7658–7662 [View Article][PubMed]
    [Google Scholar]
  5. Edgcomb V., Orsi W., Bunge J., Jeon S. O., Christen R., Leslin C., Holder M., Taylor G. T., Suarez P. other authors 2011a; Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness. ISME J 5:1344–1356 [View Article][PubMed]
    [Google Scholar]
  6. Edgcomb V., Orsi W., Taylor G. T., Vdacny P., Taylor C. T., Suarez P., Epstein S. 2011b; Accessing marine protists from the anoxic Cariaco Basin. ISME J 5:1237–1241 [View Article][PubMed]
    [Google Scholar]
  7. Epstein S., Lopez-Garcia P. 2008; “Missing” protists: a molecular prospective. Biodivers Conserv 17:261–276 [View Article]
    [Google Scholar]
  8. Fan X., Miao M., Al-Rasheid K. A. S., Song W. 2009; A new genus of marine scuticociliate (Protozoa, Ciliophora) from northern China, with a brief note on its phylogenetic position inferred from small subunit ribosomal DNA sequence data. J Eukaryot Microbiol 56:577–582 [View Article][PubMed]
    [Google Scholar]
  9. Finlay B. J., Corliss J. O., Esteban G., Fenchel T. 1996; Biodiversity at the microbial level: the number of free-living ciliates in the biosphere. Q Rev Biol 71:221–237 [View Article]
    [Google Scholar]
  10. Foissner W. 1991; Basic light and scanning electron microscopic methods for taxonomic studies of ciliated protozoa. Eur J Protistol 27:313–330 [View Article]
    [Google Scholar]
  11. Foissner W. 2003; Deciliation of ciliated protozoa for scanning electron microscopy: a fast, simple method using tensides.. In Abstracts of the 4th European Congress of Protistology and 10th European Conference on Ciliate Biology, 31 August–5 September 2003, San Benedetto del Tronto (AP), Italy, p. 133
    [Google Scholar]
  12. Foissner W., Agatha S., Berger H. 2002; Soil ciliates (Protozoa, Ciliophora) from Namibia (Southwest Africa), with emphasis on two contrasting environments, the Etosha region and the Namib Desert. Denisia 5:1–1459
    [Google Scholar]
  13. Foissner W., Chao A., Katz L. A. 2008; Diversity and geographic distribution of ciliates (Protista: Ciliophora). Biodivers Conserv 17:345–363 [View Article]
    [Google Scholar]
  14. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. other authors 2004; arb: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  15. Lynn D. H. 2008 The Ciliated Protozoa: Characterization, Classification, and Guide to the Literature, 3rd edn. New York: Springer;
    [Google Scholar]
  16. Muller-Karger F. E., Varela R., Thunell R., Scranton M., Bohrer R., Taylor G. T., Capelo J., Astor Y., Tappa E. other authors 2001; Annual cycle of primary production in the Cariaco Basin: Response to upwelling and implications for vertical export. Geophys Res 106:C34527–4542 [View Article]
    [Google Scholar]
  17. Orsi W., Edgcomb V., Jeon S. O., Leslin C., Bunge J., Taylor G. T., Varela R., Epstein S. 2011; Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization. ISME J 5:1357–1373 [View Article][PubMed]
    [Google Scholar]
  18. Posada D., Crandall K. A. 1998; modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818 [View Article][PubMed]
    [Google Scholar]
  19. Ronquist F., Huelsenbeck J. P. 2003; MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574 [View Article][PubMed]
    [Google Scholar]
  20. Song W., Warren A., Hu X. (editors) 2009 Free-living Ciliates in the Bohai and Yellow Seas, China Beijing: Science Press;
    [Google Scholar]
  21. Stamatakis A., Hoover P., Rougemont J. 2008; A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57:758–771 [View Article][PubMed]
    [Google Scholar]
  22. Stoeck T., Fowle W. H., Epstein S. S. 2003a; Methodology of protistan discovery: from rRNA detection to quality scanning electron microscope images. Appl Environ Microbiol 69:6856–6863 [View Article][PubMed]
    [Google Scholar]
  23. Stoeck T., Taylor G. T., Epstein S. S. 2003b; Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea). Appl Environ Microbiol 69:5656–5663 [View Article][PubMed]
    [Google Scholar]
  24. Stoeck T., Hayward B., Taylor G. T., Varela R., Epstein S. S. 2006; A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157:31–43 [View Article][PubMed]
    [Google Scholar]
  25. Taylor C. D., Doherty K. W. 1990; Submersible Incubation Device (SID), autonomous instrumentation for the in situ measurement of primary production and other microbial rate processes. Deep-Sea Res 37:343–358 [View Article]
    [Google Scholar]
  26. Taylor C. D., Howes B. L., Doherty K. W. 1993; Automated instrumentation for time-series measurements of primary production and nutrient status in production platform-accessible environments. Mar Technol Soc J 27:32–44
    [Google Scholar]
  27. Taylor G. T., Iabichella M., Ho T.-Y., Scranton M. I., Thunell R. C., Muller-Karger F., Varela R. 2001; Chemoautotrophy in the redox transition zone of the Cariaco Basin: A significant midwater source of organic carbon production. Limnol Oceanogr 46:148–163 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.034710-0
Loading
/content/journal/ijsem/10.1099/ijs.0.034710-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error