Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column

Applied and Environmental Microbiology

Volumn 72, Issue 10, 2006, Pages 6578-6583

  Jeon, S O ^a,d   Bunge, J ^b   Stoeck, T ^c   Barger, K J A ^b   Hong, S H ^a,d   Epstein, S S ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

^b Department of Obstetrics Gynecology   (United States)

^c Rheinland Pfälzische Technische Universität Kaiserslautern Landau   (Germany)

^d Kangwon National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOLOGY; DATA ACQUISITION; GENES; MATHEMATICAL MODELS; RNA; STATISTICAL METHODS;

ANOXIC WATER COLUMN; MICROBIAL EUKARYOTES; OPERATIONAL TAXONOMIC UNITS (OTU);

MICROBIOLOGY;

RNA 18S;

ANOXIC CONDITIONS; PROTIST; SPECIES DIVERSITY; SPECIES RICHNESS; STATISTICAL ANALYSIS; WATER COLUMN;

ARTICLE; BIODIVERSITY; EUKARYOTE; GENE LIBRARY; GENE SEQUENCE; MICROBIAL POPULATION DYNAMICS; MICROFLORA; MOLECULAR CLONING; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; NONPARAMETRIC TEST; NUCLEOTIDE SEQUENCE; QUALITATIVE ANALYSIS; SAMPLING; SAMPLING ERROR; STATISTICAL ANALYSIS; TAXONOMY; WATER SAMPLING;

ANAEROBIOSIS; ECOSYSTEM; EUKARYOTIC CELLS; OXYGEN; RNA, RIBOSOMAL, 18S; SEAWATER;

ATLANTIC OCEAN; CARIACO BASIN; CARIBBEAN SEA;

EUKARYOTA; OTUS; PROTISTA;

EID: 33750071107     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00787-06     Document Type: Article

References (40)

1. Amaral Zettler, L. A., F. Gomez, E. Zettler, B. G. Keenan, R. Amils, and M. L. Sogin. 2002. Microbiology: eukaryotic diversity in Spain's River of Fire. Nature 417:137.
2. Baldauf, S. L. 2003. The deep roots of eukaryotes. Science 300:1703-1706.
3. Barger, K. J.-A. 2006. Mixtures of exponential distributions to describe the distribution of Poisson means in estimating the number of unobserved classes. M.S. thesis. Cornell University, Ithaca, N.Y. [Online.] http://hdl.handle.net/1813/2953.
4. 2S gradient in a supersulfidic anoxic fjord (Framvaren, Norway). Appl. Environ. Microbiol. 72:3626-3636.
5. Bunge, J., M. Fitzpatrick, and J. Handley. 1995. Comparison of 3 estimators of the number of species. J. Appl. Stat. 22:45-59.
6. Burnham, K. P., and D. R. Anderson. 1998. Model selection and inference: a practical information-theoretic approach. Springer-Verlag Inc., New York, N.Y.
7. Caron, D. A., P. D. Countway, and M. V. Brown. 2004. The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools. J. Eukaryot. Microbiol. 51:38-48.
8. Chao, A., and J. Bunge. 2002. Estimating the number of species in a stochastic abundance model. Biometrics 58:531-539.
9. Chao, A., and S.-M. Lee. 1992. Estimating the number of classes via sample coverage. J. Am. Stat. Assoc. 87:210-217.
10. Coleman, A. W. 2002. Microbial eukaryote species. Science 297:337.
11. Colwell, R. K. 2005, posting date. Estimates: statistical estimation of species richness and shared species from samples, version 7.5. [Online.] http://purl.oclc.org/estimates.
12. Countway, P. D., R. J. Gast, P. Savai, and D. A. Caron. 2005. Protistan diversity estimates based on 18S rDNA from seawater incubations in the Western North Atlantic. J. Eukaryot. Microbiol. 52:95-106.
13. Edgcomb, V. P., D. T. Kysela, A. Teske, A. de Vera Gomez, and M. L. Sogin. 2002. Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc. Natl. Acad. Sci. USA 99:7658-7662.
14. Feldmann, A., and W. Whitt. 1998. Fitting mixtures of exponentials to long-tail distributions to analyze network performance models. Perform. Eval. 31:245-279.
15. Finlay, B. J., and T. Fenchel. 1999. Divergent perspectives on protist species richness. Protist 150:229-233.
16. Foissner, W. 1999. Protist diversity: estimates of the near-imponderable. Protist 150:363-368.
17. Hong, S.-H., J. Bunge, S.-O. Jeon, and S. Epstein. 2006. Predicting microbial species richness. Proc. Natl. Acad. Sci. USA 103:117-122.
18. Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
19. Hughes, J. B., J. J. Hellmann, T. H. Ricketts, and B. J. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:4399-4406.
20. Kemp, P. F., and J. Y. Aller. 2004. Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol. Ecol. 47:161-177.
21. Lane, D. J. 1991. 16S/23S sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid technologies in bacterial systematics. John Wiley and Sons, Chichester, United Kingdom.
22. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker, Jr., P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:173-174.
23. Mao, C. X., and R. K. Colwell. 2005. Estimation of species richness: mixture models, the role of rare species, and inferential challenges. Ecology 86:1143-1153.
24. Massana, R., V. Balagué, L. Guillou, and C. Pedros-Alió. 2004. Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches. FEMS Microbiol. Ecol. 50:231-243.
25. McLachlan, G. J., and D. Peel. 2000. Finite mixture models. Wiley, New York, N.Y.
26. Medlin, L., H. J. Elwood, S. Stickel, and M. L. Sogin. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71:491-499.
27. Muller-Karger, F., R. Varela, R. Thunell, M. Scranton, R. Bohrer, G. T. Taylor, J. Capelo, Y. Asto, E. Tappa, T.-Y. Ho, and J. J. Walsh. 2001. Annual cycle of primary production in the Cariaco Basin: response to upwelling and implications for vertical export. J. Geophys. Res. 106:4527-4542.
28. Richards, F. A., and R. F. Vaccaro. 1956. The Cariaco Trench, an anaerobic basin in the Caribbean. Deep Sea Res. 3:214-228.
29. Robison-Cox, J. F., M. M. Bateson, and D. M. Ward. 1995. Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl. Environ. Microbiol. 61:1240-1245.
30. Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
31. Shopsin, B., M. Gomez, S. O. Montgomery, D. H. Smith, M. Waddington, D. E. Dodge, D. A. Bost, M. Riehman, S. Naidich, and B. N. Kreiswirth. 1999. Evaluation of protein A gene polymorphic region DNA sequencing for typing of Staphylococcus aureus strains. J. Clin. Microbiol. 37:3556-3563.
32. Stoeck, T., B. Hayward, G. T. Taylor, R. Varela, and S. S. Epstein. 2006. A multiple PCR-primer approach to access the microeukaryotic diversity in the anoxic Cariaco Basin (Caribbean Sea). Protist 157:31-43.
33. Stoeck, T., G. Taylor, and S. S. Epstein. 2003. Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea). Appl. Environ. Microbiol. 69:5656-5663.
34. Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
35. Taylor, G. T., M. I. Scranton, M. Iabichella, T.-Y. Ho, R. C. Thunell, F. Muller-Karger, and R. Varela. 2001. Chemoautotrophy in the redox transition zone of the Cariaco Basin: a significant midwater source of organic carbon production. Limnol. Oceanogr. 46:148-163.
36. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 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.
37. Tollenaar, N., and A. Mooijaart. 2003. Type I errors and power of the parametric bootstrap goodness-of-fit test: full and limited information. Br. J. Math. Stat. Psychol. 56:271-288.
38. Wang, J.-P. Z., and B. G. Lindsay. 2005. A penalized nonparametric maximum likelihood approach to species richness estimation. J. Am. Stat. Assoc. 100:942-959.
39. Williamson, M., and K. J. Gaston. 2005. The lognormal distribution is not an appropriate null hypothesis for the species-abundance distribution. J. Anim. Ecol. 74:409-422.
40. Zuendorf, A., A. Behnke, J. A. Bunge, K. J. Barger, and T. Stoeck. Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord. FEMS Microbiol. Ecol., in press.