Comparative approach to capture bacterial diversity of coastal waters

Journal of Microbiology

Volumn 49, Issue 5, 2011, Pages 729-740

  Na, Hyunsoo ^a,b   Kim, Ok Sun ^b,c   Yoon, Seok Hwan ^b   Kim, Yunmin ^b   Chun, Jongsik ^b  

^a AARHUS UNIVERSITY   (Denmark)

^b Seoul National University   (South Korea)

^c Korea Polar Research Institute (KOPRI)   (South Korea)

Author keywords

cloning; DGGE; diversity; high throughput culturing (HTC); plate washing PCR (PWPCR); pyrosequencing; Roche 454 GS FLX titanium

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA; RNA 16S; SEA WATER;

ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; EVALUATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METAGENOMICS; METHODOLOGY; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; SOUTH KOREA;

BACTERIA; BACTERIOLOGICAL TECHNIQUES; BIODIVERSITY; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; METAGENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; REPUBLIC OF KOREA; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); RHODOBACTERACEAE;

EID: 80955142289     PISSN: 12258873     EISSN: 19763794     Source Type: Journal    
DOI: 10.1007/s12275-011-1205-z     Document Type: Article

References (47)

1. Ampe, F., N. ben Omar, C. Moizan, C. Wacher, and J. P. Guyot. 1999. Polyphasic study of the spatial distribution of microorganisms in Mexican pozol, a fermented maiz dough, demostrates the need for cultivation-independent methods to investigate traditional fermentations. Appl. Environ. Microbiol. 65, 5464-5473.
2. Buchan, A., J. M. Gonzalez, and M. A. Moran. 2005. Overview of the marine roseobacter lineage. Appl. Environ. Microbiol. 71, 5665-5677.
3. Cheng, S. M. and J. M. Foght. 2007. Cultivation-independent and-dependent characterization of bacteria resident beneath John Evans Glacier. FEMS Microbiol. Ecol. 59, 318-330.
4. Cho, J. C. and S. J. Giovannoni. 2004. Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl. Environ. Microbiol. 70, 432-440.
5. Chouari, R., D. Le Paslier, C. Dauga, P. Daegelen, J. Weissenbach, and A. Sghir. 2005. Novel major bacterial candidate division within a municipal anaerobic sludge digester. Appl. Environ. Microbiol. 71, 2145-2153.
6. Chun, J. and M. Goodfellow. 1995. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 45, 240-245.
7. Chun, J., K. Y. Kim, J. H. Lee, and Y. Choi. 2010. The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiol. 10, 101.
8. Chun, J., J. H. Lee, Y. Jung, M. Kim, S. Kim, B. K. Kim, and Y. W. Lim. 2007. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57, 2259-2261.
9. Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, and et al. 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31, 442-443.
10. Connon, S. A. and S. J. Giovannoni. 2002. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68, 3878-3885.
11. Curtis, T. P., W. T. Sloan, and J. W. Scannell. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 99, 10494-10499.
12. Derakshani, M., T. Lukow, and W. Liesack. 2001. Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Appl. Environ. Microbiol. 67, 623-631.
13. DeSantis, T. Z., Jr., P. Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, and G. L. Andersen. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34, W394-399.
14. Donachie, S. P., J. S. Foster, and M. V. Brown. 2007. Culture clash: challenging the dogma of microbial diversity. ISME J. 1, 97-99.
15. Dyksterhouse, S. E., J. P. Gray, R. P. Herwig, J. C. Lara, and J. T. Staley. 1995. Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int. J. Syst. Bacteriol. 45, 116-123.
16. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
17. Edwards, R. A., B. Rodriguez-Brito, L. Wegley, M. Haynes, M. Breitbart, D. M. Peterson, M. O. Saar, S. Alexander, E. C. Alexander Jr., and F. Rohwer. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7, 57.
18. Elshahed, M. S., N. H. Youssef, Q. Luo, F. Z. Najar, B. A. Roe, T. M. Sisk, S. I. Buhring, K. U. Hinrichs, and L. R. Krumholz. 2007. Phylogenetic and metabolic diversity of Planctomycetes from anaerobic, sulfide- and sulfur-rich Zodletone Spring, Oklahoma. Appl. Environ. Microbiol. 73, 4707-4716.
19. Giovannoni, S. J., L. Bibbs, J. C. Cho, M. D. Stapels, R. Desiderio, K. L. Vergin, M. S. Rappe, and et al. 2005. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438, 82-85.
20. Gonzalez, J. M., R. Simo, R. Massana, J. S. Covert, E. O. Casamayor, C. Pedr'os-Ali'o, and M. A. Moran. 2000. Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl. Environ. Microbiol. 66, 4237-4246.
21. Griffiths, R. I., A. S. Whiteley, A. G. O'Donnell, and M. J. Bailey. 2000. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66, 5488-5491.
22. Harwati, T. U., Y. Kasai, Y. Kodama, D. Susilaningsih, and K. Watanabe. 2009. Tropicibacter naphthalenivorans gen. nov., sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Semarang Port in Indonesia. Int. J. Syst. Evol. Microbiol. 59, 392-396.
23. Huse, S. M., J. A. Huber, H. G. Morrison, M. L. Sogin, and D. M. Welch. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8, R143.
24. Jeon, Y. S., H. Chung, S. Park, I. Hur, J. H. Lee, and J. Chun. 2005. jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. Bioinformatics 21, 3171-3173.
25. Kim, B. S. 2007. Molecular ecology of prokaryotic community in Korean tidal flat. Seoul National University, Seoul.
26. Kim, B. S., B. K. Kim, J. H. Lee, M. Kim, Y. W. Lim, and J. Chun. 2008. Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing. J. Microbiol. 46, 357-363.
27. Kormas, K. A., A. Meziti, A. Dahlmann, G. J. De Lange, and V. Lykousis. 2008. Characterization of methanogenic and prokaryotic assemblages based on mcrA and 16S rRNA gene diversity in sediments of the Kazan mud volcano (Mediterranean Sea). Geobiology 6, 450-460.
28. Kunin, V., A. Engelbrektson, H. Ochman, and P. Hugenholtz. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12, 118-123.
29. Li, W. and A. Godzik. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659.
30. Morris, R. M., M. S. Rappe, S. A. Connon, K. L. Vergin, W. A. Siebold, C. A. Carlson, and S. J. Giovannoni. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420, 806-810.
31. Morris, R. M., K. L. Vergin, J. C. Cho, S. J. Giovannoni, M. S. Rappe, and C. A. Carlson. 2005. Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic time-series study. Limnol. Oceanogr. 50, 1687-1696.
32. O'sullivan, L. A., K. E. Fuller, E. M. Thomas, C. M. Turley, J. C. Fry, and A. J. Weightman. 2004. Distribution and culturability of the uncultivated 'AGG58 cluster' of the Bacteroidetes phylum in aquatic environments. FEMS Microbiol. Ecol. 47, 359-370.
33. Pedr'os-Ali'o, C. 2006. Marine microbial diversity: can it be determined? Trends Microbiol. 14, 257-263.
34. Porter, K. G. and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25, 943-948.
35. Quince, C., A. Lanzen, T. P. Curtis, R. J. Davenport, N. Hall, I. M. Head, L. F. Read, and W. T. Sloan. 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6, 639-641.
36. Schellenberg, J., M. G. Links, J. E. Hill, T. J. Dumonceaux, G. A. Peters, S. Tyler, T. B. Ball, A. Severini, and F. A. Plummer. 2009. Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition. Appl. Environ. Microbiol. 75, 2889-2898.
37. Schloss, P. D., S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, R. A. Lesniewski, and et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541.
38. Selje, N., M. Simon, and T. Brinkhoff. 2004. A newly discovered Roseobacter cluster in temperate and polar oceans. Nature 427, 445-448.
39. Shaw, A. K., A. L. Halpern, K. Beeson, B. Tran, J. C. Venter, and J. B. Martiny. 2008. It's all relative: ranking the diversity of aquatic bacterial communities. Environ. Microbiol. 10, 2200-2210.
40. Stevenson, B. S., S. A. Eichorst, J. T. Wertz, T. M. Schmidt, and J. A. Breznak. 2004. New strategies for cultivation and detection of previously uncultured microbes. Appl. Environ. Microbiol. 70, 4748-4755.
41. Sun, Y., Y. Cai, L. Liu, F. Yu, M. L. Farrell, W. McKendree, and W. Farmerie. 2009. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res. 37, e76.
42. Sundquist, A., S. Bigdeli, R. Jalili, M. L. Druzin, S. Waller, K. M. Pullen, Y. Y. El-Sayed, M. M. Taslimi, S. Batzoglou, and M. Ronaghi. 2007. Bacterial flora-typing with deep, targeted, chip-based pyrosequencing. BMC Microbiol. 7, 108.
43. Suzuki, M. T., C. M. Preston, O. Beja, J. R. de la Torre, G. F. Steward, and E. F. DeLong. 2004. Phylogenetic screening of ribosomal RNA gene-containing clones in Bacterial Artificial Chromosome (BAC) libraries from different depths in Monterey Bay. Microbiol. Ecol. 48, 473-488.
44. 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.
45. Wagner-Dobler, I. and H. Biebl. 2006. Environmental biology of the marine Roseobacter lineage. Annu. Rev. Microbiol. 60, 255-280.
46. Webster, N. S., R. E. Cobb, R. Soo, S. L. Anthony, C. N. Battershill, S. Whalan, and E. Evans-Illidge. 2010. Bacterial community dynamics in the marine sponge Rhopaloeides odorabile under in situ and ex situ cultivation. Mar. Biotechnol. 13, 296-304.
47. Zubkov, M. V., B. M. Fuchs, S. D. Archer, R. P. Kiene, R. Amann, and P. H. Burkill. 2002. Rapid turnover of dissolved DMS and DMSP by defined bacterioplankton communities in the stratified euphotic zone of the North Sea. Deep-Sea Res. II. 49, 3017-3038.