"Bring to Lab" of 19 novel species among 60 isolates retrieved from a freshwater pond

Journal of Microbiology and Biotechnology

Volumn 17, Issue 1, 2007, Pages 168-175

  Song, Jaeho ^a   Yang, Seung Jo ^a   Cho, Jang Cheon ^a  

^a Inha University   (South Korea)

Author keywords

16S rRNA gene; Bacterial diversity; Cultivation; Freshwater; Novel species

Indexed keywords

BACTERIAL RNA; RIBOSOME RNA; RNA 16S;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL STRAIN; BACTERIUM; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; BACTERIUM ISOLATION; BETAPROTEOBACTERIA; DEINOCOCCUS; FIRMICUTES; FRESHWATER SPECIES; GAMMAPROTEOBACTERIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA SEQUENCE; STRAIN DIFFERENCE; UNINDEXED SEQUENCE;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA; BACTERIOLOGICAL TECHNIQUES; BACTEROIDETES; BETAPROTEOBACTERIA; CULTURE MEDIA; DEINOCOCCUS; DNA PRIMERS; DNA, BACTERIAL; FRESH WATER; GAMMAPROTEOBACTERIA; KOREA; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; WATER MICROBIOLOGY;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; DEINOCOCCI; FIRMICUTES; GAMMAPROTEOBACTERIA;

EID: 33846874971     PISSN: 10177825     EISSN: 17388872     Source Type: Journal    
DOI: None     Document Type: Article

References (36)

1. Acinas, S. G, V. Klepac-Ceraj, D. E. Hunt, C. Pharino, I. Ceraj, D. L. Distel, and M. F. Polz. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551-554.
2. Ahn, J.-H., M.-S. Kim, M.-C. Kim, J.-S. Lirn, G-T. Lee, J. K. Yun, T. Kim, T. Kim, and J.-O. Ka. 2006. Analysis of bacterial diversity and community structure in forest soils contaminated with fuel hydrocarbon. J. Microbiol. Biotechnol. 16: 704-715.
3. Bruns, A., H. Hoffelner, and J. Overmann. 2003. A novel approach for high throughput cultivation assays and the isolation of plank-tonic bacteria. FEMS Microbiol. Ecol. 45: 161-171.
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. Cho, W, E.-H. Lee, E.-H. Shim, J. Kim, H. W. Ryu, and K.-S. Cho. 2005. Bacterial communities of biofilms sampled from seepage groundwater contaminated with petroleum oil. J. Microbiol. Biotechnol. 15: 952-964.
6. Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56: 457-487.
7. 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.
8. DeLong, E. F., C. M. Preston, T. Mincer, V. Rich, S. J. Hallam, N. U. Frigaard, A. Martinez, M. B. Sullivan, R. Edwards, B. R. Brito, S. W. Chisholm, and D. M. Karl. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
9. Gich, F., J. Garcia-Gil, and J. Overmann. 2001. Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes. Arch. Microbiol. 177: 1-10.
10. Gich, F. and J. Overmann. 2006. Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll a-containing, obligately aerobic bacterium isolated from freshwater lakes. Int. J. Syst. Evol. Microbiol. 56: 847-854.
11. Gich, F., K. Schubert, A. Bruns, H. Hoffelner, and J. Overmann. 2005. Specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. Appl. Environ. Microbiol. 71: 5908-5919.
12. Giovannoni, S. and M. Rappé. 2000. Evolution, diversity and molecular ecology of marine prokaryotes, pp. 47-84. In D. L. Kirchman (ed.), Microbial Ecology of the Oceans. John Wiley & Sons, Inc., New York.
13. 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.
14. Hugenholtz, P., C. Pitulle, K. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180: 366-376.
15. Hwang, C. Y and B. C. Cho. 2006. Flectobacillus lacus sp. nov., isolated from a highly eutrophic pond in Korea. Int. J Syst. Evol. Microbiol. 56: 1197-1201.
16. Kim, B. S., H. M. Oh, H. J. Kang, S. S. Park, and J. S. Chun. 2004. Remarkable bacterial diversity in the tidal flat sediment as revealed by 16S rDNA analysis. J. Microbiol. Biotechnol. 14: 205-211.
17. Kim, M.-S., J.-H. Ahn, M.-K. Jung, J.-H. Yu, D.-H. Joo, M.-C. Kim, H.-C. Shin, T. Kim, T.-H. Ryu, S.-J. Kweon, T. Kim, D.-H. Kim, and J.-O. Ka. 2005. Molecular and cultivation-based characterization of bacterial community structure in rice field soil. J. Microbiol. Biotechnol. 15: 1087-1093.
18. Kim, W-K., R. Cui, and D. Jahng. 2005. Enrichment of ammonia-oxidizing bacteria for efficient nitrification of wastewater. J. Microbiol. Biotechnol. 15: 772-779.
19. Konneke, M., A. E. Bernhard, J. R. de la Torre, C. B. Walker, J. B. Waterbury, and D. A. Stahl. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.
20. Lee, S.-H., H.-R. Oh, J.-H. Lee, S.-J. Kim, and J.-C. Cho. 2004. Cold-seep sediment harbors phylogenetically diverse uncultured bacteria. J. Microbiol. Biotechnol. 14: 906-913.
21. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K. H. Schleifer. 2004. ARB: A software environment for sequence data. Nucleic Acids Res. 32: 1363 -1371.
22. Moore, L. R., G Rocap, and S. W. Chisholm. 1998. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393: 464-467.
23. Page, K. A., S. A. Connon, and S. J. Giovannoni. 2004. Representative freshwater bacterioplankton isolated from Crater Lake, Oregon. Appl. Environ. Microbiol. 70: 6542-6550.
24. Rappe, M. S., S. A. Connon, K. L. Vergin, and S. J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630-633.
25. Reasoner, D. J. and E. E. Geldreich. 1985. A new medium for the enumeration and subculture of bacteria from potable water. Appl. Environ. Microbiol. 49: 1-7.
26. Rocap, G., F. W. Larimer, J. Lamerdin, S. Malfatti, P. Chain, N. A. Ahlgren, A. Arellano, M. Coleman, L. Hauser, W. R. Hess, Z. I. Johnson, M. Land, D. Lindell, A. F. Post, W. Regala, M. Shah, S. L. Shaw, C. Steglich, M. B. Sullivan, C. S. Ting, A. Tolonen, E. A. Webb, E. R. Zinser, and S. W. Chisholm. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047.
27. Simu, K. and A. Hagstrom. 2004. Oligotrophic bacterioplankton with a novel single-cell life strategy. Appl. Environ. Microbiol. 70: 2445-2451.
28. Stackebrandt, E. and B. M. Göebel. 1994. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44: 846-849.
29. Swofford, D. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). 4b8 Ed. Sinauer Associates, Sunderland, Massachusetts.
30. Tamaki, H., Y. Sekiguchi, S. Hanada, K. Nakamura, N. Nomura, M. Matsumura, and Y. Kamagata. 2005. Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl. Environ. Microbiol. 71: 2162-2169.
31. Thompson, J. R., M. A. Randa, L. A. Marcelino, A. Tomita-Mitchell, E. Lim, and M. F. Polz. 2004. Diversity and dynamics of a north atlantic coastal Vibrio community. Appl. Environ. Microbiol. 70: 4103-4110.
32. Wang, Z.-W., Y.-H. Liu, X. Dai, B.-J. Wang, C.-Y. Jiang, and S.-J. Liu. 2006. Flavobacterium saliperosum sp. nov., isolated from freshwater lake sediment. Int. J. Syst. Evol. Microbiol. 56: 439-442.
33. Wayne, L. G, D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Trüfer. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-464.
34. Xiang, Z., X. Xiao, P. Wang, and F. P. Wang. 2004. Screening and characterization of psychrotrophic, lipolytic bacteria from deep-sea sediments. J. Microbiol. Biotechnol. 14: 952-958.
35. Zwart, G, W. D. Hiorns, B. A. Methe, M. P. van Agterveld, R. Huismans, S. C. Nold, J. P. Zehr, and H. J. Laanbroek. 1998. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst. Appl. Microbiol. 21: 546-556.
36. Zwart, G., R. Huismans, M. P. van Agterveld, Y. Van de Peer, P. De Rijk, H. Eenhoorn, G. Muyzer, E. J. van Hannen, H. J. Gons, and H. J. Laanbroek. 1998. Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake. FEMS Microbiol. Ecol. 25: 159-169.