Browse > Article

'Bring to Lab' of 19 Novel Species Among 60 Isolates Retrieved from a Freshwater Pond  

Song, Jae-Ho (Division of Biology and Ocean Sciences, Inha University)
Yang, Seung-Jo (Division of Biology and Ocean Sciences, Inha University)
Cho, Jang-Cheon (Division of Biology and Ocean Sciences, Inha University)
Publication Information
Journal of Microbiology and Biotechnology / v.17, no.1, 2007 , pp. 168-175 More about this Journal
Abstract
We report here on the cultivation of numerous novel bacterial species from a eutrophic freshwater pond. A total of 60 strains, 15 strains per each culture medium, were obtained from the surface of a eutrophic freshwater pond by employing a conventional dilution-plating method with four different kinds of culture media, including R2A, 1/10R2A, PCA, and 1/10PCA. Among the 60 strains isolated, 27 strains showed less than 97% 16S rRNA gene sequence similarities to validly published species, and thus they are considered to comprise 19 novel species. Of the 27 strains assigned to the novel species, the majority of the strains (20 strains) were affiliated with the Alphaproteobacteria and Betaproteobacteria. The remaining 7 strains were affiliated with the Gammaproteobacteria, Firmicutes, Actinobacteria, and Deinococci. Because we have isolated 19 novel species from a usual freshwater pond using a conventional culturing technique, our results suggest that an unexplored ecosystem, even if it looks like a common ecosystem found elsewhere, harbors diverse unidentified microbes, which will be definitely further characterized.
Keywords
Cultivation; freshwater; novel species; 16S rRNA gene; bacterial diversity;
Citations & Related Records
Times Cited By KSCI : 7  (Citation Analysis)
Times Cited By Web Of Science : 6  (Related Records In Web of Science)
연도 인용수 순위
1 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   DOI   ScienceOn
2 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   DOI
3 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   DOI   ScienceOn
4 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
5 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   과학기술학회마을
6 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   DOI
7 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   DOI   ScienceOn
8 Stackebrandt, E. and B. M. Goebel. 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   DOI   ScienceOn
9 Bruns, A., H. Hoffelner, and J. Overmann. 2003. A novel approach for high throughput cultivation assays and the isolation of planktonic bacteria. FEMS Microbiol. Ecol. 45: 161-171   DOI   ScienceOn
10 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: 546-55   DOI   ScienceOn
11 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
12 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   DOI   ScienceOn
13 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   DOI   ScienceOn
14 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   DOI   ScienceOn
15 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   DOI   ScienceOn
16 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   DOI   ScienceOn
17 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   과학기술학회마을
18 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   DOI   ScienceOn
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   DOI   ScienceOn
20 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   DOI   ScienceOn
21 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
22 Ahn, J.-H., M.-S. Kim, M.-C. Kim, J.-S. Lim, 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   과학기술학회마을
23 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   DOI   ScienceOn
24 Swofford, D. 2002. PAUP$^{\ast}$. Phylogenetic Analysis Using Parsimony ($^{\ast}$and Other Methods). 4b8 Ed. Sinauer Associates, Sunderland, Massachusetts
25 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. Trufer. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-464   DOI
26 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
27 Giovannoni, S. and M. Rappe. 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
28 Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56: 457-487   DOI   ScienceOn
29 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   DOI   ScienceOn
30 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   DOI
31 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   DOI   ScienceOn
32 Simu, K. and A. Hagstrom. 2004. Oligotrophic bacterioplankton with a novel single-cell life strategy. Appl. Environ. Microbiol. 70: 2445-2451   DOI   ScienceOn
33 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   과학기술학회마을
34 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
35 Moore, L. R., G. Rocap, and S. W. Chisholm. 1998. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393: 464-467   DOI   ScienceOn
36 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