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http://dx.doi.org/10.5352/JLS.2014.24.5.522

Seasonal Variations in the Bacterial Community of Gwangyang Bay Seawater  

Park, Seong Chan (Woogene B&G Rearch Institute)
Lee, Ji Hee (Department of Biology, Sunchon National University)
Kang, Joo Won (Department of Biology, Sunchon National University)
Baik, Keun Sik (Division of Life Sciences, Korea Basic Science Institute)
Seong, Chi Nam (Department of Biology, Sunchon National University)
Publication Information
Journal of Life Science / v.24, no.5, 2014 , pp. 522-531 More about this Journal
Abstract
Seasonal variations in the bacterial community of Gwangyang Bay seawater were analyzed using both isolation and cultivation-independent methods. Amplified rDNA restriction analysis was applied to 200 bacterial isolates. Bacterial isolates were composed of four phyla: Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Pyrosequencing was conducted, in addition to denaturing gradient gel electrophoresis (DGGE) of genomic DNA extracted directly from the water samples. The bacterial sequences obtained by pyrosequencing of 16S rRNA genes consisted of 24 phyla in the spring and summer, 39 in the fall, and 32 in the winter. The diversity index was high in the fall, whereas the dominancy index was high in the spring. In the spring, phylum Firmicutes was dominant, whereas phylum Proteobacteria dominated in the other three seasons. The second most dominant phyla were Proteobacteria in the spring, Firmicutes in the summer, and Bacteroidetes both in the fall and winter. Bacilliaceae was the most predominant family in the spring. Rhodobacteraceae and Bacilliaceae dominated in the summer, and Rhodobacteraceae dominated in the winter. Neither was dominant in the fall Twenty-seven bands purified from DGGE profiles were cloned and analyzed phylogenetically. In the spring, phylum Firmicutes dominated, followed by Proteobacteria. Proteobacteria dominated in all other seasons. Thus, two cultivation-independent methods for determination of seasonal variation patterns at the phylum level were in accordance with each other.
Keywords
Amplified rDNA restriction analysis; bacterial community; denaturing gradient gel electrophoresis; pyrosequencing;
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1 Ghosh, A., Maity, B., Chakrabarti, K. and Chattopadhyay, D. 2007. Bacterial diversity of East Calcutta wet land area: possible identification of potential bacterial population for different biotechnological uses. Microb Ecol 54, 452-459.   DOI
2 Heck, K. L., Van Belle, G. and Simberloff, D. 1975. Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecol 56, 1459-1461.   DOI   ScienceOn
3 Henriques, I. S., Almeida, A., Cunha, A. and Correia, A. 2004. Molecular sequence analysis of prokaryotic diversity in the middle and outer sections of the Portuguese estuary Ria de Aveiro. FEMS Microbiol Ecol 49, 269-279.   DOI   ScienceOn
4 Hurlbert, S. H. 1971. The nonconcept of species diversity: a critique and alternative parameters. Ecol 52, 577-586.   DOI   ScienceOn
5 Chun, J., Huq, A. and Colwell, R. R. 1999. Analysis of 16S-23S rRNA intergenic spacer regions of Vibrio cholerae and Vibrio mimicus. Appl Environ Microbiol 65, 2202-2208.
6 Chao, A. and Lee, S. M. 1992. Estimating the number of classes via sample coverage. J Am Stat Assoc 87, 210-217.   DOI   ScienceOn
7 Choi, C. G. and Huh, S. H. 2008. Composition of marine algal community at the intertidal zone in Gwangyang bay, South Sea, Korea. Korran J Fisher Aqua Sci 41, 201-207.   과학기술학회마을   DOI
8 Chun, J. and Goodfellow, M. 1995. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45, 240-245.   DOI   ScienceOn
9 Sokal, D. M. and Michener, C. D. 1958. A statistical method for evaluating systematic relationship. Univ. Kansas. Sci Bull 38, 1409-1438.
10 Polymenakou, P. N., Lampadariou, N., Mandalakis, M. and Tselepides, A. 2009. Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea. Syst Appl Microbiol 32, 17-26.   DOI   ScienceOn
11 Schloss, P. D. and Handelsman, J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71, 1501-1506.   DOI   ScienceOn
12 Somerville, C. C., Knight, I. T., Straube, W. L. and Colwell, R. R. 1989. Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl Environ Microbiol 55, 548-554.
13 Wright, E. S., Yilmaz, L. S. and Noguera, D. R. 2012. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol 78, 717-725.   DOI   ScienceOn
14 Na, H., Kim, O.-S., Yoon, S.-H., Kim, Y. and Chun, J. 2011. Comparative approach to capture bacterial diversity of coastal waters. J Microbiol 49, 729-740.   과학기술학회마을   DOI
15 Park, S. C., Baik, K. S., Choe, H. N., Lim, C. H., Kim, H. J., Ka, J. O. and Seong, C. N. 2011. Altererythrobacter namhicola sp. nov., and Altererythrobacter aestuarii sp. nov., isolated from seawater. Int J Syst Evol Microbiol 61, 709-715.   DOI   ScienceOn
16 Ling, J., Dong, J. D., Wang, Y. S., Zhang, Y. Y., Deng, C., Lin, L., Wu, M. L. and Sun, F. L. 2012. Spatial variation of bacterial community structure of the Northern South China Sea in relation to water chemistry. Ecotoxicol 21, 1669-1679.   DOI
17 Lozupone, C. and Knight, R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71, 8228-8235.   DOI   ScienceOn
18 Park, S. C, Baik, K. S., Kim, M. S., Kim, D. and Seong, C. N. 2009. Shewanella marina sp. nov., isolated from seawater. Int J Syst Evol Microbiol 59, 1888-1894.   DOI   ScienceOn
19 Park, S. C., Lim, C. H., Baik, K. S., Lee, K. H., Lee, J. S. and Seong, C. N. 2010. Pseudidiomarina aestuarii sp. nov., a marine bacterium isolated from shallow coastal seawater. Int J Syst Evol Microbiol 60, 2071-2075.   DOI   ScienceOn
20 Chao, A. 1984. Nonparametric-estimation of the number of classes in a population. Scand J Stat 11, 265-270.
21 American Public Health Association. 1989. Standard Methods for the Examination of Water and Wastewater, 17th ed., Washington, D. C., USA.
22 Baek, S. H., Kim, D. S., Hyun, B. G., Choi, H. W. and Kim, Y. O. 2011. Characteristics of horizontal community distribution and nutrient limitation on growth rate of phytoplankton during a winter in Gwangyang bay, Korea. Ocean Polar Res 33, 99-111.   과학기술학회마을   DOI
23 Baik, K. S. 2005. Prokaryotic diversity of Woopo wetland estimated by phylogenetic analysis. Ph. D. Thesis, Sunchon National University. Korea.
24 Lee, Y. S., Kang, C.-K., Choi, Y.-K. and Leem S. Y. 2007. Origin and spatial distribution of organic matter at Gwangyang bay in the fall. Ocean Science J 12, 1-8.   과학기술학회마을
25 Lane, D. J. 1991. 16S/23S rRNA sequencing, pp. 115-175. In E. Stackebrandt & M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics, Wiley, Chichester, U.K.
26 Joshi, A. A., Kanekar, P. P., Kelkar, A. S., Shouche, Y. S., Vani, A. A., Borgave, S. B. and Sarnaik, S. S. 2008. Cultivable bacterial diversity of alkaline Lonar lake, India. Microb Ecol 55, 163-172.   DOI
27 Kim, B.-S., Kim, B. K., Lee, J.-H., Kim, M., Lim, Y. W. and Chun, J. 2008. Rapid phylogenetic dissection of prokaryotic structure in tidal flat using pyrosequencing. J Microbiol 46, 357-363.   과학기술학회마을   DOI   ScienceOn
28 Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H., Yi, H., Won, S. and Chun, J. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62, 716-721.   DOI   ScienceOn
29 Kirchman, D. L., Cottrell, M. T. and Lovejoy, C. 2010. The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes. Environ Microbiol 12, 1132-1143.   DOI
30 Galand, P. E., Bourrain, M., De Maistre, E., Catala, P., Desdevises, Y., Elifantz, H., Kirchman, D. L. and Lebaron, P. 2012. Phylogenetic and functional diversity of bacteria and archaea in a unique stratified lagoon, the clipperton atoll (N Pacific). FEMS Microbiol Ecol 82, 616-628.   DOI   ScienceOn
31 Chun, J., Kim, K. Y., Lee, J.-H. and Choi, Y. 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.   DOI   ScienceOn
32 Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T., Garrity, G. M. and Tiedje, J. M. 2009. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37, D141-D145.
33 Droege, M. and Hil, B. 2008. The Genome Sequencer FLX System-longer reads, more applications, straight forward bioinformatics and more complete data sets. J Biotechnol 31, 3-10.
34 Polymenakou, P. N., Bertilsson, S., Tselepides, A. and Stephanou, E. G. 2005. Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries. Microb Ecol 50, 447-462.   DOI   ScienceOn
35 Park, S. C., Choe, H. N., Hwang, Y. M., Baik, K. S., Kim, S. N., Lee, Y. S., Jung, J. S. and Seong, C. N. 2013. Marinivirga aestuarii gen. nov., sp. nov., a novel member of the family Flavobacteriaceae, isolated from marine environment, and emended descriptions of the genera Hyunsoonleella, Jejuia and Pontirhabdus and Hyunsoonleella jejuensis, Jejuia pallidilutea and Pontirhabdus pectinivorans. Int J Syst Evol Microbiol 63, 1524-1531.   DOI   ScienceOn