Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지

Molecular and Cultivation-Based Characterization of Bacterial Community Structure in Rice Field Soil

  • KIM MI-SOON (School of Agricultural Biotechnology, Seoul National University) ;
  • AHN JAE-HYUNG (School of Agricultural Biotechnology, Seoul National University) ;
  • JUNG MEE-KUM (School of Agricultural Biotechnology, Seoul National University) ;
  • YU JI-HYEON (School of Agricultural Biotechnology, Seoul National University) ;
  • JOO DONGHUN (School of Agricultural Biotechnology, Seoul National University) ;
  • KIM MIN-CHEOL (School of Agricultural Biotechnology, Seoul National University) ;
  • SHIN HYE-CHUL (School of Agricultural Biotechnology, Seoul National University) ;
  • KIM TAESUNG (Ecosystem Disturbance Assessment Division, Nature and Ecology Research Department, National Institute of Environmental Research) ;
  • RYU TAE-HUN (National Institute of Agricultural Biotechnology, Rural Development Administration) ;
  • KWEON SOON-JONG (National Institute of Agricultural Biotechnology, Rural Development Administration) ;
  • KIM TAESAN (National Institute of Agricultural Biotechnology, Rural Development Administration) ;
  • KIM DONG-HERN (National Institute of Agricultural Biotechnology, Rural Development Administration) ;
  • KA JONG-OK (School of Agricultural Biotechnology, Seoul National University)
  • Published : 2005.10.01
Download PDF
⟨ Previous Next ⟩

Abstract

The population diversity and seasonal changes of bacterial communities in rice soils were monitored using both culture-dependent approaches and molecular methods. The rice field plot consisted of twelve subplots planted with two genetically-modified (GM) rice and two non-GM rice plants in three replicates. The DGGE analysis revealed that the bacterial community structures of the twelve subplot soils were quite similar to each other in a given month, indicating that there were no significant differences in the structure of the soil microbial populations between GM rice and non-GM rice during the experiment. However, the DGGE profiles of June soil after a sudden flooding were quite different from those of the other months. The June profiles exhibited a few intense DNA bands, compared with the others, indicating that flooding of rice field stimulated selective growth of some indigenous microorganisms. Phylogenetic analysis of l6S rDNA sequences from cultivated isolates showed that, while the isolates obtained from April soil before flooding were relatively evenly distributed among diverse genera such as Arthrobacter, Streptomyces, Terrabacter, and Bacillus/Paenibacillus, those from June soil after flooding mostly belonged to the Arthrobacter species. Phylogenetic analysis of 16S rDNA sequences obtained from the soil by cloning showed that April, August, and October had more diverse microorganisms than June. The results of this study indicated that flooding of rice fields gave a significant impact on the indigenous microbial community structure; however, the initial structure was gradually recovered over time after a sudden flooding.

Keywords

References

  1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipmann. 1990. Basic local alignment tool. J. Mol. Biol. 215: 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2
  2. Bakken, L. R. and R. A. Olsen. 1987. The relationship between cell size and viability of soil bacteria. Microb. Ecol. 13: 103-114 https://doi.org/10.1007/BF02011247
  3. Balkwill, D. L. 1990. Deep-aquifer microorganisms, pp. 183-211. In D. P. Labeda (ed.), Isolation of Biotechnological Organisms from Nature. McGraw-Hill Publ. Co., New York, U.S.A
  4. Bosio, D. A., K. M. Scow, N. Gunapala, and K. J. Graham. 1998. Determinants of soil microbial communities: Effects of agricultural management, season and soil type on phospholipid fatty acid profiles. Microb. Ecol. 36: 1-12 https://doi.org/10.1007/s002489900087
  5. Cho. M. J., Y. K. Kim, and J. O. Ka. 2004. Molecular differentiation of Bacillus spp. antagonistic against phytopathogenic fungi causing damping-off disease. J. Microbiol. Biotechnol. 14(3): 599-606
  6. de Bruijn, F. J. 1992. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ. Microbiol. 58: 2180-2187
  7. Felske, A., A. Wolterink, R. V. Lis, and A. D. L. Akkermans. 1998. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl. Environ. Microbiol. 64: 871-879
  8. Ferguson, R. L., E. N. Buckley, and A. V. Palumbo. 1984. Response of marine bacterioplankton to differential filtration and confinement. Appl. Environ. Microbiol. 47: 49-55
  9. Ferris, M. J., G. Muyzer, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62: 340-346
  10. Gelsomino, A., A. C. Keijzer- Wolters, G. Cacco, and J. D. van Elsas. 1999. Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis. J. Microbiol. Methods 38: 1-15 https://doi.org/10.1016/S0167-7012(99)00054-8
  11. Grobkopf, R., P. H. Janssen, and W Liesack. 1998. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 64: 960-969
  12. Grobkopf, R., S. Stubner, and W Liesack. 1998. Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl. Environ. Microbiol. 64: 4983-4989
  13. Hattori, T., H. Mitsui, H. Haga, N. Wakao, S. Shikano, K. Gorlach, Y. Kasahara, A. El-Beltagy, and R. Hattori. 1997. Advances in soil microbial ecology and the biodiversity. Antonie van Leeuwenhoek 72: 21-28 https://doi.org/10.1023/A:1000201017238
  14. Hengstmann, U., K.-J. Chin, P. H. Janssen, and W. Liesack. 1999. Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil. Appl. Environ. Microbiol. 65: 5050-5058
  15. 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
  16. Kim, T. S., M. S. Kim, M. K. Jung, J. H. Ahn, M. J. Joe, K. H. Oh, M. H. Lee, M. K. Kim, and J. O. Ka. 2005. Analysis of plasmid pJP4 horizontal transfer and its impact on bacterial community structure in natural soil. J. Microbiol. Biotechnol. 15(2): 376-383
  17. Kim, Y. T., B. K. Park, E. I. Hwang, N. H. Yim, N. R. Kim, T. H. Kang, S. H. Lee, and S. U. Kim. 2004. Investigation of possible gene transfer to soil microorganisms for environmental risk assessment of genetically modified organisms. J. Microbiol. Biotechnol. 14(3): 498-502
  18. Lane, D. J. 1991. 16S/23S rRNA sequencing, pp. 115-148. In E. Stackebrandt and M. Goodfellow (eds.), Nucleic Acid Techniques in Bacterial Systematics. John Wiley and Sons, Chichester, England
  19. Ludwig, W., S. H. Bauer, I. Held, G. Kirchhof, R. Schulze, I. Huber, S. Spring, A. Hartmann, and K.-H. Schleifer. 1997. Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153: 181-190 https://doi.org/10.1111/j.1574-6968.1997.tb10480.x
  20. Lueders, T. and M. Friedrich. 2000. Archaeal population dynamics during sequential reduction processes in rice field soil. Appl. Environ. Microbiol. 66: 2732-2742 https://doi.org/10.1128/AEM.66.7.2732-2742.2000
  21. MacNaughton, S. J., J. R. Stephen, A. D. Venosa, G. A. Davis, Y.-J. Chang, and D. C. White. 1999. Microbial population changes during bioremediation of an experimental dil spill. Appl. Environ. Microbiol. 65: 3566-3574
  22. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker Jr., P. R. Saxman, J. M. Stredwick, G. M. Garrity, B. Li, G. J. Olsen, S. Pramanik, T. M. Schmidt, and J. M. Tiedje. 2000. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28(1): 173-174 https://doi.org/10.1093/nar/28.1.173
  23. Mansoor, E. Y. and T. R. G. Gray. 1995. Growth of Arthrobacter globiformis in soil observed by fluorescent antibody and ELISA techniques. Microbiology 141: 505-511 https://doi.org/10.1099/13500872-141-2-505
  24. McCaig, A. E., L. A. Glover, and J. I. Prosser. 1999. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl. Environ. Microbiol. 65: 1721-1730
  25. Nielsen, K. M., A. M. Bones, K. Smalla, and J. D. van Elsas. 1998. Horizontal gene transfer from transgenic plants to terrestrial bacteria - a rare event? FEMS Microbiol. Rev. 22: 79-103 https://doi.org/10.1111/j.1574-6976.1998.tb00362.x
  26. Norris, T. B., J. M. Wraith, R. W. Castenholz, and T. R. McDermott. 2002. Soil microbial community structure across a thermal gradient following a geothermal heating event. Appl. Environ. Microbiol. 68: 6300-6309 https://doi.org/10.1128/AEM.68.12.6300-6309.2002
  27. Ou, L. T., J. M. Davidson, and D. F. Rothwell. 1978. Response of soil microflora to high 2,4-D applications. Soil Biol. Biochem. 10: 443-445 https://doi.org/10.1016/0038-0717(78)90074-3
  28. Park, I. H. and J. O. Ka. 2003. Isolation and characterization of 4-(2,4-dichlorophenoxy)butyric acid-degrading bacteria from agricultural soils. J. Microbiol. Biotechnol. 13(2): 243-250
  29. Reichardt, W., G. Mascarina, B. Padre, and J. Doll. 1997. Microbial communities of continuously cropped, irrigated rice fields. Appl. Environ. Microbiol. 63: 233-238
  30. Roger, P. A., W. J. Zimmerman, and T. A. Lumpkin. 1993. Microbiological management of wetland rice fields, pp. 417-455. In F. B. Metting, Jr. (ed.), Soil Microbial Ecology. Marcel Dekker, Inc., New York, U.S.A
  31. Saxena, A. D. and G. Stotzky. 2000. Insecticidal toxin from Bacillus thuringiensis is released from roots of transgenic Bt corn in vitro and in situ. FEMS Microbiol. Ecol. 33: 35-39 https://doi.org/10.1111/j.1574-6941.2000.tb00724.x
  32. Smit, E., P. Leefang, S. Gommans, and J. Van Den Broek. 2001. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl. Environ. Microbiol. 67: 2284-2291 https://doi.org/10.1128/AEM.67.5.2284-2291.2001
  33. Sneath, P. H. A. and R. R. Sokal. 1973. Numerical Taxonomy. Freeman, San Francisco, California, U.S.A
  34. Swofford, D. L. 2002. PAUP: Phylogenetic analysis using parsimony, version 4.0. Computer program distributed by Sinauer Associates, Sunderland, Massachusetts, U.S.A
  35. Versalovic, J., M. Schneider, F. J. de Bruijn, and J. R. Lupski. 1994. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell Biol. 5: 25-40
  36. Watanabe, I. and C. Furusaka. 1980. Microbial ecology of flooded rice soils. Adv. Microb. Ecol. 4: 125-168
  37. Weaver, R. W, J. S. Angle, and P. S. Bottomley. 1999. Methods of Soil Analysis: Part 2 - Microbiological and Biochemical Properties. Soil Science Society of America, Madison, U.S.A