Research in Plant Disease (식물병연구)

The Korean Society of Plant Pathology (한국식물병리학회)
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Draft Genome Sequence of a Chitinase-producing Biocontrol Bacterium Serratia sp. C-1

  • Park, Seur Kee (Department of Plant Medicine, Sunchon National University) ;
  • Kim, Young Cheol (Institute of Environmentally-Friendly Agriculture, Chonnam National University)
  • Received : 2015.07.30
  • Accepted : 2015.08.31
  • Published : 2015.09.30
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Abstract

The chitinase-producing bacterial strain C-1 is one of the key chitinase-producing biocontrol agents used for effective bioformulations for biological control. These bioformulations are mixed cultures of various chitinolytic bacteria. However, the precise identification, biocontrol activity, and the underlying mechanisms of the strain C-1 have not been investigated so far. Therefore, we evaluated in planta biocontrol efficacies of C-1 and determined the draft genome sequence of the strain in this study. The bacterial C-1 strain was identified as a novel Serratia sp. by a phylogenic analysis of its 16S rRNA sequence. The Serratia sp. C-1 bacterial cultures showed strong in planta biocontrol efficacies against some major phytopathogenic fungal diseases. The draft genome sequence of Serratia sp. C-1 indicated that the C-1 strain is a novel strain harboring a subset of genes that may be involved in its biocontrol activities.

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References

  1. Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A. L., Overbeek, R. A., McNeil, L. K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A. and Zagnitko, O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9: 75. https://doi.org/10.1186/1471-2164-9-75
  2. Clarke-Pearson, M. and Brady, S. F. 2008. Paerucumarin, a new metabolite produced by the pvc gene cluster from Pseudomonas aeruginosa. J. Bacteriol. 190: 6927-6930. https://doi.org/10.1128/JB.00801-08
  3. De Vleesschauwer, D. and Hofte, M. 2003. Using Serratia plymutica to control fungal pathogens of plants. CAB Reviews 2: 189-257.
  4. Ha, W. J., Kim, Y. C., Jung, H. and Park, S. K. 2014. Control of the rootknot nematode (Meloidogyne spp.) on cucumber by a liquid bio-formulation containing chitinolytic bacteria, chitin, and their products. Res. Plant Dis. 20: 112-118. (In Korean) https://doi.org/10.5423/RPD.2014.20.2.112
  5. Harris, A. K. P., Williamson, N. R., Slater, H., Cox, A., Abbasi, S., Foulds, I., Simonsen, H. T., Leeper, F. J. and Salmond, G. P. C. 2004. The Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species-and strain-dependent genome context variation. Microbiology 150: 3547-3560. https://doi.org/10.1099/mic.0.27222-0
  6. Han, S. H., Kang, B. R., Lee, J. H., Kim, H. J., Park, J. Y., Kim, J. J. and Kim, Y. C. 2012. Isolation and characterization of oligotrophic bacteria possessing induced systemic disease resistance against plant pathogens. Plant Pathol. J. 28: 68-74. https://doi.org/10.5423/PPJ.NT.11.2011.0218
  7. Kim, H. J., Choi, H. S., Yang, S. Y., Kim, I. S., Yamaguchi, T., Sohng, J. K., Park, S. K., Kim, J.-C, Lee, C. H., McSpadden Gardener, B. B. and Kim, Y. C. 2014. Both extracellular chitinase and a new cyclic lipopeptide, chromobactomycin, contribute to the biocontrol activity of Chromobacterium sp. C61. Mol. Plant Pathol. 15: 122-132. https://doi.org/10.1111/mpp.12070
  8. Kim, H. J., Park, J. Y., Han, S. H., Lee, J. H., Rong, X., McSpadden Gardener, B. B., Park, S. K. and Kim, Y. C. 2011a. Draft genome sequence of the biocontrol bacterium Chromobacterium sp. Strain C-61. J. Bacteriol. 193: 6803-6804. https://doi.org/10.1128/JB.06191-11
  9. Kim, J. C., Choi, G. J., Park, J. H., Kim, H. T. and Cho, K. Y. 2001. Activity against plant pathogenic fungi of phomalactone isolated from Nigrospora sphaerica. Pest Manag. Sci. 57: 554-559. https://doi.org/10.1002/ps.318
  10. Kim, Y. C., Jung, H., Kim, K. Y. and Park, S. K. 2008. An effective biocontrol bioformulation against Phytopathora blight of pepper using growth mixtures of combined chitinolytic bacteria under different field conditions. Eur. J. Plant Pathol. 120: 373-382. https://doi.org/10.1007/s10658-007-9227-4
  11. Kim, Y. C., Lee, J. H., Bae, Y.-S., Sohn, B.-K. and Park, S. K. 2010. Development of effective environmentally-friendly approaches to control Alternaria blight and anthracnose disease of Korean ginseng. Eur. J. Plant Pathol. 127: 443-450. https://doi.org/10.1007/s10658-010-9610-4
  12. Kim, Y. C., Leveau, J., McSpadden Gardener, B. B., Pierson, E. A., Pierson, L. S. and Ryu, C.-M. 2011b. The multifactorial basis for plant health promotion by plant-associated bacteria. Appl. Environ. Microbiol. 77: 15848-1555.
  13. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120. https://doi.org/10.1007/BF01731581
  14. Li, P. Kwok, A. H. Y., Jiang, J., Ran, T., Xu, D. Wang, W. and Leung F. C. 2015. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential. PLoS One 10: e0123061. https://doi.org/10.1371/journal.pone.0123061
  15. McSpadden Gardener, B. B., Kim, I. S., Kim, K. Y. and Kim, Y. C. 2014. Draft genome sequence of a chitinase-producing biocontrol bacterium, Lysobacter antibioticus HS124. Res. Plant Dis. 20: 216-218. https://doi.org/10.5423/RPD.2014.20.3.216
  16. Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V., Chuang, H.-Y., Cohoon, M., de Crecy-Lagard, V., Diaz, N., Disz, T., Edwards, R., Fonstein, M., Frank, E. D., Gerdes, S., Glass, E. M., Goesmann, A., Hanson, A., Iwata-Reuyl, D., Jensen, R., Jamshidi, N., Krause, L., Kubal, M., Larsen, N., Linke, B., McHardy, A. C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Osterman, A., Portnoy, V., Pusch, G. D., Rodionov, D. A., Ruckert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Y., Zagnitko, O. and Vonstein, V. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research 33: 5691-5702. https://doi.org/10.1093/nar/gki866
  17. Park, J.-K., Lee, S.-H., Lee, J.-H., Han, S., Kang, H., Kim, J.-C., Kim, Y. C. and McSpadden Gardener, B. B. 2013. Sampling and selection factors that enhance the diversity of microbial collections: application to biopesticide development. Plant Pathol. J. 29: 144-153. https://doi.org/10.5423/PPJ.SI.01.2013.0015
  18. Ugras, S., Sezen, K., Kati, H. and Demibag, Z. 2014. Purification and characterization of an antibacterial substance produced by pest-originated Serratia marcescens Mm3. Turk. J. Biol. 38: 177-184. https://doi.org/10.3906/biy-1305-46
  19. Zerbino, D. R. and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829. https://doi.org/10.1101/gr.074492.107
  20. Zerbino, D. R., McEwen, G. K., Margulies, E. H. and Birney, E. 2009. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de Novo assembler. PLoS ONE 4: e8407. https://doi.org/10.1371/journal.pone.0008407

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