Journal of Microbiology and Biotechnology

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

Diversity of Root-Associated Paenibacillus spp. in Winter Crops from the Southern Part of Korea

  • CHEONG HOON (Laboratory of Microbial Genomics, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Department of Applied Biology and Environmental Sciences, College of Agriculture and Life Sciences, Gyeongsang National University) ;
  • PARK SOO-YOUNG (Laboratory of Microbial Genomics, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • RYU CHOONG-MIN (Laboratory of Microbial Genomics, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • KIM JIHYUN F. (Laboratory of Microbial Genomics, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • PARK SEUNG-HWAN (Laboratory of Microbial Genomics, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • PARK CHANG SEUK (Department of Applied Biology and Environmental Sciences, College of Agriculture and Life Sciences, Gyeongsang National University)
  • Published : 2005.12.01
Download PDF
⟨ Previous Next ⟩

Abstract

The genus Paenibacillus is a new group of bacilli separated from the genus Bacillus, and most of species have been isolated from soil. In the present study, we collected 450 spore-forming bacilli from the roots of winter crops, such as barley, wheat, onion, green onion, and Chinese cabbage, which were cultivated in the southern part of Korea. Among these 450 isolates, 104 Paenibacillus-like isolates were selected, based on their colony shape, odor, color, and endospore morphology, and 41 isolates were then finally identified as Paenibacillus spp. by 16S rDNA sequencing. Among the 41 Paenibacillus isolates, 23 were classified as P. polymyxa, a type species of the genus Paenibacillus, based on comparison of the 16S rDNA sequences with those of 32 type strains of the genus Paenibacillus from the GenBank database. Thirty-five isolates among the 41 Paenibacillus isolates exhibited antagonistic activity towards plant fungal and bacterial pathogens, whereas 24 isolates had a significant growth-enhancing effect on cucumber seedlings, when applied to the seeds. An assessment of the root-colonization capacity under gnotobiotic conditions revealed that all 41 isolates were able to colonize cucumber roots without any significant difference. Twenty-one of the Paenibacillus isolates were shown to contain the nifH gene, which is an indicator of $N_{2}$ fixation. However, the other 20 isolates, including the reference strain E681, did not incorporate the nifH gene. To investigate the diversity of the isolates, a BOX-PCR was performed, and the resulting electrophoresis patterns allowed the 41 Paenibacillus isolates to be divided into three groups (Groups A, B, and C). One group included Paenibacillus strains isolated mainly from barley or wheat, whereas the other two groups contained strains isolated from diverse plant samples. Accordingly, the present results showed that the Paenibacillus isolates collected from the rhizosphere of winter crops were diverse in their biological and genetic characteristics, and they are good candidates for further application studies.

Keywords

References

  1. Ash, C., F. G. Priest, and M. D. Collins. 1993. Molecular identification of rRNA group 3 Bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek 64: 253-260 https://doi.org/10.1007/BF00873085
  2. Berge, O., T. Heulin, and J. Balandreau. 1991. Diversity of diazotroph populations in the rhizosphere of maize (Zea mays L.) growing on different French soil. Biol. Fertil. Soils 11: 210-215 https://doi.org/10.1007/BF00335769
  3. Budi, S. W., D. van Tuinen, C. Arnould, E. Dumas-Gaudot, V. Gianinazzi-Pearson, and S. Gianinazzi. 2000. Hydrolytic enzyme activity of Paenibacillus sp. strain B2 and effects of the antagonistic bacterium on cell integrity of two soil-borne pathogenic fungi. Appl. Soil Ecol. 15: 191-199 https://doi.org/10.1016/S0929-1393(00)00095-0
  4. Bae, Y. S., H. K. Kim, and C. S. Park. 1990. An improved method for rapid screening and analysis of root colonizing biocontrol agents. Korean J. Plant Pathol. 6: 325-332
  5. Berge, O., G. Marie-Helene, W. Achouak, P. Normand, and T. Heulin. 2002. Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Int. J. Syst. Evol. Microbiol. 52: 607-616 https://doi.org/10.1099/00207713-52-2-607
  6. Bezzate, S., S. Aymerich, R. Chambert, S. Czarnes, O. Berge, and T. Heulin. 2000. Disruption of the Paenibacillus polymyxa levansucrase gene impairs its ability to aggregate soil in the wheat rhizosphere. Environ. Microbiol. 2: 333-342 https://doi.org/10.1046/j.1462-2920.2000.00114.x
  7. Choi, O. H., J. W. Kim, C. M. Ryu, and C. S. Park. 2004. Colonization and population changes of a biocontrol agent, Paenibacillus polymyxa E681, in seeds and roots. Plant Pathol. J. 20(2): 97-102 https://doi.org/10.5423/PPJ.2004.20.2.097
  8. Choo, Q. C., M. R. Samian, and N. Najimudin. 2003. Phylogeny and characterization of three nifH-homologous genes from Paenibacillus azotofixans. Appl. Environ.Microbiol. 69: 3658-3662 https://doi.org/10.1128/AEM.69.6.3658-3662.2003
  9. Coelho, M. R., I. von der Weid, V. Zahner, and L. Seldin. 2003. Characterization of nitrogen-fixing Paenibacillus species by polymerase chain reaction restriction fragment length polymophism analysis of part of genes encoding 16S rRNA and 23S rRNA and by multilocus enzyme electrophoresis. FEMS Microbiol. Lett. 222: 243-250 https://doi.org/10.1016/S0378-1097(03)00300-8
  10. Chung, Y. R., C. H. Kim, I. H. Hwang, and J. S. Chun. 2000. Paenibacillus koreensis sp. nov., a new species that produces an iturin-like antifungal compound. Int. J. Syst. Evol. Microbiol. 50: 1495-1500 https://doi.org/10.1099/00207713-50-4-1495
  11. Helbig, J. 2001. Biological Control of Botrytis cinerea Pers. ex Fr. in strawberry by Paenibacillus polymyxa (isolate 18191). J. Phytopathol. 149: 265-273 https://doi.org/10.1046/j.1439-0434.2001.00609.x
  12. Heulin, T., O. Berge, P. Mavingui, L. Gouzou, K. P. Hebbar, and J. Balandreau. 1994. Bacillus polymyxa and Rahnella aquatilis, the dominant $N_2$-fixing bacteria associated with wheat rhizosphere in French soils. Eur. J. Soil Biol. 30: 35- 42
  13. Huddleston, A. S., N. Cresswell, M. C. P Neves, J. E. Beringer, S. Baumberg, D. I. Thomas, and E. M. H. Wellington. 1997. Molecular detection of streptomycin-producing Streptomycetes in Brazilian soil. Appl. Environ. Microbiol. 63: 1288-1297
  14. Hwang, S. F., K. F. Chang, R. J. Howard, B. A. Deneka, and G. D. Turnbull. 1996. Decrease in incidence of Pythium damping-off of field pea by seed treatment with Bacillus spp. and metalaxyl. J. Plant Dis. Protect. 103: 31-41
  15. Jeon, Y. H., S. P. Chang, I. Hwang, and Y. H. Kim. 2003. Involvement of growth-promoting rhizobacterium Paenibacillus polymyxa in root rot of stored Korean ginseng. J. Microbiol.Biotechnol. 13: 881-891
  16. Kim, D. S., R. J. Cook, and D. M. Weller. 1997. Bacillus sp. L324-92 for biological control of three root diseases of wheat grown with reduced tillage. Phytopathology 87: 551- 558 https://doi.org/10.1094/PHYTO.1997.87.5.551
  17. Kim, J., J.-G. Kim, B.-K. Park, O. Choi, C. S. Park, and I. G. Hwang. 2003. Identification of genes for biosynthesis of antibacterial compound from Pseudomonas fluorescens B16, and its activity against Ralstonia solanacearum. J.Microbiol. Biotechnol. 13: 292-331
  18. Kloepper, J., R. Lifshitz, and R. M. Zablotowicz. 1989. Freeliving bacterial inocula for enhancing crop productivity. Trends Biotechnol. 7: 39-44 https://doi.org/10.1016/0167-7799(89)90057-7
  19. Lebuhn, M., T. Heulin, and A. Hartmann. 1997. Production of auxin and other indolic and phenolic compounds by Paenibacillus polymyxa strains isolated from different proximity to plant roots. FEMS Microbiol. Ecol. 22: 325- 334 https://doi.org/10.1111/j.1574-6941.1997.tb00384.x
  20. Lee, Y. E. and P. O. Lim. 2004. Purification and characterization of two thermostable xylanases from Paenibacillus sp. DG- 22. J. Microbiol. Biotechnol. 14: 1014-1021
  21. Mavingui, P. and T. Heulin. 1994. In vitro chitinase antifungal activity of soil, rhizosphere and rhizoplane populations of Bacillus polymyxa. Soil Biol. Biochem. 26: 801-803 https://doi.org/10.1016/0038-0717(94)90277-1
  22. Mavingui, P., G. Laguerre, O. Berge, and T. Heulin. 1992. Genetic and phenotypic diversity of Bacillus polymyxa in soil and in the wheat rhizosphere. Appl. Environ. Microbiol. 58: 1894-1903
  23. Moon, G. S., C. H. Kang, Y. R. Pyun, and W. J. Kim. 2004. Isolation, identification, and characterization of a bacteriocinproducing Enterococcus sp. from kimchi and its application to kimchi fermentation. J. Microbiol. Biotechnol. 14: 924- 931
  24. Nielsen, J. and G. Sorensen. 1997. Multi-target and mediumindependent fungal antagonism by hydrolytic enzymes in Paenibacillus polymyxa and Bacillus pumilus strains from barley rhizosphere. FEMS Microbiol. Ecol. 22: 183-192 https://doi.org/10.1111/j.1574-6941.1997.tb00370.x
  25. Oedjijono, M. A. and C. Dragar. 1993. Isolation of bacteria antagonistic to a range of plant pathogenic fungi. Soil Biol. Biochem. 25: 247-250 https://doi.org/10.1016/0038-0717(93)90034-9
  26. Petersen, D. J., M. Shishido, F. B. Holl, and C. P. Chanway. 1995. Use of species and strain-specific PCR primers for identification of conifer root associated Bacillus spp. FEMS Microbiol. Lett. 133: 71-76 https://doi.org/10.1111/j.1574-6968.1995.tb07863.x
  27. Pichard, J. P., D. Larue, and J. L. Thouvenot. 1995. Gavaserin and Saltavalin, new peptide antibiotics produced by Bacillus polymyxa. FEMS Microbiol. Lett. 133: 215- 218 https://doi.org/10.1111/j.1574-6968.1995.tb07887.x
  28. Pusey, P. L. and C. L. Wilson. 1984. Postharvest biological control of stone fruit brown rot by Bacillus subtilis. Plant Disease 68: 753-756 https://doi.org/10.1094/PD-69-753
  29. Rovira, A. D. 1963. Microbial inoculation of plants. 1. Establishment of free-living nitrogen-fixing bacteria in the rhizosphere and their effects on maize, tomato and wheat. Plant Soil 19: 304-314 https://doi.org/10.1007/BF01379484
  30. Ryu, C. M. and C. S. Park. 1997. Enhancement of plant growth induced by endospore forming PGPR strain, Bacillus polymyxa E681, pp. 186-190. Proceedings of the Fourth International Workshop on Plant Growth-Promoting Rhizobacteria Japan-OECD Joint Workshop
  31. Ryu, C. M., M. A. Farag, C. H. Hu, M. S. Reddy, H. X. Wei, P. W. Pare, and J. W. Kloepper. 2003. Bacterial volatiles promote growth in Arabidopsis. Proc. Natl. Acad. Sci. USA 100: 4927-4932
  32. Sambrook, J. and D. W. Russell. 2001. Molecular Cloning: A Laboratory Manual, 3rd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, U.S.A
  33. Schloter, M., M. Lebuhn, T. Heulin, and A. Hartmann. 2000. Ecology and evolution of bacterial microdiversity. FEMS Microbiol. Rev. 24: 647-660 https://doi.org/10.1111/j.1574-6976.2000.tb00564.x
  34. Seldin, L., A. S. Rosado, D. W. da Cruz, A. Nobrega, J. D. van Elsas, and E. Paiva. 1998. Comparison of Paenibacillus azotofixans strains isolated from rhizoplane, rhizoshere, and non-root-associated soil from maize planted in two different Brazilian soils. Appl. Environ. Microbiol. 64: 3860-3868
  35. Seldin, L., J. D. van Elsas, and E. G. C. Phnido. 1983. Bacillus nitrogen fixers from Brazilian soils. Plant Soil 70: 243-255 https://doi.org/10.1007/BF02374784
  36. Storm, K. S., P. E. Rosenthal, and A. Swanson. 1977. Polymixin and related peptide antibiotics. Annu. Rev. Biochem. 46: 723-763 https://doi.org/10.1146/annurev.bi.46.070177.003451
  37. Ueda, T., Y. Suga, N. Yahiro, and T. Matsuguchi. 1995. Remarkable $N_2$-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J. Bacteriol. 177: 1414-1417 https://doi.org/10.1128/jb.177.5.1414-1417.1995
  38. 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
  39. Von Bredemann, G. 1908. Untersuchungen uber die Variation und das Stickstoffbindungsvermogen des Bacillus asterosporus A. M., ausgefuhrt an 27 Sta mmen verschiedener Herkunft. Zbl. Bakteriol. Parasitenkd. Infektionskr. Hyg. 2: 44-89
  40. Von der Weid, I., E. Paiva, A. Nobrega, J. D. van Elsas, and L. Seldin. 2000. Diversity of Paenibacillus polymyxa strains isolated from the rhizosphere of maize planted in cerrado soil. Res. Microbiol. 151: 369-381 https://doi.org/10.1016/S0923-2508(00)00160-1
  41. Von der Weid, I., G. F. Duarte, J. D. van Elsas, and L. Seldin. 2002. Paenibacillus sp. nov., a novel nitrogen-fixing species isolated from the maize rhizosphere in Brazil. Int. J. Syst. Evol. Microbiol. 52: 2147-2153 https://doi.org/10.1099/ijs.0.02272-0
  42. Walker, R., A. A. Powell, and B. Seddon. 1998. Bacillus isolates from the spermosphere of peas and dwarf French beans with antifungal activity against Botrytis cinerea and Pythium species. J. Appl. Microbiol. 84: 791-801 https://doi.org/10.1046/j.1365-2672.1998.00411.x