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Phylogenetic characteristics of actinobacterial population in bamboo (Sasa borealis) soil

조릿대 대나무림 토양 내 방선균군집의 계통학적 특성

  • Lee, Hyo-Jin (Institute of Microbial Ecology and Resources, Mokwon University) ;
  • Han, Song-Ih (Department of Microbial & Nano Materials, Mokwon University) ;
  • Whang, Kyung-Sook (Institute of Microbial Ecology and Resources, Mokwon University)
  • 이효진 (목원대학교 미생물생태자원연구센터) ;
  • 한송이 (목원대학교 미생물나노소재학과) ;
  • 황경숙 (목원대학교 미생물생태자원연구센터)
  • Received : 2016.02.17
  • Accepted : 2016.03.22
  • Published : 2016.03.31

Abstract

In this study, a pyrosequencing was performed and analyzed to verify the phylogenetic diversity of actinomycetes in the bamboo (Sasa borealis) soil as a base study to obtain the genetic resources of actinomycetes. It was found that the rhizosphere soil had much various distribution in bacterial communities showing a diversity of 8.15 with 2,868 OTUs, while the litter layer showed a diversity of 7.55 with 2,588 OTUs. The bacterial community in the bamboo soil was composed of 35 phyla and the predominant phyla were Proteobacteria (51-60%), Bacteroidetes (16-20%), Acidobacteria (4-16%) and Actinobacteria (4-14%). In particular, Actinobacteria including Micromonosporaceae and Streptomycetaceae had a diverse distribution of actinomycetes within the six orders, 35 families and 121 genera, and it was characterized that about 83% of actinomycetes within Actinomycetales belonged to the 28 families. Among the dominant actinobacterial populations, Micromonosporaceae, Pseudonocardiaceae and Streptomycetaceae were representative family groups in the bamboo soils.

Acknowledgement

Supported by : 농촌진흥청

References

  1. Berdy, J. 2005. Bioactive microbial metabolites. J. Antibiot. (Tokyo). 58, 1-26. https://doi.org/10.1038/ja.2005.1
  2. 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., et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37, 141-145.
  3. Cordovez, V., Carrion, V.J., Etalo, D.W., Mumm, R., Zhu, H., van Wezel, G.P., and Raaijmakers, J.M. 2015. Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil. Front. Microbiol. 6, 1081.
  4. Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., and Knight, R. 2011. Uchime improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200. https://doi.org/10.1093/bioinformatics/btr381
  5. Hayakawa, M. 2008. Studies on the isolation and distribution of rare actinomycetes in soil. Actinomycetol. 22, 12-19. https://doi.org/10.3209/saj.SAJ220103
  6. Jog, R., Nareshkumar, G., and Rajkumar, S. 2012. Plant growth promoting potential and soil enzyme production of the most abundant Streptomyces spp. from wheat rhizosphere. J. Appl. Microbiol. 113, 1154-1164. https://doi.org/10.1111/j.1365-2672.2012.05417.x
  7. Kim, P.K., Kwon, O.S., Lim, C.Y., Park, D.J., and Kim, C.J. 1997. Genus distribution of soil actinomycetes on different depth. Kor. J. Appl. Microbiol. Biotechnol. 5, 534-536.
  8. Lee, H.W., Ahn, J.H., Kim, M.W., Weon, H.Y., Song, J.K., Lee, S.J., and Kim, B.Y. 2013. Diversity and antimicrobial activity of actinomycetes from fecal sample of rhinoceros beetle larvae. Kor. J. Microbiol. 49, 156-164. https://doi.org/10.7845/kjm.2013.3041
  9. Lee, H.J. and Whang, K.S. 2010. Biodiversity and phylogenetic analysis of Streptomyces collected from bamboo forest soil. Kor. J. Microbiol. 46, 262-269.
  10. Miyadoh, S. 1993. Research on antibiotic screening in Japan over the last decade: a producing microorganism approach. Actinomycetologica 7, 100-106. https://doi.org/10.3209/saj.7_100
  11. Morales, D.K., Ocampo, W., and Zambrano, M.M. 2007. Efficient removal of hexavalent chromium by a tolerant Streptomyces sp. affected by the toxic effect of metal exposure. J. Appl. Microbiol. 103, 2704-2712. https://doi.org/10.1111/j.1365-2672.2007.03510.x
  12. Nimnoi, P., Pongsilp, N., and Lumyong, S. 2010. Genetic diversity and community of endophytic actinomycetes within the roots of Aquilaria crassna Pierre ex Lec assessed by actinomycetes-specific PCR and PCR-DGGE of 16S rRNA gene. Biochem. Syst. Ecol. 38, 595-601. https://doi.org/10.1016/j.bse.2010.07.005
  13. Olano, C., Mendez, C., and Salas, J.A. 2009. Antitumor compounds from marine actinomycetes. Mar. Drugs 7, 210-248. https://doi.org/10.3390/md7020210
  14. Piepersberg, W. 1994. Pathway engineering in secondary metabolite-producing actinomycetes. Crit. Rev. Biotechnol. 14, 251-285. https://doi.org/10.3109/07388554409079835
  15. Quince, C., Lanzen, A., Davenport, R.J., and Turnbaugh, P.J. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38. https://doi.org/10.1186/1471-2105-12-38
  16. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J., et al. 2009. Introducing mothur: open-source, platform-independent, community supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541. https://doi.org/10.1128/AEM.01541-09
  17. Sun, W., Dai, S., Jiang, S., Wang, G., Liu, G., Wu, H., and Li, X. 2010. Culture-dependent and culture-independent diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve from the South China Sea. Antonie van Leeuwenhoek 98, 65-75. https://doi.org/10.1007/s10482-010-9430-8
  18. Takada-Hoshino, Y. and Matsumoto, M. 2004. An improved DNA extraction method using skim milk from soils that strongly adsorb DNA. Microbes Environ. 19, 13-19. https://doi.org/10.1264/jsme2.19.13
  19. Warnecke, F., Amann, R., and Pernthaler, J. 2004. Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environ. Microbiol. 6, 242-253. https://doi.org/10.1111/j.1462-2920.2004.00561.x
  20. Whang, K.S. 2001. Taxonomic characteristics of nitrogen-fixing oligotrophic bacteria from forest soil. Kor. J. Microbiol. 37, 114-119.
  21. Yadav, A.K., Kumar, R., Saikia, R., Bora, T.C., and Arora, D.K. 2009. Novel copper resistant and antimicrobial Streptomyces isolated from Bay of Bengal, India. J. Med. Mycol. 19, 234-240. https://doi.org/10.1016/j.mycmed.2009.07.005
  22. Yasir, M., Aslam, Z., Song, G.C., Bibi, F., Jeon, C.O., and Chung, Y.R. 2011. Chitinophaga vermicomposti sp. nov., with antifungal activity, isolated from vermicompost. Int. J. Syst. Evol. Microbiol. 61, 2373-2378. https://doi.org/10.1099/ijs.0.023028-0