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Phylogenetic diversity of bacterial communities in a gray solar saltern and isolation of extremely halophilic bacteria using culturomics

토판염전 결정지 내 세균군집의 계통학적 다양성 및 Culturomics법을 이용한 고도 호염균의 분리

  • Cho, Geon-Yeong (Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University) ;
  • Han, Song-Ih (Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University) ;
  • Whang, Kyung-Sook (Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University)
  • 조건영 (목원대학교 미생물나노소재학과) ;
  • 한송이 (목원대학교 미생물나노소재학과) ;
  • 황경숙 (목원대학교 미생물나노소재학과)
  • Received : 2017.03.08
  • Accepted : 2017.03.25
  • Published : 2017.03.31

Abstract

In this study, we investigated the phylogenetic diversity of the bacterial community and isolation of extremely halophilic bacteria using culturomics in a gray solar saltern. The number of bacterial living cells, enumerated in a gray solar saltern by direct fluorescence microscopy was three to four orders of magnitude greater than those enumerated by plate counts, suggesting the distribution of 'viable but non-culturable bacteria'. The biodiversity of bacterial communities in a gray solar saltern was investigated by pyrosequencing, 1,778 OTUs of bacteria were comprised of 18 phyla 46 classes 85 orders 140 families 243 genera with 6.16 diversity index. Archaea communities were composed of 3 phyla 6 classes 7 orders 7 families 38 genera with 4.95 diversity index from 643 OTUs. Totally 137 isolates were isolated by 59 different cultural methods based on culturomics considering culture media and conditions suitable for the growth of extremely halophilic bacteria. Phylogenetic analyses of extremely halophilic isolates based on 16S rRNA gene sequences, extremely halophilic isolates were composed of 4 phyla and 11 genera. Haloterrigena and Haloferax can be successfully isolated from culturomics. These culturomics were effective methods for collection of diversity of extremely halophilic bacteria.

본 연구에서는 토판염전 결정지에 서식하는 세균군집의 계통학적 다양성을 분석하고 culturomics법에 기반하여 고도 호염균의 다양성을 확보하고자 하였다. 토판염전 내 세균밀도를 조사한 결과, 직접검경법에 의한 생균수는 평판배양법에 비해 $10^3{\sim}10^4$ 배 이상 높은 계수치를 나타내어 배양이 곤란한 세균(viable but non-culturable bacteria, VBNC)이 다수 존재해 있음으로 판단되었다. 토판염전 결정지 내 세균군집 다양성 해석을 위해 배양비의존적 방법인 pyrosequencing 분자기법을 이용하였다. 세균군집의 경우 1,778 OTUs, 다양성 지수 6.16로 나타났으며, 18문46강85목140과 243속으로 확인되었다. Archaea군집은 643 OTUs, 다양성 지수 4.95로 3문6강7목7과 38속이 분포해 있음이 확인되었다. 고도 호염균 생육에 적합한 배양배지 및 배양조건을 고려한 총 59가지의 다양한 배양 방법을 이용하여 137균주를 순수 분리하였다. 분리된 고도호염균의 16S rRNA 유전자 분석결과, 총4문11속의 다양한 계통군으로 확인되었으며 호염성 archaea 계통군 Haloterrigena 속과 haloferax 속이 culturomics법을 통해 성공적으로 분리되었다. 고도 호염균 다양성 확보를 위해 culturomics법이 매우 효과적임을 밝혔다.

Keywords

References

  1. Ben-Amotz, A. and Avron, M. 1989. The biotechnology of mass culturing Dunaliella for products of commercial interest, pp. 91-114. In Cresswell, R.C., Rees, T.A.V., and Shah, N. (eds.), Algal and cyanobacteiral Biotechnology. Longman Scientific and Technical Press.
  2. 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, 101-108. https://doi.org/10.1186/1471-2180-10-101
  3. 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.
  4. DeLong, E.F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89, 5685-5689. https://doi.org/10.1073/pnas.89.12.5685
  5. 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
  6. Eichler, J. 2000. Novel glycoproteins of the halophilic archaeon Haloferax volcanii. Arch. Microbiol. 173, 445-448. https://doi.org/10.1007/s002030000152
  7. Jiang, Y.X., Wu, J.G., Yu, K.Q., Ai, C.X., Zou, F., and Zhou, H.W. 2011. Integrated lysis procedures reduce extraction biases of microbial DNA from mangrove sediment. J. Biosci. Bioeng. 111, 153-157. https://doi.org/10.1016/j.jbiosc.2010.10.006
  8. Kamekura, M. 1986. Production and function of enzymes from eubacterial halophiles. FEMS Microbiol. Rev. 39, 145-150. https://doi.org/10.1111/j.1574-6968.1986.tb01855.x
  9. Kim, H.N. 2012. The structure of microbial communities at solar saltern in Korea as revealed by pyrosequeincing of 16S rRNA genes. 51. BS thesis. Graduate School, Hankuk Univ. Foreign, Korea.
  10. Koh, H.W., Kim, S.J., Rhee, S.K. and Park, S.J. 2015. Isolation and characterization analysis of the halophilic archaea isolated from solar saltern, Gomso. Korean J. Microbiol. 51, 427-434. https://doi.org/10.7845/kjm.2015.5041
  11. Lagier, J.C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., Bittar, F., Fournous, G., Gimenez, G., Maraninchi, M., et al. 2012. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin. Microbiol. Infect. 18, 1185-1193. https://doi.org/10.1111/1469-0691.12023
  12. Lee, K.D., Park, J.W., Choi, C.R., Song, H.W., Yun, S.K., Yang, H.C., and Ham, K.S. 2007. Salinity and heavy metal contents of solar salts produced in Jeollanamdo province of Korea. Korean J. Food Sci. Nutr. 36, 753-758. https://doi.org/10.3746/jkfn.2007.36.6.753
  13. Li, W. and Godzik, A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659. https://doi.org/10.1093/bioinformatics/btl158
  14. Oren, A. 2008. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Systems 4, 2. https://doi.org/10.1186/1746-1448-4-2
  15. Oren, A. 2015. Halophilic microbial communities and their environments. Curr. Opin. Biotechnol. 33, 119-124. https://doi.org/10.1016/j.copbio.2015.02.005
  16. Park, J.W., Kim, S.J., Kim, S.H., Kim, B.H., Kang, S.G., Nam, S.H., and Jung, S.T. 2000. Determination of mineral and heavy metal contents of various salts. Korean J. Food Sci. Technol. 32, 1442-1445.
  17. Park, S.H. and Lee, G.H. 2015. Diversity and identification of halophilic bacteria by pyrosequencing in a solar salterns of Jeungdo, Korea. Korean J. Nat. Conservation 9, 149-156. https://doi.org/10.11624/KJNC.2015.9.2.149
  18. Park, J.S., Whang, K.S., and Cheon, J.S. 2005. Procedure of microbial classification and identification. Worldscience. Korea.
  19. Pastor, J.M., Bernal, V., Salvador, M., Argandona, M., Vargas, C., Csonka, L., Sevilla, A., Iborra, J.L., Nieto, J.J., and Canovas, M., et al. 2013. Role of central metabolism in the osmoadaptation of the halophilic bacterium Chromohalobacter salexigens. J. Biol. Chem. 288, 17769-17781. https://doi.org/10.1074/jbc.M113.470567
  20. Perez-Pomares , F., Bautista, V., Ferrer, J., Pire , C., Marhuenda-Egea, F.C., Bonete, M.J. 2003. Alpha-amylase activity from the halophilic archaeon Haloferax mediterranei. Extremophiles 7, 299-306 https://doi.org/10.1007/s00792-003-0327-6
  21. Pfluger, K., Baumann, S., Gottschalk, G., Lin, W., Santos, H., and Muller, V. 2003. Lysine-2, 3-aminomutase and ${\beta}$-lysine acetyltransferase genes of methanogenic Archaea are salt induced and are essential for the biosynthesis of NE-acetyl-${\beta}$-lysine and growth at high salinity. Appl. Environ. Microbiol. 69, 6047-6055. https://doi.org/10.1128/AEM.69.10.6047-6055.2003
  22. Qian, P.Y., Wang, Y., Lee, O.O., Lau, S.C.K., Yang, J.K., Lafi, F.F., Al-Suwailem, A., and Wong, T.Y.H. 2011. Vertical stratification of microbial communities in the Red sea revealed by 16S rDNA pyrosequencing. ISME J. 5, 507-518. https://doi.org/10.1038/ismej.2010.112
  23. 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
  24. Santorelli, M., Maurelli, L., Pocsfalvi, G., Fiume, I., Squillaci, G., La Cara, F., Del Monaco, G., and Morana, A. 2016. Isolation and characterisation of a novel alpha-amylase from the extreme haloarchaeon Haloterrigena turkmenica. Int. J. Biol. Macromol. 92, 174-184. https://doi.org/10.1016/j.ijbiomac.2016.07.001
  25. Saum, R., Mingote, A., Santos, H., and Muller, V. 2009. A novel limb in the osmoregulatory network of Methanosarcina mazei Go1: Ne-acetyl-${\beta}$-lysine can be substituted by glutamate and alanine. Environ. Microbiol. 11, 1056-1065. https://doi.org/10.1111/j.1462-2920.2008.01826.x
  26. 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
  27. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504. https://doi.org/10.1101/gr.1239303
  28. Ventosa, A., de la Haba, R.R., Sanchez-Porro, C., and Papke, R.T. 2015. Microbial diversity of hypersaline environments: a metagenomic approach. Curr. Opin. Microbiol. 25, 80-87. https://doi.org/10.1016/j.mib.2015.05.002
  29. Whang, K.S., Yang, H.C., and Someya, T. 2003. The detection and a quantitative evaluation of viable but non-culturable soil bacteria using a modified direct viable count method. Korean J. Microbiol. 39, 181-186.
  30. Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697-703. https://doi.org/10.1128/jb.173.2.697-703.1991