미생물학회지 (Korean Journal of Microbiology)

  • 제49권2호
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  • Pages.150-155
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  • 2013
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  • 0440-2413(pISSN)
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  • 2383-9902(eISSN)
한국미생물학회 (The Microbiological Society of Korea)
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Pyrosequencing을 이용한 하절기 영산강 유역의 Phylum 계층의 세균 군집 조사

Use of Pyrosequencing for Characterizing Microbial Community at Phylum Level in Yeongsan River Watershed during Early Summer

  • Chung, Jin (National Institute of Environmental Research) ;
  • Park, Sang Jung (National Institute of Environmental Research) ;
  • Unno, Tatsuya (College of molecular life sciences, Jeju National University)
  • 투고 : 2013.05.09
  • 심사 : 2013.06.19
  • 발행 : 2013.06.30
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초록

Pyrosequencing을 이용하여 영산강 유역의 세균 군집 현황을 조사하였다. 영산강 본류 및 지천 14개 지점을 선정하여 5-7월동안 시료채취를 하였다. 총 42개의 시료를 가지고 총 989,380 reads을 얻었으며 taxonomic 분류와 OTU 분포도 분석을 실시하였다. Phylum 계층의 세균 구조 결과를 통해서 지천의 특성, 토지 이용, 시기적인 요인 등 환경적 요인에 따라 세균 군집 구조가 민감하게 변하는 경향을 나타내었다. 또한, OTU 분석을 근거한 오염원 추적기법(microbial source tracking; MST)을 통해 분변오염을 추적해보았다. Firmicutes가 가장 수질에 영향을 주는 taxa로 관찰되었다. 본 연구를 통해서, 현재 사용하는 수질 지표, BOD, pH 등에 더하여 pyrosequencing을 이용한 세균군집 조사 결과가 보다 효율적인 하천의 물관리 정책을 위해서 유용한 정보가 될 수 있을 것으로 기대한다.

We have conducted pyrosequencing for freshwater microbial community analyses. Fourteen sites along the Yeongsan river were selected for this study, and samples were collected monthly from May to July, 2012. Total 987,380 reads were obtained from 42 samples and used for taxonomic classification and OTU distribution analysis. Our results showed that high geographical and temporal variation in the phylum level bacterial composition, suggesting that microbial community is a very sensitive parameter affected by the surrounding environments including tributaries and land use nearby. In addition, we conducted an OTU-based Microbial Source Tracking to identify sources of fecal pollution in the same region. From this study Firmicutes was found to be the most influential taxa in this region. Here, we report that the use of pyrosequencing based microbial community analysis may give an additional information on freshwater quality monitoring, in addition to the currently used water quality parameters, such as BOD and pH.

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참고문헌

  1. Bibby, K., Viau, E., and Peccia, J. 2010. Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids. Wat. Res. 44, 4252-4260. https://doi.org/10.1016/j.watres.2010.05.039
  2. Eiler, A. and Bertilsson, S. 2004. Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes. Environ. Microbiol. 6, 1228-1243. https://doi.org/10.1111/j.1462-2920.2004.00657.x
  3. Foley, J.A., Defries, R., Asner, G.P., Barford, C., Bonan, G., Carpenter, S.R., Chapin, F.S., Coe, M.T., Daily, G.C., Gibbs, H.K., and et al. 2005. Global consequences of land use. Science 309, 570-574. https://doi.org/10.1126/science.1111772
  4. Gentry-Shields, J., Rowny, J.G., and Stewart, J.R. 2012. HuBac and nifH source tracking markers display a relationship to land use but not rainfall. Wat. Res. 46, 6163-6174. https://doi.org/10.1016/j.watres.2012.09.016
  5. Han, D., Unno, T., Jang, J., Lim, K., Lee, S.N., Ko, G., Sadowsky, M.J., and Hur, H.G. 2011. The occurrence of virulence traits among high-level aminoglycosides resistant Enterococcus isolates obtained from feces of humans, animal, and birds in South Korea. Int. J. Food Microbiol. 144, 387-392. https://doi.org/10.1016/j.ijfoodmicro.2010.10.024
  6. Hu, M., Wang, X., Wen, X., and Xia, Y. 2012. Microbial community structures in different wastewater treatment plants as revealed by 454-pyrosequencing analysis. Bioresour. Technol. 117, 72-79. https://doi.org/10.1016/j.biortech.2012.04.061
  7. Jang, J., Suh, Y.S., Di, D.Y., Unno, T., Sadowsky, M.J., and Hur, H.G. 2013. Pathogenic Escherichia coli strains producing extendedspectrum beta-latamases in the Yeongsand River basin of South Korea. Environ. Sci. Technol. 47, 1128-1136. https://doi.org/10.1021/es303577u
  8. Jang, J., Unno, T., Lee, S.W., Cho, K.H., Sadowsky, M.J., Ko, G., Kim, J.H., and Hur, H.G. 2011. Prevalence of season-specific Escherichia coli strains in the Yeongsan River basin of South Korea. Environ. Microbiol. 13, 3103-3113. https://doi.org/10.1111/j.1462-2920.2011.02541.x
  9. Lauber, C.L., Hamady, M., Knight, R., and Fierer, N. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75, 5111-5120. https://doi.org/10.1128/AEM.00335-09
  10. Lee, J. and Kim, I.S. 2011. Microbial community in seawater reverse osmosis and rapid diagnosis of membrane. Desalination 273, 118-126. https://doi.org/10.1016/j.desal.2010.12.005
  11. Lee, H., Kim, H., Park, H., Cho, Y., Ryu, S., Lee, K., Jung, J., and Ko, G. 2008. Evaluation of influent water quality using indicator microorganisms in Lake Shiwha. J. Environ. Health Sci. 34, 86-94. https://doi.org/10.5668/JEHS.2008.34.1.086
  12. Lindstrom, E.S., Kamst-Van Agterveld, M.P., and Zwart, G. 2005. Distribution of typical freshwayer bacterial groups is associated with pH, temperature, and lake water retention time. Appl. Environ. Microbiol. 71, 8201-8206. https://doi.org/10.1128/AEM.71.12.8201-8206.2005
  13. Nam, Y.D., Lee, S.Y., and Lim, S.I. 2012. Microbial community analysis of Korean soybean pastes by next-generation sequencing. Int. J. Food Microbiol. 155, 36-42. https://doi.org/10.1016/j.ijfoodmicro.2012.01.013
  14. Schloss, P.D., Gevers, D., and Westcott, S.L. 2011. Reducing the effects of PCR amplification and seqeunecing artifacts on 16S rRNA-based studies. PLoS ONE 6, e27310. https://doi.org/10.1371/journal.pone.0027310
  15. Schloss, P.D. and Westcott, S.L. 2011. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl. Environ. Microbiol. 77, 3219-3226. https://doi.org/10.1128/AEM.02810-10
  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., and 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. Scott, T.M., Rose, J.B., Jenkins, T.M., Farrah, S.R., and Lukasik, J. 2002. Microbial source tracking: Current methodology and future directions. Appl. Environ. Microbiol. 68, 5796-5803. https://doi.org/10.1128/AEM.68.12.5796-5803.2002
  18. Simpson, J.M., Santo Domingo, J.W., and Reasoner, D.J. 2002. Microbial source tracking: State of the science. Environ. Sci. Technol. 36, 5279-5288. https://doi.org/10.1021/es026000b
  19. Stoeckel, D.M. and Harwood, V.J. 2007. Performance, design, and analysis in microbial source tracking studies. Appl. Environ. Microbiol. 73, 2405-2415. https://doi.org/10.1128/AEM.02473-06
  20. Unno, T., Han, D., Jang, J., Lee, S.N., Ko, G., Choi, H.Y., Kim, J.H., Sadowsky, M.J., and Hur, H.G. 2009. Absence of Escherichia coli phylogenetic group B2 strains in humans and domesticated animals from Jeonnam Province, Republic of Korea. Appl. Environ. Microbiol. 75, 5659-5666. https://doi.org/10.1128/AEM.00443-09
  21. Unno, T., Han, D., Jang, J., Lee, S.N., Kim, J.H., Ko, G., Kim, B.G., Ahn, J.H., Kanaly, R.A., Sadowsky, M.J., and et al. 2010a. High diversity and abundance of antibiotic-resistant Escherichia coli isolated from humans and farm animal hosts in Jeonnam Province, South Korea. Sci. Total Environ. 408, 3499-3506. https://doi.org/10.1016/j.scitotenv.2010.04.046
  22. Unno, T., Jang, J., Han, D., Kim, J.H., Sadowsky, M.J., Kim, O., Chun, J., and Hur, H.G. 2010b. Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watershed. Environ. Sci. Technol. 44, 7777-7782. https://doi.org/10.1021/es101500z
  23. Unno, T., Han, D., Jang, J., Widmer, K., Ko, G., Sadowsky, M.J., and Hur, H.G. 2011. Genotypic and phenotypic trends in antibiotic resistant pathogenic Escherichia coli isolated from humans and farm animals in South Korea. Microbes Environ. 26, 198-204. https://doi.org/10.1264/jsme2.ME10194
  24. Unno, T., Di, D.Y.W., Jang, J., Suh, Y.S., Sadowsky, M.J., and Hur, H.-G. 2012. Integrated online system for a pyrosequencing-based microbial source tracking method that targets bacteroidetes 16S rDNA. Environ. Sci. Technol. 46, 93-98. https://doi.org/10.1021/es201380c
  25. Vishnivetskaya, T.A., Mosher, J.J., Palumbo, A.V., Yang, Z.K., Podar, M., Brown, S.D., Brooks, S.C., Gu, B., Southworth, G.R., Crake, M.M., and et al. 2011. Mercury and other heavy metals influence bacterial community structure in contaminated Tennessee streams. Appl. Environ. Microbiol. 77, 302-311. https://doi.org/10.1128/AEM.01715-10
  26. Will, C., Thurmer, A., Wollherr, A., Nacke, H., Herold, N., Schrumpf, M., Gutknecht, J., Wubet, T., Buscot, F., and Daniel, R. 2010. Horison-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl. Environ. Microbiol. 76, 6751-6759. https://doi.org/10.1128/AEM.01063-10
  27. Youssef, N.H., Couger, M.B., and Elshahed, M.S. 2010. Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone Spring, OK, USA): The role of the rare biosphere. PLoS ONE 5, 1-12.