Microbiology and Biotechnology Letters (한국미생물·생명공학회지)

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Phylogenetic Analysis and Diversity of Marine Bacteria Isolated from Rhizosphere Soils of Halophyte in Suncheon Bay

순천만에 자생하는 염생식물 근권에서 유래한 해양세균의 계통학적 분석 및 다양성

  • 유영현 (경북대학교 생명과학부) ;
  • 박종명 (롯데중앙연구소) ;
  • 이명철 (농촌진흥청 국립농업과학원 농업유전자원센터) ;
  • 김종국 (경북대학교 생명과학부)
  • Received : 2015.01.13
  • Accepted : 2015.02.17
  • Published : 2015.03.28
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Abstract

The bacterial diversity of the rhizosphere soil of S. japonica native to Suncheon bay was analyzed. Ninety two strains showing different morphological characteristics were isolated from the soils around the community of S. japonica. Bacterial diversity and distributions were studied by phylogenetic analysis of the partial 16S rDNA sequences. Ninety two strains were partially sequenced and analyzed phylogenetically. These strains were composed of 5 phyla firmicutes (56.5%), gamma-proteobacteria (29.3%), alpha-proteobacteria (5.4%), actinobacteria (5.4%), bacteroidetes (3.3%) and Shannon’s diversity index (H') were different from each of sampling sites (1.675, 1.924 and 2.04). Eleven isolates were presumed to be novel species candidates based on similarity analysis of the 16s rRNA gene sequences. Overall, Firmicutes and gamma-proteobacteria of the rhizosphere soil of S. japonica showed a high diversity.

순천만의 염생식물 근권에서 정주하는 세균의 분리를 위해 순천만에서 우점하는 자생식물인 칠면초 군락 3개 지점을 선발하여 샘플링 하였다. 시료는 marine broth, tryptic soy broth 한천배지를 통해 분리되었으며, 형태학적인 구분을 통해 순수분리되었다. 분리주의 16S rDNA를 분석하여 총 92 균주가 동정되었다. 이들의 유연관계 확인을 위한 계통수 작성 결과, 각각 firmicutes (56.5%), gamma-proteobacteria (29.3%), alpha-proteobacteria (5.4%), actinobacteria (5.4%), bacteroidetes (3.3%)에 속하였다. Shannon’s Diversity index (H')를 산출하였을 때 각각 1.675, 1.924, 2.04로, 채취 지점별로 종 다양성의 차이를 보였다.

Keywords

Acknowledgement

Grant : 하천 및 습지등 생태계복원을 위한 생물소재 개발

References

  1. Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169.
  2. Campbell BJ, Engel AS, Porter ML, Takai K. 2006. The versatile ε-proteobacteria: key players in sulphidic habitats. Nat. Rev. Microbiol. 4: 458-468. https://doi.org/10.1038/nrmicro1414
  3. Chapman VJ. 1974. Salt marshes and salt deserts of the world in ecology of halophytes. Academic Press, New York. pp. 3-22.
  4. Cottrell MT, Kirchman DL. 2000. Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl. Environ. Microbiol. 66: 5116-5122. https://doi.org/10.1128/AEM.66.12.5116-5122.2000
  5. Cottrell MT, Kirchman DL. 2000. Natural assemblages of marine proteobacteria and members Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 66: 1692-1697. https://doi.org/10.1128/AEM.66.4.1692-1697.2000
  6. Dai JM, Sun Y, Culp RA, Noakes JE. 2009. A laboratory study on biochemical degradation and microbial utilization of organic matter comprising a marine diatom, land grass, and salt marsh plant in estuarine ecosystems. Aquat. Ecol. 43: 825-841. https://doi.org/10.1007/s10452-008-9211-x
  7. Felsenstein J. 1985. Confidence limits on phylogenesis: an approach using the bootstrap. Evolution 39: 783-791. https://doi.org/10.2307/2408678
  8. Fierer N, Jackson RB. 2006. The diversity and bio-geography of soil bacterial communities. Proc. Natl. Acad. Sci. U.S.A. 103: 626-631. https://doi.org/10.1073/pnas.0507535103
  9. Glöckner FO, Fuchs BM, Aman R. 1999. Bacterio-plankton compositions of lakesand oceans: a first comparison based on fluorescence- in situ-hybridization. Appl. Environ. Microbiol. 65: 3721-3726.
  10. Gonzalez JM, Moran MA. 1997. Numerical dominance of a group of marine bacteria in the α-subclass of the class Proteobacteria in coastal seawater. Appl. Environ. Microbiol. 63: 4237-4242.
  11. Hill TC, Walsh KA, Harris JA, Moffett BF. 2003. Using ecological diversity measures with bacterial communities. FEMS Microbiol. Ecol. 43: 1-11. https://doi.org/10.1111/j.1574-6941.2003.tb01040.x
  12. I von der Weid, Alviano DS, Santos AL, Soares RM, Alviano CS, Seldin L. 2003. Antimicrobial activity of Paenibacillus peoriae strain NRRL BD-62 against a broad spectrum of phytopathogenic bacteria and fungi. J. Appl. Microbiol. 95: 1143-1151. https://doi.org/10.1046/j.1365-2672.2003.02097.x
  13. Ihm BS, Leem JS, Kim JW, Kim HS, Ihm HB. 1998. Studies on the vegetation at the wetland of Suncheonman. Bull. Inst. Litt. Envi. Mokpo. Nat. Univ. 15: 1-8.
  14. Jang SK, Cheong CJ. 2010. Characteristics of grain size and organic matters in the tidal flat sediments of the Suncheon Bay. J. Korean. Soc. Mar. Environ. Eng. 13: 198-205.
  15. Jeon SA, Sung HR, Park YM, Park JH, Ghim SY. 2009. Analysis of endospore-forming bacteria or nitrogen-fixing bacteria community isolated from plants rhizosphere in Dokdo island. Korean J. Microbiol. Biotechnol. 37: 189-196.
  16. Jeong SM, Lee MB. 2004. Change of estuary landscape in Suncheon Bay, South coast of Korea. J. Korean Geomorphological Association. 11: 127-139.
  17. Kim BS, Oh HM, Kang HJ, Park SS, Chun JS. 2004. Archaeal diversity in the tidal flat sediment as revealed by 16S rDNA analysis. J. Microbiol. 14: 205-211.
  18. Kim YE, Yoon HJ, You YH, Kim H, Seo YG, Kim M, et al. 2014. Diversity and characteristics of rhizosphere microorganisms isolated from the soil around the roots of three plants native to the Dokdo Islands. J. Life. Sci. 24: 461-466. https://doi.org/10.5352/JLS.2014.24.4.461
  19. Kim YG, Jin YA, Hwang CY, Cho BC. 2008. Marinobacterium rhizophilum sp. nov., isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica. Int. J. Syst. Evol. Microbiol. 58: 164-167. https://doi.org/10.1099/ijs.0.65176-0
  20. Lee S, Ka JO, Song HG. 2012. Growth promotion of Xanthium italicum by application of rhizobacterial isolates of Bacillus aryabhattai in microcosm soil. J. Microbiol. 50: 45-49. https://doi.org/10.1007/s12275-012-1415-z
  21. Li H, Qiao G, Li Q, Zhou W, Won KM, Xu DH, Park SI. 2010. Biological characteristics and pathogenicity of a highly pathogenic Shewanella marisflavi infecting sea cucumber, Apostichopus japonicus. J. Fish. Disease. 33: 865-867. https://doi.org/10.1111/j.1365-2761.2010.01189.x
  22. Lim JM, Jeon CO, Kim CJ. 2006. Bacillus taeanensis sp. nov.,a halophilic Gram-positive bacterium from a solar saltern in Korea. Int. J. Syst. Evol. Microbiol. 56: 2903-2908. https://doi.org/10.1099/ijs.0.64036-0
  23. Madhaiyan M, Poonguzhali S, Kwon SW, Sa TM. 2010. Bacillus methylotrophicus sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil. Int. J. Syst. Evol. Microbiol. 60: 2490-2495. https://doi.org/10.1099/ijs.0.015487-0
  24. Maidak BL, Cole JR, Parker TG, Jr CT, Saxman PR, Stredwick JM, et al. 2000. The RDP (Ribosomal Database project) continues. Nucleic Acids Res. 28: 73-174. https://doi.org/10.1093/nar/28.1.73
  25. Mani A, Arga CA, Jane D, Nithyalakshmy R, Kaveh E, Ehsan M. 2012. Carbohydrate degrading bacteria losely associated with Tetraselmis indica: influence on algal growth. Aquat. Biol. 15: 61-71. https://doi.org/10.3354/ab00402
  26. Mauricio Gutiérrez A, Peña Cabriales JJ, Maldonado Vega M. 2010. Isolation and characterization of hexavalent chromiumreducing rhizospheric bacteria from a wetland. Int. J. Phytoremediation. 12: 317-334. https://doi.org/10.1080/15226510902968118
  27. Ma Y, Prasad MN, Rajkumar M, Freitas H. 2010. Plant growth promoting rhizobacteria and endophytes accelerate phytoremediation of metalliferous soils. Biotechnol. Adv. 29: 248-258.
  28. MEthé BA, Hiorns WD, Zehr JP. 1998. Contrasts between marine and freshwater bacterial community com-position: analyses of communities in Lake George and six other Adirondack lakes. Limnol. Oceanogr. 43: 368-374. https://doi.org/10.4319/lo.1998.43.2.0368
  29. Nelson DM, Glawe AJ, Labeda DP, Cann IK, Mackie RI. 2009. Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundra. Int. J. Syst. Evol. Microbiol. 59: 1708-1714. https://doi.org/10.1099/ijs.0.004572-0
  30. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40: 337-365. https://doi.org/10.1146/annurev.mi.40.100186.002005
  31. QL Liu, GM YA, Miao LL, Zheng HY, Liu ZP. 2012. The characteristics of a novel heterotrophic nitrification-aerobic denitrification bacterium, Bacillus methylotrophicus strain L7. Bioresour. Technol. 108: 35-44. https://doi.org/10.1016/j.biortech.2011.12.139
  32. Rodriguez RJ, Henson J, Van VE, Hoy M, Wright L, Beckwith F, Kim Y, Redman RS. 2008. Stress tolerance in plants via habitat-adapted symbiosis. ISME J. 2: 404-416. https://doi.org/10.1038/ismej.2007.106
  33. Sandana Mala JG, Sujatha D, Rose C. 2015. Inducible chromate reductase exhibiting extracellular activity in Bacillus methylotrophicus for chromium bioremediation. Microbiol. Res. 170: 235-241. https://doi.org/10.1016/j.micres.2014.06.001
  34. Seo Y, Kim M, You YH, Yoon JH, Woo JR, Lee G, et al. 2012. Genetic diversity of endophytic fungi isolated from the roots of halophytes naturally growing in Suncheon Bay. Korean J. Mycol. 40: 7-10. https://doi.org/10.4489/KJM.2012.40.1.007
  35. Siddikee MA, Chauhan PS, Anandham R, Han GH, Sa TM. 2010. Isolation, characterization, and use for plant growth promotion under salt stress, of ACC deaminase-producing halotolerant bacteria derived from coastal soil. J. Microbiol. Biotechnol. 20: 1577-1584. https://doi.org/10.4014/jmb.1007.07011
  36. Sunar K, Dey P, Chakraborty U, Chakraborty B. 2015. Biocontrol efficacy and plant growth promoting activity of Bacillus altitudinis isolated from Darjeeling hills, India. J. Basic Microbiol. 55: 91-104. https://doi.org/10.1002/jobm.201300227
  37. Tang YW, Von GA, Waddington MG, Hopkins MK, Smith DH, Li H, et al. 2000. Identification of coryneform bacterial isolates by ribosomal DNA sequence analysis. J. Clin. Microbiol. 38: 1676-1678.
  38. Waller F, Achatz B, Baltruscha TH, Fodor J, Becker K, Fischer M, et al. 2005. The endophytic fungus Piriformospora indica reprograms barley to saltstress tolerance, disease resistance, and higher yield. Proc. Natl. Acad. Sci. U.S.A. 102: 13386-13391. https://doi.org/10.1073/pnas.0504423102
  39. Woo PC, Lau SK, Teng JL, Tse H, Yuen KY. 2008 Then and now: use of 16S rDNA gene se-quencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin. Microbiol. Infect. 14: 908-934. https://doi.org/10.1111/j.1469-0691.2008.02070.x
  40. Yamamura S, Yamashita M, Fujimoto N, Kuroda M, Kashiwa M, Sei K, et al. 2007. Bacillus selenatarsenatis sp. nov., a selenate- and arsenate-reducing bacterium isolated from the effluent drain of a glass-manufacturing plant. Int. J. Syst. Evol. Microbiol. 57: 1060-1064. https://doi.org/10.1099/ijs.0.64667-0
  41. Yamamura S, Watanabe M, Kanzaki M, Soda S, Ike M. 2008. Removal of arsenic from contaminated soils by microbial reduction of arsenate and quinone. Environ. Sci. Technol. 42: 6154-6159. https://doi.org/10.1021/es703146f
  42. Yoon JH, Kim IG, Kang KH, Oh TK, Park YH. 2003. Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. Int. J. Syst. Evol. Microbiol. 53: 1297-1303. https://doi.org/10.1099/ijs.0.02365-0
  43. Yoon JH, Lee ST, Park YH. 1998. Inter- and intraspecific phylogenetic analysis of the genus Norcardioides and related taxa based on 16s rRNA gene sequences. Int. J. Syst. Bacteriol. 48: 187-194. https://doi.org/10.1099/00207713-48-1-187
  44. You YH, Yoon H, Kang SM, Shin JH, Choo YS, Lee IJ, et al. 2012. Fungal diversity and plant growth promotion of endophytic Fungi from six halophytes in Suncheon Bay. J. Microbiol. Biotechnol. 22: 1550-1557.
  45. Zhiyong L, He L, Miao X. 2007. Cultivable bacterial community from south China sea sponge as revealed by DGGE fingerprinting and 16S rDNA phylogenetic analysis. Curr. Microbiol. 55: 654-672.

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