Skip to main content
SpringerLink
Log in

Phylogenetic analysis of culturable marine bacteria in sediments from South Korean Yellow Sea

  • Experimental Articles
  • Published:
Microbiology Aims and scope Submit manuscript

Abstract

Biogeochemical and microbiological characterization of marine sediments taken from the Yellow Sea of South Korea was carried out. One hundred and thirty six bacterial strains were isolated, characterized and phylogenetic relationship was evaluated. The gene sequences of 16S rDNA regions were examined to study the phylogenetic analysis of bacterial community in the marine sediments. Among 136 isolates, 5 bacterial isolates were identified as novel members, remaining 131 isolates were fall into 5 major linkages of bacterial phyla represented as follows: Firmicutes,, -@Proteobacteria, High G + C and Bacteroidetes. Bacterial community in sediments mainly dominated by Firmicute (58.77%) and followed by @-Proteobacteria (38.16%). @-Proteobacteria domain highly diverged and mainly consists of the genera Vibrio, Marinobacterium, Photobacterium, Pseudoalteromonas, Oceanisphaera, Halomonas, Alteromonas, Stenotrophomas and Pseudomonas. Total N and Organic matter content in Yellow Sea of South Korea were relatively high. The Total-N content in the sediments was varied from 177.31 to 1974.96 (mg/kg) and organic matter ranged from 0.82 to 4.23 (g/100 g−1). The current research work provides clear explanation obtained for the phylogenetic affiliation of the culturable bacterial community in sediments of South Korean Yellow Sea and revealed the relationship with biogeochemical characteristics of the sediments.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Giovannoni, S.J., Britschgi, T.B., Moyer, C.L., and Field, K.G., Genetic Diversity in Sargasso Sea Bacterioplankton, Nature, 1990, vol. 345, pp. 60–63.

    Article  PubMed  CAS  Google Scholar 

  2. Urakawa, H., Kita-Tsukamoto, K., and Ohwada, K., Microbial Diversity in Marine Sediments from Sagami Bay and Tokyo Bay, Japan, as Determined by 16SrRNA Gene Analysis, Microbiol., 1999, vol. 145, pp. 3305–3315.

    CAS  Google Scholar 

  3. Gray, J.P. and Herwig, R.P., Phylogenetic Analysis of the Bacterial Communities in Marine Sediments, Appl. Environ. Microbiol., 1996, vol. 62, pp. 4049–4059.

    PubMed  CAS  Google Scholar 

  4. Hongxiang, X., Min, W., Xiaogu, W., Junyi, Y., and Chunsheng, W., Bacterial Diversity in Deep-Sea Sediment from Northeastern Pacific Ocean, Acta Ecol. Sinica., 2008, vol. 28, pp. 479–485.

    Article  Google Scholar 

  5. Lee, J.H., Shin, H.H., Lee, D.S., Kwon, K.K., Kim, S.J., and Lee, H.K., Bacterial Diversity of Culturable Isolates from Seawater and a Marine Coral, Plexauridae sp., Near Mun-Sum, Cheju-Island, J. Microbiol., 1999, vol. 37, pp. 193–199.

    Google Scholar 

  6. Cetecioglu, Z., Ince, B.K., Kolukirik, M., and Ince, O., Biogeographical Distribution and Diversity of Bacterial and Archaeal Communities Within Highly Polluted Anoxic Marine Sediments from the Marmara Sea, Mar. Pollut. Bull., 2009, vol. 58, pp. 384–395.

    Article  PubMed  CAS  Google Scholar 

  7. Peroni, C. and Rossi, G., Determination of Microbial Activity in Marine Sediments by Resazurin Reduction, Chem. Ecol., 1986, vol. 2, pp. 205–209.

    Article  CAS  Google Scholar 

  8. Suzuki, M.T., Rappe, M.S., Haimberger, Z.W., Winfield, H., Adair, N., Strobel, J., and Giovannoni, S.J., Bacterial Diversisty among Small-Subunit rRNA Gene Clones and Cellular Isolates from the Same Seawater Sample, Appl. Environ. Microbiol., 1997, vol. 63, pp. 983–989.

    PubMed  CAS  Google Scholar 

  9. Dunbar, J., Takala, S., Barns, S.M., Davis, J.A., and Kuske, C.R., Levels of Bacterial Community Diversity in Four arid Soils Compared by Cultivation and 16S rRNA Gene Cloning, Appl. Environ. Microbiol., 1999, vol. 65, pp. 1662–1669.

    PubMed  CAS  Google Scholar 

  10. D’Hondt, S., Jorgensen, B.B., Miller, D.J., Batzke, A., Blake, R., Cragg, B.A., Cypionka, H., Dickens, G.R., Ferdelman, T., Hinrichs, K.U., Holm, N.G., Mitterer, R., Spivack, A., Wang, G., Bekins, B., Engele, B., Ford, K., Gettemy, G., Rutherford, S.D., Sass, H., Skilbeck, G., Aiello, I.W., Guerin, G., House, C.H., Inagaki, F., Meister, P., Naehr, T., Siitsuma, S., Parkes, R.J., Schippers, A., Smith, D.C., Teske, A., Wiegel, J., Padilla, C.N., and Acosta, J.L.S., Distribution of Microbial Activities in Deep Subseafloor Sediments, Science, 2004, vol. 306, pp. 2216–2221.

    Article  PubMed  Google Scholar 

  11. Muller, P.J., C/N Ratios of Pacific Deep Sediments: Effect of Inorganic Ammonium and Organic Nitrogen Compounds Sorbed by Clays, Geochim. Cosmochim. Acta, 1977, vol. 41, pp. 765–776.

    Article  Google Scholar 

  12. Berner, R.A., Burial of Organic Carbon and Pyrite Sulphur in Modern Ocean: Its Geochemical and Environmental Significance, Amer. J. Sci., 1982, vol. 282, pp. 451–473.

    Article  CAS  Google Scholar 

  13. Geetha, R., Chandramohanakumar, N., and Mathews, L., Geochemical Reactivity of Surficial and Core Sediment of a Tropical Mangrove Ecosystem, Int. J. Environ. Res., 2008, vol. 2, pp. 329–342.

    Google Scholar 

  14. Lee, J.W., Nam, J.H., Kim, Y.H., Lee, K.H., and Lee, D.H., Bacterial Communities in the Initial Stage of Marine Biofilm Formation on Artificial Surfaces, J. Microbiol., 2008, vol. 46, pp. 174–182.

    Article  PubMed  CAS  Google Scholar 

  15. Ordonez, O.F., Flores, M.R., Bib, J.R., Paz, A., and Farias, M.E., Extremophile Culture Collection from Andean Lakes: Extreme Pristine Environments that Host a Wide Diversity of Microorganisms with Tolerance to UV Radiation, Microbiol. Ecol., 2009, vol. 58, pp. 461–473.

    Article  Google Scholar 

  16. Zhou, M.Y., Chen, X.L., Zhao, H.L., Dang, H.Y., Luan, X.W., Zhang, X.Y., He, H.L., Zhou, B.C., and Zhang, Y.Z., Diversity of Both the Cultivable Protease-Producing Bacteria and Their Extracellular Proteases in the Sediments of the South China Sea, Microbiol. Ecol., 2009, vol. 58, pp. 582–590.

    Article  Google Scholar 

  17. Jensen, P.R. and Fenical, W., Marine Bacterial Diversity as a Resource for Novel Microbial Products. J. Ind. Microbiol., 1996, vol. 17, pp. 346–351.

    Article  CAS  Google Scholar 

  18. Walkley, A. and Black, I.A., An Examination of the Degtjareff Method for Determining Soil Organic Matter and a Proposed Modification of the Chromic Acid Titration Method, Soil Sci., 1934, vol. 37, pp. 29–38.

    Article  CAS  Google Scholar 

  19. Maloy, S.R., Experimental Techniques in Bacterial Genetics, Boston: Jones et Bartlett, 1990.

    Google Scholar 

  20. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J., Gapped BLAST and PSI-BLAST: a New Generation of Protein Database Search Programs, Nucl. Acid. Res., 1997, vol. 25, pp. 3389–3402.

    Article  CAS  Google Scholar 

  21. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G., The ClustalX Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools, Nucl. Acid Res., 1997, vol. 24, pp. 4876–4882.

    Article  Google Scholar 

  22. Li, Z., Hu, Y., Liu, Y., Huang, Y., He, L., and Miao, X., 16S rDNA Clone Library-Based Bacterial Phylogenetic Diversity Associated with Three South China Sea Sponges, World J. Microbiol. Biotechnol., 2007, vol. 23, pp. 1265–1272.

    Article  CAS  Google Scholar 

  23. Quan, Z.X., Xiao, Y.P., Roh, S.W., Nam, Y.D., Chang, H.W., Shin, K.S., Rhee, S.K., Park, Y.H., and Bae, J.W., Joostella marina gen. nov., sp. nov., a Novel Member of the Family Flavobacteriaceae Isolated from the East Sea, Int. J. Syst. Evol. Microbiol., 2008, vol. 58, pp. 1388–1392.

    Article  PubMed  CAS  Google Scholar 

  24. Radke, L.C., Howard, K.W.F., and Gell, P.A., Chemical Diversity in Southeastern Australian Saline Lakes I. Geochemical Causes, Mar. Freshwater Res., 2002, vol. 53, pp. 1–19.

    Article  Google Scholar 

  25. Shaw, G.A., Adams, J.B., and Bornman, T.G., Sediment Characteristics and Vegetation Dynamics as Indicators for the Potential Rehabilitation of an Estuary Salt Marsh on the Arid West Coast of South Africa, J. Arid Environments., 2008, vol. 72, pp. 1097–1109.

    Article  Google Scholar 

  26. Huston, A.L. and Deming, J.W., Relationships between Microbial Extracellular Enzymatic Activity and Suspended and Sinking Particulate Organic Matter: Seasonal Transformations in the North Water, Deep-Sea Res. II, 2002, vol. 49, pp. 5211–5225.

    Article  CAS  Google Scholar 

  27. Koster, M. and Meyer-Reil, L.A., Characterization of Carbon and Microbial Biomass Pools in Shallow Water Coastal Sediments of the Southern Baltic Sea (Nordrugensche Bodden), Mar. Ecol. Prog. Ser., 2001, vol. 214, pp. 25–41.

    Article  CAS  Google Scholar 

  28. Ast, J.C., Cleenweck, I., Engelbeen, K., Ubanczyk, H., Thompson, F.L., De-Vos, P., and Dunlap, P.V., Photobacterium kishitanii sp. nov., a Luminous Marine Bacterium Symbiotic with Deep-Sea Fishes, Int. J. Syst. Evol. Microbiol., 2007, vol. 57, pp. 2073–2078.

    Article  PubMed  CAS  Google Scholar 

  29. Ast, J.C. and Dunlap, P.V., Phylogenetic Resolution and Habitat Specificity of Members of the Photobacterium phosphoreum Species Group, Environ. Microbiol., 2005, vol. 7, pp. 1641–1654.

    Article  PubMed  CAS  Google Scholar 

  30. Grant, W.D., Rhodes, L.L., Porsser, B.A., and Asher, R.A., Production of Bacteriolytic Enzymes and Degradation of Bacteria by Filamentous Fungi, J. Eng. Microbiol., 1986, vol. 132, pp. 2353–2358.

    CAS  Google Scholar 

  31. Wang, G., Shuai, L., Li, Y., Lin, W., Zhao, X., and Duan, D., Phylogenetic Analysis of Epiphytic Marine Bacteria on Hole-Rotten Diseased Sporophytes of Laminaria japonica, J. Appl. Phycol., 2008, vol. 20, pp. 403–409.

    Article  Google Scholar 

  32. Takamoto, S., Yamada, K., and Ezura, Y., Production of Bacteriolytic Enzymes during the Growth of a Marine Bacterium Alteromonas sp. No. 8-R, J. Gen. Appl. Microbiol., 1994, vol. 40, pp. 499–508.

    Article  CAS  Google Scholar 

  33. Ivanova, E.P., Sawabe, T., Alexeeva, Y.V., Lysenko, A.M., Gorshkova, N.M., Hayashi, K., Zhukova, N.V., Christen, R., and Mikhailov, V.V., Pseudoalteromonas issachenkonii sp. nov., a Bacterium That Degrades the Thallus of the Brown Alga Focus evanescens, Int. J. Syst. Evol. Microbiol., 2002, vol. 52, pp. 229–234.

    PubMed  CAS  Google Scholar 

  34. Wichels, A., Wurtz, S., Dopke, H., Schutt, C., and Gerdts, G., Bacterial Diversity in the Breadcrumb Sponge Halichondria panacea (pallas), FEMS Microbiol. Ecol., 2006, vol. 56, pp. 102–118.

    Article  PubMed  CAS  Google Scholar 

  35. Farrow, J.A.E., Wallbanks, S., and Collins, M.D., Phylogenetic Interrealtionships of Round-Spore-Forming Bacilli Containing Cell Walls Based on Lysine and the Non-Spore-Forming Genera Caryophanon, Fiiguobacterium, Kurthia and Planococcus, Int. J. Syst. Bacteriol., 1994, vol. 44, pp. 74–82.

    Article  PubMed  CAS  Google Scholar 

  36. Yoon, J.H., Kang, S.J., Schumann, P., and Oh, T.-K., Jeotgalibacillus salarius sp. nov., Isolated from a Marine Saltern, and Reclassification of Marinibacillus marinus and Marinibacillus campisalis into the Genus Jeotgalibacillus as Jeotgalibacillus marinus comb. nov. and Jeotgalibacillus campisalis comb. nov., Respectively, Int. J. Syst. Evol. Microbiol., 2010, V. 60. P. 15–20.

    Article  PubMed  CAS  Google Scholar 

  37. Reddy, G.S.N., Matsumoto, G.I., and Shivaji S., Sporosarcina macmurdoensis sp. nov., from a Cyanobacterial Mat Sample from a Pond in the McMurdo Dry Valleys, Antarctica, Int. J. Syst. Evol. Microbiol., 2003, vol. 53, pp. 1363–1367.

    Article  PubMed  CAS  Google Scholar 

  38. Nakamura, L.K., Bacillus psychrophilus sp. nov., nom. rev, Int. J. Syst. Bacteriol., 1984, vol. 34, pp. 121–123.

    Article  Google Scholar 

  39. Yoon, J.H., Lee, K.C., Weiss, N., Kho, Y.H., Kang, K.H., and Park, Y.H., Sporosarcina aquimarina sp. nov., a Bacterium Isolated from Seawater in Korea, and Transfer of Bacillus globisporus (Larkin & Stokes 1967), Bacillus psychrophilus (Nakamura 1984) and Bacillus pasteurii (Chester 1898) to the genus Sporosarcina as Sporosarchina globispora comb. nov., Sporosarcina psycrophila comb. nov. and Sporosarcina pasteurii comb. nov., and Emended Description of the Genus Sporosarcina, Int. J. Syst. Evol. Microbiol., 2001, vol. 51, pp. 1079–1086.

    PubMed  CAS  Google Scholar 

  40. Maldonado, L.A., Stach, J.E., Pathom-aree, W., Ward, A.C., Bull, A.T., and Goodfellow, M., Diversity of Cultivable Actinobacteria in Geographically Widespread Marine Sediments, Antonie van Leeuwenhoek, 2005, vol. 87, pp. 11–18.

    Article  PubMed  Google Scholar 

  41. Wu, J., Guan, T., Jiang, H., Zhi, X., Tang, S., Dong, H., Zhang, L., and Li, W., Diversity of Actinobacterial Community in Saline Sediments from Yunnan and Xinjiang, China, Extremophiles, 2009, vol. 13, pp. 623–632.

    Article  PubMed  Google Scholar 

  42. Stach, J.E., Maldonado, L.A., Masson, D.G., Ward, A.C., Goodfellow, M., and Bull, A.T., Statistical Approaches for Estimating Actinobacterial Diversity in Marine Sediments, Appl. Environ. Microbiol., 2003, vol. 69, pp. 6189–6200.

    Article  PubMed  CAS  Google Scholar 

  43. Jensen, P.R. and Fenical, W., The Relative Abundance and Seawater Requirements of Gram-Positive Bacteria in Near Shore Tropical Marine Samples, Microb. Ecol., 1995, vol. 29, pp. 249–257.

    Article  Google Scholar 

  44. Moran, M.A., Rutherford, L.T., and Hodson, R.E., Evidence for Indigenous Streptomyces Populations in a Marine Environment Determined with a 16S rRNA Probe, Appl. Environ. Microbiol., 1995, vol. 61, pp. 3695–3700.

    PubMed  CAS  Google Scholar 

  45. Park, J.R., Bae, J.W., Nam, Y.D., Chang, H.W., Kwon, H.Y., Quan, Z.X., and Park, Y.H., Sulfitobacter litoralis sp. nov., a Marine Bacterium Isolated from the East Sea, Korea, Int. J. Syst. Evol. Microbiol., 2007, vol. 57, pp. 692–695.

    Article  PubMed  CAS  Google Scholar 

  46. Sorokin, D.Y., Sulfitobacter pontiacus gen. nov., sp. nov. — a New Heterotrophic Bacterium from the Black Sea, Specialized on Sulfite Oxidation, Microbiology (English version of Mikrobiologiya), 1995, vol. 64, pp. 295–305.

    Google Scholar 

  47. Ivanova, E.P., Gorshkova, N.M., Sawabe, T., Zhukova, N.V., Hayashi, K., Kurilenko, V.V., Alexeeva, Y., Buljan, V., Nicolau, D.V., Mikhailov, V.V. and Christen, R., Sulfitobacter delicates sp. nov. and Sulfitobacter dubius sp. nov., Respectively from a Starfish (Stellaster equestris) and Sea Grass (Zostera marina), Int. J. Syst. Evol. Mocrobiol., 2004, vol. 54, pp. 475–480.

    Article  CAS  Google Scholar 

  48. Widdel, R., Microbiology and Ecology of Sulfate and Sulfur Reducing Bacteria, In A. J. B. Zehnder (ed.), Biology of Anaerobic Microorganisms. John Wiley & Sons Inc New York, 1991, pp. 469–585.

Download references

Author information

Authors and Affiliations

  1. Department of Forest Science and Technology, Institute of Agricultural Science and Technology, Chonbuk National University, Jeonju, South Korea

    Natarajan Velmurugan, Duraisamy Kalpana & Yang-Soo Lee

  2. Department of Agricultural Chemistry, Chonbuk National University, Jeonju, South Korea

    Jae-Young Cho

  3. Biological Science Major, School of Science and Technology, Kunsan National University, Kunsan, South Korea

    Geon-Hyoung Lee & Suk-Hwan Park

Authors
  1. Natarajan Velmurugan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Duraisamy Kalpana
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jae-Young Cho
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Geon-Hyoung Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Suk-Hwan Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yang-Soo Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yang-Soo Lee.

Additional information

The article is published in the original.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Velmurugan, N., Kalpana, D., Cho, JY. et al. Phylogenetic analysis of culturable marine bacteria in sediments from South Korean Yellow Sea. Microbiology 80, 261–272 (2011). https://doi.org/10.1134/S0026261711010188

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0026261711010188

Key words

Search

Navigation