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.
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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.
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.
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.
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.
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.
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.
Peroni, C. and Rossi, G., Determination of Microbial Activity in Marine Sediments by Resazurin Reduction, Chem. Ecol., 1986, vol. 2, pp. 205–209.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Maloy, S.R., Experimental Techniques in Bacterial Genetics, Boston: Jones et Bartlett, 1990.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Nakamura, L.K., Bacillus psychrophilus sp. nov., nom. rev, Int. J. Syst. Bacteriol., 1984, vol. 34, pp. 121–123.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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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
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DOI: https://doi.org/10.1134/S0026261711010188