Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Biogeographical Distribution and Diversity of Bacterial Communities in Surface Sediments of the South China Sea

  • Li, Tao (State Key Laboratory of Marine Geology, Tongji University) ;
  • Wang, Peng (State Key Laboratory of Marine Geology, Tongji University)
  • Received : 2012.09.13
  • Accepted : 2012.12.26
  • Published : 2013.05.28
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Abstract

This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

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References

  1. Abulencia, C. B., D. L. Wyborski, J. A. Garcia, M. Podar, W. Chen, S. H. Chang, et al. 2006. Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl. Environ. Microbiol. 72: 3291-3301. https://doi.org/10.1128/AEM.72.5.3291-3301.2006
  2. Bowman, J. P. and R. D. McCuaig. 2003. Biodiversity, community structural shifts, and biogeography of prokaryotes within antarctic continental shelf sediment. Appl. Environ. Microbiol. 69: 2463-2483. https://doi.org/10.1128/AEM.69.5.2463-2483.2003
  3. Briee, C., D. Moreira, and P. Lopez-Garcia. 2007. Archaeal and bacterial community composition of sediment and plankton from asuboxic freshwater pond. Res. Microbiol. 158: 213-227. https://doi.org/10.1016/j.resmic.2006.12.012
  4. Briggs, B. R., F. Inagaki, Y. Morono, T. Futagami, C. Huguet, A. Rosell-Mele, et al. 2012. Bacterial dominance in subseafloor sediments characterized by methane hydrates. FEMS Microbiol. Ecol. 81: 88-98. https://doi.org/10.1111/j.1574-6941.2012.01311.x
  5. Cao, H., Y. Hong, M. Li, and J. Gu. 2011. Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the Western Pacific. Microb. Ecol. 62: 813-823. https://doi.org/10.1007/s00248-011-9901-0
  6. Chao, A. and T. J. Shen. Program SPADE (Species prediction and diversity estimation). Program and user's guide. Available at http://chao.stat.nthu.edu.tw.
  7. Colwell, F., A. Schwartz, and B. Briggs. 2011. Microbial community distribution in sediments from the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope. Maine Petrol. Geol. 28: 404-410. https://doi.org/10.1016/j.marpetgeo.2009.12.012
  8. D'Hondt, S., B. B. Jorgensen, D. J. Miller, A. Batzke, R. Blake, B. A. Cragg, et al. 2004. Distributions of microbial activities in deep subseafloor sediments. Science 306: 2216-2221. https://doi.org/10.1126/science.1101155
  9. D'Hondt, S., F. Inagaki, T. Ferdelman, B. B. Jorgensen, K. Kato, P. Kemp, et al. 2007. Exploring subseafloor life with the integrated ocean drilling program. Scientific Drilling 5: 26-37.
  10. Dai, X., H. Zhou, Y. Chen, C. Cai, Y. Zhou, S. Zhou, and L. Qu. 2002. A preliminary study on 16S rDNA diversity of bacteria in the Nansha marine sediment, the South China Sea. Progress Natural Science 12: 479-484.
  11. 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
  12. Etter, R. J. and J. F. Grassle. 1992. Patterns of species diversity in the deep sea as a function of sediment particle size diversity. Nature 360: 576-578. https://doi.org/10.1038/360576a0
  13. Fry, J. C., R. J. Parkes, B. A. Cragg, A. J. Weightman, and G. Webster. 2008. Prokaryotic biodiversity and activity in the deep subseafoor biosphere. FEMS Microbiol. Ecol. 66: 181-196. https://doi.org/10.1111/j.1574-6941.2008.00566.x
  14. Girvan, M. S., J. Bullimore, J. N. Pretty, A. M. Osborn, and A. S. Ball. 2003. Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl. Environ. Microbiol. 69: 1800-1809. https://doi.org/10.1128/AEM.69.3.1800-1809.2003
  15. Glatz, R. E., P. W. Lepp, B. B. Ward, and C. A. Francis. 2006. Planktonic microbial community composition across steep physical/chemical gradients in permanently ice-covered Lake Bonney, Antarctica. Geobiology 4: 53-67. https://doi.org/10.1111/j.1472-4669.2006.00057.x
  16. Huneke, H. and T. Mulder (eds.). 2011. Deep-Sea Sediments, Vol. 63 (Developments in Sedimentology). Elsevier Science, Oxford.
  17. Harris, J. K., S. T. Kelley, and N. R. Pace. 2004. New perspective on uncultured bacterial phylogenetic division OP11. Appl. Environ. Microbiol. 70: 845-849. https://doi.org/10.1128/AEM.70.2.845-849.2004
  18. Heijs, S. K., G. Aloisi, I. Bouloubassi, R. D. Pancost, C. Pierre, J. S. S. Damste, et al. 2006. Microbial community structure in three deep-sea carbonate crusts. Microb. Ecol. 52: 451-462.
  19. Heijs, S. K., R. R. Haese, P. W. J. J. Wielen, L. J. Forney, and J. D. Elsas. 2007. Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep. Microb. Ecol. 53: 384-398. https://doi.org/10.1007/s00248-006-9172-3
  20. Huber, J. A., H. P. Johnson, D. A. Butterfield, and J. A. Baross. 2006. Microbial life in ridge flank crustal fluids. Environ. Microbiol. 8: 88-99. https://doi.org/10.1111/j.1462-2920.2005.00872.x
  21. Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180: 366-376.
  22. Inagaki, F., M. M. M. Kuypers, U. Tsunogai, J.-I. Ishibashi, K.- I. Nakamura, T. Treude, et al. 2006. Microbial community in a sediment-hosted $CO_2$ lake of the southern Okinawa Trough hydrothermal system. Proc. Natl. Acad. Sci. USA 103: 14164-14169. https://doi.org/10.1073/pnas.0606083103
  23. Inagaki, F., T. Nunoura, S. Nakagawa, A. Teske, M. Lever, A. Lauer, et al. 2006. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc. Natl. Acad. Sci. USA 103: 2815-2820. https://doi.org/10.1073/pnas.0511033103
  24. Inagaki, F., Y. Sakihama, A. Inoue, C. Kato, and K. Horikoshi. 2002. Molecular phylogenetic analyses of reverse-transcribed bacterial rRNA obtained from deep-sea cold seep sediments. Environ. Microbiol. 4: 277-286. https://doi.org/10.1046/j.1462-2920.2002.00294.x
  25. Inagaki, F., M. Suzuki, K. Takai, H. Oida, T. Sakamoto, K. Aoki, et al. 2003. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl. Environ. Microbiol. 69: 7224-7235. https://doi.org/10.1128/AEM.69.12.7224-7235.2003
  26. Jorgensen, B. B. and A. Boetius. 2007. Feast and famine - microbial life in the deep-sea bed. Nat. Rev. Microbiol. 5: 770-781. https://doi.org/10.1038/nrmicro1745
  27. Jiao, L., X. Su, F. Chen, Y. Zhang, H. Jiang, Y. Luo, and H. Dong. 2011. Microbial diversity in sediments of core HS-PC 500 from Shenhu Area, northern South China Sea. Wei Sheng Wu Xue Bao 51: 876-890.
  28. Knittela, K., A. Boetius, A. Lemkea, H. Eilersa, K. Lochted, O. Pfannkuchee, et al. 2003. Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia Margin, Oregon). Geomicrobiol. J. 20: 269-294. https://doi.org/10.1080/01490450303896
  29. Kormas, K. A., D. C. Smith, V. Edgcomb, and A. Teske. 2003. Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol. Ecol. 45: 115-125. https://doi.org/10.1016/S0168-6496(03)00128-4
  30. Lopez-Garcia, P., S. Duperron, P. Philippot, J. Foriel, J. Susini, and D. Moreira. 2003. Bacterial diversity in hydrothermal sediment and epsilon-proteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ. Microbiol. 5: 961-971. https://doi.org/10.1046/j.1462-2920.2003.00495.x
  31. Li, T., P. Wang, and P. Wang. 2008. Bacterial and archaeal diversity in surface sediment from the south slope of the South China Sea. Wei Sheng Wu Xue Bao 48: 323-329.
  32. Li, T., P. Wang, and P. Wang. 2008. Microbial diversity in surface sediments of the Xisha Trough, the South China Sea. Acta Ecol. Sin. 28: 1166-1173. https://doi.org/10.1016/S1872-2032(08)60036-0
  33. Marchesi, J. R., A. J. Weightman, B. A. Cragg, R. J. Parkes, and J. C. Fry. 2001. Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol. Ecol. 34: 221-228. https://doi.org/10.1111/j.1574-6941.2001.tb00773.x
  34. Musata, N., U. Wernera, K. Knittela, S. Kolba, T. Dodenhofa, J. E. E. V. Beusekomb, et al. 2006. Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Romo Basin, Wadden Sea. Syst. Appl. Microbiol. 29: 333-348. https://doi.org/10.1016/j.syapm.2005.12.006
  35. Neef, A., R. Amann, H. Schlesner, and K.-H. Schleifer. 1998. Monitoring a widespread bacterial group: In situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144: 3257-3266. https://doi.org/10.1099/00221287-144-12-3257
  36. Nercessian, O., Y. Fouquet, C. Pierre, D. Prieur, and C. Jeanthon. 2005. Diversity of bacteria and archaea associated with a carbonate-rich metalliferous sediment sample from the rainbow vent field on the mid-atlantic ridge. Environ. Microbiol. 7: 698-714. https://doi.org/10.1111/j.1462-2920.2005.00744.x
  37. Newberry, C. J., G. Webster, B. A. Cragg, R. J. Parkes, A. J. Weightman, and J. C. Fry. 2004. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ. Microbiol. 6: 274-287. https://doi.org/10.1111/j.1462-2920.2004.00568.x
  38. Niemann, H., T. Losekann, D. D. Beer, M. Elvert, T. Nadalig, K. Knittel, et al. 2006. Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443: 854-858. https://doi.org/10.1038/nature05227
  39. Orcutt, B. N., J. B. Sylvan, N. J. Knab, and K. J. Edwards. 2011. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol. Molec. Biol. Rev. 75: 361-422. https://doi.org/10.1128/MMBR.00039-10
  40. Pachiadaki, M. G., V. Lykousis, E. G. Stefanou, and K. A. Kormas. 2010. Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea). FEMS Microbiol. Ecol. 72: 429-444. https://doi.org/10.1111/j.1574-6941.2010.00857.x
  41. Parkes, R. J., B. A. Cragg, N. Banning, F. Brock, G. Webster, J. C. Fry, et al. 2007. Biogeochemistry and biodiversity of methane cycling in subsurface marine sediments (Skagerrak, Denmark). Environ. Microbiol. 9: 1146-1161. https://doi.org/10.1111/j.1462-2920.2006.01237.x
  42. Parkes, R. J., G. Webster, B. A. Cragg, A. J. Weightman, C. J. Newberry, T. G. Ferdelman, et al. 2005. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436: 390-394. https://doi.org/10.1038/nature03796
  43. Penton, C. R., A. H. Devol, and J. M. Tiedje. 2006. Molecular evidence for the broad distribution of anaerobic ammoniumoxidizing bacteria in freshwater and marine sediments. Appl. Environ. Microbiol. 72: 6829-6832. https://doi.org/10.1128/AEM.01254-06
  44. Prell, W. L., P. Wang, P. Blum, D. K. Rea, and S. C. Clemens. 1999. Isotopic chemistry of organic carbon in sediments from Leg 184. In J. S. Leventhal (ed.). Proceedings of the Ocean Drilling Program, Scientific Results. Available at http://www.odp.tamu.edu/publications/184_SR/VOLUME/CHAPTERS/215.PDF.
  45. Reed, D. W., Y. Fujita, M. E. Delwiche, D. B. Blackwelder, P. P. Sheridan, T. Uchida, and F. S. Colwell. 2002. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microbiol. 68: 3759-3770. https://doi.org/10.1128/AEM.68.8.3759-3770.2002
  46. Rochelle, P. A., B. A. Cragg, J. C. Fry, R. J. Parkes, and A. J. Weightman. 1994. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S ribosomal-RNA gene sequence analysis. FEMS Microbiol. Ecol. 15: 215-225. https://doi.org/10.1111/j.1574-6941.1994.tb00245.x
  47. Sapp, M., E. R. Parker, L. R. Teal, and M. Schratzberger. 2010. Advancing the understanding of biogeography-diversity relationships of benthic microorganisms in the North Sea. FEMS Microbiol. Ecol. 74: 410-429. https://doi.org/10.1111/j.1574-6941.2010.00957.x
  48. Schäfer, H., T. G. Ferdelman, H. Fossing, and G. Muyzer. 2007. Microbial diversity in deep sediments of the Benguela Upwelling System. Aquat. Microb. Ecol. 50: 1-9. https://doi.org/10.3354/ame01164
  49. Schloss, P. D. and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71: 1501-1506. https://doi.org/10.1128/AEM.71.3.1501-1506.2005
  50. Sun, H., S. Dai, G. Wang, L. Xie, and X. Li. 2010. Phylogenetic diversity analysis of bacteria in the deep-sea sediments from the Bashi Channel by 16S rDNA BLAST. J. Trop. Oceanogr. 29: 41-46.
  51. Swofford, D. L. (ed.). 1999. PAUP: Phylogenetic Analysis Using Parsimony ($^*and$ other methods), Version 4.0. Sinauer Associates, Sunderland, Massachusetts.
  52. Teske, A., K. U. Hinrichs, V. Edgcomb, A. V. Gomez, D. Kysela, S. P. Sylva, et al. 2002. Microbial diversity of hydrothermal sediments in the Guaymas Basin: Evidence for anaerobic methanotrophic communities. Appl. Environ. Microbiol. 68: 1994-2007 https://doi.org/10.1128/AEM.68.4.1994-2007.2002
  53. Wagner, C., M. Mau, M. Schlomann, J. Heinicke, and U. Koch. 2007. Characterization of the bacterial flora in mineral waters in upstreaming fluids of deep igneous rock aquifers. J. Geophys. Res. 112: G01003.
  54. Walker, A. W., J. D. Sanderson, C. Churcher, G. C. Parkes, B. N. Hudspith, N. Rayment, et al. 2011. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol. 11: 7. https://doi.org/10.1186/1471-2180-11-7
  55. Wang, G., J. Dong, X. Li, and H. Sun. 2010. The bacterial diversity in surface sediment from the South China Sea. Acta Oceanol. Sin. 29: 98-105.
  56. Wang, J., C. Jenkins, R. I. Webb, and J. A. Fuerst. 2002. Isolation of Gemmata-like and Isosphaera-like planctomycete bacteria from soil and freshwater. Appl. Environ. Microbiol. 68: 417-422. https://doi.org/10.1128/AEM.68.1.417-422.2002
  57. Wang, P. and Q. Li (eds.). 2009. The South China Sea: Paleoceanography and Sedimentology. Springer, Berlin.
  58. Wang, P., T. Li, A. Hu, Y. Wei, W. Guo, N. Jiao, and C. Zhang. 2010. Community structure of Archaea from deep-sea sediments of the South China Sea. Microb. Ecol. 60: 796-806. https://doi.org/10.1007/s00248-010-9746-y
  59. Webster, G., R. J. Parkes, B. A. Cragg, C. J. Newberry, A. J. Weightman, and J. C. Fry. 2006. Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol. Ecol. 58: 65-85. https://doi.org/10.1111/j.1574-6941.2006.00147.x
  60. Wegener, G., M. Shovitri, K. Knittel, H. Niemann, M. Hovland, and A. Boetius. 2008. Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea). Biogeosci. Discuss. 5: 971-1015. https://doi.org/10.5194/bgd-5-971-2008
  61. Wei, Y., J. Wang, J. Liu, L. Dong, L. Li, H. Wang, et al. 2011. Spatial variations in archaeal lipids of surface water and coretop sediments in the South China Sea and their implications for paleoclimate studies. Appl. Environ. Microbiol. 77: 7479-7489. https://doi.org/10.1128/AEM.00580-11
  62. Wilms, R., B. Kopke, H. Sass, T. S. Chang, H. Cypionka, and B. Engelen. 2006. Deep biosphere-related bacteria within the subsurface of tidal flat sediments. Environ. Microbiol. 8: 709-719. https://doi.org/10.1111/j.1462-2920.2005.00949.x
  63. Wilms, R., H. Sass, B. Kopke, J. Koster, H. Cypionka, and B. Engelen. 2006. Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters. Appl. Environ. Microbiol. 72: 2756-2764. https://doi.org/10.1128/AEM.72.4.2756-2764.2006
  64. Xu, F., X. Dai, Y. Chen, H. Zhou, J. Cai, and L. Qu. 2004. Phylogenetic diversity of bacteria and archaea in the Nansha marine sediment, as determined by 16S rDNA analysis. Oceanol. Limnol. Sin. 35: 89-94.
  65. Zeng, R., J. Zhao, R. Zhang, and N. Lin. 2004. Bacterial community in sediment from the Western Pacific "Warm Pool" and its relationship to environment. Sci. China Ser. D Earth Sci. 42: 282-290.
  66. Zhang, Y., X. Su, F. Chen, Y. Wang, L. Jiao, H. Dong, et al. 2012. Microbial diversity in cold seep sediments from the northern South China Sea. Geosci. Frontiers 3: 301-316. https://doi.org/10.1016/j.gsf.2011.11.014
  67. Zhou, J., M. E. Davey, J. B. Figueras, E. Rivkina, D. Gilichinsky, and J. M. Tiedje. 1997. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143: 3913-3919. https://doi.org/10.1099/00221287-143-12-3913

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