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Acta Oceanologica Sinica

, Volume 35, Issue 6, pp 85–93 | Cite as

A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean

  • Jing Wang
  • Jinjun Kan
  • Laura Borecki
  • Xiaodong Zhang
  • Dongxiao Wang
  • Jun SunEmail author
Article

Abstract

Besides being critical components of marine food web, microorganisms play vital roles in biogeochemical cycling of nutrients and elements in the ocean. Currently little is known about microbial population structure and their distributions in the eastern Indian Ocean. In this study, we applied molecular approaches including polymerase chain reaction-denaturant gradient gel electrophoresis (PCR-DGGE) and High-Throughput next generation sequencing to investigate bacterial 16S rRNA genes from the equatorial regions and the adjacent Bay of Bengal in the eastern Indian Ocean. In general, Bacteroidetes, Proteobacteria (mainly Alpha, and Gamma), Actinobacteria, Cyanobacteria and Planctomycetes dominated the microbial communities. Horizontally distinct spatial distribution of major microbial groups was observed from PCR-DGGE gel image analyses. However, further detailed characterization of community structures by pyrosequencing suggested a more pronounced stratified distribution pattern: Cyanobacteria and Actinobacteria were more predominant at surface water (25 m); Bacteroidetes dominated at 25 m and 150 m while Proteobacteria (mainly Alphaproteobacteria) occurred more frequently at 75 m water depth. With increasing water depth, the bacterial communities from different locations tended to share high similarity, indicating a niche partitioning for minor groups of bacteria recovered with high throughput sequencing approaches. This study provided the first “snapshot” on biodiversity and spatial distribution of Bacteria in water columns in the eastern Indian Ocean, and the findings further emphasized the potential functional roles of these microbes in energy and resource cycling in the eastern Indian Ocean.

Keywords

eastern Indian Ocean water column bacterial community pyrosequencing 

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References

  1. Amaral-Zettler L, Artigas L F, Baross J, et al. 2010. A global census of marine microbes. In: McIntyre A D, ed. Life in the World’s Oceans: Diversity, Distribution, and Abundance. Oxford: Wiley-Blackwell Publishing Ltd, 223–245Google Scholar
  2. Arrigo K R. 2005. Marine microorganisms and global nutrient cycles. Nature, 437(7057): 349–355CrossRefGoogle Scholar
  3. Azam F, Steward G F, Smith D C, et al. 1994. Significance of bacteria in carbon fluxes in the Arabian Sea. Proc Proceedings of the Indian Academy of Sciences-Earth and Planetary Sciences, 103(2): 341–351Google Scholar
  4. Bharathi P A L, Nair S. 2005. Rise of the dormant: simulated disturbance improves culturable abundance, diversity, and functions of deep-sea bacteria of Central Indian Ocean Basin. Mar Georesour Geotechnol, 23(4): 419–428CrossRefGoogle Scholar
  5. Bouteiller A L, Blanchot J, Rodier M. 1992. Size distribution patterns of phytoplankton in the western Pacific: towards a generalization for the tropical open ocean. Deep Sea Research Part A: Oceanographic Research Papers, 39(5): 805–823CrossRefGoogle Scholar
  6. Brinkhoff T, Giebel H A, Simon M. 2008. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol, 189(6): 531–539CrossRefGoogle Scholar
  7. Brown M V, Philip G K, Bunge J A, et al. 2009. Microbial community structure in the North Pacific Ocean. ISME J, 3(12): 1374–1386CrossRefGoogle Scholar
  8. Buchan A, Neidle E L, Moran M A. 2004. Diverse organization of genes of the β-ketoadipate pathway in members of the marine Roseobacter lineage. Appl Environ Microbiol, 70(3): 1658–1668CrossRefGoogle Scholar
  9. Burkill P H. 2002. Microbial dynamics. In: Watts L, Burkill P, Smith S, eds. Arabian, Sea Process Study. Bergen, Norway: JGOFS International Planning OfficeGoogle Scholar
  10. Clarke K R. 1993. Non-parametric multivariate analyses of changes in community structure. Aust J Ecol, 18(1): 117–143CrossRefGoogle Scholar
  11. Cole S E, LaRiviere F J, Merrikh C N, et al. 2009. A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay. Mol Cell, 34(4): 440–450CrossRefGoogle Scholar
  12. da Silva M A C, Cavalett A, Spinner A, et al. 2013. Phylogenetic identification of marine bacteria isolated from deep-sea sediments of the eastern South Atlantic Ocean. SpringerPlus, 2(1): 127, doi: 10.1186/2193–1801–2127CrossRefGoogle Scholar
  13. Du Jikun, Xiao Kai, Li Li, et al. 2013. Temporal and spatial diversity of bacterial communities in coastal waters of the South China Sea. PLoS One, 8(6): e66968CrossRefGoogle Scholar
  14. Edgar R C, Haas B J, Clemente J C, et al. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16): 2194–2200CrossRefGoogle Scholar
  15. Emerson D, Fleming E J, McBeth J M. 2010. Iron-oxidizing bacteria: an environmental and genomic perspective. Annu Rev Microbiol, 64(1): 561–583CrossRefGoogle Scholar
  16. Fennel K, Follows M, Falkowski P G. 2005. The co-evolution of the nitrogen, carbon and oxygen cycles in the Proterozoic ocean. Am J Sci, 305(6–8): 526–545CrossRefGoogle Scholar
  17. Fernández-Gómez B, Richter M, Schüler M, et al. 2013. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J, 7(5): 1026–1037CrossRefGoogle Scholar
  18. Fine R A, Smethie W M, Bullister J L, et al. 2008. Decadal ventilation and mixing of Indian Ocean waters. Deep Sea Research Part I: Oceanographic Research Papers, 55(1): 20–37CrossRefGoogle Scholar
  19. Fuhrman J A, McCallum K, Davis A A. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol, 59(5): 1294–1302Google Scholar
  20. Fuhrman J A, Steele J A. 2008. Community structure of marine bacterioplankton: patterns, networks, and relationships to function. Aquat Microb Ecol, 53(1): 69–81CrossRefGoogle Scholar
  21. Glöckner F O, Fuchs B M, Amann R. 1999. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol, 65(8): 3721–3726Google Scholar
  22. Goñi-Urriza M, de Montaudouin X, Guyoneaud R, et al. 1999. Effect of macrofaunal bioturbation on bacterial distribution in marine sandy sediments, with special reference to sulphur-oxidising bacteria. J Sea Res, 41(4): 269–279CrossRefGoogle Scholar
  23. Han D, Ha H K, Hwang C Y, et al. 2014. Bacterial distribution along stratified water columns in the Pacific sector of the Arctic Ocean. Deep Sea Research Part II: Topical Studies in Oceanography, doi: 10.1016/j.dsr2.2014.06.007Google Scholar
  24. Hoek J, Banta A, Hubler F, et al. 2003. Microbial diversity of a sulphide spire located in the Edmond deep-sea hydrothermal vent field on the Central Indian Ridge. Geobiology, 1(2): 119–127CrossRefGoogle Scholar
  25. Hood R R, Wiggert J D, Naqvi S W A. 2009. Indian ocean research: opportunities and challenges. In: Wiggert J D, Hood R R, Naqvi S W A, eds. Indian Ocean Biogeochemical Processes and Ecological Variability. Geophysical Monograph Series Washington, DC: American Geophysical Union, 409–429CrossRefGoogle Scholar
  26. Ivanova E P, Gorshkova N M, Sawabe T, et al. 2004. Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina). Int J Syst Evol Microbiol, 54(2): 475–480CrossRefGoogle Scholar
  27. Jason S, Siddiqui P J A, Walsby A E, et al. 1995. Cytomorphological characterization of the planktonic diazotrophic cyanobacteria Trichodesmium spp. from the Indian Ocean and Caribbean and Sargasso Seas. J Phycol, 31(3): 463–477CrossRefGoogle Scholar
  28. Jiao Nianzhi, Zhang Yao, Zeng Yonghui, et al. 2007. Distinct distribution pattern of abundance and diversity of aerobic anoxygenic phototrophic bacteria in the global ocean. Environ Microbiol, 9(12): 3091–3099CrossRefGoogle Scholar
  29. Johnson R M, Schwent R M, Press W. 1968. The characteristics and distribution of marine bacteria isolated from the Indian Ocean. Limnol Oceanogr, 13(4): 656–664CrossRefGoogle Scholar
  30. Kabisch A, Otto A, König S, et al. 2014. Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803. ISME J, 8(7): 1492–1502CrossRefGoogle Scholar
  31. Kan Jinjun, Crump B C, Wang Kui, et al. 2006a. Bacterioplankton community in Chesapeake Bay: predictable or random assemblages. Limnol Oceanogr, 51(5): 2157–2169CrossRefGoogle Scholar
  32. Kan Jinjun, Wang Kui, Chen Feng. 2006b. Temporal variation and detection limit of an estuarine bacterioplankton community analyzed by denaturing gradient gel electrophoresis (DGGE). Aquat Microb Ecol, 42(1): 7–18CrossRefGoogle Scholar
  33. Keller M, Zengler K. 2004. Tapping into microbial diversity. Nat Rev Microbiol, 2(2): 141–150CrossRefGoogle Scholar
  34. Khandeparker R, Meena R M, Deobagkar D. 2014. Bacterial diversity in deep-sea sediments from Afanasy Nikitin seamount, equatorial Indian Ocean. Geomicrobiol J, 31(10): 942–949CrossRefGoogle Scholar
  35. Kirchman D L. 2002. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol, 39(2): 91–100Google Scholar
  36. Konstantinidis K T, DeLong E F. 2008. Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J, 2(10): 1052–1065CrossRefGoogle Scholar
  37. Kumar S P, Muraleedharan P M, Prasad T G, et al. 2002. Why is the Bay of Bengal less productive during summer monsoon compared to the Arabian Sea?. Geophys Res Lett, 29(24): 881–884, doi: 10.1029/2002GL016013CrossRefGoogle Scholar
  38. Kumar S P, Narvekar J, Nuncio M, et al. 2009. What drives the biological productivity of the northern Indian Ocean?. In: Wiggert J D, Hood R R, Naqvi S W A, et al., eds. Indian Ocean Biogeochemical Processes and Ecological Variability. Washington, DC: American Geophysical Union, 33–56CrossRefGoogle Scholar
  39. Kumar S P, Nuncio M, Narvekar J, et al. 2004. Are eddies nature’s trigger to enhance biological productivity in the Bay of Bengal?. Geophys Res Lett, 31(7): L07309, doi: 10.1029/2003GL019274Google Scholar
  40. McCreary J P, Yu Z, Hood R R, et al. 2013. Dynamics of the Indian-Ocean oxygen minimum zones. Prog Oceanogr, 112–113: 15–37CrossRefGoogle Scholar
  41. Madhupratap M, Gauns M, Ramaiah N, et al. 2003. Biogeochemistry of the Bay of Bengal: physical, chemical and primary productivity characteristics of the central and western Bay of Bengal during summer monsoon 2001. Deep Sea Research Part II: Topical Studies in Oceanography, 50(5): 881–896CrossRefGoogle Scholar
  42. Moran M A, Armbrust E V. 2007. Genomes of sea microbes. Oceanogr, 20(2): 47–55CrossRefGoogle Scholar
  43. Moran M A, Belas R, Schell M A, et al. 2007. Ecological genomics of marine Roseobacters. Appl Environ Microbiol, 73(14): 4559–4569CrossRefGoogle Scholar
  44. Mosher J J, Bernberg E L, Shevchenko O, et al. 2013. Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples. J Microbiol Methods, 95(2): 175–181CrossRefGoogle Scholar
  45. Muyzer G, de Waal E C, Uitterlinden A G. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol, 59(3): 695–700Google Scholar
  46. Nair S, Bharathi P A L, Chandramohan D. 1994. Culturable heterotrophic bacteria from the euphotic zone of the Indian-Ocean during the summer monsoon. Oceanologica Acta, 17(1): 63–68Google Scholar
  47. Nyadjro E, Subrahmanyam B, Giese B S. 2013. Variability of salt flux in the Indian Ocean during 1960–2008. Remote Sens Environ, 134: 175–193CrossRefGoogle Scholar
  48. Oren A. 2014. Cyanobacteria: biology, ecology and evolution. In: Sharma N K, Rai A K, Stal L, eds. Cyanobacteria: An Economic Perspective. Oxford: Wiley-Blackwell, 1–20Google Scholar
  49. Pace N R. 1997. A molecular view of microbial diversity and the biosphere. Science, 276(5313): 734–740CrossRefGoogle Scholar
  50. Parkes R J, Sellek G, Webster G, et al. 2009. Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG). Environ Microbiol, 11(12): 3140–3153CrossRefGoogle Scholar
  51. Parsons T R, Maita Y, Lalli C M. 1984. Determination of chlorophylls and total carotenoids: spectrophotometric method. In: Parsons T R, Maita Y, Lalli C M, eds. A Manual of Chemical and Biological Methods for Seawater Analysis. Oxford: Pergamin Press, 101–112CrossRefGoogle Scholar
  52. Priest F G. 1993. Systematics and ecology of Bacillus. In: Sonenshein A L, Hoch J A, Losick R, eds. Bacillus Subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology and Molecular Genetics. Washington: American Society for Microbiology PressGoogle Scholar
  53. Pukall R, Buntefuβ D, Frühling A, et al. 1999. Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the a-Proteobacteria. Int J Syst Evol Microbiol, 49(2): 513–519Google Scholar
  54. Rao C K, Naqvi S W A, Kumar M D, et al. 1994. Hydrochemistry of the Bay of Bengal: possible reasons for a different water-column cycling of carbon and nitrogen from the Arabian Sea. Mar Chem, 47(3–4): 279–290CrossRefGoogle Scholar
  55. Rixen T, Ramaswamy V, Gaye B, et al. 2008. Monsoonal and ENSO impacts on particle fluxes and the biological pump in the Indian Ocean. In: Wiggert J D, Hood R R, Naqvi S W A, et al., eds. Indian Ocean Biogeochemical Processes and Ecological Variability. Geophysical Monograph Series. Washington, DC: American Geophysical Union, 365–383Google Scholar
  56. SAS Institute Inc. 2008. SAS/STAT® 9.2 User’s Guide. Cary, NC: SAS Institute IncGoogle Scholar
  57. Schauer R, Bienhold C, Ramette A, et al. 2010. Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME J, 4(2): 159–170CrossRefGoogle Scholar
  58. Schloss P D, Westcott S L, Ryabin T, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 75(23): 7537–7541CrossRefGoogle Scholar
  59. Schott F A, McCreary J P. 2001. The monsoon circulation of the Indian Ocean. Prog Oceanogr, 51(1): 1–123CrossRefGoogle Scholar
  60. Srinivas B, Sarin M M. 2013. Atmospheric deposition of N, P and Fe to the Northern Indian Ocean: implications to C-and N-fixation. Sci Total Environ, 456–457: 104–114CrossRefGoogle Scholar
  61. Srinivas B, Sarin M M, Sarma V V S S. 2011. Atmospheric dry deposition of inorganic and organic nitrogen to the Bay of Bengal: impact of continental outflow. Mar Chem, 127(1–4): 170–179CrossRefGoogle Scholar
  62. Suess E. 1980. Particulate organic carbon flux in the oceans-surface productivity and oxygen utilization. Nature, 288(5788): 260–263CrossRefGoogle Scholar
  63. Suh S S, Park M, Hwang J, et al. 2014. Distinct patterns of marine bacterial communities in the South and North Pacific Oceans. J Microbiol, 52(10): 834–841CrossRefGoogle Scholar
  64. Treusch A H, Vergin K L, Finlay L A, et al. 2009. Seasonality and vertical structure of microbial communities in an ocean gyre. ISME J, 3(10): 1148–1163CrossRefGoogle Scholar
  65. Ward A C, Bora N. 2006. Diversity and biogeography of marine actinobacteria. Curr Opin Microbiol, 9(3): 279–286CrossRefGoogle Scholar
  66. Whitman W B, Coleman D C, Wiebe W J. 1998. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A, 95(12): 6578–6583CrossRefGoogle Scholar
  67. Wilkins D, van Sebille E, Rintoul S R, et al. 2013. Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects. Nat Commun, 4: 2457, doi: 10.1038/ncomms3457CrossRefGoogle Scholar
  68. Woebken D, Lam P, Kuypers M M M, et al. 2008. A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones. Environ Microbiol, 10(11): 3106–3119CrossRefGoogle Scholar
  69. Wu Houbo, Guo Yatao, Wang Guanghua, et al. 2011. Composition of bacterial communities in deep-sea sediments from the South China Sea, the Andaman Sea and the Indian Ocean. Afr J Microbiol Res, 5(29): 5273–5283Google Scholar
  70. Yuan Jun, Lai Qiliang, Zheng Tianling, et al. 2009. Novosphingobium indicum sp. Nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment. Int J Syst Evol Microbiol, 59(8): 2084–2088CrossRefGoogle Scholar

Copyright information

© The Chinese Society of Oceanography and Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Jing Wang
    • 1
    • 2
  • Jinjun Kan
    • 3
  • Laura Borecki
    • 3
  • Xiaodong Zhang
    • 1
    • 2
  • Dongxiao Wang
    • 4
  • Jun Sun
    • 1
    • 2
    Email author
  1. 1.College of Marine and Environmental SciencesTianjin University of Science and TechnologyTianjinChina
  2. 2.Tianjin Key Laboratory of Marine Resources and ChemistryTianjin University of Science and TechnologyTianjinChina
  3. 3.Stroud Water Research CenterAvondaleUSA
  4. 4.State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina

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