한국해양생명과학회지 (Journal of Marine Life Science)

한국해양생명과학회 (The Korean Society of Marine Life Science)
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Bacterial Communities from the Water Column and the Surface Sediments along a Transect in the East Sea

  • Lee, Jeong-Kyu (Department of Marine Environmental Science, Chungnam National University) ;
  • Choi, Keun-Hyung (Department of Marine Environmental Science, Chungnam National University)
  • 투고 : 2021.03.22
  • 심사 : 2021.04.26
  • 발행 : 2021.05.31
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초록

We determined the composition of water and sediment bacterial assemblages from the East Sea using 16S rRNA gene sequencing. Total bacterial reads were greater in surface waters (<100 m) than in deep seawaters (>500 m) and sediments. However, total OTUs, bacterial diversity, and evenness were greater in deep seawaters than in surface waters with those in the sediment comparable to the deep sea waters. Proteobacteria was the most dominant bacterial phylum comprising 67.3% of the total sequence reads followed by Bacteriodetes (15.8%). Planctomycetes, Verrucomicrobia, and Actinobacteria followed all together consisting of only 8.1% of the total sequence. Candidatus Pelagibacter ubique considered oligotrophic bacteria, and Planctomycetes copiotrophic bacteria showed an opposite distribution in the surface waters, suggesting a potentially direct competition for available resources by these bacteria with different traits. The bacterial community in the warm surface waters were well separated from the other deep cold seawater and sediment samples. The bacteria exclusively associated with deep sea waters was Actinobacteriacea, known to be prevalent in the deep photic zone. The bacterial group Chromatiales and Lutibacter were those exclusively associated with the sediment samples. The overall bacterial community showed similarities in the horizontal rather than vertical direction in the East Sea.

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과제정보

We are grateful to the captain and crew of R/V Nara for the ship time and numerous undergraduate students for assisting in sampling on board. We also thank Seongmin Cheon, Young-Hee Kim, Chungoo Park for assisting this paper. This research was supported by Chungnam National University.

참고문헌

  1. A Bazylinski D, Morillo V, Lefevre C, Viloria NL, Dubbels B, Williams T. 2016. Endothiovibrio diazotrophicus gen. nov., sp. nov., a Novel Nitrogen-Fixing, Sulfur-Oxidizing Gammaproteobacterium Isolated from a Salt Marsh.
  2. Agogue H, Lamy D, Neal PR, Sogin ML, Herndl GJ. 2011. Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Molecular Ecology 20: 258-274. https://doi.org/10.1111/j.1365-294X.2010.04932.x
  3. Azam F. 1998. Microbial control of oceanic carbon flux: the plot thickens. Science 280: 694-696. https://doi.org/10.1126/science.280.5364.694
  4. Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA, Thingstad F. 1983. The ecological role of water-column microbes in the sea. Marine Ecology Progress Series 10: 257-263. https://doi.org/10.3354/meps010257
  5. Barbeyron T, Carpentier F, L'Haridon S, Schuler M, Michel G, Amann R. 2008. Description of Maribacter forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of the genus Maribacter. International Journal of Systematic and Evolutionary Microbiology 58: 790-797. https://doi.org/10.1099/ijs.0.65469-0
  6. Bernardet J, Nakagawa Y. 2006. An introduction to the family Flavobacteriaceae, p 455-480. The prokaryotes 7.
  7. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
  8. Bolhuis H, Stal LJ. 2011. Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing. The ISME Journal 5: 1701. https://doi.org/10.1038/ismej.2011.52
  9. Britschgi TB, Giovannoni SJ. 1991. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Applied and Environmental Microbiology 57: 1707-1713. https://doi.org/10.1128/aem.57.6.1707-1713.1991
  10. Caceres MD, Legendre P. 2009. Associations between species and groups of sites: indices and statistical inference. Ecology 90: 3566-3574. https://doi.org/10.1890/08-1823.1
  11. Campbell BJ, Kirchman DL. 2013. Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. The ISME Journal 7: 210. https://doi.org/10.1038/ismej.2012.93
  12. Choi A, Yang S-J, Cho J-C. 2013. Lutibacter flavus sp. nov., a marine bacterium isolated from a tidal flat sediment. International Journal of Systematic and Evolutionary Microbiology 63: 946-951. https://doi.org/10.1099/ijs.0.043471-0
  13. Choi DH, Cho BC. 2006. Lutibacter litoralis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment. International Journal of Systematic and Evolutionary Microbiology 56: 771-776. https://doi.org/10.1099/ijs.0.64146-0
  14. Ciok A, Dziewit L, Grzesiak J, Budzik K, Gorniak D, Zdanowski MK, Bartosik D. 2016. Identification of miniature plasmids in psychrophilic Arctic bacteria of the genus Variovorax. FEMS Microbiology Ecology 92: fiw043-fiw043. https://doi.org/10.1093/femsec/fiw043
  15. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Research 42: D633-D642. https://doi.org/10.1093/nar/gkt1244
  16. Cottrell MT, Waidner LA, Yu L, Kirchman DL. 2005. Bacterial diver- sity of metagenomic and PCR libraries from the Delaware River. Environmental Microbiology 7: 1883-1895. https://doi.org/10.1111/j.1462-2920.2005.00762.x
  17. DeLong EF. 2009. The microbial ocean from genomes to biomes. Nature 459: 200. https://doi.org/10.1038/nature08059
  18. Dyksma S, Bischof K, Fuchs BM, Hoffmann K, Meier D, Meyerdierks A, Pjevac P, Probandt D, Richter M, Stepanauskas R. 2016. Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. The ISME Journal 10: 1939. https://doi.org/10.1038/ismej.2015.257
  19. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200. https://doi.org/10.1093/bioinformatics/btr381
  20. Feng BW, Li XR, Wang JH, Hu ZY, Meng H, Xiang LY, Quan ZX. 2009. Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea. FEMS Microbiology Ecology 70: 236-248. https://doi.org/10.1111/j.1574-6941.2009.00772.x
  21. Franco DC, Signori CN, Duarte RT, Nakayama CR, Campos LS, Pellizari VH. 2017. High prevalence of gammaproteobacteria in the sediments of admiralty bay and north bransfield Basin, Northwestern Antarctic Peninsula. Frontiers in Microbiology 8: 153.
  22. Fuhrman J, McCallum K, Davis A. 1993a. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Applied and Environmental Microbiology 59: 1294-1302. https://doi.org/10.1128/aem.59.5.1294-1302.1993
  23. Fuhrman JA, McCallum K, Davis AA. 1993b. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Applied and Environmental Microbiology 59: 1294-1302. https://doi.org/10.1128/aem.59.5.1294-1302.1993
  24. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D, Bibbs L, Eads J, Richardson TH, Noordewier M, Rappe MS, Short JM, Carrington JC, Mathur EJ. 2005. Genome Streamlining in a Cosmopolitan Oceanic Bacterium. Science 309: 1242-1245. https://doi.org/10.1126/science.1114057
  25. Giovannoni SJ, Vergin KL. 2012. Seasonality in ocean microbial communities. Science 335: 671-676. https://doi.org/10.1126/science.1198078
  26. Glockner FO, Kube M, Bauer M, Teeling H, Lombardot T, Ludwig W, Gade D, Beck A, Borzym K, Heitmann K. 2003. Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proceedings of the National Academy of Sciences 100: 8298-8303. https://doi.org/10.1073/pnas.1431443100
  27. Grasshoff K, Kremling K, Ehrhardt M. 2009. Methods of seawater analysis. John Wiley & Sons.
  28. Guilini K, Oevelen DV, Soetaert K, Middelburg JJ, Vanreusela A. 2010. Nutritional importance of benthic bacteria for deepsea nematodes from the Arctic ice margin: Results of an isotope tracer experiment. Limnology and Oceanography 55: 1977-1989. https://doi.org/10.4319/lo.2010.55.5.1977
  29. Henson MW, Lanclos VC, Faircloth BC, Thrash JC. 2018. Cultivation and genomics of the first freshwater SAR11 (LD12) isolate. bioRxiv, 093567.
  30. Ichiye T. 1984. Some problems of circulation and hydrography of the Japan Sea and the Tsushima Current, Elsevier oceanography series. Elsevier, pp 15-54.
  31. Jenkins C, Kedar V, Fuerst JA. 2002. Gene discovery within the planctomycete division of the domain Bacteria using sequence tags from genomic DNA libraries. Genome Biology 3: research0031.
  32. Kirchman DL. 2002. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiology Ecology 39: 91-100. https://doi.org/10.1111/j.1574-6941.2002.tb00910.x
  33. Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'dwyer J, Koeppel AF, Green JL, Pollard KS. 2013. Global marine bacterial diversity peaks at high latitudes in winter. The ISME Journal 7: 1669. https://doi.org/10.1038/ismej.2013.37
  34. Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, DeMaere MZ, Ting L, Ertan H, Johnson J, Ferriera S, Lapidus A, Anderson I, Kyrpides N, Munk AC, Detter C, Han CS, Brown MV, Robb FT, Kjelleberg S, Cavicchioli R. 2009. The genomic basis of trophic strategy in marine bacteria. Proceedings of the National Academy of Sciences 106: 15527-15533. https://doi.org/10.1073/pnas.0903507106
  35. Lavy A, Keren R, Yu K, Thomas BC, Alvarez-Cohen L, Banfield JF, Ilan M. 2018. A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges. Environmental Microbiology 20: 800-814. https://doi.org/10.1111/1462-2920.14013
  36. Mizuno CM, Rodriguez-Valera F, Ghai R. 2015. Genomes of planktonic acidimicrobiales: widening horizons for marine actinobacteria by metagenomics. MBio 6: e02083-02014.
  37. Moeseneder MM, Arrieta JM, Muyzer G, Winter C, Herndl GJ. 1999. Optimization of Terminal-Restriction Fragment Length Polymorphism Analysis for Complex Marine Bacterioplankton Communities and Comparison with Denaturing Gradient Gel Electrophoresis. Applied and Environmental Microbiology 65: 3518-3525. https://doi.org/10.1128/AEM.65.8.3518-3525.1999
  38. Moriarty DJW, Skyring GW, O'Brien GW, Heggie DT. 1991. Heterotrophic bacterial activity and growth rates in sediments of the continental margin of eastern Australia. Deep Sea Research Part A. Oceanographic Research Papers 38: 693-712.
  39. Morris R, Longnecker K, Giovannoni S. 2006. Pirellula and OM43 are among the dominant lineages identified in an Oregon coast diatom bloom. Environmental Microbiology 8: 1361-1370. https://doi.org/10.1111/j.1462-2920.2006.01029.x
  40. Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806. https://doi.org/10.1038/nature01240
  41. Mullins TD, Britschgi TB, Krest RL, Gioivannoni SJ. 1995. Genetic comparisons communities. Limnology and Oceanography 40: 148-158. https://doi.org/10.4319/lo.1995.40.1.0148
  42. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'hara R, Simpson GL, Solymos P, Stevens MHH, Wagner H. 2013. Package 'vegan'. Community ecology package, version 2.
  43. Onitsuka G, Yanagi T, Yoon JH. 2007. A numerical study on nutrient sources in the surface layer of the Japan Sea using a coupled physical-ecosystem model. Journal of Geophysical Research: Oceans 112.
  44. Pommier T, Neal PR, Gasol JM, Coll M, Acinas SG, Pedros-Alio C. 2010. Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA. Aquatic Microbial Ecology 61: 221-233. https://doi.org/10.3354/ame01484
  45. Price PB, Sowers T. 2004. Temperature dependence of metabolic rates for microbial growth, maintenance, and survival. Proceedings of the National Academy of Sciences of the United States of America 101: 4631-4636. https://doi.org/10.1073/pnas.0400522101
  46. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macian MC. 2014. The Family Rhodobacteraceae, in: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. (Eds.), The Prokaryotes: Alphaproteobacteria and Betaproteobacteria. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 439-512.
  47. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41: D590-D596. https://doi.org/10.1093/nar/gks1219
  48. R Core Team, 2018. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
  49. Ravenschlag K, Sahm K, Amann R. 2001. Quantitative molecular analysis of the microbial community in marine Arctic sediments (Svalbard). Applied and Environmental Microbiology 67: 387-395. https://doi.org/10.1128/AEM.67.1.387-395.2001
  50. Rogers Y-H, Venter JC. 2005. Massively parallel sequencing. Nature 437: 326. https://doi.org/10.1038/437326a
  51. Rothberg BEG, Rothberg JM. 2015. Massively Parallel ("NextGeneration") DNA Sequencing. Clinical Chemistry 61: 997-998. https://doi.org/10.1373/clinchem.2014.237461
  52. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Applied and Environmental Microbiology 75: 7537-7541. https://doi.org/10.1128/AEM.01541-09
  53. Sekiguchi H, Watanabe M, Nakahara T, Xu B, Uchiyama H. 2002. Succession of Bacterial Community Structure along the Changjiang River Determined by Denaturing Gradient Gel Electrophoresis and Clone Library Analysis. Applied and Environmental Microbiology 68: 5142-5150. https://doi.org/10.1128/AEM.68.10.5142-5150.2002
  54. Seo J-H, Kang I, Yang S-J, Cho J-C. 2017. Characterization of spatial distribution of the bacterial community in the South Sea of Korea. PLOS ONE 12: e0174159. https://doi.org/10.1371/journal.pone.0174159
  55. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences 103: 12115-12120. https://doi.org/10.1073/pnas.0605127103
  56. Sundararaman A, Lee S-S. 2017. Lutibacter oceani sp. nov., isolated from marine sediment in South Korea. Antonie van Leeuwenhoek 110: 45-51. https://doi.org/10.1007/s10482-016-0772-8
  57. Teramoto M, Nishijima M. 2014. Amylibacter marinus gen. nov., sp. nov., isolated from surface seawater. International Journal of Systematic and Evolutionary Microbiology 64: 4016-4020. https://doi.org/10.1099/ijs.0.065847-0
  58. Wagner M, Horn M. 2006. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Current Opinion in Biotechnology 17: 241-249. https://doi.org/10.1016/j.copbio.2006.05.005
  59. Walsh EA, Kirkpatrick JB, Rutherford SD, Smith DC, Sogin M, D'Hondt S. 2015. Bacterial diversity and community composition from seasurface to subseafloor. The ISME Journal 10: 979. https://doi.org/10.1038/ismej.2015.175
  60. Wang YP, Gu J-D. 2006. Degradability of dimethyl terephthalate by Variovorax paradoxus T4 and Sphingomonas yanoikuyae DOS01 isolated from deep-ocean sediments. Ecotoxicology 15: 549-557. https://doi.org/10.1007/s10646-006-0093-1
  61. Yoon J-H, Kang S-J, Oh T-K. 2006. Variovorax dokdonensis sp. nov., isolated from soil. International Journal of Systematic and Evolutionary Microbiology 56: 811-814. https://doi.org/10.1099/ijs.0.64070-0
  62. Zure M, Munn CB, Harder J. 2015a. Diversity of Rhodopirellula and related planctomycetes in a North Sea coastal sediment employing carB as molecular marker. FEMS Microbiology Letters 362.
  63. Zure M, Munn CB, Harder J. 2015b. Diversity of Rhodopirellula and related planctomycetes in a North Sea coastal sediment employing carB as molecular marker. FEMS Microbiology Letters 362: fnv127-fnv127. https://doi.org/10.1093/femsle/fnv127