DOI QR코드

DOI QR Code

Community Structure, Diversity, and Vertical Distribution of Archaea Revealed by 16S rRNA Gene Analysis in the Deep Sea Sediment of the Ulleung Basin, East Sea

16S rRNA 유전자 분석방법을 이용한 동해 울릉분지 심해 퇴적물 내 고세균 군집 구조 및 다양성의 수직분포 특성연구

  • Kim, Bo-Bae (Department of Environmental Marine Sciences Division of Science and Technology Hanyang University) ;
  • Cho, Hye-Youn (Department of Environmental Marine Sciences Division of Science and Technology Hanyang University) ;
  • Hyun, Jung-Ho (Department of Environmental Marine Sciences Division of Science and Technology Hanyang University)
  • 김보배 (한양대학교 과학기술학부 해양환경과학과) ;
  • 조혜연 (한양대학교 과학기술학부 해양환경과학과) ;
  • 현정호 (한양대학교 과학기술학부 해양환경과학과)
  • Received : 2010.08.11
  • Accepted : 2010.09.13
  • Published : 2010.09.30

Abstract

To assess community structure and diversity of archaea, a clone sequencing analysis based on an archaeal 16S rRNA gene was conducted at three sediment depths of the continental slope and Ulleung Basin in the East Sea. A total of 311 and 342 clones were sequenced at the slope and basin sites, respectively. Marine Group I, which is known as the ammonia oxidizers, appeared to predominate in the surface sediment of both sites (97.3% at slope, 88.5% at basin). In the anoxic subsurface sediment of the slope and basin, the predominant archaeal group differed noticeably. Marine Benthic Group B dominated in the subsurface sediment of the slope. Marine Benthic Group D and Miscellaneous Crenarchaeotal Group were the second largest archaeal group at 8-9 cm and 18-19 cm depth, respectively. Marine Benthic Group C of Crenarchaeota occupied the highest proportion by accounting for more than 60% of total clones in the subsurface sediments of the basin site. While archaeal groups that use metal oxide as an electron acceptor were relatively more abundant at the basin sites with manganese (Mn) oxide-enriched surface sediment, archaeal groups related to the sulfur cycle were more abundant in the sulfidogenic sediments of the slope. Overall results indicate that archaeal communities in the Ulleung Basin show clear spatial variation with depth and sites according to geochemical properties the sediment. Archaeal communities also seem to play a significant role in the biogeochemical carbon (C), nitrogen (N), sulfur (S), and metal cycles at each site.

Acknowledgement

Supported by : 한국학술진흥재단

References

  1. 유옥례, 목진숙, 김성한, 최동림, 현정호 (2010) 동해 울릉분지에서 대륙사면과 분지 퇴적물의 지화학적 특성에 따른 황산염 환원 비교. Ocean Polar Res Submitted
  2. 이명숙, 홍순규, 이동훈, 김치경, 배경숙 (2001) 16S rRNA 유전자 분석에 의한 전남 순천만 갯벌의 세균 다양성. 한국미생물학회지 37:137-144
  3. 조혜연, 이정현, 현정호 (2004) 16S rDNA 분석을 이용한 강화도 장화리 갯벌 퇴적물 내 미생물 군집구조 및 다양성. 한국미생물학회지 40:189-198
  4. 현정호, 이홍금, 권개경 (2003) 해양환경의 황산염 환원율 조절요인 및 유기물 분해에 있어 황산염 환원의 중요성. 바다 8:210-224
  5. Arakawa S, Sato T, Sato R, Zhang J, Gamo T, Tsunogai U, Hirota A, Yoshida Y, Usami R, Inagaki F, Kato C (2006) Molecular phylogenetic and chemical analysis of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea. Extremophiles 10:311-319 https://doi.org/10.1007/s00792-005-0501-0
  6. Beal EJ, House CH, Orphan VJ (2009) Manganese- and iron-dependent marine methane oxidation. Science 325:184-187 https://doi.org/10.1126/science.1169984
  7. Belkin S, Jannasch HW (1985) A new extremely thermophilic sulfur-reducing heterotrophic marine bacterium. Arch Microbiol 141:181-186 https://doi.org/10.1007/BF00408055
  8. Bowman JP, McCuaig RD (2003) Biodiversity, community structural shifts, and biogeography of prokaryotes within Antartic continental shelf sediment. Appl Environ Microbial 69:2463-2483 https://doi.org/10.1128/AEM.69.5.2463-2483.2003
  9. Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sorensen KB, Anderson R (2006) Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA 103:3846-3851 https://doi.org/10.1073/pnas.0600035103
  10. Chandler DP, Brockman FJ, Bailey TJ, Fredrickson JK (1998) Phylogenetic diversity of archaea and bacteria in a deep subsurface paleosol. Microb Ecol 36:37-50 https://doi.org/10.1007/s002489900091
  11. Dang H, Luan X, Zhao J, Li J (2009) Diverse and novel nifH and nifH-like gene sequences in the deep-sea methane-seep sediments of the Okhotsk Sea. Appl Environ Microbiol 75:2238-2245 https://doi.org/10.1128/AEM.02556-08
  12. Dang H, Luan XW, Chen R, Zhang X, Guo L, Klotz MG (2010) Diversity, abundance and distribution of amoAencoding archaea in deep-sea methane seep sediments of the Okhotsk Sea. FEMS Microbiol Ecol 72(3):370-85 https://doi.org/10.1111/j.1574-6941.2010.00870.x
  13. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685-5689 https://doi.org/10.1073/pnas.89.12.5685
  14. Gray JP, Herwig RP (1996) Phylogenetic analysis of the bacterial communities in marine sediment. Appl Environ Microbiol 62(11):4049-4059
  15. Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y, Sugahara J, Preston C, de la Torre J, Richardson PM, Delong EF (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci USA 103:18296-18301 https://doi.org/10.1073/pnas.0608549103
  16. Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci USA 105:2134-2139 https://doi.org/10.1073/pnas.0708857105
  17. Hyun JH, Kim D, Shin CW, Noh JH, Yang EJ, Mok JS, Kim SH, Kim HC, Yoo S (2009) Enhanced phytoplankton and bacterioplankton production coupled to coastal upwelling and an anticyclonic eddy in the Ulleung basin, East Sea. Aquatic Microbial Ecolpgy 54:45-54
  18. Hyun JH, Mok JS, You OR, Kim D, Choi DL (2010) Variations and controls of sulfate reduction in the continental slope and rise of the Ulleung Basin off the southeast Korean upwelling system in the East Sea. Geomicrobiol J 27:212-222 https://doi.org/10.1080/01490450903456731
  19. Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aok K, Nealson KH, Horikoshi K (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
  20. Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever MA, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH, Horikoshi K, D'Hondt S, Jorgensen BB (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments in the Pacific ocean margin. Proc Natl Acad Sci USA 103:2815-2820 https://doi.org/10.1073/pnas.0511033103
  21. Kim BS, Oh HM, Kang H, Chun J (2005) Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis. J Microbiol 43:144-151
  22. Kendall MM, Wardlaw GD, Tang CF, Bonin AS, Liu Y, Valentine DL (2007) Diversity of Archaea in marine sediments from Skan Bay, Alaska, Including cultivated methanogens, and description of Methanogenium boonei sp. nov. Appl Environ Microbiol 73(2):407-414 https://doi.org/10.1128/AEM.01154-06
  23. Knittel K, Losekann T, Boetius A, Kort R, Amann R (2005) Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microbiol 71:467-479 https://doi.org/10.1128/AEM.71.1.467-479.2005
  24. Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543-546 https://doi.org/10.1038/nature03911
  25. Lee T, Hyun JH, Mok JS, Kim D (2008) Organic carbon accumulation and sulfate reduction rates in slope and basin sediments of the Ulleung Basin, East/Japan Sea. Geo-Marine Lett 28:153-159 https://doi.org/10.1007/s00367-007-0097-8
  26. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia -oxidizing prokaryototes in soils. Nature 442:806-809 https://doi.org/10.1038/nature04983
  27. Lloyd KG, Lapham L, Teske A (2006) An anaerobic methane-oxidizing community of ANME-1b archaea in hypersaline Gulf of Mexico sediments. Appl Environ Microbiol 72:7218-7230 https://doi.org/10.1128/AEM.00886-06
  28. Madigan MT, Martinko JM (2006) Brock biology of microorganisms. Prentic Hall. USA
  29. Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976-979 https://doi.org/10.1038/nature08465
  30. Nelson KA, Moin NS, Bernhard AE (2009) Archaeal diversity and the prevalence of Crenarchaeota in salt marsh sediments. Appl Environ Microbiol 75:4211-4215 https://doi.org/10.1128/AEM.00201-09
  31. Newberry CJ, Webster G, Weightman AJ, Fry JC (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
  32. Nicol GW, Schleper C (2006) Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends in Microbiol 14:207-212 https://doi.org/10.1016/j.tim.2006.03.004
  33. Park SJ, Park BJ, Rhee SK (2008) Comparative analysis of archaeal 16S rRNA and amoA genes to estimates the abundance and diversity of ammonia -oxidizing archaea in marine sediments. Extremophiles 12:605-615 https://doi.org/10.1007/s00792-008-0165-7
  34. Ravenschlag K, Sahm K, Pernthaler J, Amann R (1999) High bacterial diversity in permanently cold, marine sediments. Appl Environ Microbiol 65:3982-3989
  35. Reed D, Fujita Y, Delwiche ME, Blackwelder DB, Sheridan PP, Uchida T, Colwell FS (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl Environ Microbiol 66:3798-3806 https://doi.org/10.1128/AEM.66.9.3798-3806.2000
  36. Reysenbach AL, Longnecker K, Kirshtein J (2000) Novel bacterial and archaeal lineages from an in-situ growth chamber deployed at a mid-atlantic ridge hydrothermal vent. Appl Environ Microbiol 66:3798-3806 https://doi.org/10.1128/AEM.66.9.3798-3806.2000
  37. Sorensen KB, Lauer A, Teske A (2004) Archaeal phylotypes in a metal-rich, low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology 2:151-161 https://doi.org/10.1111/j.1472-4677.2004.00028.x
  38. Sorensen KB, Teske A (2006) Stratified communities of active archaea in deep marine subsurface sediments. Appl Environ Microbiol 72:4596-4603 https://doi.org/10.1128/AEM.00562-06
  39. Stein LY, Jones G, Alexander B, Elmund K, Wrightjones C, Nealson KH (2002) Intriguing microbial diversity associated with metal-rich particles from a freshwater reservoir. FEMS Microbial Ecol 42:431-440 https://doi.org/10.1111/j.1574-6941.2002.tb01032.x
  40. Takai K, Horikoshi K (1999) Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152:1285-1297
  41. Teske A, Hinrichs KU, Edgcomb V, Gomez AdV, Kysela D, Sylva SP, Colwell FS (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
  42. Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA, Reysenbach AL (1999) Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microbiol 65:4375-4384
  43. Wilms R, Sass H, Kopke B, Koster J, Cypionka H, Engelen B (2006) Specific Bacterial, Archaeal, and Eukaryotic Communities in Tidal-Flat sediments along a Vertical profile of Several meters. Appl Environ Microbiol 72(4):2756-2764 https://doi.org/10.1128/AEM.72.4.2756-2764.2006
  44. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088-5090 https://doi.org/10.1073/pnas.74.11.5088
  45. Yayanos AA, Dietz AS, Van Boxtel R (1979) Isolation of a deep-sea barophilic bacterium and some of its growth characteristics. Science 205:808-810 https://doi.org/10.1126/science.205.4408.808

Cited by

  1. Prokaryotic community composition revealed by denaturing gradient gel electrophoresis in the East Sea vol.50, pp.4, 2015, https://doi.org/10.1007/s12601-015-0057-6
  2. Characteristics of Microbial Community Structures of the Methane Hydrate Sediments in the Ulleung Basin, East Sea of Korea vol.50, pp.3, 2014, https://doi.org/10.7845/kjm.2014.4033
  3. Seasonal Variation of Bacterial Community Composition in Sediments and Overlying Waters of the South East Sea vol.19, pp.2, 2014, https://doi.org/10.7850/jkso.2014.19.2.147
  4. Microbial community structures of methane hydrate-bearing sediments in the Ulleung Basin, East Sea of Korea vol.47, 2013, https://doi.org/10.1016/j.marpetgeo.2013.06.002