Skip to main content
SpringerLink
Log in

Bacterial and archaeal community structure of pan-Arctic Ocean sediments revealed by pyrosequencing

  • Published:
Acta Oceanologica Sinica Aims and scope Submit manuscript

Abstract

This study was to investigate bacterial and archaeal community structure of pan-Arctic Ocean sediments by pyrosequencing. In total, investigation of three marine sediments revealed 15 002 bacterial and 4 362 archaeal operational taxonomic units (OTUs) at the 97% similarity level. Analysis of community structure indicated that these three samples had high bacterial and archaeal diversity. The most relatively abundant bacterial group in Samples CC1 and R05 was Proteobacteria, while Firmicutes was dominant in Sample BL03. Thaumarchaeota was the most relatively abundant archaeal phylum in Samples CC1 and R05, and the relative abundance of Thaumarchaeota was almost as high as that of Euryarchaeota in Sample BL03. These two phyla accounted for nearly 100% of the archaeal OTUs. δ-Proteobacteria and γ-Proteobacteria were the two most relatively abundant classes at Proteobacterial class level, and their relative abundance was more than 60% in Samples CC1 and R05. There were also differences in the top 10 relatively abundant bacterial and archaeal OTUs among the three samples at the 97% similarity, and only 12 core bacterial OTUs were detected. Overall, this study indicated that there were distinct microbial communities and many unique OTUs in these three samples.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Abbai N S, Govender A, Shaik R, et al. 2012. Pyrosequence analysis of unamplified and whole genome amplified DNA from hydrocarbon-contaminated groundwater. Mol Biotechnol, 50(1): 39–48

    Article  Google Scholar 

  • Albers S V, Pohlschröder M. 2009. Diversity of archaeal type IV pilinlike structures. Extremophiles, 13(3): 403–410

    Article  Google Scholar 

  • Bowman J S, Rasmussen S, Blom N, et al. 2012. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene. ISMEJ, 6(1): 11–20

    Article  Google Scholar 

  • Brochier-Armanet C, Boussau B, Gribaldo S, et al. 2008. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nature Reviews Microbiology, 6(3): 245–252

    Article  Google Scholar 

  • Chaban B, Ng S Y M, Jarrel K F. 2006. Archaeal habitats-from the extreme to the ordinary. Can J Microbiol, 52(2): 73–116

    Article  Google Scholar 

  • Chelius M K, Triplett E W. 2001. The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb Ecol, 41(3): 252–263

    Article  Google Scholar 

  • Chun J, Kim K Y, Lee J H, et al. 2010. The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiol, 10(1): 101

    Article  Google Scholar 

  • Comeau A M, Harding T, Galand P E, et al. 2012. Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters. Sci Rep, 2: 604

    Article  Google Scholar 

  • Comeau A M, Li W K W, Tremblay J É, et al. 2011. Arctic Ocean microbial community structure before and after the 2007 record sea ice minimum. PLoS One, 6(11): e27492

    Article  Google Scholar 

  • Cooper L W, Whitledge T E, Grebmeier J M, et al. 1997. The nutrient, salinity, and stable oxygen isotope composition of Bering and Chukchi Seas waters in and near the Bering Strait. J Geophys Res, 102(C6): 12563–12573

    Article  Google Scholar 

  • Galand P E, Casamayor E O, Kirchman D L, et al. 2009. Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci USA, 106(52): 22427–22432

    Article  Google Scholar 

  • Hamdan L J, Coffin R B, Sikaroodi M, et al. 2013. Ocean currents shape the microbiome of Arctic marine sediments. ISME J, 7(4): 685–696

    Article  Google Scholar 

  • Hetzer A, Morgan H W, McDonald I R, et al. 2007. Microbial life in Champagne Pool, a geothermal spring in Waiotapu, New Zealand. Extremophiles, 11(4): 605–614

    Article  Google Scholar 

  • Jaenicke S, Ander C, Bekel T, et al. 2011. Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS One, 6(1): e14519

    Article  Google Scholar 

  • Jørgensen B B, Boetius A. 2007. Feast and famine—microbial life in the deep-sea bed. Nat Rev Microbiol, 5(10): 770–781

    Article  Google Scholar 

  • Jorgensen S L, Hannisdal B, Lanzén A, et al. 2012. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc Natl Acad Sci USA, 109(42): E2846–E2855

    Article  Google Scholar 

  • Kirchman D L, Cottrell M T, Lovejoy C. 2010. The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes. Environ Microbiol, 12(5): 1132–1143

    Article  Google Scholar 

  • Kormas K A, Tivey M K, Von Damm K, et al. 2006. Bacterial and archaeal phylotypes associated with distinct mineralogical layers of a white smoker spire from a deep-sea hydrothermal vent site (9°N, East Pacific Rise). Environ Microbiol, 8(5): 909–920

    Article  Google Scholar 

  • Li An, Chu Ya’nan, Wang Xumin, et al. 2013. A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol Biof, 6(1): 3

    Article  Google Scholar 

  • Li Huirong, Yu Yong, Luo Wei, et al. 2009. Bacterial diversity in surface sediments from the Pacific Arctic Ocean. Extremophiles, 13(2): 233–246

    Article  Google Scholar 

  • Muller F, Brissac T, Le Bris N, et al. 2010. First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat. Environ Microbiol, 12(8): 2371–2383

    Article  Google Scholar 

  • Nunoura T, Oida H, Nakaseama M, et al. 2010. Archaeal diversity and distribution along thermal and geochemical gradients in hydrothermal sediments at the Yonaguni Knoll IV hydrothermal field in the southern Okinawa Trough. Appl Environ Microbiol, 76(4): 1198–1211

    Article  Google Scholar 

  • Pester M, Schleper C, Wagner M. 2011. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr Opin Microbiol, 14(3): 300–306

    Article  Google Scholar 

  • Rahkila R, Nieminen T, Johansson P, et al. 2012. Characterization and evaluation of the spoilage potential of Lactococcus piscium isolates from modified atmosphere packaged meat. Int J Food Microbiol, 156(1): 50–59

    Article  Google Scholar 

  • Ravenschlag K, Sahm K, Knoblauch C, et al. 2000. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments. Appl Environ Microbiol, 66(8): 3592–3602

    Article  Google Scholar 

  • Reddy P V V, Rao S S S N, Pratibha M S, et al. 2009. Bacterial diversity and bioprospecting for cold-active enzymes from culturable bacteria associated with sediment from a melt water stream of Midtre Lovénbreen glacier, an Arctic glacier. Research in Microbiology, 160(8): 538–546

    Article  Google Scholar 

  • Rothberg J M, Leamon J H. 2008. The development and impact of 454 sequencing. Nat Biotechnol, 26(10): 1117–1124

    Article  Google Scholar 

  • Roussel E G, Bonavita M A C, Querellou J, et al. 2008. Extending the sub-sea-floor biosphere. Science, 320(5879): 1046

    Article  Google Scholar 

  • Segerer A H, Burggraf S, Fiala G, et al. 1993. Life in hot springs and hydrothermal vents. Origins Life Evol Biosphere, 23(1): 77–90

    Article  Google Scholar 

  • Tian Fei, Yu Yong, Chen Bo, et al. 2009. Bacterial, archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis. Polar Biol, 32(1): 93–103

    Article  Google Scholar 

  • Torsvik V, Øvreås L, Thingstad T F. 2002. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science, 296(5570): 1064–1066

    Article  Google Scholar 

  • Trevors J T, Kevan P G, Tam L. 2010. Microbial diversity across a Canadian sub-Arctic, isostatically rebounding, soil transect. Polar Sci, 4(1): 81–91

    Article  Google Scholar 

  • Wang Shufang, Xiao Xiang, Jiang Lijing, et al. 2009. Diversity and abundance of ammonia-oxidizing archaea in hydrothermal vent chimneys of the Juan De Fuca Ridge. Appl Environ Microbiol, 75(12): 4216–4220

    Article  Google Scholar 

  • Whitman W B, Coleman D C, Wiebe W J. 1998. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA, 95(12): 6578–6583

    Article  Google Scholar 

  • Williams A M, Fryer J L, Collins M D. 1990. Lactococcus piscium sp. nov. a new Lactococcus species from salmonid fish. FEMS Microbiol Lett, 68(1-2): 109–113

    Article  Google Scholar 

  • Wu Shangong, Wang Guitang, Angert E R, et al. 2012. Composition, diversity, and origin of the bacterial community in grass carp intestine. PLoS One, 7(2): e30440

    Article  Google Scholar 

  • Zeng Yinxin, Zou Yang, Chen Bo, et al. 2011. Phylogenetic diversity of sediment bacteria in the northern Bering Sea. Polar Biol, 34(6): 907–919

    Article  Google Scholar 

  • Zeng Yinxin, Zhang Fang, He Jianfeng, et al. 2013. Bacterioplankton community structure in the Arctic waters as revealed by pyrosequencing of 16S rRNA genes. Antonie van Leeuwenhoek, 103(6): 1309–1319

    Article  Google Scholar 

  • Zheng Xiong, Su Yinglong, Li Xiang, et al. 2013. Pyrosequencing reveals the key microorganisms involved in sludge alkaline fermentation for efficient short-chain fatty acids production. Environ Sci Technol, 47(9): 4262–4268

    Article  Google Scholar 

Download references

Acknowledgements

The authors thank the sampling assistances of the 5th Chinese National Arctic Expedition.

Author information

Authors and Affiliations

  1. The First Institute of Oceanography, State Oceanic Administration, Qingdao, 266061, China

    Xuezheng Lin, Liang Zhang, Yanguang Liu & Yang Li

Authors
  1. Xuezheng Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Liang Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yanguang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xuezheng Lin.

Additional information

Foundation item: The Chinese Polar Environment Comprehensive Investigation and Assessment Program under contract No. CHINARE2014-03-05; the National Natural Science Foundation of China under contract No. 41176174; the Innovation and Development Regional Demonstration Program of Marine Economy under contract No. 12PYY001SF08-HYYS-1.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lin, X., Zhang, L., Liu, Y. et al. Bacterial and archaeal community structure of pan-Arctic Ocean sediments revealed by pyrosequencing. Acta Oceanol. Sin. 36, 146–152 (2017). https://doi.org/10.1007/s13131-017-1030-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13131-017-1030-2

Keywords

Search

Navigation