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Bacterial diversity in surface sediments from the Pacific Arctic Ocean

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Abstract

In order to assess bacterial diversity within four surface sediment samples (0–5 cm) collected from the Pacific Arctic Ocean, 16S ribosomal DNA clone library analysis was performed. Near full length 16S rDNA sequences were obtained for 463 clones from four libraries and 13 distinct major lineages of Bacteria were identified (α, β, γ, δ and ε-Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Firmicutes, Planctomycetes, Spirochetes, and Verrucomicrobia). α, γ, and δ-Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria were common phylogenetic groups from all the sediments. The γ-Proteobacteria were the dominant bacterial lineage, representing near or over 50% of the clones. Over 35% of γ-Proteobacteria clones of four clone library were closely related to cultured bacterial isolates with similarity values ranging from 94 to 100%. The community composition was different among sampling sites, which potentially was related to geochemical differences.

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References

  • Bano N, Hollibaugh JT (2002) Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl Environ Microbiol 68:505–518

    Article  PubMed  CAS  Google Scholar 

  • Belicka LL, Macdonald RW, Harvey HR (2002) Sources and transport of organic carbon to shelf, slope, and basin surface sediments of the Arctic Ocean. Deep-Sea Res I 49:1463–1483

    Article  CAS  Google Scholar 

  • Blazejak A, Kuever J, Erseus C, Amann R, Dubilier N (2006) Phylogeny of 16S rRNA, ribulose 1, 5-bisphosphate carboxylase/oxygenase, and adenosine 5′-phosphosulfate reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (oligochaeta) from Bermuda and the Bahamas. Appl Environ Microbiol 72:5527–5536

    Article  PubMed  CAS  Google Scholar 

  • Bosshard PP, Santini Y, Grüter D, Stettler R, Bachofen R (2000) Bacterial diversity and community composition in the chemocline of the meromictic alpine lake Cadagno a reveal by 16S rDNA analysis. FEMS Microbiol Ecol 31:173–182

    Article  PubMed  CAS  Google Scholar 

  • Bowman JP, McCuaig RD (2003) Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69:2463–2483

    Article  PubMed  CAS  Google Scholar 

  • Bowman JP, McCammon SA, Brown MV, Nichols DS, McMeekin TA (1997) Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl Environ Microbiol 63:3068–3078

    PubMed  CAS  Google Scholar 

  • Bowman JP, McCammon SA, Gibson JAE, Robertson L, Nichols PD (2003) Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediment. Appl Environ Microbiol 69:2448–2462

    Article  PubMed  CAS  Google Scholar 

  • Bowman JP, McCammon SA, Dann AL (2005) Biogeographic and quantitative analyses of abundant uncultivated γ-Proteobacterial clades from marine sediment. Microb Ecol 49:451–460

    Article  PubMed  CAS  Google Scholar 

  • Brinkmeyer R, Knittel K, Jurgens J, Weyland H, Amann R, Helmke E (2003) Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl Environ Microbiol 69:6610–6619

    Article  PubMed  CAS  Google Scholar 

  • Chao A (1987) Estimating the population size for capture recapture data with unequal catchability. Biometrics 43:783–791

    Article  PubMed  CAS  Google Scholar 

  • Chen L (2000) The report of the first Chinese Arctic Research Expedition (in Chinese). China Ocean Press, Beijing

    Google Scholar 

  • Dhillon A, Teske A, Dillon J, Stahl DA, Sogin ML (2003) Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl Environ Microbiol 69:2765–2772

    Article  PubMed  CAS  Google Scholar 

  • D’Hondt S, Rutherford S, Spivack AJ (2002) Metabolic activity of subsurface life in deep-sea sediments. Science 295:2067–2070

    Article  PubMed  CAS  Google Scholar 

  • Garrity GM, Winters M, Kuo AW, Searles DB (2002) Taxonomic outline of the Prokaryotes, Bergey’s Manual of Systematic Bacteriology, 2nd edn edn. Springer, New York

    Google Scholar 

  • Gillan DC, Pernet P (2007) Adherent bacteria in heavy metal contaminated marine sediments. Biofouling 23:1–13

    Article  PubMed  CAS  Google Scholar 

  • Glatz RE, Lepp PW, Ward BB, Francis CA (2006) Planktonic microbial community composition across steep physical/chemical gradients in permanently ice-covered Lake Bonney, Antarctica. Geobiology 4:53–67

    Article  CAS  Google Scholar 

  • Gooday AJ, Turley CM (1990) Responses by benthic organisms to inputs of organic material to the ocean floor: a review. Phil Trans R Soc Lond A 331:119–138

    Article  CAS  Google Scholar 

  • Gradinger R, Bluhm BA (2005) Arctic Ocean exploration, 2002. Polar Biol 28:169–170

    Article  Google Scholar 

  • Gray JP, Herwig RP (1996) Phylogenetic analysis of the bacterial communities in marine sediments. Appl Environ Microbiol 62:4049–4059

    PubMed  CAS  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser No.41 41:95–98

    CAS  Google Scholar 

  • Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67:4399–4406

    Article  PubMed  CAS  Google Scholar 

  • Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K, Neaslon 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

    Article  PubMed  CAS  Google Scholar 

  • Knoblauch C, Jørgensen BB, Harder J (1999) Community size and metabolic rates of psychrophilic sulfate-reducing bacteria in Arctic marine sediments. Appl Environ Microbiol 65:4230–4233

    PubMed  CAS  Google Scholar 

  • Kostka JE, Thamdrup B, Glud RN, Canfield DE (1999) Rates and pathways of carbon oxidation in permanently cold Arctic sediments. Mar Ecol Prog Ser 180:7–21

    Article  CAS  Google Scholar 

  • Kwon KK, Lee HS, Yang SH, Kim SJ (2005) Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the ‘Alphaproteobacteria’. Int J Syst Evol Microbiol 55(PT 5):2033–2037

    Article  PubMed  CAS  Google Scholar 

  • Li L, Kato C, Horikoshi K (1999a) Bacterial diversity in deep-sea sediments from different depths. Biodivers Conserv 8:659–677

    Article  Google Scholar 

  • Li L, Kato C, Horikoshi K (1999b) Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar Biotechnol 1:391–400

    Article  PubMed  CAS  Google Scholar 

  • Llobet-Brossa E, Rossello-Mora R, Amann R (1998) Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl Environ Microbiol 64:2691–2696

    PubMed  Google Scholar 

  • Losekann T, Knittel K, Nadalig T, Fuchs B, Niemann H, Boetius A, Amann R (2007) Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby mud volcano, Barents Sea. Appl Environ Microbiol 73:3348–3362

    Article  PubMed  CAS  Google Scholar 

  • Macdonald RW, Solomon SM, Cranston RE, Welch HE, Yunker MB, Gobeil C (1998) A sediment and organic carbon budget for the Canadian Beaufort Shelf. Marine Geol 144:255–273

    Article  CAS  Google Scholar 

  • Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29:173–174

    Article  PubMed  CAS  Google Scholar 

  • Methé BA, Hiorns WD, Zehr JP (1998) Contrasts between marine and freshwater bacterial community composition: analyses of communities in Lake George and six other Adirondack lakes. Limnol Oceanogr 43:368–374

    Google Scholar 

  • Minana-Galbis D, Farfan M, Loren JG, Fuste MC (2002) Biochemical identification and numerical taxonomy of Aeromonas spp. isolated from environmental and clinical samples in Spain. J Appl Microbiol 93:420–430

    Article  PubMed  CAS  Google Scholar 

  • Minana-Galbis D, Farfan M, Fuste MC, Loren JG (2004) Aeromonas molluscorum sp. nov. isolated from bivalve mollusks. Int J Syst Evol Microbiol 54:2073–2078

    Article  PubMed  CAS  Google Scholar 

  • Mu C, Bao Z, Chen G, Hu J, Hao L, Qi Z, Li G (2005) Bacterial diversity in the sediments collected from the Shikoku Basin. Acta Oceanol Sinica 24:114–121

    Google Scholar 

  • Mullins TD, Britschgi TB, Krest RL, Giovannoni SJ (1995) Genetic comparisons revealed that the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limno Oceanogr 40:148–158

    Article  CAS  Google Scholar 

  • Nedashkovskaya OI, Vancanneyt M, De Vos P, Kim SB, Le MS, Mikhailov VV (2007) Maribacter polysiphoniae sp. nov., isolated from a red alga. Int J Syst Evol Microbiol 57(PT 12):2840–2843

    Article  PubMed  CAS  Google Scholar 

  • Prabagaran SR, Manorama R, Delille D, Shivaji S (2007) Predominance of Roseobacter, Sulfitobacter, Glaciecola and Psychrobacter in seawater collected off Ushuaia, Argentina, Sub-Antarctica. FEMS Microbiol Ecol 59(2):342–355

    PubMed  CAS  Google Scholar 

  • Parkes RJ, Cragg BA, Bale SJ, Getliff JM, Goodman K, Rochelle PA, Fry JC, Weightman AJ, Harvey SM (1994) Deep bacterial biosphere in Pacific Ocean sediments. Nature 371:410–413

    Article  Google Scholar 

  • Perreault NN, Andersen DT, Pollard WH, Greer CW, Whyte LG (2007) Characterization of the prokaryotic diversity in cold saline perennial springs of the Canadian high Arctic. Appl Environ Microbiol 73:1532–1543

    Article  PubMed  CAS  Google Scholar 

  • Polymenakou PN, Bertilsson S, Tselepides A, Stephanou EG (2005) Bacterial community composition in different sediments from the eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries. Microb Ecol 50:447–462

    Article  PubMed  CAS  Google Scholar 

  • Purkhold U, Wagner M, Timmermann G, Pommerening-Roser A, Koops HP (2003) 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. Int J Syst Evol Microbiol 53(Pt 5):1485–1494

    Article  PubMed  CAS  Google Scholar 

  • Ravenschlag K, Sahm K, Pernthaler J, Amann R (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65:3982–3989

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Ravenschlag K, Sahm K, Amann R (2001) Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Appl Environ Microbiol 67:387–395

    Article  PubMed  CAS  Google Scholar 

  • Romanenko LA, Schumann P, Rohde M, Zhukova NV, Mikhailov VV, Stackebrandt E (2005) Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp. nov., novel bacteria from the marine environment. Int J Syst Evol Microbiol 55:143–148

    Article  PubMed  CAS  Google Scholar 

  • Rysgaard S, Thamdrup B, Risgaard-Petersen N, Fossing H, Berg P, Christensen PB, Dalsgaard T (1999) Seasonal carbon and nutrient mineralization in a high-Arctic coastal marine sediment, Young Sound, Northeast Greenland. Mar Ecol Prog Ser 175:261–276

    Article  Google Scholar 

  • Sahm K, Berninger UG (1998) Abundance, vertical distribution and community structure of benthic prokaryotes from permanently cold marine sediments (Svalbard, Arctic Ocean). Mar Ecol Prog Ser 165:71–80

    Article  Google Scholar 

  • Sahm K, MacGregor BJ, Jørgensen BB, Stahl DA (1999) Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment. Environ Microbiol 1:65–74

    Article  PubMed  CAS  Google Scholar 

  • Santelli CM, Orcutt BN, Banning E, Bach W, Moyer CL, Sogin ML, Staudigel H, Edwards KJ (2008) Abundance and diversity of microbial life in ocean crust. Nature 453(7195):653–656

    Article  PubMed  CAS  Google Scholar 

  • Sorensen KB, Glazer B, Hannides A, Gaidos E (2007) Spatial structure of the microbial community in sandy carbonate sediment. Mar Ecol Prog Ser 346:61–74

    Article  CAS  Google Scholar 

  • Swingley WD, Sadekar S, Mastrian SD, Matthies HJ, Hao J, Ramos H, Acharya CR, Conrad AL, Taylor HL, Dejesa LC, Shah MK, O’huallachain ME, Lince MT, Blankenship RE, Beatty JT, Touchman JW (2007) The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J Bacteriol 189(3):683–690

    Article  PubMed  CAS  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  PubMed  CAS  Google Scholar 

  • Taylor MW, Radax R, Steger D, Wagner M (2007) Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 71(2):295–347

    Article  PubMed  CAS  Google Scholar 

  • Teske A, Hinrichs KU, Edgcomb V, de Vera Gomez A, Kysela D, Sylva SP, Sogin ML, Jannasch HW (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68:1994–2007

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Uphoff HU, Felske A, Fehr W, Wagner-Dobler I (2001) The microbial diversity in picoplankton enrichment cultures: a molecular screening of marine isolates. FEMS Microbiol Ecol 35:249–258

    Article  PubMed  CAS  Google Scholar 

  • Webster G, Parkes RJ, Fry JC, Weightman AJ (2004) Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl Environ Microbiol 70:5708–5713

    Article  PubMed  CAS  Google Scholar 

  • Webster G, Parkes RJ, Cragg BA, Newberry CJ, Weightman AJ, Fry JC (2006) Prokaryotic community composition and biogeochemical processes in deep subseafoor sediments from the Peru Margin. FEMS Microbiol Ecol 58:65–85

    Article  PubMed  CAS  Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583

    Article  PubMed  CAS  Google Scholar 

  • Zhang Z (2004) The report of 2003 Chinese Arctic Research Expedition (in Chinese). Ocean press, Beijing

    Google Scholar 

  • Zhang W, Ki JS, Qian PY (2008) Microbial diversity in polluted harbor sediments I: Bacterial community assessment based on four clone libraries of 16S rDNA. Estuar Coast Shelf Sci 76(3):668–681

    Article  Google Scholar 

  • Zeng R, Zhao J, Zhang R, Lin N (2005) Bacterial community in sediment from the western Pacific Warm Pool and its relationship to environment. China Environ. Sci 48:282–290

    Article  CAS  Google Scholar 

  • Zubkov MV, Fuchs BM, Archer SD, Kiene RP, Amann R, Burkill PH (2002) A population of the alpha-proteobacteria dominates the bacterioplankton and dimethylsulphoniopropionate uptake after an algal bloom in the North Sea. Deep-sea Res II, Top Stud Oceanogr 49(15):3017–3038

    Article  CAS  Google Scholar 

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Acknowledgments

We appreciate the assistance of the crew of the Xuelong and the scientists who collected samples for us on the CHINARE 2003 cruise, especially A.G. Gao, R.J. Wang and M.H. Cai. H.B. Teng, Q. Luo and M. Wang provided useful data analysis and other support during the preparation of the manuscript. Y.H. Su and A.B. Chen helped with sample analysis. We also thank Dr. H.S. Bi for assistance in editing and discussing this manuscript. This work was supported by the National Natural Science Foundation of China (No. 40876097, 40806073), Chinese National Basic Research Program (No. 2004CB719601), Polar Strategic Research Foundation of China, and the program of the Science and Technology Committee of Shanghai, China (052307053). This work is also a part of the Project ‘Second Chinese National Arctic Research Expedition’ or CHINARE-2003 supported by the Ministry of Finance of China and organized by the Chinese Arctic and Antarctic Administration (CAA). The participants in this joint work are from the institutions (e.g., PRIC, FIO, SIO, etc.).

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  1. SOA Key Laboratory for Polar Science, Polar Research Institute of China, 200136, Shanghai, China

    Huirong Li, Yong Yu, Wei Luo, Yinxin Zeng & Bo Chen

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  1. Huirong Li
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Correspondence to Huirong Li.

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Communicated by F. Robb.

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Li, H., Yu, Y., Luo, W. et al. Bacterial diversity in surface sediments from the Pacific Arctic Ocean. Extremophiles 13, 233–246 (2009). https://doi.org/10.1007/s00792-009-0225-7

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