Bacterial diversity in surface sediments from the Pacific Arctic Ocean

Extremophiles

Volumn 13, Issue 2, 2009, Pages 233-246

  Li, Huirong ^a   Yu, Yong ^a   Luo, Wei ^a   Zeng, Yinxin ^a   Chen, Bo ^a  

^a POLAR RESEARCH INSTITUTE OF CHINA   (China)

Author keywords

16S rDNA; Bacterial; Sediment; The Pacific Arctic Ocean

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA; RNA 16S; SEA WATER;

ARCTIC; ARTICLE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; GAMMAPROTEOBACTERIA; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR CLONING; PACIFIC OCEAN; PHYLOGENY; SEA; SEDIMENT;

ARCTIC REGIONS; BACTERIA; BIODIVERSITY; CLONING, MOLECULAR; DNA, BACTERIAL; DNA, RIBOSOMAL; GAMMAPROTEOBACTERIA; GEOLOGIC SEDIMENTS; OCEANS AND SEAS; PACIFIC OCEAN; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER;

ACIDOBACTERIA; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CHLOROFLEXI; CHLOROFLEXI (CLASS); DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; FIRMICUTES; GAMMAPROTEOBACTERIA; PLANCTOMYCETES; SPIROCHAETALES; VERRUCOMICROBIA;

EID: 61449227230     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-009-0225-7     Document Type: Article

References (64)

1. N Bano JT Hollibaugh 2002 Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean Appl Environ Microbiol 68 505 518
2. LL Belicka RW Macdonald HR Harvey 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
3. A Blazejak J Kuever C Erseus R Amann N Dubilier 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
4. PP Bosshard Y Santini D Grüter R Stettler R Bachofen 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
5. JP Bowman RD McCuaig 2003 Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment Appl Environ Microbiol 69 2463 2483
6. JP Bowman SA McCammon MV Brown DS Nichols TA McMeekin 1997 Diversity and association of psychrophilic bacteria in Antarctic sea ice Appl Environ Microbiol 63 3068 3078
7. JP Bowman SA McCammon JAE Gibson L Robertson PD Nichols 2003 Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediment Appl Environ Microbiol 69 2448 2462
8. JP Bowman SA McCammon AL Dann 2005 Biogeographic and quantitative analyses of abundant uncultivated γ-Proteobacterial clades from marine sediment Microb Ecol 49 451 460
9. R Brinkmeyer K Knittel J Jurgens H Weyland R Amann E Helmke 2003 Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice Appl Environ Microbiol 69 6610 6619
10. A Chao 1987 Estimating the population size for capture recapture data with unequal catchability Biometrics 43 783 791
11. Chen L (2000) The report of the first Chinese Arctic Research Expedition (in Chinese). China Ocean Press, Beijing
12. A Dhillon A Teske J Dillon DA Stahl ML Sogin 2003 Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin Appl Environ Microbiol 69 2765 2772
13. S D'Hondt S Rutherford AJ Spivack 2002 Metabolic activity of subsurface life in deep-sea sediments Science 295 2067 2070
14. 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
15. DC Gillan P Pernet 2007 Adherent bacteria in heavy metal contaminated marine sediments Biofouling 23 1 13
16. RE Glatz PW Lepp BB Ward CA Francis 2006 Planktonic microbial community composition across steep physical/chemical gradients in permanently ice-covered Lake Bonney, Antarctica Geobiology 4 53 67
17. AJ Gooday CM Turley 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
18. R Gradinger BA Bluhm 2005 Arctic Ocean exploration, 2002 Polar Biol 28 169 170
19. JP Gray RP Herwig 1996 Phylogenetic analysis of the bacterial communities in marine sediments Appl Environ Microbiol 62 4049 4059
20. TA Hall 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
21. JB Hughes JJ Hellmann TH Ricketts BJM Bohannan 2001 Counting the uncountable: statistical approaches to estimating microbial diversity Appl Environ Microbiol 67 4399 4406
22. F Inagaki M Suzuki K Takai H Oida T Sakamoto K Aoki KH Neaslon K Horikoshi 2003 Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk Appl Environ Microbiol 69 7224 7235
23. C Knoblauch BB Jørgensen J Harder 1999 Community size and metabolic rates of psychrophilic sulfate-reducing bacteria in Arctic marine sediments Appl Environ Microbiol 65 4230 4233
24. JE Kostka B Thamdrup RN Glud DE Canfield 1999 Rates and pathways of carbon oxidation in permanently cold Arctic sediments Mar Ecol Prog Ser 180 7 21
25. KK Kwon HS Lee SH Yang SJ Kim 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
26. L Li C Kato K Horikoshi 1999 Bacterial diversity in deep-sea sediments from different depths Biodivers Conserv 8 659 677
27. L Li C Kato K Horikoshi 1999 Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench Mar Biotechnol 1 391 400
28. E Llobet-Brossa R Rossello-Mora R Amann 1998 Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization Appl Environ Microbiol 64 2691 2696
29. T Losekann K Knittel T Nadalig B Fuchs H Niemann A Boetius R Amann 2007 Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby mud volcano, Barents Sea Appl Environ Microbiol 73 3348 3362
30. RW Macdonald SM Solomon RE Cranston HE Welch MB Yunker C Gobeil 1998 A sediment and organic carbon budget for the Canadian Beaufort Shelf Marine Geol 144 255 273
31. BL Maidak JR Cole TG Lilburn CT Parker PR Saxman RJ Farris GM Garrity GJ Olsen TM Schmidt JM Tiedje 2001 The RDP-II (Ribosomal Database Project) Nucleic Acids Res 29 173 174
32. BA Methé WD Hiorns JP Zehr 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
33. D Minana-Galbis M Farfan JG Loren MC Fuste 2002 Biochemical identification and numerical taxonomy of Aeromonas spp. isolated from environmental and clinical samples in Spain J Appl Microbiol 93 420 430
34. D Minana-Galbis M Farfan MC Fuste JG Loren 2004 Aeromonas molluscorum sp. nov. isolated from bivalve mollusks Int J Syst Evol Microbiol 54 2073 2078
35. C Mu Z Bao G Chen J Hu L Hao Z Qi G Li 2005 Bacterial diversity in the sediments collected from the Shikoku Basin Acta Oceanol Sinica 24 114 121
36. TD Mullins TB Britschgi RL Krest SJ Giovannoni 1995 Genetic comparisons revealed that the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities Limno Oceanogr 40 148 158
37. OI Nedashkovskaya M Vancanneyt P De Vos SB Kim MS Le VV Mikhailov 2007 Maribacter polysiphoniae sp. nov., isolated from a red alga Int J Syst Evol Microbiol 57 PT 12 2840 2843
38. SR Prabagaran R Manorama D Delille S Shivaji 2007 Predominance of Roseobacter, Sulfitobacter, Glaciecola and Psychrobacter in seawater collected off Ushuaia, Argentina, Sub-Antarctica FEMS Microbiol Ecol 59 2 342 355
39. RJ Parkes BA Cragg SJ Bale JM Getliff K Goodman PA Rochelle JC Fry AJ Weightman SM Harvey 1994 Deep bacterial biosphere in Pacific Ocean sediments Nature 371 410 413
40. NN Perreault DT Andersen WH Pollard CW Greer LG Whyte 2007 Characterization of the prokaryotic diversity in cold saline perennial springs of the Canadian high Arctic Appl Environ Microbiol 73 1532 1543
41. PN Polymenakou S Bertilsson A Tselepides EG Stephanou 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
42. U Purkhold M Wagner G Timmermann A Pommerening-Roser HP Koops 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
43. K Ravenschlag K Sahm J Pernthaler R Amann 1999 High bacterial diversity in permanently cold marine sediments Appl Environ Microbiol 65 3982 3989
44. K Ravenschlag K Sahm C Knoblauch BB Jørgensen R Amann 2000 Community structure, cellular rRNA content and activity of sulfate reducing bacteria in marine arctic sediments Appl Environ Microbiol 66 3592 3602
45. K Ravenschlag K Sahm R Amann 2001 Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard) Appl Environ Microbiol 67 387 395
46. LA Romanenko P Schumann M Rohde NV Zhukova VV Mikhailov E Stackebrandt 2005 Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp. nov., novel bacteria from the marine environment Int J Syst Evol Microbiol 55 143 148
47. S Rysgaard B Thamdrup N Risgaard-Petersen H Fossing P Berg PB Christensen T Dalsgaard 1999 Seasonal carbon and nutrient mineralization in a high-Arctic coastal marine sediment, Young Sound, Northeast Greenland Mar Ecol Prog Ser 175 261 276
48. K Sahm UG Berninger 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
49. K Sahm BJ MacGregor BB Jørgensen DA Stahl 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
50. CM Santelli BN Orcutt E Banning W Bach CL Moyer ML Sogin H Staudigel KJ Edwards 2008 Abundance and diversity of microbial life in ocean crust Nature 453 7195 653 656
51. KB Sorensen B Glazer A Hannides E Gaidos 2007 Spatial structure of the microbial community in sandy carbonate sediment Mar Ecol Prog Ser 346 61 74
52. WD Swingley S Sadekar SD Mastrian HJ Matthies J Hao H Ramos CR Acharya AL Conrad HL Taylor LC Dejesa MK Shah ME O'huallachain MT Lince RE Blankenship JT Beatty JW Touchman 2007 The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism J Bacteriol 189 3 683 690
53. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 Mol Biol Evol 24 1596 1599
54. MW Taylor R Radax D Steger M Wagner 2007 Sponge-associated microorganisms: evolution, ecology, and biotechnological potential Microbiol Mol Biol Rev 71 2 295 347
55. A Teske KU Hinrichs V Edgcomb A de Vera Gomez D Kysela SP Sylva ML Sogin HW Jannasch 2002 Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities Appl Environ Microbiol 68 1994 2007
56. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 4876 4882
57. HU Uphoff A Felske W Fehr I Wagner-Dobler 2001 The microbial diversity in picoplankton enrichment cultures: a molecular screening of marine isolates FEMS Microbiol Ecol 35 249 258
58. G Webster RJ Parkes JC Fry AJ Weightman 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
59. G Webster RJ Parkes BA Cragg CJ Newberry AJ Weightman JC Fry 2006 Prokaryotic community composition and biogeochemical processes in deep subseafoor sediments from the Peru Margin FEMS Microbiol Ecol 58 65 85
60. WB Whitman DC Coleman WJ Wiebe 1998 Prokaryotes: the unseen majority Proc Natl Acad Sci USA 95 6578 6583
61. Zhang Z (2004) The report of 2003 Chinese Arctic Research Expedition (in Chinese). Ocean press, Beijing
62. W Zhang JS Ki PY Qian 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
63. R Zeng J Zhao R Zhang N Lin 2005 Bacterial community in sediment from the western Pacific Warm Pool and its relationship to environment China Environ. Sci 48 282 290
64. MV Zubkov BM Fuchs SD Archer RP Kiene R Amann PH Burkill 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