Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (∼13°N)

Extremophiles

Volumn 12, Issue 4, 2008, Pages 573-585

  Li, Youxun ^a,b   Li, Fuchao ^a   Zhang, Xiaowen ^a,b   Qin, Song ^a   Zeng, Zhigang ^a   Dang, Hongyue ^a   Qin, Yunshan ^a  

^a INSTITUTE OF OCEANOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Cold sediment; East Pacific Rise (EPR); Geochemical features; Microbial diversity; Vertical distribution

Indexed keywords

DNA; RIBOSOME DNA; RNA 16S;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BIOLOGICAL MODEL; CHEMICAL MODEL; CHINA; COLD; ECOSYSTEM; GENETIC VARIABILITY; GENETICS; METABOLISM; MICROBIOLOGY; PHYLOGENY; POLYMERASE CHAIN REACTION; SEDIMENT; STATISTICAL MODEL;

ARCHAEA; BACTERIA; CHINA; COLD; DNA; DNA, RIBOSOMAL; ECOSYSTEM; GEOLOGIC SEDIMENTS; MODELS, CHEMICAL; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; VARIATION (GENETICS);

ACTINOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); CHLOROFLEXI; CHLOROFLEXI (CLASS); CRENARCHAEOTA; GAMMAPROTEOBACTERIA; PROKARYOTA; UNIDENTIFIED BACTERIUM;

EID: 46149112581     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-008-0159-5     Document Type: Article

References (64)

1. Alain K, Marteinsson VT, Miroshnichenko ML, Bonch-Osmolovskaya EA, Prieur D, Birrien JL (2002) Marinitoga piezophila sp. nov., a rod-shaped, thermo-piezophilic bacterium isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 52:1331-1339
2. Arakawa S, Sato T, Yoshida Y, Usami R, Kato C (2006) Comparison of the microbial diversity in cold-seep sediments from different depths in the Nankai Trough. J Gen Appl Microbiol 52:47-54
3. Audiffrin C, Cayol JL, Joulian C, Casalot L, Thomas P, Garcia JL, Ollivier B (2003) Desulfonauticus submarinus gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 53:1585-1590
4. Barbier G, Godfroy A, Meunier JR, Querellou J, Cambon MA, Lesongeur F, Grimont PA, Raguenes G (1999) Pyrococcus glycovorans sp. nov., a hyperthermophilic archaeon isolated from the East Pacific Rise. Int J Syst Bacteriol 49(Pt 4):1829-1837
5. Barns SM, Fundyga RE, Jeffries MW, Pace NR (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci USA 91:1609-1613
6. Briee C, Moreira D, Lopez-Garcia P (2007) Archaeal and bacterial community composition of sediment and plankton from a suboxic freshwater pond. Res Microbiol 158:213-227
7. 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
8. Colwell F, Matsumoto R, Reed D (2004) A review of the gas hydrates, geology, and biology of the Nankai Trough. Chem Geol 205:391-404
9. Ehrhardt CJ, Haymon RM, Lamontagne MG, Holden PA (2007) Evidence for hydrothermal Archaea within the basaltic flanks of the East Pacific Rise. Environ Microbiol 9:900-912
10. Excoffier L, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:4
11. Fry JC, Webster G, Cragg BA, Weightman AJ, Parkes RJ (2006) Analysis of DGGE profiles to explore the relationship between prokaryotic community composition. FEMS Microbiol Ecol 58:86-98
12. GB18668 (2002) Marine sediment quality General administration of quality supervision, inspection and quarantine of the People's Republic of China
13. Hekinian R, Fevrier M, Avedik F, Cambon P, Charlou JL, Needham HD, Raillard J, Boulegue J, Merlivat L, Moinet A, Manganini S, Lange J (1983) East Pacific Rise near 13{degrees}N: geology of new hydrothermal fields. Science 219:1321-1324
14. Hoj L, Olsen RA, Torsvik VL (2005) Archaeal communities in High Arctic wetlands at Spitsbergen, Norway (78 degrees N) as characterized by 16S rRNA gene fingerprinting. FEMS Microbiol Ecol 53:89-101
15. Holoman TR, Elberson MA, Cutter LA, May HD, Sowers KR (1998) Characterization of a defined 2,3,5,6-tetrachlorobiphenyl-ortho-dechlorinating microbial community by comparative sequence analysis of genes coding for 16S rRNA. Appl Environ Microbiol 64:3359-3367
16. Huber JA, Butterfield DA, Baross JA (2002) Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Appl Environ Microbiol 68:1585-1594
17. Inagaki F, Kuypers MM, Tsunogai U, Ishibashi J, Nakamura K, Treude T, Ohkubo S, Nakaseama M, Gena K, Chiba H, Hirayama H, Nunoura T, Takai K, Jorgensen BB, Horikoshi K, Boetius A (2006a) Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system. Proc Natl Acad Sci USA 103:14164-14169
18. Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH, Horikoshi K, D'Hondt S, Jorgensen BB (2006b) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci USA 103:2815-2820
19. Jeanthon C, L'Haridon S, Reysenbach AL, Corre E, Vernet M, Messner P, Sleytr UB, Prieur D (1999) Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213T as Methanococcus fervens sp. nov. Int J Syst Bacteriol 49(Pt 2):583-589
20. Kanagawa T (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng 96:317-323
21. Kanokratana P, Chanapan S, Pootanakit K, Eurwilaichitr L (2004) Diversity and abundance of Bacteria and Archaea in the Bor Khlueng Hot Spring in Thailand. J Basic Microbiol 44:430-444
22. Kato C, Li L, Tamaoka J, Horikoshi K (1997) Molecular analyses of the sediment of the 11,000-m deep Mariana Trench. Extremophiles 1:117-123
23. 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 73:407-414
24. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150-163
25. Larkin JM, Henk MC (1996) Filamentous sulfide-oxidizing bacteria at hydrocarbon seeps of the Gulf of Mexico. Microsc Res Tech 33:23-31
26. 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
27. MacGregor BJ, Moser DP, Baker BJ, Alm EW, Maurer M, Nealson KH, Stahl DA (2001) Seasonal and spatial variability in Lake Michigan sediment small-subunit rRNA concentrations. Appl Environ Microbiol 67:3908-3922
28. Madrid VM, Taylor GT, Scranton MI, Chistoserdov AY (2001) Phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the Cariaco Basin. Appl Environ Microbiol 67:1663-1674
29. Margalef R (1958) Information theory in ecology. Gen Syst 3:36
30. Marteinsson VT, Hauksdottir S, Hobel CF, Kristmannsdottir H, Hreggvidsson GO, Kristjansson JK (2001) Phylogenetic diversity analysis of subterranean hot springs in Iceland. Appl Environ Microbiol 67:4242-4248
31. Martin AP (2002) Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68:3673-3682
32. Martiny JB, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin PJ, Naeem S, Ovreas L, Reysenbach AL, Smith VH, Staley JT (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102-112
33. Menard HW (1960) The East Pacific Rise. Science 132:1737-1746
34. Miroshnichenko ML, Kostrikina NA, L'Haridon S Jeanthon C, Hippe H, Stackebrandt E, Bonch-Osmolovskaya EA (2002) Nautilia lithotrophica gen. nov., sp. nov., a thermophilic sulfur-reducing epsilon-proteobacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 52:1299-1304
35. Moussard H, Corre E, Cambon-Bonavita MA, Fouquet Y, Jeanthon C (2006a) Novel uncultured Epsilonproteobacteria dominate a filamentous sulphur mat from the 13 degrees N hydrothermal vent field, East Pacific Rise. FEMS Microbiol Ecol 58:449-463
36. Moussard H, Moreira D, Cambon-Bonavita MA, Lopez-Garcia P, Jeanthon C (2006b) Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeote. FEMS Microbiol Ecol 57:452-469
37. Munson MA, Nedwell DB, Embley TM (1997) Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl Environ Microbiol 63:4729-4733
38. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695-700
39. Nercessian O, Bienvenu N, Moreira D, Prieur D, Jeanthon C (2005) Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments. Environ Microbiol 7:118-132
40. Nercessian O, Reysenbach AL, Prieur D, Jeanthon C (2003) Archaeal diversity associated with in situ samplers deployed on hydrothermal vents on the East Pacific Rise (13 degrees N). Environ Microbiol 5:492-502
41. Newberry CJ, Webster G, Cragg BA, Parkes RJ, 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
42. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734-740
43. Pielou EC (1966) Species-diversity and pattern-diversity in the study of ecological succession. J Theor Biol 10:370-383
44. Reed AJ, Lutz RA, Vetriani C (2006) Vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the Florida Escarpment. Extremophiles 10:199-211
45. Rohlf FJ (1998) NTSYS-pc, numerical taxonomy and multivariate analysis system version 2.02. Exeter Publications, Setauket
46. Schrenk MO, Kelley DS, Delaney JR, Baross JA (2003) Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl Environ Microbiol 69:3580-3592
47. Schwarz JI, Eckert W, Conrad R (2007) Community structure of Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel). Syst Appl Microbiol 30:239-254
48. Shannon C, Weaver (1949) The mathematical theory of communication. University of Illinois Press, Urbana
49. Slobodkin A, Campbell B, Cary SC, Bonch-Osmolovskaya E, Jeanthon C (2001) Evidence for the presence of thermophilic Fe(III)-reducing microorganisms in deep-sea hydrothermal vents at 13 degrees N (East Pacific Rise). FEMS Microbiol Ecol 36:235-243
50. Sorensen KB, Lauer A, Teske A (2004) Archaeal phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology 2:151-161
51. Staley JT, Gosink JJ (1999) Poles apart: biodiversity and biogeography of sea ice bacteria. Annu Rev Microbiol 53:189-215
52. Takai K, Oida H, Suzuki Y, Hirayama H, Nakagawa S, Nunoura T, Inagaki F, Nealson KH, Horikoshi K (2004) Spatial distribution of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems. Appl Environ Microbiol 70:2404-2413
53. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
54. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74
55. von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213-229
56. Wang P, Xiao X, Wang F (2005) Phylogenetic analysis of Archaea in the deep-sea sediments of west Pacific Warm Pool. Extremophiles 9:209-217
57. Wani AA, Surakasi VP, Siddharth J, Raghavan RG, Patole MS, Ranade D, Shouche YS (2006) Molecular analyses of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area. Res Microbiol 157:928-937
58. Wawrik B, Kutliev D, Abdivasievna UA, Kukor JJ, Zylstra GJ, Kerkhof L (2007) Biogeography of actinomycete communities and type II polyketide synthase genes in soils collected in New Jersey and Central Asia. Appl Environ Microbiol 73:2982-2989
59. 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 72:2756-2764
60. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
61. Yan B, Hong K, Yu ZN (2006a) Archaeal communities in mangrove soil characterized by 16S rRNA gene clones. J Microbiol 44:566-571
62. Yan T, Ye Q, Zhou J, Zhang CL (2006b) Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. FEMS Microbiol Ecol 57:251-259
63. Yanagibayashi M, Nogi Y, Li L, Kato C (1999) Changes in the microbial community in Japan Trench sediment from a depth of 6292 m during cultivation without decompression. FEMS Microbiol Lett 170:271-279
64. Zeidner G, Beja O (2004) The use of DGGE analyses to explore eastern Mediterranean and Red Sea marine picophytoplankton assemblages. Environ Microbiol 6:528-534