Microbila diversity in the deep marine sediment from the Qiongdongnan Basin in China Sea

Geomicrobiology Journal

Volumn 24, Issue 6, 2007, Pages 505-517

  Jiang, Hongchen ^a   Dong, Hailiang ^a   Ji, Shanshan ^a   Ye, Ying ^b   Wu, Nengyou ^c  

^a MIAMI UNIVERSITY   (United States)

^b ZHEJIANG UNIVERSITY   (China)

^c Guangzhou Marine Geological Survey CGS   (China)

Author keywords

16S rRNA gene analysis; Archaea; Bacteria; Diversity; South China Sea

Indexed keywords

BACTERIUM; CARBON CYCLE; CONTINENTAL SHELF; CONTINENTAL SLOPE; DEEP-SEA SEDIMENT; GAS HYDRATE; GENE; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; PHYLOGENETICS;

PACIFIC OCEAN; QIONGDONGNAN BASIN; SOUTH CHINA SEA;

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; DELTAPROTEOBACTERIA; EURYARCHAEOTA; FIRMICUTES; METHANOSARCINA; METHANOSARCINALES;

EID: 35148845696     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490450701572473     Document Type: Conference Paper

References (69)

1. Acinas, S. G., Sarma-Rupavtarm, R., Klepac-Ceraj, V. and Polz, M. F. (2005) PCR-induced sequence artifacts and bias: Insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol, 71, pp. 8966-8969.
2. Biddle, J. F., House, C. H. and Brenchley, J. E. (2005) Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane profiles. Geobiology, 3, pp. 287-295.
3. Bidle, K. A., Kastner, M. and Bartlett, D. H. (1999) A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia Margin (ODP site 892B). FEMS Microbiol Lett, 177, pp. 101-108.
4. Boetius, A., Ravenschlag, K., Schubert, C. J., Rickert, D., Widdel, F., Gieseke, A., Amann, R., Jorgensen, B. B., Witte, U. and Pfannkuche, O. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature, 407, pp. 623-626.
5. Brisbarre, N., Fardeau, M. L., Cueff, V., Cayol, J. L., Barbier, G., Cilia, V., Ravot, G., Thomas, P., Garcia, J. L. and Ollivier, B. (2003) Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney. Int J Syst Evol Microbiol, 53, pp. 1043-1049.
6. Bruns, A. and Berthe-Corti, L. (1999) Fundibacter jadensis gen. nov., sp. nov., a new slightly halophilic bacterium, isolated from intertidal sediment. Int J Syst Bacteriol, 49, pp. 441-448.
7. Chen, D-F and Xia, B. (2004) Distribution of gas hydrate stable zones and resource prediction in the Qiongdongnan Basin of the South China Sea (in Chinese). Chin J Geophy, 47, pp. 483-489.
8. D'Hondt, S., Jorgensen, B. B., Miller, D. J., Batzke, A., Blake, R., Cragg, B. A., Cypionka, H., Dickens, G. D., Ferdelman, T., Hinrichs, K-U, Holm, N. G., Mitterer, R., Spivack, A., Wang, G., Bekins, B., Engelen, B., Ford, K., Gettemy, G., Rutherford, S. D., Sass, H., Skilbeck, C GI, Aiello, I. W., Guerin, G., House, C. H., Inagaki, F., Meister, P., Naehr, T., Niitsuma, S., Parkes, R. J., Schippers, A., Smith, D. C., Teske, A., Wiegel, J., Padilla, C. N. and Acosta, J LS (2004) Distributions of microbial activities in deep subseafloor sediments. Science, 306, pp. 2216-2221.
9. Fernandez-Martinez, J., Pujalte, M. J., Garcia-Martinez, J., Mata, M., Garay, E. and Rodriguez-Valera, F. (2003) Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 12178T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax. Int J Syst Evol Microbiol, 53, pp. 331-338.
10. Franzmann, P. D., Springer, N., Ludwig, W., de Macario, E Conway and Rhode, M. (1992) A methanogenic archaeon from Ace Lake, Antarctica: Methanococcoides burtonii sp. nov. Syst Appl Microbiol, 15, pp. 573-581.
11. Gonzalez, J. M. and Moran, M. A. (1997) Numerical dominance of a group of marine bacteria in the alpha-subclass of the class Proteobacteria in coastal seawater. Appl Environ Microbiol, 63, pp. 4237-4242.
12. Gonzalez, J. M. and Whitman, W. B. (2004) Oceanospirillum and Related Genera. The Prokaryotes: An evolving electronic resource for the microbiological community, Springer-Verlag, New York
13. Grimberg, S. J., Stringfellow, W. T. and Aitken, M. D. (1996) Quantifying the biodegradation of phenanthrene by Pseudomonas stutzeri P16 in the presence of a nonionic surfactant. Appl Environ Microbiol, 62, pp. 2387-2392.
14. Grosskopf, R., Stubner, S. and Liesack, W. (1998) Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microbiol, 64, pp. 4983-4989.
15. Guo, T. M., Wu, B. H., Zhu, Y. H., Fan, S. S. and Chen, G. J. (2004) A review on the gas hydrate research in China. J Petro Sci Eng, 41, pp. 11-20.
16. Xia, B., Sun, D., Zhang, S. and Liu, B. (2006) Hydrocarbon accumulation, migration and play targets in the Qiongdongnan Basin, South China Sea (in Chinese). Petrol Expl Devel, 33, pp. 53-58.
17. Hinrichs, K. U., Hayes, J. M., Sylva, S. P., Brewer, P. G. and Delong, E. F. (1999) Methane-consuming archaebacteria in marine sediments. Nature, 398, pp. 802-805.
18. Hugenholtz, P., Goebel, B. M. and Pace, N. R. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol, 180, pp. 4765-4774.
19. Humayoun, S. B., Bano, N. and Hollibaugh, J. T. (2003) Depth distribution of microbial diversity in Mona Lake, A mermictic soda lake in California. Appl Environ Microbiol, 69, pp. 1030-1042.
20. Inagaki, F., Nunoura, T., Nakagawa, S., Teske, A., Lever, M., Lauer, A., Suzuki, M., Takai, K., Delwiche, M., Colwell, F. S., Nealson, K. H., Horikoshi, K., D'Hondt, S. and Jorgensen, B. B. (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. PNAS, 103, pp. 2815-2820.
21. Inagaki, F., Suzuki, M., Takai, K., Oida, H., Sakamoto, T., Aoki, K., Nealson, K. H. and Horikoshi, K. (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of okhotsk. Appl Environ Microbiol, 69, pp. 7224-7235.
22. Jiang, H., Dong, H., Zhang, G., Chapman, L. R. and Fields, M. W. (2006) Microbial diversity in water and sediment of Lake Chaka: An athalassohaline lake in northwestern China. Appl Environ Microbiol, 72, pp. 3832-3845.
23. Jiang, S., Yang, T., Xue, Z., Yand, J., Ling, H., Huang, Y., Liu, J. and Chen, D. (2005) Chlorine and sulfate concentrations in pore waters from marine sediments in the north margin of the South China Sea and their implications for gas hydrate exploration (in Chinese). Geoscience, 19, pp. 45-54.
24. Joye, S. B., Boetius, A., Orcutt, B., Montoya, J. P., Schulz, H. N., Erickson, M. J. and Lugo, S. K. (2004) The anaerobic oxidation of methane and sulfate reduction in sediments from Gulf of Mexico cold seeps. Chem Geol, 205, pp. 219-238.
25. Kaye, J. Z., Marquez, M. C., Ventosa, A. and Baross, J. A. (2004) Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: Halophilic bacteria isolated from deep-sea hydrothermal-vent environments. Int J Syst Evol Microbiol, 54, pp. 499-511.
26. Kim, B. S., Oh, H. M., Kang, H. and Chun, J. (2005) Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis. J Microbiol, 43, pp. 144-151.
27. Knittel, K., Losekann, T., Boetius, A., Kort, R. and Amann, R. (2005) Diversity and distribution of methanotrophic Archaea at cold seeps. Appl Environ Microbiol, 71, pp. 467-479.
28. Kormas, K., Smith, D. C., Edgcomb, V. and Teske, A. (2003) Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol Ecol, 45, pp. 115-125.
29. Kvenvolden, K. A. (1988) Methane hydrales and global climate. Global Biogeochemical Cycles, 2, pp. 221-229.
30. Kwon, K. K., Lee, H. S., Yang, S. H. and Kim, S. J. (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, pp. 2033-2037.
31. Lanoil, B. D., Sassen, R., La Duc, M. T., Sweet, S. T. and Nealson, K. H. (2001) Bacteria and archaea physically associated with Gulf of Mexico gas hydrates. Appl Environ Microbiol, 67, pp. 5143-5153.
32. Liu, J. and Wang, C. (2004) Oil-gas geological implication of geothermal fluids in Yingge Sea Basin-Qingdongnan Basin (in Chinese). Natl Gas Expl Devel, 27, pp. 7-15.
33. Marchesi, J. R., Weightman, A. J., Cragg, B. A., Parkes, R. J. and Fry, J. C. (2001) Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol Ecol, 34, pp. 221-228.
34. McDonnell, S. L. and Czarnecki, M. (2000) A note on gas hydrate in the northern sector of the South China Sea. Natural gas hydrate: In oceanic and permafrost environments, pp. 239-244. Kluwer Academic Publishers, Dordrecht, Boston
35. Milkov, A. V. (2004) Global estimates of hydrate-bound gas in marine sediments: How much is really out there?. Earth-Science Reviews, 66, pp. 183-197.
36. Mills, H. J., Hodges, C., Wilson, K., MacDonald, I. R. and Sobecky, P. A. (2003) Microbial diversity in sediments associated with suface-breaching gas hydrate mounds in the Gulf of Mexico. FEMS Microbiol Ecol, 46, pp. 39-52.
37. Mills, H. J., Martinez, R. J., Story, S. and Sobecky, P. A. (2005) Characterization of microbial community structure in Gulf of Mexico gas hydrates: Comparative analysis of DNA- and RNA-derived clone libraries. Appl Environ Microbiol, 71, pp. 3235-3247.
38. Miyazaki, M., Nogi, Y., Usami, R. and Horikoshi, K. (2006) Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan. Int J Syst Evol Microbiol, 56, pp. 1607-1613.
39. Mullins, T. D., Theresa, B. B., Robin, L. K. and Stephen, J. G. (1995) Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol Oceanogr, 40, pp. 148-158.
40. Newberry, C. J., Webster, G., Cragg, B. A., Parkes, R. J., Weightman, A. J. and Fry, J. C. (2004) Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ Microbiol, 6, pp. 274-287.
41. Niewohner, C., Hensen, C., Kasten, S., Zabel, M. and Schulz, H. D. (1998) Deep sulfate reduction completely mediated by anaerobic methane oxidation in sediments of the upwelling area off Namibia. Geochim Cosmochim Acta, 62, pp. 455-464.
42. Nunoura, T., Oida, H., Toki, T., Ashi, J., Takai, K. and Horikoshi, K. (2006) Quantification of mcrA by quantitative fluorescent PCR in sediments from methane seep of the Nankai Trough. FEMS Microbiol Ecol, 57, pp. 149-157.
43. Orcutt, B., Boetius, A., Elvert, M., Samarkin, V. and Joye, S. B. (2005) Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps. Geochim Cosmochim Acta, 69, pp. 4267-4281.
44. Orphan, V. J., House, C. H., Hinrichs, K. U., McKeegan, K. D. and De Long, E. F. (2001) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science, 293, pp. 484-487.
45. Parkes, R. J., Cragg, B. A. and Wellsbury, P. (2000) Recent studies on bacterial populations and processes in marine sediments: A review. Hydrogeol J, 8, pp. 11-28.
46. Pimenov, N. V., Rusanov, I. I., Poglazova, M. N., Mityushina, L. L., Sorokin, D. Y., Khmelenina, V. N. and Trotsenko, Y. A. (1997) Bacterial mats on coral-like structures at methane seeps in the Black Sea. Microbiology, 66, pp. 354-360.
47. Pinhassi, J. and Berman, T. (2003) Differential growth response of colony-forming alpha- and gamma-proteobacteria in dilution culture and nutrient addition experiments from Lake Kinneret (Israel), the eastern Mediterranean Sea, and the Gulf of Eilat. Appl Environ Microbiol, 69, pp. 199-211.
48. Purdy, K. J., Nedwell, D. B. and Embley, T. M. (2003) Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting antarctic sediments. Appl Environ Microbiol, 69, pp. 3181-3191.
49. Reed, D. W., Fujita, Y., Delwiche, M. E., Blackwelder, D. B., Sheridan, P. P., Uchida, T. and Colwell, F. S. (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl Environ Microbiol, 68, pp. 3759-3770.
50. Sassen, R., MacDonald, I. R., Requejo, A. G., Guinasso, N. L., Kennicutt, M. C., Sweet, S. T. and Brooks, J. M. (1994) Organic geochemistry of sediments from chemosynthetic communities, Gulf of Mexico slope. Geo-Mar Lett, 14, pp. 110-119.
51. Schippers, A., Neretin, L. N., Kallmeyer, J., Ferdelman, T. G., Cragg, B. A., Parkes, R. J. and Jorgensen, B. B. (2005) Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature, 433, pp. 861-864.
52. Schloss, P. D. and Handelsman, J. (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol, 71, pp. 1501-1506.
53. Singh, N., Kendall, M. M., Liu, Y. and Boone, D. R. (2005) Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: Description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica. Int J Syst Evol Microbiol, 55, pp. 2531-2538.
54. Sorensen, K. B. and Teske, A. (2006) Stratified communities of active archaea in deep marine subsurface sediments. Appl Environ Microbiol, 72, pp. 4596-4603.
55. Stevens, H., Stubner, M., Simon, M. and Brinkhoff, T. (2005) Phylogeny of Proteobacteria Bacteroidetes from oxic habitats of a tidal flat ecosystem. FEMS Microbiol Ecol, 54, pp. 351-365.
56. Strous, M. and Jetten, M SM (2004) Anaerobic oxidation of methane and ammonium. Annu Rev Microbiol, 58, pp. 99-117.
57. Chen, F. and Huang, Y. (2005) A pilot study on Miocene through Holocene dediments from the continental slope of the South China Sea in correlation with possible distribution of gas hydrates (in Chinese). Geoscience, 19, pp. 1-13.
58. Takai, K. and Horikoshi, K. (1999) Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics, 152, pp. 1285-1297.
59. Takai, K., Moser, D. P., DeFlaun, M., Onstott, T. C. and Fredrickson, J. K. (2001) Archaeal diversity in waters from deep south African Gold Mines. Appl Environ Microbiol, 67, pp. 5750-5760.
60. Teske, A., Brinkhoff, T., Muyzer, G., Moser, D. P., Rethmeier, J. and Jannasch, H. W. (2000) Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. Appl Environ Microbiol, 66, pp. 3125-3133.
61. Thamdrup, B., Rossello-Mora, R. and Amann, R. (2000) Microbial manganese and sulfate reduction in Black Sea shelf sediments. Appl Environ Microbiol, 66, pp. 2888-2897.
62. Treude, T., Boetius, A., Knittel, K., Wallmann, K. and Jb, B. (2003) Anaerobic oxidation of methane above gas hydrates (Hydrate Ridge, OR). Mar Ecol Prog Ser, 264, pp. 1-14.
63. Treude, T., Niggemann, J., Kallmeyer, J., Wintersteller, P., Schubert, C. J., Boetius, A. and Jorgensen, B. B. (2005) Anaerobic oxidation of methane and sulfate reduction along the Chilean continental margin. Geochim Cosmochim Acta, 69, pp. 2767-2779.
64. Valentine, D. L. and Reeburgh, W. S. (2000) New perspectives on anaerobic methane oxidation. Environ Microbiol, 2, pp. 477-484.
65. Vetriani, C., Jannasch, H. W., MacGregor, B. J., Stahl, D. A. and Reysenbach, A. L. (1999) Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl Environ Microbiol, 65, pp. 4375-4384.
66. Zhang, G., Zhu, Y. and Chen, B. (2003) Progress of gas hydrate investigation in China off shore (in Chinese). Earth Sci Front, 10, pp. 177-189.
67. Zhang, G., Huang, Y., Liang, J. and Wong, H. K. (2005) Gas hydrate occurrence on the continental slope of the northern South China Sea. Mar Petro Geol, 22, pp. 403-412.
68. Zeng, R., Zhao, J., Zhang, R. and Lin, N. (2005) Bacterial community in sediment from the western Pacific Warm Pool and its relationship to environment. Science in China (Series D), 48, pp. 282-290.
69. Zhu, W. and Wang, Z. (2004) Exploration potential of atectonic oil-gas pools in the northern shelf basin of the South China Sea. Petrol Sci, 1, pp. 22-30.