A Preliminary Study of Microbial Diversity of the Top Sediment from the MD06-3047
Received date: 2009-12-14
Revised date: 2009-12-30
Online published: 2010-02-10
Total DNA was extracted from the top sediment layer (0-10 cm) of MD06-3047 in the Kuroshio and was used as template for polymerase chain reaction (PCR) amplification employing specific primers for bacterial and archaeal 16S rRNA genes. The 16S rDNA libraries were then constructed. Microbial diversity was analyzed by using restriction fragment length polymorphism (RFLP), DNA sequencing and phylogenetic analysis. The results show that there are six phyla in the Bacteria domain: Proteobacteria, Acidbacterium, Planctanycenea, Verrucomicrobia, Candidate division OP8 and Bacteroidetes, and the phylum Proteobacteria is predominant. In the Archaea domain, Crenarchaeota dominates over Euryarchaeota. There are four divisions in the Crenarchaeota kingdom: MCG, C3, Marine Benthic Group A, Marine Group; three divisions in Euryarchaeota kingdom: South Africa Golden mine Euryarchaeota Group、Marine Benthic Group E and MEG, and the Marine Benthic Group E is the dominating group.
Key words： Kuroshio; 16S rDNA; Archaea; Bacteria; Microbial diversity
WEI Yu-Li . A Preliminary Study of Microbial Diversity of the Top Sediment from the MD06-3047[J]. Advances in Earth Science, 2010 , 25(2) : 212 -219 . DOI: 10.11867/j.issn.1001-8166.2010.02.0212
[1] Chu T Y. The fluctuations of the Kuroshio Current in the eastern sea area of Taiwan[J].Acta Oceanography Taiwan,1974,(4): 1-12.
[2] Wang Zheng, Hou Yijun, Le Kentang, et al. Advances in study on the Kuroshio in the source region [J].Studia Marina Sinica,2007, 48:35-41.[王铮, 侯一筠, 乐肯堂, 等. 源区黑潮研究进展 [J]. 海洋科学集刊, 2007, 48: 35-41.]
[3] Zhao Jingtao, Chang Fengming, Li Tiegang, et al. Carbonate cycle and its control factors in Kuroshio source during the last 190 ka BP[J].Acta Petrologica Sinica,2008, 24:1 401-1 410.[赵京涛, 常凤鸣, 李铁刚, 等. 近190 ka BP 以来菲律宾海黑潮源区的碳酸盐旋回记起控制因素 [J]. 岩石学报，2008, 24:1 401-1 410.]
[4] Yuan Yaochu, Kaneko Arata, Su Jilan, et al. The Kuroshio east of Taiwan and in the East China Sea and the currents east of the Ryukyu Islands during early summer of 1996[J].Oceanography,1998, 54: 217-226.
[5] Johns W E, Lee T N, Liu C T, et al. PCM-1 array monitors Kuroshio transport [J].WOCE Notes,1995, 7: 10-13.
[6] Whitman W B, Coleman D C, Wiebe W J. Prokaryotes: The unseen majority [J].Proceedings of the National Academy of Sciences of the United States of America,1998, 95: 6 578-6 583.
[7] Claypool G E, Kaplan I R. The origin and distribution of methane in marine sediments, in Kaplan[C]//Natural Gases in Marine Sediments. New York: N Y Plenum Press, 1974:99-139.
[8] Fisk M R, Giovannoni S J, Thorseth I H. Alteration of oceanic volcanic glass: Textural evidence of microbial activity [J].Science,1998, 281: 978-980.
[9] Dang H, Li J, Zhang X, et al. Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin [J].Journal of Applied Microbiology, 2009, 106: 1 482-1 493.
[10] Zhou J Z, Davery E, Figure J B. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA [J].Microbiology,1997, 143: 3 913-3 919.
[11] Gurtler V, Stanisich V A. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region[J].Microbiology,1996, 142: 3-16.
[12] DeLong E F. Archaea in coastal marine environments[J].Proceedings of the Natlional Academy of Sciences USA,1992, 89: 5 685-5 689.
[13] Maidak B L, Cole J R, Lilburn T G, et al. The RDP-II (ribosome database project) [J].Nucleic Acids Research,2001, 29: 173-174.
[14] Thompson J D, Higgins D G, Gibson T J. CLUSTAL-W-Improving the sensitivy of progressive multiple sequence alignment through sequence weighting, position-specific gap penalies and weight martix choice [J].Nucleic Acids Research,1994, 22: 4 673-4 680.
[15] Kumar S, Tamura K, Nei M. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment [J].Briefings in Bioinformatics,2004, 5: 150-163.
[16] Li Tao, Wang Peng, Wang Pinxian. Microbial diversity in surface sediments of the Xisha Trough, the South China Sea [J].Acta Ecologica Sinica,2008, 28 (3) : 1 166-1 173.[李涛, 王鹏，汪品先. 南海西沙海槽表层沉积物微生物多样性 [J]. 生态学报, 2008, 28 (3): 1 166-1 173.]
[17] Inagaki F, Sakihama Y, Inoue A, et al. Molecular phylogenetic analyses of reversetranscribed bacterial rRNA obtained from deep-sea cold seep sediments [J].EnvironmentalMicrobiology,2002, 4(5): 277-286.
[18] Marchesi J R, Weightman A J, Cragg B A, et al. Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia margin as revealed by 16S rRNA molecular analysis[J].FEMS Microbiology Ecology,2001, 34: 221-228.
[19] Urakawa H, Kita-Tsukamoto K, Ohwada K. Restriction fragment length polymorphism (RFLP) analysis of psychrophilic and psychrotrophic Vibrio and photobacterium from the western North Pacific Ocean and Otsuchi Bay, Japan [J].FEMS Microbiology Letters,1998, 165(2): 373-378.
[20] Doronina N V, Darmaeva T D, Trotsenko Y A. Methylophaga alcalica sp. nov., a novel alkaliphilic and moderately halophilic, obligately methylotrophic bacterium from an East Mongolian saline soda lake [J].International Journal of Systematic and Evolutionary Microbiology, 2003, 53 (1): 223-229.
[21] Zeng R, Zhao J, Zhang R, et al. Bacterial Community in sediment from the western Pacific Warm Pool and its relationship to environment [J].China Environmental Science, 2005, 48: 282-290.
[22] Barns S M, Fundyga R E, Jeffries M W, et al. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment [J].Proceedings of the Natlconal Academy Sciences USA,1994,91:1 609-1 613.
[23] Coolen M J, Cypionka H, Sass A M, et al. Ongoing modification of Mediterranean sapropels mediated by prokaryotes [J].Science,2002, 296: 2 407-2 410.
[24] Inagaki F, Suzuki M, Takai K, et al. Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of Ohkotsk [J]. Applied Environmental Microbiology,2003, 69: 7 224-7 235.
[25] Knittel K, Losekann T, Boetius A, et al. Diversity and distribution of methanotrophic Archaea at cold seeps [J]. Applied and Environmental Microbiol,2005,71: 467-479.
[26] Vetriani C, Jannasch H W, MacGregor B, et al. Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments[J]. Applied and Environmental Microbiology, 1999, 65: 4 375-4 384.
[27] Inagaki F, Nunoura T, Nakagawa S, et al. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin[J]. Proceedings of Natlioual Academy of the Sciences USA,2006, 103: 2 815-2 820.
[28] Institut Polaire Francais.MD155-Marco Polo 2 Images XIV Cruise Report[R]. Technopôle Brest-Iroise: Institut Polaire Francais, 2006.
[29] Inagaki F, SuzukiM, Takai K, et al. Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of Okhotsk[J]. Applied and Environmental Microbiology, 2003,69(12): 7 224-7 235.
/
| 〈 |
|
〉 |
甘公网安备62010202000687
