A Preliminary Study on the Diversity of Bacteria in the Xisha Trough Sediment, the South China Sea
Received date: 2006-02-27
Revised date: 2006-08-20
Online published: 2006-10-15
The bulk DNA was isolated from bacterial habits in sediments of the Xisha trough, the south China sea. Using a pair of primers special for most common bacteria, the researchers amplified partial sequences of bacterial 16S rDNA gene and thus constructed a 16S rDNA clone library. A total of 22 clones were used to reconstruct the bacterial 16S rDNA phylogenetic tree. Guided by the phylogenetic tree, bacteria fell into four main lineages: Proteobacteria, Planctomycene, Actinabacteria and Low G+C Gram-positive bacterium. Among them, 49% belonged to Proteobacteria, 22% to Planctomycene,the same to Low G+C Gram-positive bacterium,and the remaining 7% to Planctomycene. The group of Proteobacteria clustered in three subgroups: α-, γ- and δ-Proteobacteria, and the subgroup of δ-Proteobacteria predominated in them. Furthermore, the abundance of two groups of Planctomycene and Low G+C Gram-positive bacterium, living commonly in shallow marine deposits, was higher in sediments of the Xisha Trough than in other deep-sea sediments. Most members of these two groups were probably brought from the shelf into the trough sediment by the turbid.
Key words： Marine sediment; Bacterial diversity.; The Xisha trough; 16S rDNA
WANG Pin-xian , LI Tao , WANG Peng . A Preliminary Study on the Diversity of Bacteria in the Xisha Trough Sediment, the South China Sea[J]. Advances in Earth Science, 2006 , 21(10) : 1058 -1062 . DOI: 10.11867/j.issn.1001-8166.2006.10.1058
[1] Aller R C, Hall P O J, Rude P D, et al. Biogeochemical heterogeneity and suboxic deagenesis in hemipelagic sediments of the Panama Basin[J]. Deep-Sea Research, 1998, 45: 133-165.
[2] Nealson K H. Sediment bacteria:Who's there,what are they doing, and what's new?[J]. Annual Review of Earth and Planetary Sciences, 1997, 25: 403-434.
[3] Bell P E, Mills A L, Herman J S. Biogeochemical conditions favoring magnetite formation during anaerobic iron reduction[J]. Applied and Environmental Microbiology, 1987, 53: 2 610-2 616.
[4] Kostka J E, Nealson K H. Dissolution and reduction of magnetite by bacteria[J]. Environmental Science and Technology, 1995, 29: 2 535-2 540.
[5] Wang Pinxian. Earth system science in China quo vadis?[J]. Advances in Earth Science, 2003, 18: 837-851.[汪品先. 我国的地球系统科学研究向何处去[J]. 地球科学进展, 2003, 18: 837-851.]
[6] Parkes R J, Cragg B A, Bale S J, et al. Deep bacterial biosphere in Pacific Ocean sediments[J]. Nature, 1994, 371: 410-413.
[7] Ward D M, Weller R, Bateson M M. 16S rRNA sequences reveal uncultured inhabitants of a well studied thermal community[J]. FEMS Microbiology Reviews, 1990, 6: 105-115.
[8] Dai Xin, Zhou Hui, Cai Chuanghua, et al. A preliminary study on the novel taxa of bacteria as determined by 16S rDNA gene analysis[J]. Acta Scientiarum Naturalium University Sumyatseni, 2001, 40: 51-54. [戴欣, 周惠, 蔡创华, 等. 海洋沉积物中特有细菌类群的初步探讨[J]. 中山大学学报:自然科学版, 2001, 40: 51-54.]
[9] Dai Xin, Zhou Hui, Chen Yueqin, et al. A preliminary study on 16S rDAN diversity of bacteria in the Xisha marine sediment, the South China Sea[J]. Progress in Matural Science, 2002, 12: 479-484.[戴欣, 周惠, 陈月琴, 等. 中国南海南沙海区沉积物中细菌16S rDNA多样性的初步研究[J]. 自然科学进展, 2002, 12: 479-484.]
[10] Xu Fei, Dai Xin, Chen Yueqin, et al. Phylogenetic diversity of bacteria and archaea in the Nansha marine sediment, as determined by 16S rDNA analysis[J]. Oceanologia et Limnologia Sinica, 2004, 35: 89-94. [许飞, 戴欣, 陈月琴, 等. 南沙海区沉积物中细菌和古细菌16S rDNA多样性的研究[J]. 海洋与湖沼, 2004, 35: 89-94.]
[11] 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.
[12] 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.
[13] Thompson J D, Higgins D G, Gibson T J. CLUSTAL-W-Improving the sensitivy of progressive multiple sequence alignment through sequence weighting, postiton-specific gap penalies and weight martix choice[J]. Nucleic Acids Research, 1994, 22:4 673-4 680.
[14] 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.
[15] Roose-Amsaleg C L, Garnier-Sillam E M H. Extraction and purification of microbial DNA from soil and sediment samples[J]. Applied Soil Ecology, 2001, 18: 47-60.
[16] Webster G, Newberry C J, Fry J C, et al. Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: A cautionary tale[J]. Journal of Microbiological Methods, 2003, 55: 155-164.
[17] Li L, Kato C, Horikoshi K. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench[J]. Marine Biotechnology (NY), 1999, 1: 391-400.
[18] Li L, Kato C, Horikoshi K. Bacterial diversity in deep-sea sediments from different depths[J]. Biodiversity and Conservation, 1999, 8: 659-677.
[19] Newberry C J, Webster G, Cragg B A, et al. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai trough, Ocean Drilling Program Leg 190[J]. Environmental Microbiology, 2004, 6: 274-287.
/
| 〈 |
|
〉 |
甘公网安备62010202000687
