The bacterial diversity in surface sediment from the South China Sea
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The bacterial diversity in surface sediment from the South China Sea WANG Guanghua1,2 , DONG Junde1 , LI Xiang1∗ , SUN Huimin1,2 1
2
Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, China Graduate University of Chinese Academy of Science, Beijing 100049, China
Received 27 April 2009; accepted 4 December 2009 ©The Chinese Society of Oceanography and Springer-Verlag Berlin Heidelberg 2010
Abstract 16S rDNA sequencing results from this study and literatures demonstrate that sediment bacteria in the South China Sea (SCS) were very diverse, which contained 22 of the 24 phyla of bacteria investigated from marine sediment, however, it was very imbalance among stations. So bacterial diversity from 15 samples which covered a wide range of sediment types from 20 to 3 888 m in depth was studied in DGGE (denature gradient gel electrophoresis) in this paper. The DGGE results indicate that both sediment bacterial diversity and diversity difference among stations were significant. Thirty representative and differential fingerprints among samples were recovered and sequenced, phylogenetic analysis indicates that they may belong to Proteobacteria (α-, β-, γ-, δ-, ε-), Planctomycetes, Firmicutes, Chloroflexi, Acidobacteria, Actinobacteria, Nitrospirae, Gemmatimonadetes, candidate division WS3 and so on, of which, Gemmatimonadetes and candidate division WS3 bacteria were first detected in SCS sediment. This study also shows that bacterial diversity analysis based on DGGE was more potential than traditional 16S rDNA clone library in multiple sample analysis. Key words: bacterial diversity, DGGE, marine sediment, South China Sea
1 Introduction Over the last decade, the understanding of microbial diversity and dynamics in marine sediment has significantly increased due to the rapid development of culture-independent molecular technologies (Zhang et al., 2008). According to data extrapolation, marine sediment may contain two thirds of the Earth’s total prokaryotic biomass (Teske, 2005), and now it has been testified that there were bacteria survival 1626 m below the sea floor (Roussel et al., 2008). Although the bias for 16S rDNA cultureindependent methods in copy numbers, preferential amplification of certain sequences, and different PCR efficiencies of DNA from environmental samples (Zhang et al., 2008; Roudi` ere et al., 2007; Von Wintzingerode et al., 1997), conservative 16S rDNA was still indispensable in microbial community composition study. So far, 16S rDNA clone library, fluorescent in situ hybridization (FISH) and denature gradient gel electrophoresis (DGGE) were the most pre-
vailing 16S rDNA microbial community composition study methods. 16S rDNA clone library was the most matured and controversy one (Roudi` ere et al., 2007). FISH was a sensitive and intuitive method, which can more reasonably represent the marine environment microbial community diversity to date (Ishii et al., 2004), but it is still limited by insufficient probes an
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