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Construction and Preliminary Analysis of a Deep-Sea Sediment Metagenomic Fosmid Library from Qiongdongnan Basin, South China Sea

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Abstract

Preliminary characterization of the microbial phylogeny and metabolic potential of a deep-sea sediment sample from the Qiongdongnan Basin, South China Sea, was carried out using a metagenomic library approach. An effective and rapid method of DNA isolation, purification, and library construction was used resulting in approximately 200,000 clones with an average insert size of about 36 kb. End sequencing of 600 individual clones from the fosmid library generated 1,051 sequences with an average sequence length of 619 bp. Phylogenetic ascription indicated that this library was dominated by Bacteria, predominately Proteobacteria, though Planctomycetes were also relatively abundant. Sulfate-reducing and anaerobic ammonium-oxidizing bacteria, which play important roles in the cycling of sedimentary nutrients, were abundant in the library. Cluster of orthologous groups category analysis showed that most of the genes contained in the end sequences were related to metabolism, and with cellular processes and signaling. Functional groups assigned by SEED (subsystems-based annotations) highlighted the existence of ‘one-carbon’ metabolism within this community as well as identifying functional genes involved in methanogenesis. Furthermore, diverse genes involved in the biodegradation of xenobiotics were found using Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis.

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Acknowledgments

This work was partly supported by the National High Technology Research and Development Program of China (2007AA09Z443 and 2007AA021301) and Knowledge Innovation Project of The Chinese Academy of Sciences (KSCX2-YW-G-022).

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Authors and Affiliations

  1. Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, People’s Republic of China

    Yongfei Hu, Chengzhang Fu, Yeshi Yin, Gong Cheng, Fang Lei, Xi Yang, Jing Li, Elizabeth Jane Ashforth, Lixin Zhang & Baoli Zhu

  2. Graduate University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China

    Yongfei Hu, Chengzhang Fu, Yeshi Yin, Gong Cheng & Fang Lei

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  1. Yongfei Hu
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Correspondence to Lixin Zhang or Baoli Zhu.

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Yongfei Hu and Chengzhang Fu contributed equally to this article.

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Hu, Y., Fu, C., Yin, Y. et al. Construction and Preliminary Analysis of a Deep-Sea Sediment Metagenomic Fosmid Library from Qiongdongnan Basin, South China Sea. Mar Biotechnol 12, 719–727 (2010). https://doi.org/10.1007/s10126-010-9259-1

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