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Phylogenetic diversity of Archaea in prawn farm sediment

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Abstract

The structure and diversity of the Archaea collected from prawn farm sediment were investigated for the first time. A partial 16S ribosomal DNA library was constructed with Archaea-specific primers. Subsequently, 80 randomly selected archaeal clones from the library were analyzed by restriction fragment length polymorphism (RFLP), and resulted in 50 different RFLP patterns. Sequence analysis of representatives from each unique RFLP type revealed high diversity in the archaeal populations, and the majority of archaeal clones were either members of novel lineages or most closely related to uncultured clones. In the phylogenetic analysis, the archaeal clones could be grouped into discrete phylogenetic lineages within the two kingdoms Crenarchaeota and Euryarchaeota. Euryarchaeota dominated in our archaeal library, with up to 72.2% of the total clones, and Crenarchaeota represented 27.8%. Of all the Euryarchaeota clones, three clones (5.6%) were affiliated with Methanosarcinales, four clones (7.4%) were related to Methanomicrobiales, three clones (5.6%) were related to Halobacterium (with 93% similarity), and the remaining clones (81.5%) were related to those uncultured Euryarchaeota in the aquatic sediment ecosystem. None of the crenarchaeal clones were associated with any known cultured lineages. The selective dispersal of the archaeal population indicates that their ecological niches are associated with environmental characteristics. Novel phylotypes of Archaea would expand our understanding of the genetic diversity of Archaea in aquatic sediment systems and would be significant in the phylogenetic study of Archaea.

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Acknowledgements

This study was supported by NSFC projects (no. 40176037, 40232021) and the Red Tide Key Project of the National Natural Science Foundation of Guangdong province, China (no. 011208). The experiments comply with current laws of the country in which the experiments were performed.

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Authors and Affiliations

  1. Key Laboratory of Gene Engineering of the Ministry of Education, Biotechnology Research Center, Zhongshan University, 510275, Guangzhou, P.R. China

    Peng Shao, Yueqin Chen, Hui Zhou & Lianghu Qu

  2. Key Laboratory for Marine Environmental Science of the Ministry Education, Environmental Science Research Center, Xiamen University, 361005, Xiamen, P.R. China

    Ying Ma, Heyang Li & Nianzhi Jiao

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  1. Peng Shao
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  2. Yueqin Chen
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Correspondence to Yueqin Chen.

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Communicated by O. Kinne, Oldendorf/Luhe

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Shao, P., Chen, Y., Zhou, H. et al. Phylogenetic diversity of Archaea in prawn farm sediment. Marine Biology 146, 133–142 (2004). https://doi.org/10.1007/s00227-004-1431-6

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