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Culture-independent nested PCR method reveals high diversity of actinobacteria associated with the marine sponges Hymeniacidon perleve and Sponge sp.

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Abstract

A culture-independent nested polymerase chain reaction (PCR) technique was used to investigate the diversity of actinobacteria communities associated with the sponges Hymeniacidon perleve and Sponge sp. The phylogenetic affiliation of sponge-derived actinobacteria was then assessed by 16S rRNA sequencing of cloned DNA fragments. A total of 196 positive clones were screened by restriction fragment length polymorphism (RFLP) analysis; 48 unique operational taxonomic units (OTUs) were selected for sequencing. Rarefaction analysis indicated that the clone libraries represented 93% and 94% of the total estimated diversity for the two species, respectively. Phylogenetic analysis of sequence data revealed representatives of various phylogenetic divisions, which were related to the following ten actinobacterial genera: Acidimicrobium, Corynebacterium, Propionibacterium, Actinomyces, Micrococcus, Microbacterium, Streptomyces, Mycobacterium, Cellulosimicrobium, Sporichthya, and unidentified actinobacterial clones. A sponge-specific, previously uncultured actinobacteria community grouped within the subclass Acidimicrobidae was discovered from both H. perleve and Sponge sp. Sequences belonging to Acidimicrobium in the H. perleve and the Sponge sp. clone libraries represented 33% and 24% of the clones, respectively. In the Sponge sp. clone library Mycobacterium dominated, accounting for 70% of all clones. The presence of Acidimicrobium and mycobacteria within two sponges can lay the groundwork for attempts to culture these interesting bacteria for industrial applications.

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Acknowledgements

The authors gratefully acknowledge the financial support from the “Innovation Fund” of the Dalian Institute of Chemical Physics and the “973 Hi-Tech Research and Development Program of China” (2003CB716001). We thank Prof. Li-Jinhe of the Qingdao Institute of Oceanology at the Chinese Academy of Sciences for identifying the sponges used in this study.

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Authors and Affiliations

  1. Marine Bioproducts Engineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China

    Yanjuan Xin, Jianyu Huang & Wei Zhang

  2. Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100039, China

    Yanjuan Xin, Jianyu Huang & Maicun Deng

  3. Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia

    Wei Zhang

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  1. Yanjuan Xin
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  2. Jianyu Huang
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Correspondence to Wei Zhang.

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Xin, Y., Huang, J., Deng, M. et al. Culture-independent nested PCR method reveals high diversity of actinobacteria associated with the marine sponges Hymeniacidon perleve and Sponge sp.. Antonie van Leeuwenhoek 94, 533–542 (2008). https://doi.org/10.1007/s10482-008-9270-y

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