Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Gelliodes carnosa Collected from the Hainan Island Coastal Waters of the South China Sea

Abstract

Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse with representatives of the high G + C Gram-positive bacteria, cyanobacteria, low G + C Gram-positive bacteria, and proteobacteria (α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall, 300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes. Approximately 1,000 16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs (19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity (≤97%) with their closest matches in GenBank and were probably new species. Our data provide strong evidence for the presence of a diverse variety of unidentified bacteria in the marine sponge G. carnosa. A relatively high proportion of the isolates exhibited antimicrobial activity, and the deferred antagonism assay showed that over half of the active isolates exhibited a much stronger bioactivity when grown on medium containing seawater. In addition to demonstrating that the sponge-associated bacteria could be a rich source of new biologically active natural products, the results may have ecological implications. This study expands our knowledge of the diversity of sponge-associated bacteria and contributes to the growing database of the bacterial communities within sponges.

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Acknowledgments

This work was supported in part by the National Science and Technology Project of China (no. 2009ZX09301-003-4-1, 2009ZX09301-003-11-1). We thank Professor Jin-He Li at the Institute of Oceanology, Chinese Academy of Science, for the sponge identification and gratefully acknowledge the help of the personnel at Sanya Nanfan Sci-Tech Institute during the sampling of the sponge. We also thank Mr. Rui-shan Wang and Ms. Ruo-meng Song in our lab for assistance in the antimicrobial assay. Finally, we thank Ms. Amy Blass at Brigham and Women’s Hospital, Harvard Medical School, USA, for proofreading this manuscript.

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Correspondence to Ping Zhu.

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Phylogenetic affiliation of the cultured isolates from the sponge G. carnosa (DOC 121 kb)

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Li, C., Liu, W., Zhu, P. et al. Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Gelliodes carnosa Collected from the Hainan Island Coastal Waters of the South China Sea. Microb Ecol 62, 800 (2011). https://doi.org/10.1007/s00248-011-9896-6

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Keywords

  • Sponge
  • Operational Taxonomic Unit
  • Marine Sponge
  • Restriction Fragment Length Polymorphism Analysis
  • Restriction Fragment Length Polymorphism Pattern