Bacterial diversity of the Marine Sponge, Halichondria panicea by ARDRA and DGGE

ARDRA와 DGGE를 이용한 Halichondria panicea 해면의 공생세균 다양성

  • Park, Jin-Sook (Department of Biological Science and Biotechnology, Hannam University)
  • 박진숙 (한남대학교 생명시스템과학과)
  • Received : 2015.12.23
  • Accepted : 2015.12.24
  • Published : 2015.12.31


Culture-dependent ARDRA and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Halichondria panicea collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and Marine agar media. PCR amplicons of the 16S rRNA gene from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rRNA gene sequences derived from ARDRA patterns showed more than 96% similarities compared with known bacterial species, and the isolates belonged to four classes, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rRNA genes amplified from the sponge-derived total gDNA showed 14 DGGE bands, and their sequences showed 100% similarities compared with the sequences available in GenBank. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven classes, including Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteira, Bacteroidetes, Cyanobacteria, and Chloroflexi. According to both the ARDRA and DGGE methods, three classes, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, were commonly found in H. panicea. However, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture independent method than in culture-dependent method.


Halichondria panicea;16S rRNA gene;ARDRA;bacterial diversity;DGGE;marine sponge


Supported by : 한국해양과학기술진흥원, 한국연구재단


  1. Abe, T., Sahin, F.P., Akiyama, K., Naito, T., Kishigami, M., Miyamoto, K., Sakakibara, Y., and Uemura, D. 2012. Construction of a metagenomic library for the marine sponge Halichondria okadai. Biosci. Biotechnol. Biochem. 76, 633-639.
  2. Althoff, K., Schutt, C., Steffen, R., Batel, R., and Mueller, W.E. 1998. Evidence for a symbiosis between bacteria of the genus Rhodobacter and the marine sponge Halichondria panicea: harbor also for putatively toxic bacteria?. Mar. Biol. 130, 529-536.
  3. Barthel, D. and Wolfrath, B. 1989. Tissue sloughing in the sponge Halichondria panicea: a fouling organism prevents being fouled. Ocecologia 78, 357-360.
  4. Hentschel, U., Usher, K.M., and Talor, M.W. 2006 Marine sponges as microbial fermenters. FEMS Microbiol. Ecol. 55, 167-177.
  5. Imhoff, J.F. and Stohr, R. 2003. Sponge-associated bacteria: general overview and special aspects of bacteria associated with Halichondria panicea, pp. 35-57. In Muller, W.E.G. (eds.), Sponges (Porifera). Springer-Verlag Berlin Heidelberg, New York, USA.
  6. Jackson, S.A., Kennedy, J., Morrissey, J.P., O'Gara, F., and Dobson, A.W. 2012. Pyrosequencing reveals diverse and distinct sponge-specific microbial communities in sponges from a single geographical location in irish waters. Microb. Ecol. 64, 105-116.
  7. Jeong, I.H. and Park, J.S. 2012a. Phylogenetic analysis of bacterial diversity in the marine sponge, Asteropus simplex, collected from Jeju Island. Korean J. Microbiol. 48, 275-283.
  8. Jeong, J.B. and Park, J.S. 2012b. Seasonal differences of bacterial communities associated with the marine sponge, Hymeniacidon sinapium. Korean J. Microbiol. 48, 262-269.
  9. Kennedy, J., Flemer, B., Jackson, S.A., Morrissey, J.P., O'Gara, F., and Dobson, A.D. 2014. Evidence of a putative deep sea specific microbiome in marine sponges. PLoS 9, e91092.
  10. Li, Z., He, L., and Miao, X. 2007. Cultivable bacterial community from South China sea sponge as revealed by DGGE fingerprinting and 16S rDNA phylogenetic analysis. Curr. Microbiol. 55, 465-472.
  11. Nagle, D.G., McClatchey, W.C., and Gerwick, W.H. 1992. New glycosphingolipids from the marine sponge Halichondria panicea. J. Nat. Prod. 55, 1013-1017.
  12. Perovic, S., Wichels, A., Schutt, C., Gerdts, G., Pahler, S., Steffen, R., and Muller, W.E. 1998. Neuroactive compounds produced by bacteria from the marine sponge Halichondria panicea: activation of the neuronal NMDA receptor. Environ. Toxicol. Pharmacol. 6, 125-133.
  13. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
  14. Schmitt, S., Tsai, P., Bell, J., Fromont, J., Ilan, M., Lindquist, N., Perez, T., Rodrigo, A., Schupp, P.J., Vacelet, J., et al. 2012. Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME J. 6, 564-576.
  15. Schneemann, I., Kajahn, I., Ohlendorf, B., Zinecker, H., Erhard, A., Nagel, K., Wiese, J., and Imhoff, J.F. 2010a. Mayamycin, a cytotoxic polyketide from a Streptomyces strain isolated from the marine sponge Halichondria panicea. J. Nat. Prod. 73, 1309-1312.
  16. Schneemann, I., Nagel, K., Kajahn, I., Labes, A., Wiese, J., and Imhoff, J.F. 2010b. Comprehensive investigation of marine Actinobacteria associated with the sponge Halichondria panicea. Appl. Environ. Microbiol. 76, 3702-3714.
  17. Schneemann, I., Ohlendorf, B., Zinecker, H., Nagel, K., Wiese, J., and Imhoff, J.F. 2010c. Nocapyrones A-D, ${\gamma}$-pyrones from a Nocardiopsis strain isolated from the marine sponge Halichondria panicea. J. Nat. Prod. 73, 1444-1447.
  18. Sipkema, D., Schippers, K., Maalcke, W.J., Yang, Y., Salim, S., and Blanch, H.W. 2011. Multiple approaches to enhance the cultivability of bacteria associated with the marine sponge Haliclona (gellius) sp. Appl. Environ. Microbiol. 77, 2130-2140.
  19. Tamura, K., Dudley, J., Nei, M., and Kumar, S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599.
  20. Taylor, M.W., Radax, R., Steger, D., and Wagner, M. 2007. Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol. Mol. Biol. Rev. 71, 295-347.
  21. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
  22. Webster, N.S., Negri, A.P., Munro, M.M., and Battershill, C.N. 2004. Diverse microbial communities inhabit Antarctic sponges. Environ. Microbiol. 6, 288-300.
  23. Wichels, A., Wurtz, S., Dopke, H., Schutt, C., and Gerdts, G. 2006. Bacterial diversity in the breadcrumb sponge Halichondria panicea (Pallas). FEMS Microbiol. Ecol. 56, 102-118.