Advertisement

Antonie van Leeuwenhoek

, Volume 90, Issue 2, pp 159–169 | Cite as

Culturable Actinobacteria from the Marine Sponge Hymeniacidon perleve: Isolation and Phylogenetic Diversity by 16S rRNA gene-RFLP Analysis

  • Haitao Zhang
  • Yoo Kyung Lee
  • Wei Zhang
  • Hong Kum Lee
Original paper

Abstract

A total of 106 actinobacteria associated with the marine sponge Hymeniacidon perleve collected from the Yellow Sea, China were isolated using eight different media. The number of species and genera of actinobacteria recovered from the different media varied significantly, underlining the importance of optimizing the isolation conditions. The phylogenetic diversity of the actinobacteria isolates was assessed using 16S rRNA gene amplification–restriction fragment length polymorphism (RFLP) analysis of the 106 strains with different morphologies. The RFLP fingerprinting of selected strains by HhaI-digestion of the 16S rRNA genes resulted in 11 different patterns. The HhaI-RFLP analysis gave good resolution for the identification of the actinobacteria isolates at the genus level. A phylogenetic analysis using 16S rRNA gene sequences revealed that the isolates belonged to seven genera of culturable actinobacteria including Actinoalloteichus, Micromonospora, Nocardia, Nocardiopsis, Pseudonocardia, Rhodococcus, and Streptomyces. The dominant genus was Streptomyces, which represented 74% of the isolates. Three of the strains identified are candidates for new species.

Keywords

Marine sponge Actinobacteria RFLP Streptomycetes Nocardiopsis Pseudonocardia Nocardia Micromonospora Rhodococcus Actinoalloteichus 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Notes

Acknowledgements

The authors wish to thank financial supports from “Innovation Fund” from the Dalian Institute of Chemical Physics, “973 Hi-Tech Research and Development Program of China” (2003CB716001). This research was also funded by National Research Laboratory Program of the Korean Ministry of Science & Technology (PE05009). We appreciate Professor Li-Jinhe, at Qingdao Institute of Oceanology, Chinese Academy of Sciences for the sponge identification.

References

  1. Blunt JW, Copp BR, Munro MH, Northcote PT, Prinsep MR (2003) Marine natural products. Nat Prod Rep 20:1–48PubMedCrossRefGoogle Scholar
  2. Blunt JW, Copp BR, Munro MH, Northcote PT, Prinsep MR (2004) Marine natural products. Nat Prod Rep 21:1–49PubMedCrossRefGoogle Scholar
  3. Bultel-Ponce VC, Debitus JP, Berge GP, Guyot M (1998) Metabolites from the marine sponge-associated bacterium Micrococcus luteus. J Mar Biotech 6:233–236Google Scholar
  4. Chun J (1995) Computer-assisted classification and identification of actinomycetes. Ph.D. Thesis, Univ. Newcastle, Newcastle upon Tyne, UKGoogle Scholar
  5. Cifuentes A, Anton J, Benlloch S, Donnelly A, Herbert RA, Rodriguez-Valera F (2000) Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl Environ Microbiol 66:1715–1719PubMedCrossRefGoogle Scholar
  6. Colquhoun JA, Heald SC, Li L, Tamaoka J, Kato C, Horikoshi K, Bull AT (1998) Taxonomy and biotransformation activities of some deep-sea actinomycetes. Extremophiles 2:269–277PubMedCrossRefGoogle Scholar
  7. Cook AE, Meyers PR (2003) Rapid identification of filamentous actinomycetes to the genus level using genus-specific 16S rRNA gene restriction fragment patterns. Int J Syst Evol Microbiol 53:1907–1915PubMedCrossRefGoogle Scholar
  8. Faulkner DJ (2002) Marine natural products. Nat Prod Rep 19:1–48PubMedGoogle Scholar
  9. Felsenstein J (1993) PHYLIP (Phylogeny inference package), version 3.5c. Department of Genetics, University of Washington, seattle, WA, USAGoogle Scholar
  10. Fenical W, Baden D, Burg M, Goyet CV, Grimes JD, Katz M, Marcus NH, Pomponi S, Rhines P, Tester P, Vena J (1999) Marine-derived pharmaceuticals and related bioactive compounds. In: Fenical W (ed) From monsoons to microbes: understanding the ocean’s role in human health, Washington, D.C. pp 71–86Google Scholar
  11. Friedrich AB, Merkert H, Fendert T, Hacker J, Pietra F, Proksch P, Hentschel U (1999) Microbial diversity in the marine sponge Aplysina cavernicola (formerly Verongia cavernicola) analyzed by fluorescence in situ hybridization (FISH). Mar Bio 134:461–470CrossRefGoogle Scholar
  12. Hentschel U, Hopke J, Horn M, Friedrich AB, Wagner M, Hacker J, Moore BS (2002) Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol 68:4431–4440PubMedCrossRefGoogle Scholar
  13. Hentschel U, Schmid M, Wagner M, Fieseler L, Gernert C, Hacker J (2001) Isolation and phylogenetic analysis of bacteria with antimicrobial activities from the Mediterranean spongesAplysina aerophoba and Aplysina cavernicola. FEMS Microbiol Ecol 35:305–312PubMedCrossRefGoogle Scholar
  14. Hobel CFV, Marteinsson VT, Hreggvidsson GÓ, Kristjánsson JK (2005) Investigation of the marine ecology of intertidal hot springs by using diversity analysis of 16S rRNA and chitinase genes. Appl Environ Microbiol 71: 2771–2776PubMedCrossRefGoogle Scholar
  15. Imhoff JF, Stöhr R (2003) Sponge-associated bacteria: general overview and special aspects of bacteria association with Halichondria panacea. In: Müller WEG (ed) Sponge (Porifera). Springer, Berlin, pp 35–58Google Scholar
  16. Itoh T, Kinoshita M, Aoki S, Kobayashi M (2003) Komodoquinone A, a novel neuritogenic anthracycline, from␣marine Streptomyces sp. KS3. J Nat Prod 66:1373–1377PubMedCrossRefGoogle Scholar
  17. Jayatilake GS, Thornton MP, Leonard AC, Grimwade JE, Baker BJ (1996) Metabolites from an Antarctic sponge-associated bacterium, Pseudomonas aeruginosa. J Nat Prod 59:293–296PubMedCrossRefGoogle Scholar
  18. Jensen PR, Dwight R, Fenical W (1991) Distribution of actinomycetes in near-shore tropical marine sediments. Appl Environ Microbiol 57:1102–1108PubMedGoogle Scholar
  19. Labeda D, Shearer M (1990) Isolation of Actinomycetes for biotechnological applications. In: Labeda DP (ed) Isolation of biotechnological organisms from nature. McGraw-Hill Publishing Company, New York, pp 1–19Google Scholar
  20. Lanoot B, Cancanneyt M, Hostea B, Vandemeulebroecke K, Cnockaert MC, Dawyndt P, Liu Z, Huang Y, Swings J (2005) Grouping of streptomycetes using 16S-ITS RFLP fingerprinting. Res Microbiol 156:755–762PubMedCrossRefGoogle Scholar
  21. Lazzarini AL, Cavaletti GT, Marinelli F (2000) Rare genera of actinomycetes as potential producers of new antibiotics. Antonie van Leeuwenhoek 78:99–405CrossRefGoogle Scholar
  22. Lee HK, Lee DS, Lim J, Kim JS, Im KS, Jung JH (1998) Topoisomerase I inhibitors from the Streptomyces sp. strain KM86–9B isolated from a marine sponge. Arch Pharm Res 21:729–733PubMedCrossRefGoogle Scholar
  23. Lee YK, Lee JH, Lee HK (2001) Microbial symbiosis in marine sponges. J Microbiol 39:254–264Google Scholar
  24. Lee YK, Kim HW, Liu CL, Lee HK (2003) A simple method for DNA extraction from marine bacteria that produce extracellular materials. J Microbiol Methods 52:245–250PubMedCrossRefGoogle Scholar
  25. Macleod RA (1965) The question of existence of specific marine bacteria. Bacteriol Rev 29:9–23PubMedGoogle Scholar
  26. Maldonado LA, Stach JEM, Pathom W, Ward AC, Bull AT, Goodfellow M (2005) Diversity of cultivable actinobacteria in geographically widespread marine sediments. Antonie van Leeuwenhoek 87:11–18PubMedCrossRefGoogle Scholar
  27. Mincer TJ, Fenical W, Jensen P (2005) Culture-dependent and culture-independent diversity within the obligate marine actinomycete genus Salinispora. Appl Environ Microbiol 71:7019–7028PubMedCrossRefGoogle Scholar
  28. Mincer TJ, Jensen PR, Kauffman CA, Fenical W (2002) Widespread and persistent populations of a major new marine actinobacteria taxon in ocean sediments. Appl Environ Microbiol 68:5005–5011PubMedCrossRefGoogle Scholar
  29. Montalvo NF, Mohnmed NM, Enticknap JJ, Hill RT (2005) Novel actinobacteria from marine sponge. Antonie van Leeuwenhoek 87:29–36PubMedCrossRefGoogle Scholar
  30. Oclarit JM, Okada H, Ohta S, Kaminura K, Yamaoka Y, Iizuka T, Miyashiro S, Ikegami S (1994) Anti-bacillus substance in the marine sponge, Hyatella species, produced by an associated Vibrio species bacterium. Microbios 78:7–16PubMedGoogle Scholar
  31. Peltola JS, Andersson MA, Kampfer P, Auling G, Kroppenstedt RM, Busse HJ, Salkinoja-Salonen MS, Rainey FA (2001) Isolation of toxigenic Nocardiopsis strains from indoor environments and description of two new Nocardiopsis species, N. exhalans sp. nov. and N. umidischolae sp. nov. Appl Environ Microbiol 67:4293–4304PubMedCrossRefGoogle Scholar
  32. Piza FF, Prado PI, Manfio GP (2004) Investigation of bacterial diversity in Brazilian tropical estuarine sediments reveals high actinobacterial diversity. Antonie van Leeuwenhoek. 86:317–328PubMedCrossRefGoogle Scholar
  33. Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633PubMedCrossRefGoogle Scholar
  34. Sabry SA, Ghanem NB, Bu-Ella GA, Schumann P, Stackebrandt E, Kroppenstedt RM (2004) Nocardiopsis aegyptia sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 54:453–456PubMedCrossRefGoogle Scholar
  35. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 4:406–425Google Scholar
  36. Sanchez LJM, Martinez IM, Perez BJ, Fernandez PJL, Canedo HLM (2003) New cytotoxic indolic metabolites from a marine Streptomyces. J Nat Prod 66:863–864CrossRefGoogle Scholar
  37. Singla AK, Mayilraj S, Kudo T, Krishnamurthi S, Prasad GS, Vohra1 RM (2005) Actinoalloteichus spitiensis sp. nov., a novel actinobacterium isolated from a cold desert of the Indian Himalayas. Int J Syst Evol Microbiol 55:2561–2564PubMedCrossRefGoogle Scholar
  38. Stach JEM, Bull AT (2005) Estimating and comparing the diversity of marine actinobacteria. Antonie van Leeuwenhoek. 87:3–9PubMedCrossRefGoogle Scholar
  39. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  40. Tamura T, Liu Z, Zhang Y, Kazunori H (2000) Actinoalloteichus cyanogriseus gen. nov., sp. nov. Int J Syst Evol Microbiol 50:1435–1440PubMedGoogle Scholar
  41. Webster NS, Negri AP, Munro MM, Battershill CN (2004) Diverse microbial community inhabit Antarctic sponges. Environ Microbiol 6:288–300PubMedCrossRefGoogle Scholar
  42. Webster NS, Hill RT (2001) The culturable microbial community of the Great Barrier Reef sponge Rhopaloeides odorabile is dominated by α-Proteobacterium. Mar Bio 138:843–851CrossRefGoogle Scholar
  43. Webster NS, Wilson KJ, Blackall LL, Hill RT (2001) Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile. Appl Environ Microbiol 67:434–444PubMedCrossRefGoogle Scholar
  44. Willenz P, Hartman WD (1989) Micromorphology and ultrastructure of Caribbean sclerosponges I. Ceratoporella nicholsoni and Stromatospongia norae (Ceratoporellidae Porifera). Mar Biol 103:387–402CrossRefGoogle Scholar
  45. Xu JY, Jin Y, Yu XJ, Jin MF, Zhang W (2004) Bacteria Diversity Associated with the marine sponge Hymeniacidon perleve in China Yellow Sea. Acta Microbiol Sinica 44:576–579Google Scholar
  46. Xue S, Zhang HT, Wu PC, Zhang W, Yuan Q (2004) Study on bioactivity of extracts from marine sponges in Chinese Sea. J Exp Mar Biol Ecol 298:71–78CrossRefGoogle Scholar
  47. Yang Y, Xu L, Li Q, Jiang C (1995) A Study on Isolation Methods of Actinomycetes. Chin J Microbiol 22:88–91Google Scholar
  48. Zakharova OS, Zenova GM, Zvyagintsev DG (2003) Some Approaches to the selective isolation of actinomycetes of the genus Actinomadura from Soil. Microbiol 72:126–130CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, B.V. 2006

Authors and Affiliations

  1. 1.Marine Bioproducts Engineering Group, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
  2. 2.Polar BioCenter Korea Polar Research Institute (KOPRI)KORDISeoulKorea
  3. 3.Graduate School of the Chinese Academy of SciencesChinese Academy of SciencesBeijingChina

Personalised recommendations