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Microbial Ecology

, 62:800 | Cite as

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

  • Chang-Qing Li
  • Wen-Chao Liu
  • Ping ZhuEmail author
  • Jin-Ling Yang
  • Ke-Di Cheng
Environmental Microbiology

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.

Keywords

Sponge Operational Taxonomic Unit Marine Sponge Restriction Fragment Length Polymorphism Analysis Restriction Fragment Length Polymorphism Pattern 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

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.

Supplementary material

248_2011_9896_MOESM1_ESM.doc (141 kb)
Suppl. 1 Phylogenetic affiliation of the cultured isolates from the sponge G. carnosa (DOC 121 kb)

References

  1. 1.
    Agogué H, Joux F, Obernosterer I, Lebaron P (2005) Resistance of marine bacterioneuston to solar radiation. Appl Environ Microbiol 71:5282–5289CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169PubMedPubMedCentralGoogle Scholar
  3. 3.
    Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55:541–555CrossRefPubMedGoogle Scholar
  4. 4.
    Bhadury P, Mohammad BT, Wright PC (2006) The current status of natural products from marine fungi and their potential as anti-infective agents. J Ind Microbiol Biotechnol 33:325–337CrossRefPubMedGoogle Scholar
  5. 5.
    Carballo JL, Naranjo SA, Garciagomez JC (1996) Use of marine sponges as stress indicators in marine ecosystems at Algeciras Bay (southern Iberian Peninsula). Mar Ecol Prog Ser 135:109–122CrossRefGoogle Scholar
  6. 6.
    Carballo JL, Naranjo S (2002) Environmental assessment of a large industrial marine complex based on a community of benthic filter-feeders. Mar Pollut Bull 44:605–610CrossRefPubMedGoogle Scholar
  7. 7.
    Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35:169–172CrossRefGoogle Scholar
  8. 8.
    Lee OO, Lau SC, Qian PY (2006) Consistent bacterial community structure associated with the surface of the sponge Mycale adhaerens Bowerbank. Microb Ecol 52:693–707CrossRefPubMedGoogle Scholar
  9. 9.
    Du H, Jiao N, Hu Y, Zeng Y (2006) Diversity and distribution of pigmented heterotrophic bacteria in marine environments. FEMS Microbiol Ecol 57:92–105CrossRefPubMedGoogle Scholar
  10. 10.
    Elyakov GB, Kuznetsova T, Mikhailov VV, Maltsev II, Voinov VG, Fedoreyev SA (1991) Brominated diphenyl ethers from a marine bacterium associated with the sponge Dysidea sp. Experientia 47:632–633CrossRefGoogle Scholar
  11. 11.
    Erin AG, William F, Paul RJ (2007) Phylogenetic diversity of Gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 73:3272–3282CrossRefGoogle Scholar
  12. 12.
    Erwin PM, Thacker RW (2008) Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts. Mol Ecol 17:2937–2947CrossRefPubMedGoogle Scholar
  13. 13.
    Faulkner DJ (2000) Marine natural products. Nat Prod Rep 17:7–55CrossRefPubMedGoogle Scholar
  14. 14.
    Friedrich AB, Fischer I, Proksch P, Hacker J, Hentschel U (2001) Temporal variation of the microbial community associated with the Mediterranean sponge Aplysina aerophoba. FEMS Microbiol Ecol 38:105–113CrossRefGoogle Scholar
  15. 15.
    Gontang EA, Fenical W, Jensen PR (2007) Phylogenetic diversity of Gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 73:3272–3282CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Haefner B (2003) Drugs from the deep: marine natural products as drug candidates. Drug Discov Today 8:536–544CrossRefPubMedGoogle Scholar
  17. 17.
    Hansen MC, Tolker-Neilson T, Givskov M (1998) Biased 16S rDNA PCR amplication caused by interference from DNA flanking template region. FEMS Microbiol Ecol 26:141–149CrossRefGoogle Scholar
  18. 18.
    Hentschel U, Fieseler L, Wehrl M, Gernert C, Steinert M, Hacker J, Horn M (2003) Microbial diversity of marine sponges. In: Müller WEG (ed) Sponges (Porifera). Springer, Berlin, pp 59–88CrossRefGoogle Scholar
  19. 19.
    Hirayama H, Sunamura M, Takai K, Nunoura T, Noguchi T, Oida H, Furushima Y, Yamamoto H, Oomori T, Horikoshi K (2007) Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan. Appl Environ Microbiol 73:7642–7656CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Imamura N, Nishijima M, Adachi K, Sano H (1993) Novel antimycin antibiotics, urauchimycins A and B, produced by marine actinomycete. J Antibiot (Tokyo) 46:241–246CrossRefGoogle Scholar
  21. 21.
    Ivanova EP, Onyshchenko OM, Christen R, Lysenko AM, Zhukova NV, Shevchenko LS, Kiprianova EA (2005) Marinomonas pontica sp. nov., isolated from the Black Sea. Int J Syst Evol Microbiol 55:275–279CrossRefPubMedGoogle Scholar
  22. 22.
    Izumi H, Gauthier ME, Degnan BM, Ng YK, Hewavitharana AK, Shaw PN, Fuerst JA (2010) Diversity of Mycobacterium species from marine sponges and their sensitivity to antagonism by sponge-derived rifamycin-synthesizing actinobacterium in the genus Salinispora. FEMS Microbiol Lett 313:33–40CrossRefPubMedGoogle Scholar
  23. 23.
    Jayatilake GS, Thornton MP, Leonard AC, Grimwade JE, Baker BJ (1996) Metabolites from an Antarctic sponge-associated bacterium, Pseudomonas aeruginosa. J Nat Prod 59:293–296CrossRefPubMedGoogle Scholar
  24. 24.
    Jensen PR, Fenical WF (1996) Marine bacterial diversity as a resource for novel microbial products. J Ind Microbiol Biotechnol 17:346–351CrossRefGoogle Scholar
  25. 25.
    Kan J, Evans SE, Chen F, Suzuki MT (2008) Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay. Aquat Microb Ecol 51:55–56CrossRefGoogle Scholar
  26. 26.
    Kennedy J, Marchest J (2007) Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges. Appl Microbiol Biotechnol 75:11–20CrossRefPubMedGoogle Scholar
  27. 27.
    Kennedy J, Codling CE, Jones BV, Dobson AD, Marchesi JR (2008) Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome. Environ Microbiol 10:1888–1902CrossRefPubMedGoogle Scholar
  28. 28.
    Kennedy J, Baker P, Piper C, Cotter PD, Walsh M, Mooij MJ, Bourke MB, Rea MC, O'Connor PM, Ross RP, Hill C, O'Gara F, Marchesi JR, Dobson AD (2009) Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans collected from Irish waters. Mar Biotechnol 11:384–396CrossRefPubMedGoogle Scholar
  29. 29.
    Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546CrossRefPubMedGoogle Scholar
  30. 30.
    Levi C, Levi P (1965) Populations bacteriennes dans les eponges. J Microsc (Paris) 4:60Google Scholar
  31. 31.
    Li Q, Wang G (2009) Diversity of fungal isolated from three Hawaiian marine sponges. Microbiol Res 164:233–241CrossRefPubMedGoogle Scholar
  32. 32.
    Li Z, Liu Y (2006) Marine sponge Craniella austrialiensis associated bacterial diversity revelation based on 16S rDNA library and biologically active Actinomycetes screening, phylogenetic analysis. Lett Appl Microbiol 43:410–416CrossRefPubMedGoogle Scholar
  33. 33.
    Liu WC, Li CQ, Zhu P, Yang JL, Cheng KD (2010) Phylogenetic diversity of culturable fungi associated with two sponges: Haliclona simulans and Gelliodes carnosa, collected from the Hainan Island coastal waters of the South China Sea. Fungal Divers 42:1–15CrossRefGoogle Scholar
  34. 34.
    Maldonado LA, Stach JEM, Pathom-aree W, Ward AC, Bull AT, Goodfellow M (2005) Diversity of culturable actinobacteria in geographically widespread marine sediments. Antonie van Leeuwenhoek 87:11–18CrossRefPubMedGoogle Scholar
  35. 35.
    Michaud L, Di Cello F, Brilli M, Fani R, Lo Giudice A, Bruni V (2004) Biodiversity of cultivable psychrotrophic marine bacteria isolated from Terra Nova Bay (Ross Sea, Antarctica). FEMS Microbiol Lett 230:63–71CrossRefPubMedGoogle Scholar
  36. 36.
    Mincer TJ, Jensen PR, Kauffman CA, Fenical W (2002) Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 68:5005–5011CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Muscholl-Silberborn A, Thiel V, Imhoff JF (2008) Abundance and bioactivity of cultured sponge-associated bacteria from the Mediterranean Sea. Microb Ecol 55:94–106CrossRefGoogle Scholar
  38. 38.
    Nicolas GG, Frenette M, Lavoie MC (2010) Streptococcus salivarius mutants defective in mannose phosphotransferase systems show reduced sensitivity to mutacins I-T9 and R-3B. Can J Microbiol 56:692–696CrossRefPubMedGoogle Scholar
  39. 39.
    Nubel U, Garcia-Pichel F, Muyzer G (1997) PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl Environ Microbiol 63:3327–3332PubMedPubMedCentralGoogle Scholar
  40. 40.
    Oren M, Steindler L, Ilan M (2005) Transmission, plasticity and molecular identification of cyanobacterial symbionts in the Red Sea sponge Diacarnus erythraenus. Mar Biol 148:35–41CrossRefGoogle Scholar
  41. 41.
    Proksch P, Putz A, Ortlepp S, Kjer J, Bayer M (2010) Bioactive natural products from marine sponges and fungal endophytes. Phytochem Rev 9:475–489CrossRefGoogle Scholar
  42. 42.
    Reiswig HM (1973) Water transport, respiration and energetics of 3 tropical marine sponges. J Exp Mar Biol Ecol 14:231–249CrossRefGoogle Scholar
  43. 43.
    Santavy DL, Willenz P, Colwell RR (1990) Phenotypic study of bacteria associated with the Caribbean sclerosponge Ceratoporella nicholsoni. Appl Environ Microbiol 56:1750–1762PubMedPubMedCentralGoogle Scholar
  44. 44.
    Schmidt EW, Obraztsova AY, Davidson SK, Faulkner DJ, Haygood MG (2000) Identification of the antifungal peptide-containing symbiont of the marine sponge Theonella swinhoei as a novel δ-proteobacterium, “Candidatus Entotheonella palauensis”. Mar Biol 136:969–977CrossRefGoogle Scholar
  45. 45.
    Sekar R, Mills DK, Remily ER, Voss JD, Richardson LL (2006) Microbial communities in the surface mucopolysaccharide layer and the black band microbial mat of black band-diseased Siderastrea siderea. Appl Environ Microbiol 72:5963–5973CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Sharp KH, Eam B, Faulkner DJ, Haygood MG (2007) Vertical transimission of diverse microbes in the tropical sponge Corticium sp. Appl Environ Microbiol 73:622–629CrossRefPubMedGoogle Scholar
  47. 47.
    Taylor MW, Radax R, Steger D, Wagner M (2007) Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 71:295–347CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Thiel V, Leininger S, Schmaljohann R, Brümmer F, Imhoff JF (2007) Sponge-specific bacterial associations of the Mediterranean sponge Chondrilla nucula (Demospongiae, Tetractinomorpha). Microb Ecol 54:101–111CrossRefPubMedGoogle Scholar
  49. 49.
    Usher KM, Kuo J, Fromont J, Sutton DC (2001) Vertical transmission of cyanobacterial symbionts in the marine sponge Chondrilla australiensis (Demospongiae). Hydrobiologia 461:15–23CrossRefGoogle Scholar
  50. 50.
    Usher KM, Sutton DC, Toze S, Kuo J, Fromont J (2005) Intergenerational transmission of microbial symbionts in the marine sponge Chondrilla australiensis (Demospongiae). Mar Freshw Res 56:125–131CrossRefGoogle Scholar
  51. 51.
    Vacelet J (1975) Electron microscope study of the association between bacteria and sponges of the genus Verongia (Dictyoceratida). J Microscope Biol Cell 23:271–288Google Scholar
  52. 52.
    Vacelet J, Donadey C (1977) Electron microscope study of the association between some sponges and bacteria. J Exp Mar Ecol 30:301–314CrossRefGoogle Scholar
  53. 53.
    Watanabe K, Teramoto M, Harayama S (1999) An outbreak of nonflocculating catabolic populations caused the breakdown of a phenol-digesting activated-sludge process. Appl Environ Microbiol 65:2813–2819PubMedPubMedCentralGoogle Scholar
  54. 54.
    Webster NS, Webb RI, Ridd MJ, Hill RT, Negri AP (2001) The effects of copper on the microbial community of a coral reef sponge. Environ Microbiol 3:19–31CrossRefPubMedGoogle Scholar
  55. 55.
    Webster NS, Taylor MW, Behnam F, Lucker S, Rattei T, Whalan S, Horn M, Wagner M (2010) Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ Microbiol 12:2070–2082PubMedPubMedCentralGoogle Scholar
  56. 56.
    Zhang HT, Lee YK, ZhangW LHK (2006) Culturable actinobacteria from the marine sponge Hymeniacidon perleve: isolation and phylogenetic diversity by 16S rRNA gene-RFLP analysis. Antonie van Leeuwenhoek 90:159–169CrossRefPubMedGoogle Scholar
  57. 57.
    Zhang H, Zhang W, Jin Y, Jin M, Yu X (2008) A comparative study on the phylogenetic diversity of culturable actinobacteria isolated from five marine sponge species. Antonie van Leeuwenhoek 93:241–248CrossRefPubMedGoogle Scholar
  58. 58.
    Zhang R, Wang Y, Gu JD (2006) Identification of environmental plasmid-bearing Vibrio species isolated from polluted and pristine marine reserves of Hong Kong, and resistance to antibiotics and mercury. Antonie van Leeuwenhoek 89:307–315CrossRefPubMedGoogle Scholar
  59. 59.
    Zhu P, Li Q, Wang G (2008) Unique microbial signatures of the alien Hawaiian marine sponge Suberites zeteki. Microb Ecol 55:406–414CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Chang-Qing Li
    • 1
  • Wen-Chao Liu
    • 1
  • Ping Zhu
    • 1
    Email author
  • Jin-Ling Yang
    • 1
  • Ke-Di Cheng
    • 1
  1. 1.State Key Laboratory of Bioactive Substances and Functions of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Institute of Materia MedicaChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina

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