Application of Diffusion Growth Chambers for the Cultivation of Marine Sponge-Associated Bacteria

Marine Biotechnology

Volumn 16, Issue 5, 2014, Pages 594-603

  Steinert, Georg ^a   Whitfield, Susanna ^a   Taylor, Michael W ^b   Thoms, Carsten ^c   Schupp, Peter J ^a  

^a UNIVERSITY OF OLDENBURG   (Germany)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

^c BOGOR AGRICULTURAL UNIVERSITY   (Indonesia)

Author keywords

16S rRNA; Bacterial symbionts; Cultivation dependent; Diffusion growth chamber; In vivo cultivation; Marine sponge; Rhabdastrella globostellata; Sponge specific cluster

Indexed keywords

DIFFUSION; RNA;

16S RRNA; BACTERIAL SYMBIONTS; CULTIVATION-DEPENDENT; GROWTH CHAMBER; IN-VIVO; MARINE SPONGE; RHABDASTRELLA GLOBOSTELLATA; SPONGE-SPECIFIC CLUSTER;

BACTERIA;

CULTIVATION; MARINE ENVIRONMENT; METABOLITE; MICROBIAL COMMUNITY; RNA; SPONGE;

RNA 16S;

ANIMAL; BACTERIUM; BIOLOGICAL MODEL; BIOLOGY; CULTURE TECHNIQUE; DIFFUSION CHAMBER; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; MARINE BIOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROCEDURES; SPONGE (PORIFERA); STATISTICAL MODEL;

ANIMALS; BACTERIA; BASE SEQUENCE; CELL CULTURE TECHNIQUES; COMPUTATIONAL BIOLOGY; DIFFUSION CHAMBERS, CULTURE; LIKELIHOOD FUNCTIONS; MARINE BIOLOGY; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PORIFERA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84907596499     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-014-9575-y     Document Type: Article

References (41)

1. Alain K, Querellou J (2009) Cultivating the uncultured: Limits, advances and future challenges. Extremophiles 13: 583-94. doi: 10. 1007/s00792-009-0261-3.
2. Blunt JW, Copp BR, Munro MHG et al (2011) Marine natural products. Nat Prod Rep 28: 196-268. doi: 10. 1039/c005001f.
3. Blunt JW, Copp BR, Keyzers RA et al (2012) Marine natural products. Nat Prod Rep 29: 144-222. doi: 10. 1039/c2np00090c.
4. Blunt JW, Copp BR, Keyzers RA et al (2013) Marine natural products. Nat Prod Rep 30: 237-323. doi: 10. 1039/c2np20112g.
5. Bollmann A, Lewis K, Epstein SS (2007) Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl Environ Microbiol 73: 6386-90. doi: 10. 1128/AEM. 01309-07.
6. Bollmann A, Palumbo AV, Lewis K, Epstein SS (2010) Isolation and physiology of bacteria from contaminated subsurface sediments. Appl Environ Microbiol 76: 7413-9. doi: 10. 1128/AEM. 00376-10.
7. Ebada SS, Lin W, Proksch P (2010) Bioactive sesterterpenes and triterpenes from marine sponges: Occurrence and pharmacological significance. Mar Drugs 8: 313-46. doi: 10. 3390/md8020313.
8. Fouad M, Edrada RA, Ebel R et al (2006) Cytotoxic isomalabaricane triterpenes from the marine sponge Rhabdastrella globostellata. J Nat Prod 69: 211-8. doi: 10. 1021/np050346t.
9. Gandhimathi R, Arunkumar M, Selvin J et al (2008) Antimicrobial potential of sponge associated marine actinomycetes. J Mycol Médicale/ J Med Mycol 18: 16-22. doi: 10. 1016/j. mycmed. 2007. 11. 001.
10. Gavrish E, Bollmann A, Epstein S, Lewis K (2008) A trap for in situ cultivation of filamentous actinobacteria. J Microbiol Methods 72: 257-62. doi: 10. 1016/j. mimet. 2007. 12. 009.
11. Hentschel U, Hopke J, Horn M et al (2002) Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol 68: 4431-4440. doi: 10. 1128/AEM. 68. 9. 4431.
12. Hentschel U, Usher KM, Taylor MW (2006) Marine sponges as microbial fermenters. FEMS Microbiol Ecol 55: 167-77. doi: 10. 1111/j. 1574-6941. 2005. 00046. x.
13. Hentschel U, Piel J, Degnan SM, Taylor MW (2012) Genomic insights into the marine sponge microbiome. Nat Rev Microbiol 10: 641-54. doi: 10. 1038/nrmicro2839.
14. Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12: 1889-98. doi: 10. 1111/j. 1462-2920. 2010. 02193. x.
15. Joint I, Mühling M, Querellou J (2010) Culturing marine bacteria-an essential prerequisite for biodiscovery. Microb Biotechnol 3: 564-75. doi: 10. 1111/j. 1751-7915. 2010. 00188. x.
16. Kaeberlein T, Lewis K, Epstein SS (2002) Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296: 1127-9. doi: 10. 1126/science. 1070633.
17. Kearse M, Moir R, Wilson A et al (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647-9. doi: 10. 1093/bioinformatics/bts199.
18. Koopmans M, Martens D, Wijffels RH (2009) Towards commercial production of sponge medicines. Mar Drugs 7: 787-802. doi: 10. 3390/md7040787.
19. Lafi FF, Garson MJ, Fuerst JA (2005) Culturable bacterial symbionts isolated from two distinct sponge species (Pseudoceratina clavata and Rhabdastrella globostellata) from the Great Barrier Reef display similar phylogenetic diversity. Microb Ecol 50: 213-20. doi: 10. 1007/s00248-004-0202-8.
20. Lafi FF, Fuerst JA, Fieseler L et al (2009) Widespread distribution of poribacteria in demospongiae. Appl Environ Microbiol 75: 5695-9. doi: 10. 1128/AEM. 00035-09.
21. Lavy A, Keren R, Haber M et al (2013) Implementing sponge physiological and genomic information to enhance the diversity of its culturable associated bacteria. FEMS Microbiol Ecol. doi: 10. 1111/1574-6941. 12240.
22. Molinski TF, Dalisay DS, Lievens SL, Saludes JP (2009) Drug development from marine natural products. Nat Rev Drug Discov 8: 69-85. doi: 10. 1038/nrd2487.
23. Nichols D, Cahoon N, Trakhtenberg EM et al (2010) Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species. Appl Environ Microbiol 76: 2445-50. doi: 10. 1128/AEM. 01754-09.
24. Olson J, McCarthy P (2005) Associated bacterial communities of two deep-water sponges. Aquat Microb Ecol 39: 47-55. doi: 10. 3354/ame039047.
25. Petrosino JF, Highlander S, Luna RA et al (2009) Metagenomic pyrosequencing and microbial identification. Clin Chem 55: 856-66. doi: 10. 1373/clinchem. 2008. 107565.
26. Piel J (2009) Metabolites from symbiotic bacteria. Nat Prod Rep 26: 338-62. doi: 10. 1039/b703499g.
27. Piel J, Hui D, Wen G et al (2004) Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei. Proc Natl Acad Sci U S A 101: 16222-7. doi: 10. 1073/pnas. 0405976101.
28. Sashidhara KV, White KN, Crews P (2009) A selective account of effective paradigms and significant outcomes in the discovery of inspirational marine natural products. J Nat Prod 72: 588-603. doi: 10. 1021/np800817y.
29. Schippers KJ, Sipkema D, Osinga R et al (2012) Cultivation of sponges, sponge cells and symbionts: Achievements and future prospects. Adv Mar Biol 62: 273-337. doi: 10. 1016/B978-0-12-394283-8. 00006-0.
30. Schloss PD, Westcott SL (2011) Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77: 3219-26. doi: 10. 1128/AEM. 02810-10.
31. Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-41. doi: 10. 1128/AEM. 01541-09.
32. Simister RL, Deines P, Botté ES et al (2012) Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms. Environ Microbiol 14: 517-524. doi: 10. 1111/j. 1462-2920. 2011. 02664. x.
33. Sipkema D, Franssen MCR, Osinga R et al (2005) Marine sponges as pharmacy. Mar Biotechnol (NY) 7: 142-62. doi: 10. 1007/s10126-004-0405-5.
34. Sipkema D, Schippers K, Maalcke WJ et al (2011) Multiple approaches to enhance the cultivability of bacteria associated with the marine sponge Haliclona (gellius) sp. Appl Environ Microbiol 77: 2130-40. doi: 10. 1128/AEM. 01203-10.
35. Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456-463. doi: 10. 1093/bioinformatics/bti191.
36. Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57: 758-71. doi: 10. 1080/10635150802429642.
37. Tasdemir D, Mangalindan GC, Concepción GP et al (2002) Bioactive Isomalabaricane Triterpenes from the Marine Sponge Rhabdastrella globostellata. J Nat Prod 65: 210-214. doi: 10. 1021/np0104020.
38. Taylor MW, Radax R, Steger D, Wagner M (2007) Sponge-associated microorganisms: Evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 71: 295-347. doi: 10. 1128/MMBR. 00040-06.
39. Wang G (2006) Diversity and biotechnological potential of the sponge-associated microbial consortia. J Ind Microbiol Biotechnol 33: 545-51. doi: 10. 1007/s10295-006-0123-2.
40. Webster NS, Taylor MW (2012) Marine sponges and their microbial symbionts: love and other relationships. Environ Microbiol, 14(2): 335-46. doi: 10. 1111/j. 1462-2920. 2011. 02460. x.
41. Zhang L, An R, Wang J et al (2005) Exploring novel bioactive compounds from marine microbes. Curr Opin Microbiol 8: 276-81. doi: 10. 1016/j. mib. 2005. 04. 008.