Investigation of Oscillatoria spongeliae-dominated bacterial communities in four dictyoceratid sponges

Applied and Environmental Microbiology

Volumn 71, Issue 11, 2005, Pages 7366-7375

  Ridley, Christian P ^a   Faulkner, D John ^a   Haygood, Margo G ^a,b  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; FLUORESCENCE; GENES; RNA; TISSUE;

CYANOBACTERIAL SYMBIONT OSCILLATORIA SPONGELIAE; INVERTEBRATES; MARINE SPONGES;

BACTERIOLOGY;

RNA 16S;

BACTERIUM; MARINE ENVIRONMENT; SPONGE; SYMBIONT;

ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL GENE; BEGGIATOA; CYANOBACTERIUM; DICTYOCERATID; EPITHELIUM CELL; FLUORESCENCE IN SITU HYBRIDIZATION; GAMMAPROTEOBACTERIA; GENE INSERTION; INVERTEBRATE; LAMELLODYSIDEA CHLOREA; LAMELLODYSIDEA HERBACEA; LENDENFELDIA CHONDRODES; MARINE ENVIRONMENT; MESOPHYLL; NONHUMAN; NUCLEOTIDE SEQUENCE; OSCILLATORIA SPONGELIAE; PHYLLOSPONGIA PAPYRACEA; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPECIES; SPONGE (PORIFERA);

ANIMALS; BASE SEQUENCE; CYANOBACTERIA; DNA, BACTERIAL; ECOSYSTEM; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; PORIFERA; RHODOBACTER; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SYNECHOCYSTIS;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BEGGIATOA; CYANOBACTERIA; DICTYOCERATIDA; GAMMAPROTEOBACTERIA; INVERTEBRATA; LAMELLODYSIDEA; LAMELLODYSIDEA CHLOREA; LAMELLODYSIDEA HERBACEA; LENDENFELDIA CHONDRODES; OSCILLATORIA SPONGELIAE; PHYLLOSPONGIA PAPYRACEA; PORIFERA; RHODOBACTERACEAE; SYNECHOCYSTIS SP.;

EID: 32044431630     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.11.7366-7375.2005     Document Type: Article

References (54)

1. Acinas, S. G., L. A. Marcelino, V. Klepac-Ceraj, and M. F. Polz. 2004. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186:2629-2635.
2. Allgaier, M., H. Uphoff, A. Felske, and I. Wagner-Döbler. 2003. Aerobic anoxygenic photosynthesis in Roseobacter clade bacteria from diverse marine habitats. Appl. Environ. Microbiol. 69:5051-5059.
3. Althoff, K., C. Schütt, R. Steffen, R. Batel, and W. E. G. Müller. 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.
4. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
5. Amann, R., L. Krumholz, and D. A. Stahl. 1990. Fluorescent- oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.
6. Arillo, A., G. Bavestrello, B. Burlando, and M. Sarà. 1993. Metabolic integration between symbiotic cyanobacteria and sponges: a possible mechanism. Mar. Biol. 117:159-162.
7. Ashen, J. B., and L. J. Goff. 1996. Molecular identification of a bacterium associated with gall formation in the marine red alga Prionitis lanceolata. J. Phycol. 32:286-297.
8. Behrens, S., C. Rühland, J. Inácio, H. Huber, Á. Fonseca, I. Spencer-Martins, B. M. Fuchs, and R. Amann. 2003. In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl. Environ. Microbiol. 69:1748-1758.
9. Borowitzka, M. A., R. Hinde, and F. Pironet. 1988. Carbon fixation by the sponge Dysidea herbacea and its endosymbiont Oscillatoria spongeliae, p. 151-156. In J. H. Choat, D. J. Barnes, M. A. Borowitzka, J. C. Coll, P. J. Davies, P. Flood, B. G. Hatcher, D. Hopley, P. A. Hutchings, D. Kinsey, G. R. Orme, M. Pichon, P. F. Sale, P. W. Sammarco, C. C. Wallace, C. R. Wilkinson, E. Wolanski, and O. Bellwood (ed.), Proceedings of the Sixth International Coral Reef Symposium, Australia, vol. 3. Sixth International Coral Reef Symposium Executive Committee, Townsville, Australia.
10. Brodersen, D. E., W. M. Clemons, A. P. Carter, B. T. Wimberly, and V. Ramakrishnan. 2002. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: Structure of the proteins and their interactions with 16 S RNA. J. Mol. Biol. 316:725-768.
11. Buchan, A., L. S. Collier, E. L. Neidle, and M. A. Moran. 2000. Key aromatic-ring-cleaving enzyme, protocatechuate 3,4-dioxygenase, in the ecologically important marine Roseobacter lineage. Appl. Environ. Microbiol. 66:4662-4672.
12. Cannone, J. J., S. Subramanian, M. N. Schnare, J. R. Collelt, L. M. D'Souza, Y. Du, B. Feng, N. Lin, L. V. Madabusi, K. M. Muller, N. Pande, Z. Shang, N. Yu, and R. R. Gutell. 2002. The comparative RNA web (CRW) site: an online database of comparative sequence and structural information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3:2.
13. Cantera, J. J. L., H. Hawasaki, and T. Seki. 2004. The nitrogen-fixing gene (niflf) of Rhodopseudomonas palustris: a case of lateral gene transfer? Microbiology 150:2237-2246.
14. Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kalum, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31:442-444.
15. Cooney, R. P., O. Pantos, M. D. A. Le Tissier, M. R. Barer, A. G. O'Donnell, and J. C. Bythell. 2002. Characterization of the bacterial consortium associated with black band disease in coral using molecular microbiological techniques. Environ. Microbiol. 4:401-413.
16. Cox, G. C. 1986. Comparison of Prochloron from different hosts. I. Structural and ultrastructural characteristics. New Phytol. 104:429-445.
17. Cox, G. C., R. G. Hiller, and A. W. D. Larkum. 1985. An unusual cyanophyte, containing phycourobilin and symbiotic with ascidians and sponges. Mar. Biol. 89:149-163.
18. Erpenbeck, D., J. A. J. Breeuwer, H. C. van der Velde, and R. W. M. van Soest. 2002. Unravelling host and symbiont phylogenies of halichondrid sponges (Demospongiae, Porifera) using a mitochondrial marker. Mar. Biol. 141:377-386.
19. Fieseler, L., M. Horn, M. Wagner, and U. Hentschel. 2004. Discovery of the novel candidate phylum "Poribacteria" in marine sponges. Appl. Environ. Microbiol. 70:3724-3732.
20. Flowers, A. E., M. J. Garson, R. I. Webb, E. J. Dumdei, and R. D. Charan. 1998. Cellular origin of chlorinated diketopiperazines in the dictyoceratid sponge Dysidea herbacea (Keller). Cell Tissue Res. 292:597-607.
21. Fuchs, B. M., F. O. Glöckner, J. Wulf, and R. Amann. 2000. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labelled oligonucleotide probes. Appl. Environ. Microbiol. 66:3603-3607.
22. Good, I. J. 1953. The population frequencies of species and the estimation of population parameters. Biometrika 40:237-240.
23. Gregor, J., and G. Klug. 1999. Regulation of bacterial photosynthesis by oxygen and light. FEMS Microbiol. Lett. 179:1-9.
24. Hentscbel, U., L. Fieseler, M. Wehrl, C. Gernert, M. Steinert, J. Hacker, and M. Horn. 2003. Microbial diversity of marine sponges, p. 60-88. In W. E. G. Müller (ed.), Molecular marine biology of sponges. Springer-Verlag, Heidelburg, Germany.
25. Hentschel, U., J. Hopke, M. Horn, A. B. Friedrich, M. Wagner, J. Hacker, and B. S. Moore. 2002. Molecular evidence for a uniform microbial community in sponges from different oceans. Appl. Environ. Microbiol. 68:4431-4440.
26. Hernádez-Mariné, M., X. Turon, and J. Catalan. 1990. A marine Synechocystis (Chroococcales, Cyanophyta) epizoic on didemnid ascidians from the Mediterranean Sea. Phycologia 29:275-284.
27. Hildebrand, M., L. E. Waggoner, G. E. Lim, K. H. Sharp, C. P. Ridley, and M. G. Haygood. 2004. Approaches to identify, clone, and express symbiont bioactive metabolite genes. Nat. Prod. Rep. 21:122-142.
28. Hofacker, I. L. 2003. Vienna RNA secondary structure server. Nucleic Acids Res. 31:3429-3431.
29. Hooper, J. N. A., and R. W. M. van Soest. 2002. Introduction, p. 1-3. In J. N. A. Hooper and R. W. M. van Soest (ed.), Systema Porifera: a guide to the classification of sponges, vol. 1. Kluwer Academic/Plenum Publishers, New York, N.Y.
30. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellows (ed.), Nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, N.Y.
31. Larkum, A. W. D., G. C. Cox, R. G. Hiller, D. L. Parry, and T. P. Dibbayawan. 1987. Filamentous cyanophytes containing phycourobilin and in symbiosis with sponges and an ascidian of coral reefs. Mar. Biol. 95:1-13.
32. Lewin, R. A., and L. Cheng. 1993. Discovery, early history and phytogeny of Prochloron. Korean J. Phycol. 8:91-97.
33. Lim, G. E., and M. G. Haygood. 2004. "Candidatus Endobugula glebosa," a specific bacterial symbiont of the marine bryozoan Bugula simplex. Appl. Environ. Microbiol. 70:4921-4929.
34. Moyer, C. L., J. M. Tiedje, F. C. Dobbs, and D. M. Karl. 1996. A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl. Environ. Microbiol. 62:2501-2507.
35. Otoguro, M., M. Hayakawa, T. Yamazaki, and Y. Iimura. 2001. An integrated method for the enrichment and selective isolation of Actinokineospora spp. in soil and plant litter. J. Appl. Microbiol. 91:118-130.
36. Page, R. D. M. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:357-358.
37. Pernthaler, A., J. Pernthaler, and R. Amann. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68:3094-3101.
38. Polz, M. F., and C. M. Cavanaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.
39. Ridley, C. P., P. R. Bergquist, M. K. Harper, D. J. Faulkner, J. N. A. Hooper, and M. G. Haygood. 2005. Speciation and biosynthetic variation in four dictyoceratid sponges and their cyanobacterial symbiont, Oscillatoria spongeliae. Chem. Biol. 12:397-406.
40. Ronquist, F., and J. P. Huelsenbeck. 2003. Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
41. Schönbuber, W., B. Zarda, S. Eix, R. Rippka, M. Herdman, W. Ludwig, and R. Amann. 1999. In situ identification of cyanobacteria with horseradish peroxidase-labeled, rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 65:1259-1267.
42. Schwintner, C., M. Sabaty, B. Berna, S. Cahors, and P. Richaud. 1998. Plasmid content and localization of the genes encoding the denitrification enzyme in two strains of Rhodobacter sphaeroides. FEMS Microbiol. Lett. 165:313-321.
43. Shimada, A., N. Yano, S. Kanai, R. A. Lewin, and T. Maruyama. 2003. Molecular phylogenetic relationship between two symbiotic photo-oxygenic prokaryotes, Prochloron sp. and Synechocystis trididemni. Phycologia 42:193-197.
44. Singleton, D. R., M. A. Furlong, S. L. Rathbun, and W. B. Whitman. 2001. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67:4374-4376.
45. Springer, N., W. Ludwig, R. Amann, H. J. Schmidt, H. D. Görtz, and K. H. Schleifer. 1993. Occurrence of fragmented 16S rRNA in an obligate bacterial endosymbiont of Paramecium caudatum. Proc. Natl. Acad. Sci. USA 90:9892-9895.
46. Swofford, D. L. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods), 4th ed. Sinauer Associates, Sunderland, Mass.
47. Taylor, M. W., P. J. Schupp, I. Dahllöf, S. Kjelleberg, and P. D. Steinberg. 2004. Host specificity in marine sponge-associated bacteria, and potential implications for marine microbial diversity. Environ. Microbiol. 6:121-130.
48. Thacker, R. W., and S. Starnes. 2003. Host specificity of the symbiotic cyanobacterium Oscillatoria spongeliae in marine sponges, Dysidea spp. Mar. Biol. 142:643-648.
49. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX-Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
50. Thompson, J. R., L. A. Marcelino, and M. F. Polz. 2002. Heteroduplexes in mixed-template amplifications: formation, consequences, and elimination by 'reconditioning PCR'. Nucleic Acids Res. 30:2083-2088.
51. Webster, N. S., A. P. Negri, M. H. G. Munro, and C. N. Battershill. 2004. Diverse microbial communities inhabit Antarctic sponges. Environ. Microbiol. 6:288-300.
52. Webster, N. S., A. P. Negri, R. I. Webb, and R. T. Hill. 2002. A spongin-boring α-proteobacterium is the etiological agent of disease in the Great Barrier Reef sponge Rhopaloeides odorabile. Mar. Ecol. Prog. Ser. 232:305-309.
53. Webster, N. S., K. J. Wilson, L. L. Blackall, and R. T. Hill. 2001. Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile. Appl. Environ. Microbiol. 67:434-444.
54. Wilkinson, C. R., M. Nowak, B. Austin, and R. R. Colwell. 1981. Specificity of bacterial symbionts in the Mediterranean and Great Barrier Reef sponges. Microb. Ecol. 7:13-21.