Sponge-specific clusters revisited: A comprehensive phylogeny of sponge-associated microorganisms

Environmental Microbiology

Volumn 14, Issue 2, 2012, Pages 517-524

  Simister, Rachel L ^a   Deines, Peter ^a   Botté, Emmanuelle S ^b   Webster, Nicole S ^b   Taylor, Michael W ^a  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b AUSTRALIAN INSTITUTE OF MARINE SCIENCE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

SEA WATER;

ACIDOBACTERIA; ANIMAL; ARCHAEON; ARTICLE; BACTERIUM; BIODIVERSITY; CHLOROFLEXI; CLASSIFICATION; DENATURING GRADIENT GEL ELECTROPHORESIS; ECOSYSTEM; FUNGUS; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; SPONGE (PORIFERA); SYMBIOSIS;

ACIDOBACTERIA; ANIMALS; ARCHAEA; BACTERIA; BIODIVERSITY; CHLOROFLEXI; DENATURING GRADIENT GEL ELECTROPHORESIS; ECOSYSTEM; FUNGI; MOLECULAR SEQUENCE DATA; PHYLOGENY; PORIFERA; SEAWATER; SYMBIOSIS;

ACIDOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; CANDIDATUS PORIBACTERIA; CHLOROFLEXI; CHLOROFLEXI (CLASS); CYANOBACTERIA; EUKARYOTA; FUNGI; SYNECHOCOCCUS; SYNECHOCOCCUS ELONGATUS PCC 6301; SYNECHOCOCCUS SPONGIARUM;

EID: 84856569941     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2011.02664.x     Document Type: Article

References (32)

1. Baker, P., Kennedy, J., Morrissey, J., O'Gara, F., Dobson, A., and Marchesi, J. (2010) Endoglucanase activities and growth of marine-derived fungi isolated from the sponge Haliclona simulans. J Appl Microbiol 108: 1668-1675.
2. Bourne, D., Iida, Y., Uthicke, S., and Smith-Kuene, C. (2008) Changes in coral-associated microbial communities during a bleaching event. ISME J 2: 350-363.
3. Bugni, T., and Ireland, C. (2004) Marine-derived fungi: a chemically and biologically diverse group of microorganisms. Nat Prod Rep 21: 143-163.
4. Erwin, P.M., and Thacker, R.W. (2008) Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts. Mol Ecol 17: 2937-2947.
5. Fieseler, L., Horn, M., Wagner, M., and Hentschel, U. (2004) Discovery of the novel candidate phylum 'Poribacteria' in marine sponges. Appl Environ Microbiol 70: 3724-3732.
6. Hallam, S.J., Konstantinidis, K.T., Putnam, K., Schleper, C., Watanabe, Y., Sugahara, J., etal. (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci USA 103: 18296-18301.
7. Hentschel, U., Hopke, J., Horn, M., Friedrich, A.B., Wagner, M., Hacker, J., and Moore, B.S. (2002) Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol 68: 4431-4440.
8. Hentschel, U., Usher, K.M., and Taylor, M.W. (2006) Marine sponges as microbial fermenters. FEMS Microbiol Ecol 55: 167-177.
9. Hoffmann, F., Radax, R., Woebken, D., Holtappels, M., Lavik, G., Rapp, H.T., etal. (2009) Complex nitrogen cycling in the sponge Geodia barretti. Environ Microbiol 11: 2228-2243.
10. Höller, U., Wright, A., Matthée, G., Konig, G., Draeger, S., Aust, H.-J., and Schulz, B. (2000) Fungi from marine sponges: diversity, biological activity and secondary metabolites. Mycol Res 104: 1354-1365.
11. Kamke, J., Taylor, M.W., and Schmitt, S. (2010) Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons. ISME J 4: 498-508.
12. Liu, W., Li, C., Zhu, P., Yang, J., and Cheng, K. (2010) Phylogenetic diversity of culturable fungi associated with two marine sponges: Haliclona simulans and Gelliodes carnosa, collected from the Hainan Island coastal waters of the South China Sea. Fungal Divers 42: 1-15.
13. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, etal. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
14. Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., and Glöckner, F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
15. Reshef, L., Koren, O., Loya, Y., Rosenberg, I.Z., and Rosenberg, E. (2006) The coral probiotic hypothesis. Environ Microbiol 8: 2068-2073.
16. Richards, T., Jones, M., Leonard, G., and Bass, D. (2012) Marine fungi: their ecology and molecular diversity. Annu Rev Mar Sci 4: 12.1-12.28.
17. Rocap, G., Larimer, F.W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N.A., etal. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047.
18. Schleper, C., Swanson, R.V., Mathur, E.J., and DeLong, E.F. (1997) Characterization of a DNA polymerase from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum. J Bacteriol 179: 7803-7811.
19. Schmitt, S., Angermeier, H., Schiller, R., Lindquist, N., and Hentschel, U. (2008) Molecular microbial diversity survey of sponge reproductive stages and mechanistic insights into vertical transmission of microbial symbionts. Appl Environ Microbiol 74: 7694-7708.
20. Schmitt, S., Tsai, P., Bell, J., Fromont, J., Ilan, M., Lindquist, N., etal. (2011) Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME J. doi: 10.1038/ismej.2011.116.
21. Siegl, A., Kamke, J., Hochmuth, T., Piel, J., Richter, M., Liang, C., etal. (2010) Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J 5: 61-70.
22. Sogin, M.L., Morrison, H.G., Huber, J.A., Welch, M.D., Huse, S.M., Neal, P.R., etal. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc Natl Acad Sci USA 103: 12115-12120.
23. Sunagawa, S., Woodley, C.M., and Medina, M. (2010) Threatened corals provide underexplored microbial habitats. PLoS ONE 5: e9554.
24. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
25. 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.
26. Vacelet, J., and Donadey, C. (1977) Electron microscope study of the association between some sponges and bacteria. J Exp Mar Biol Ecol 30: 301-314.
27. Webster, N.S., and Taylor, M.W. (2011) Marine sponges and their microbial symbionts: love and other relationships. Environ Microbiol (in press) doi: 10.1111/j.1462-2920.2011.02460.x.
28. Webster, N.S., Taylor, M.W., Benham, F., Lücker, S., Rattei, T., Whalan, S., etal. (2010) Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ Microbiol 12: 2070-2082.
29. Wilkinson, C.R. (1978a) Microbial associations in sponges. I. Ecology, physiology and microbial populations of coral reef sponges. Mar Biol 49: 161-167.
30. Wilkinson, C.R. (1978b) Microbial associations in sponges. II. Numerical analysis of sponge and water bacterial populations. Mar Biol 49: 169-176.
31. Wilkinson, C.R. (1978c) Microbial associations in sponges. III. Ultrastructure of the in situ associations in coral reef sponges. Mar Biol 49: 177-185.
32. Wilkinson, C.R., Nowak, M., Austin, B., and Colwell, R.R. (1981) Specificity of bacterial symbionts in Mediterranean and Great Barrier Reef sponges. Microb Ecol 7: 13-21.