Diversity of bacterial communities on sunken woods in the mediterranean sea

Journal of Marine Science and Technology (Taiwan)

Volumn 22, Issue 1, 2014, Pages 60-66

  Bessette, Sandrine ^a,b   Fagervold, Sonja K ^a,b   Romano, Chiara ^c   Martin, Daniel ^c   Le Bris, Nadine ^a,b   Galand, Pierre E ^a,b  

^a SORBONNE UNIVERSITÉ   (France)

^b CNRS   (France)

^c CENTRE D ESTUDIS AVANÇATS DE BLANES CEAB CSIC   (Spain)

Author keywords

Bacteria; Microbial ecology; Submarine canyon; Sunken wood

Indexed keywords

BACTERIA; ECOSYSTEMS; RNA; SUBMARINES;

BACTERIAL COMMUNITY; BACTERIAL DIVERSITY; MEDITERRANEAN SEA; METABOLIC CAPABILITIES; MICROBIAL COMMUNITIES; MICROBIAL ECOLOGY; NW MEDITERRANEAN; SUBMARINE CANYON;

WOOD;

BACTERIA; ECOLOGY; ECOSYSTEMS; NUCLEIC ACIDS; WOOD;

EID: 84901799779     PISSN: 10232796     EISSN: None     Source Type: Journal    
DOI: 10.6119/JMST-013-0829-2     Document Type: Article

References (35)

1. Alain, K., Olagnon, M., Desbruyères, D., Pagé, A., Barbier, G., Juniper, S. K., Quérellou, J., and Cambon-Bonavita, M.-A., "Phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete Paralvinella palmiformis, " FEMS Microbiology Ecology, Vol. 42, pp. 463-476 (2002).
2. Ashelford, K. E., Chuzhanova, N. A., Fry, J. C., Jones, A. J., and Weightman, A. J., "At Least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies, " Applied and Environmental Microbiology, Vol. 71, pp. 7724-7736 (2005).
3. Ashelford, K. E., Chuzhanova, N. A., Fry, J. C., Jones, A. J., and Weightman, A. J., "New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras, " Applied and Environmental Microbiology, Vol. 72, pp. 5734-5741 (2006).
4. Bienhold, C., Wenzhöfer, F., Le Bris, N., Ramette, A., and Boetius, A., "Wood colonization experiments in the Eastern Mediterranean deep sea, " Geophysical Research Abstracts, Vol. 10, pp. EGU2008-A-09061 (2008).
5. Boetius, A., Ravenschlag, K., Schubert, C. J., Rickert, D., Widdel, F., Gieseke, A., Amann, R., Jorgensen, B. B., Witte, U., and Pfannkuche, O., "A marine microbial consortium apparently mediating anaerobic oxidation of methane, " Nature, Vol. 407, pp. 623-626 (2000).
6. Corliss, J. B., Dymond, J., Gordon, L. I., Edmond, J. M., von Herzen, R. P., Ballard, R. D., Green, K., Williams, D., Bainbridge, A., Crane, K., and van Andel, T. H., "Submarine thermal springs on the Galapagos Rift, " Science, Vol. 203, pp. 1073-1083 (1979).
7. Corre, E., Reysenbach, A.-L., and Prieur, D., "Alphaproteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge, " Fems Microbiology Letters, Vol. 205, pp. 329-335 (2001).
8. Distel, D., Baco, A., Chuang, E., Morrill, W., Cavanaugh, C., and Smith, C., "Do mussels take wooden steps to deep-sea vents, " Nature, Vol. 403, pp. 725-726 (2000).
9. Duperron, S., Laurent, M. C. Z., Gaill, F., and Gros, O., "Sulphuroxidizing extracellular bacteria in the gills of Mytilidae associated with wood falls, " FEMS Microbiology Ecology, Vol. 63, pp. 338-349 (2008).
10. Fagervold, S. K., Bessette, S., Romano, C., Martin, D., Plyuscheva, M., Le Bris, N., and Galand, P. E., "Microbial communities associated with the degradation of oak wood in the Blanes submarine canyon and its adjacent open slope (NW Mediterranean), " Progress In Oceanography, Vol. 118, pp. 137-143 (2013).
11. Fagervold, S. K., Galand, P. E., Zbinden, M., Gaill, F., Lebaron, P., and Palacios, C., "Sunken woods on the ocean floor provide diverse specialized habitats for microorganisms, " FEMS Microbiology Ecology, Vol. 82, pp. 616-628 (2012).
12. Fors, Y., Nilsson, T., Risberg, E. D., Sandström, M., and Torssander, P., "Sulfur accumulation in pinewood (Pinus sylvestris) induced by bacteria in a simulated seabed environment: Implications for marine archaeological wood and fossil fuels, " International Biodeterioration & Biodegradation, Vol. 62, pp. 336-347 (2008).
13. Goffredi, S. K., Wilpiszeski, R., Lee, R., and Orphan, V. J., "Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California, " ISME Journal, Vol. 2, pp. 204-220 (2008).
14. Hinrichs, K.-U., Hayes, J. M., Sylva, S. P., Brewer, P. G., and DeLong, E. F., "Methane-consuming archaebacteria in marine sediments, " Nature, Vol. 398, pp. 802-805 (1999).
15. Kim, Y. S. and Singh, A. P., "Micromorphological characteristics of wood biodegradation in wet environments: a review, " IAWA Journal, Vol. 21, pp. 135-155 (2000).
16. Laurent, M. C. Z., Gros, O., Brulport, J.-P., Gaill, F., and Le Bris, N., "Sunken wood habitat for thiotrophic symbiosis in mangrove swamps, " Marine Environmental Research, Vol. 67, pp. 83-88 (2009).
17. Letunic, I. and Bork, P., "Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy, " Nucleic Acids Research, Vol. 39, pp. W475-W478 (2011).
18. Longnecker, K. and Reysenbach, A.-L., "Expansion of the geographic distribution of a novel lineage of ε-Proteobacteria to a hydrothermal vent site on the Southern East Pacific Rise, " FEMS Microbiology Ecology, Vol. 35, pp. 287-293 (2001).
19. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., and Kumar, Y., "ARB: a software environment for sequence data, " Nucleic Acids Research, Vol. 32, pp. 1363-1371 (2004).
20. Moussard, H., Corre, E., Cambon-Bonavita, M.-A., Fouquet, Y., and Jeanthon, C., "Novel uncultured Epsilonproteobacteria dominate a filamentous sulphur mat from the 13N hydrothermal vent field, East Pacific Rise, " FEMS Microbiology Ecology, Vol. 58, pp. 449-463 (2006).
21. Niemann, H., Lösekann, T., de Beer, D., Elvert, M., Nadalig, T., Knittel, K., Amann, R., Sauter, E. J., Schlüter, M., Klages, M., Foucher, J. P., and Antje Boetius, A., "Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink, " Nature, Vol. 443, pp. 854- 858 (2006).
22. Pailleret, M., Haga, T., Petit, P., Privé-Gill, C., Saedlou, N., Gaill, F., and Zbinden, M., "Sunken wood from the Vanuatu Islands: identification of wood substrates and preliminary description of associated fauna, " Marine Ecology, Vol. 28, pp. 233-241 (2007).
23. Polz, M. F. and Cavanaugh, C. M., "Dominance of one bacterial phylotype at a Mid-Atlantic Ridge hydrothermal vent site, " Proceedings of the National Academy of Sciences, Vol. 92, pp. 7232-7236 (1995).
24. Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., and Glockner, F. O., "SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, " Nucleic Acids Research, Vol. 35, pp. 7188-7196 (2007).
25. Reichenbach, H., "The order cytophagales, " in: Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., Stackebrandt, E. (Eds.), The Prokaryotes, Springer, New York, pp. 549-590 (2006).
26. Schlesner, H., Jenkins, C., and Staley, J., "The phylum Verrucomicrobia: a phylogenetically heterogeneous bacterial group, " in: Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., Stackebrandt, E. (Eds.), The Prokaryotes, Springer, New York, pp. 881-896 (2006).
27. Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J., and Weber, C. F., "Introducing mothur: open-source, platform-independent, community- supported software for describing and comparing microbial communities, " Applied and Environmental Microbiology, Vol. 75, pp. 7537-7541 (2009).
28. Sipe, A. R., Wilbur, A. E., and Cary, S. C., "Bacterial Symbiont Transmission in the Wood-Boring Shipworm Bankia setacea (Bivalvia: Teredinidae), " Applied and Environmental Microbiology, Vol. 66, pp. 1685- 1691 (2000).
29. Smith, C. R., Kukert, H., Wheatcroft, R. A., Jumars, P. A., and Deming, J. W., "Vent fauna on whale remains, " Nature, Vol. 341, pp. 27-28 (1989).
30. Tringe, S. G., von Mering, C., Kobayashi, A., Salamov, A. A., Chen, K., Chang, H. W., Podar, M., Short, J. M., Mathur, E. J., Detter, J. C., Bork, P., Hugenholtz, P., and Rubin, E. M., "Comparative Metagenomics of Microbial Communities, " Science, Vol. 308, pp. 554-557 (2005).
31. Vergin, K. L., Urbach, E., Stein, J. L., DeLong, E. F., Lanoil, B. D., and Giovannoni, S. J., "Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of theorder planctomycetales, " Applied and Environmental Microbiology, Vol. 64, pp. 3075-3078 (1998).
32. Waterbury, J. B., Calloway, C. B., and Turner, R. D., "A Cellulolytic Nitrogen-Fixing Bacterium Cultured from the Gland of Deshayes in Shipworms (Bivalvia: Teredinidae), " Science, Vol. 221, pp. 1401-1403 (1983).
33. Weisburg, W. G., Barns, S. M., Pelletier, D. A., and Lane, D. J., "16S ribosomal DNA amplification for phylogenetic study, " Journal of Bacteriology, Vol. 173, pp. 697-703 (1991).
34. Wolff, T., "Macrofaunal utilization of plant remains in the deep sea, " Sarsia, Vol. 64, pp. 117-136 (1979).
35. Yücel, M., Galand, P. E., Fagervold, S. K., Contreira-Pereira, L., and Le Bris, N., "Sulfide production and consumption in degrading wood in the marine environment, " Chemosphere, Vol. 90, pp. 403-409 (2013).