Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents

Environmental Microbiology

Volumn 11, Issue 6, 2009, Pages 1588-1600

  Burgaud, Gaëtan ^a   Le Calvez, Thomas ^b   Arzur, Danielle ^a   Vandenkoornhuyse, Philippe ^b   Barbier, Georges ^a  

^a UNIVERSITÉ DE BREST   (France)

^b UNIVERSITÉ EUROPÉENNE DE BRETAGNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

SEA WATER;

ARTICLE; BIODIVERSITY; CLASSIFICATION; ECOSYSTEM; FUNGUS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; PHYSIOLOGY; THERMAL SPRING;

BIODIVERSITY; ECOSYSTEM; FUNGI; HOT SPRINGS; PHYLOGENY; SEAWATER; WATER MICROBIOLOGY;

EUKARYOTA; FUNGI;

EID: 66649119250     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2009.01886.x     Document Type: Article

References (68)

1. Alias, S., Kuthubutheen, A. Jones, E. (1995) Frequency of occurrence of fungi on wood in Malaysian mangroves. Hydrobiologia 295 : 97 106.
2. Alker, A., Smith, G. Kim, K. (2001) Characterization of Aspergillus sydowii (Thom et Church), a fungal pathogen of Caribbean sea fan corals. Hydrobiologia 460 : 105 111. (Pubitemid 34077753)
3. Altschul, S., Gish, W., Miller, W., Myers, E. Lipman, D. (1990) Basic local alignment search tool. J Mol Biol 215 : 403 410.
4. Atkins, M.S. (2000) Ancyromonadida: a new phylogenetic lineage among the protozoa closely related to the common ancestor of metazoans, fungi, and choanoflagellates (Opisthokonta). J Mol Evol 51 : 278 285.
5. Azmi, O. Seppelt, R. (1998) The broad-scale distribution of microfungi in the Windmill Islands region, continental Antarctica. Polar Biol 19 : 92 100. (Pubitemid 28111282)
6. Bass, D., Howe, A., Brown, N., Barton, H., Demidova, M., Michelle, H., et al. (2007) Yeast forms dominate fungal diversity in the deep oceans. Proc Biol Sci 274 : 3069 3077. (Pubitemid 350220150)
7. Bhadury, P., Mohammad, B.T. Wright, P.C. (2006) The current status of natural products from marine fungi and their potential as anti-infective agents. J Ind Microbiol Biotechnol 33 : 325 337.
8. Britayev, T.A., Martin, D., Krylova, E.M., Von Cosel, R. Aksiuk, T.S. (2007) Life-history traits of the symbiotic scale-worm Branchipolynoe seepensis and its relationships with host mussels of the genus Bathymodiolus from hydrothermal vents. Mar Ecol 28 : 36 48. (Pubitemid 46390352)
9. Buchan, A., Newell, S.Y., Moreta, J.I.L. Moran, M.A. (2002) Analysis of internal transcribed spacer (ITS) regions of rRNA genes in fungal communities in a southeastern US salt marsh. Microb Ecol 43 : 329 340. (Pubitemid 36941342)
10. Butinar, L., Zalar, P., Frisvad, J.C. Gunde-Cimerman, N. (2005) The genus Eurotium-members of indigenous fungal community in hypersaline waters of salterns. FEMS Microbiol Ecol 51 : 155 166. (Pubitemid 40038376)
11. Cancela da Fonseca, J.P. (1966) L'outil statistique en biologie du sol. III. Indices d'intérêt écologique. Rev Ecol Biol Sol 3 : 381 407.
12. Christophersen, C., Crescente, O., Frisvad, J.C., Gram, L., Nielsen, J., Nielsen, P.H. Rahbaek, L. (1998) Antibacterial activity of marine-derived fungi. Mycopathologia 143 : 135 138. (Pubitemid 29235398)
13. Cueto, M., Jensen, P.R., Kauffman, C., Fenical, W., Lobkovsky, E. Clardy, J. (2001) Pestalone, a new antibiotic produced by a marine fungus in response to bacterial challenge. J Nat Prod 64 : 1444 1446. (Pubitemid 33116688)
14. Cuomo, V., Palomba, I., Perretti, A., Guerriero, A., D'Ambrosio, M. Pietra, F. (1995) Antimicrobial activities from marine fungi. J Mar Biotechnol 2 : 199 204.
15. Damare, S. Raghukumar, C. (2008) Fungi and macroaggregation in deep-sea sediments. Microb Ecol 56 : 168 177.
16. Damare, S., Raghukumar, C. Raghukumar, S. (2006) Fungi in deep-sea sediments of the Central Indian Basin. Deep Sea Res Part I 53 : 14 27. (Pubitemid 43052559)
17. Dawson, S.C. Pace, N.R. (2002) Novel kingdom-level eukaryotic diversity in anoxic environments. Proc Natl Acad Sci USA 99 : 8324.
18. Deacon, J. (2006) Environmental conditions for growth and tolerance of extremes. In Fungal Biology, 4th edn. MA, USA : Wiley-Blackwell, pp. 142 157.
19. Desbruyères, D., Biscoito, M., Caprais, J.C., Colaço, A., Comtet, T., Crassous, P., et al. (2001) Variations in deep-sea hydrothermal vent communities on the Mid-Atlantic Ridge near the Azores plateau. Deep Sea Res Part I 48 : 1325 1346. (Pubitemid 32219164)
20. Duncan, S.M. (2007) Fungal diversity and cellulolytic activity in the historic huts, Ross Island, Antarctica. PhD Thesis. Hamilton, New Zealand : University of Waikato.
21. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32 : 1792.
22. Edgcomb, V.P., Kysela, D.T., Teske, A., de Vera Gomez, A. Sogin, M.L. (2002) Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc Natl Acad Sci USA 99 : 7658 7662. (Pubitemid 34568747)
23. Gadanho, M. Sampaio, J.P. (2005) Occurrence and diversity of yeasts in the Mid-Atlantic Ridge hydrothermal fields near the Azores Archipelago. Microb Ecol 50 : 408 417.
24. Gadanho, M. Sampaio, J.P. (2006) Microeukaryotic diversity in the extreme environments of the Iberian Pyrite Belt: a comparison between universal and fungi-specific primer sets, temperature gradient gel electrophoresis and cloning. FEMS Microbiol Ecol 57 : 139 148. (Pubitemid 43876445)
25. Guindon, S., Lethiec, F., Duroux, P. Gascuel, O. (2005) PHYML online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33 : 557 559.
26. Hawksworth, D.L., Kirk, P.M., Sutton, B.C. Pegler, D.N. (1995) Ainsworth and Bisby's Dictionary of Fungi, 8th edn. Wallingford, CT, USA : CAB International.
27. Hyde, K.D., Jones, E.B.G., Leao, E., Pointing, S.B., Poonyth, A.D. Vrijmoed, L.L.P. (1998) Role of fungi in marine ecosystems. Biodivers Conserv 7 : 1147 1161. (Pubitemid 29020172)
28. Hyde, K.D., Sarma, V.V. Jones, E.B.G. (2000) Morphology and taxonomy of higher marine fungi. In Marine Mycology: A Practical Approach. Hyde, K.D. Pointing, S.B. (eds). Hong Kong : Fungal Diversity Press, pp. 172 204.
29. James, T., Kauff, F., Schoch, C. Matheny, P. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443 : 818 822. (Pubitemid 44622687)
30. Jin, Y., Weining, S. Nevo, E. (2005) A MAPK gene from Dead Sea fungus confers stress tolerance to lithium salt and freezing-thawing: prospects for saline agriculture. Proc Natl Acad Sci USA 102 : 18992 18997. (Pubitemid 43049554)
31. Jones, E.B.G. Alias, S.A. (1997) Biodiversity of mangrove fungi. In Biodiversity of Tropical Microfungi. Hyde, K.D. (ed.). Hong Kong : Hong Kong University Press, pp. 71 92.
32. Katoh, K., Kuma, K., Toh, H. Miyata, T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33 : 511 518. (Pubitemid 40360980)
33. Kis-Papo, T. (2005) Marine fungal communities. In The Fungal Community: Its Organization and Role in the Ecosystem. Dighton, J., White, J.F. Oudemans, P. (eds). Boca Raton, FL, USA : Taylor and Francis Group, CRC Press, 23: 61 91.
34. Kochkina, G.A., Ivanushkina, N.E., Akimov, V.N., Gilichinskii, D.A. Ozerskaya, S.M. (2007) Halo- and psychrotolerant Geomyces fungi from arctic cryopegs and marine deposits. Microbiology 76 : 31 38. (Pubitemid 46352565)
35. Kohlmeyer, J. Kohlmeyer, E. (1979) Marine Mycology: The Higher Fungi. New York, USA : Academic Press.
36. Li, H., Chi, Z., Wang, X., Duan, X., Ma, L. Gao, L. (2007) Purification and characterization of extracellular amylase from the marine yeast Aureobasidium pullulans N13d and its raw potato starch digestion. Enzyme Microb Technol 40 : 1006 1012. (Pubitemid 46356507)
37. Lin, X., Huang, Y., Fang, M., Wang, J., Zheng, Z. Su, W. (2005) Cytotoxic and antimicrobial metabolites from marine lignicolous fungi, Diaporthe sp. FEMS Microbiol Lett 251 : 53 58. (Pubitemid 41306228)
38. Lopez-Garcia, P., Philippe, H., Gail, F. Moreira, D. (2003) Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge. Proc Natl Acad Sci USA 100 : 697.
39. Lopez-Garcia, P., Vereshchaka, A. Moreira, D. (2007) Eukaryotic diversity associated with carbonates and fluid-seawater interface in Lost City hydrothermal field. Environ Microbiol 9 : 546 554. (Pubitemid 46072140)
40. Lorenz, R. Molitoris, H.P. (1997) Cultivation of fungi under simulated deep-sea conditions. Mycol Res 101 : 1355 1365.
41. Maruyama, A., Honda, D., Yamamoto, H. Kitamura, K. (2000) Phylogenetic analysis of psychrophilic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov. Int J Syst Evol Microbiol 50 : 835 846. (Pubitemid 30167533)
42. Moreira, D. López-Garcia, P. (2003) Are hydrothermal vents oases for parasitic protists? Trends Parasitol 19 : 556 558. (Pubitemid 37474105)
43. Palacios, C., Zbinden, M., Baco, A.R., Treude, T., Smith, C.R., Gaill, F., et al. (2006) Microbial ecology of deep-sea sunken wood: quantitative measurements of bacterial biomass and cellulolytic activities. Cah Biol Mar 47 : 415 420. (Pubitemid 46139047)
44. Posada, D. Crandall, K. (1998) Applications note. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 : 817 818.
45. Raghukumar, C. Raghukumar, S. (1991) Fungal invasion of massive corals. Mar Ecol 12 : 251 260.
46. Raghukumar, C. Raghukumar, S. (1998) Barotolerance of fungi isolated from deep-sea sediments of the Indian Ocean. Aquat Microb Ecol 15 : 153 163. (Pubitemid 128492575)
47. Raghukumar, C., Raghukumar, S., Sheelu, G., Gupta, S.M., Nagender Nath, B. Rao, B.R. (2004) Buried in time: culturable fungi in a deep-sea sediment core from the Chagos Trench, Indian Ocean. Deep-Sea Res Part I 51 : 1759 1768. (Pubitemid 39366829)
48. Ravindran, J., Raghukumar, C. Raghukumar, S. (2001) Fungi in Porites lutea: association with healthy and diseased corals. Dis Aquat Organ 47 : 219 228. (Pubitemid 34067497)
49. Ronquist, F. Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 : 1572 1574. (Pubitemid 37038874)
50. Rowley, D.C., Kelly, S., Kauffman, C.A., Jensen, P.R. Fenical, W. (2003) Halovirs A-E, new antiviral agents from a marine-derived fungus of the genus Scytalidium. Bioorg Med Chem 11 : 4263 4274. (Pubitemid 37013577)
51. Sarma, V.V., Hyde, K. Vittal, B. (2001) Frequency of occurrence of mangrove fungi from the east coast of India. Hydrobiologia 455 : 41 53. (Pubitemid 34077726)
52. Segonzac, M., De Saint-Laurent, M. Casanova, B. (1993) L'énigme du comportement trophique des crevettes Alvinocarididae des sites hydrothermaux de la dorsale médio-atlantique. Cah Biol Mar 34 : 535 571. (Pubitemid 2049398)
53. Shearer, C.A., Descals, E., Kohlmeyer, B., Kohlmeyer, J., Marvanov, L., Padgett, D., et al. (2007) Fungal biodiversity in aquatic habitats. Biodivers Conserv 16 : 49 67. (Pubitemid 46252710)
54. Stoeck, T. Epstein, S. (2003) Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl Environ Microbiol 69 : 2657.
55. Stoeck, T., Hayward, B., Taylor, G.T., Varela, R. Epstein, S.S. (2006) A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157 : 31 43. (Pubitemid 43220715)
56. Takishita, K., Miyake, H., Kawato, M. Maruyama, T. (2005) Genetic diversity of microbial eukaryotes in anoxic sediment around fumaroles on a submarine caldera floor based on the small-subunit rDNA phylogeny. Extremophiles 9 : 185 196. (Pubitemid 40938362)
57. Tamura, K., Dudley, J., Nei, M. Kumar, S. (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software, version 4.0. Mol Biol Evol 24 : 1596 1599. (Pubitemid 47236692)
58. Thompson, J.D., Higgins, D.G. Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 : 4673 4680. (Pubitemid 24354800)
59. Tosi, S., Casado, B., Gerdol, R. Caretta, G. (2002) Fungi isolated from Antarctic mosses. Polar Biol 25 : 262 268. (Pubitemid 36058875)
60. Van Dover, C., Ward, M., Scott, J. Underdown, J. (2007) A fungal epizootic in mussels at a deep-sea hydrothermal vent. Mar Ecol 28 : 54 62. (Pubitemid 46390354)
61. Vandenkoornhuyse, P., Husband, R., Daniell, T.J., Watson, I.J., Duck, J.M., Fitter, A.H. Young, J.P.W. (2002) Arbuscular mycorrhizal community composition associated with two plant species in a grassland ecosystem. Mol Ecol 11 : 1555 1564.
62. Vilgalys, R. Hester, M. (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172 : 4238 4246. (Pubitemid 20236711)
63. Wainwright, M. (2005) Oligotrophic growth of fungi. In The Fungal Community: Its Organization and Role in the Ecosystem. Dighton, J., White, J.F. Oudemans, P. (eds). Boca Raton, FL, USA : Taylor and Francis Group, CRC Press, 23: 643 658.
64. White, T.J., Bruns, T., Lee, S. Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Chapter 38. In PCR Protocols: A Guide to Methods and Applications. Orlando, FL, USA : Academic Press, pp. 315 322.
65. Zbinden, M., Le Bris, N., Gaill, F. Compere, P. (2004) Distribution of bacteria and associated minerals in the gill chamber of the vent shrimp Rimicaris exoculata and related biogeochemical processes. Mar Ecol Prog Ser 284 : 237 251. (Pubitemid 40118218)
66. Zettler, L.A.A., Gomez, F., Zettler, E., Keenan, B.G., Amils, R. Sogin, M.L. (2001) Eukaryotic diversity in Spain's river of fire. J Eukaryot Microbiol 48 : 293 297.
67. Zettler, L.A.A., Messerli, M.A., Laatsch, A.D., Smith, P.J.S. Sogin, M.L. (2003) From genes to genomes: beyond biodiversity in Spain's Rio Tinto. Biol Bull 204 : 205 209. (Pubitemid 36516710)
68. Zuendorf, A., Bunge, J., Behnke, A., Barger, K.J.A. Stoeck, T. (2006) Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord, Denmark. FEMS Microbiol Ecol 58 : 476 491. (Pubitemid 44748156)