Fungal diversity in deep-sea extreme environments

Fungal Ecology

Volumn 5, Issue 4, 2012, Pages 463-471

  Nagano, Yuriko ^a   Nagahama, Takahiko ^a,b  

^a JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

^b Higashichikushi Junior College   (Japan)

Author keywords

Cryptomycota; Deep sea; Extreme environments; Fungal diversity; Zoosporic fungi

Indexed keywords

EUKARYOTA; FUNGI; PROKARYOTA;

EID: 84862135700     PISSN: 17545048     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.funeco.2012.01.004     Document Type: Review

References (80)

1. Abe F., Horikoshi K. Analysis of intracellular pH in the yeast Saccharomyces cerevisiae under elevated hydrostatic pressure: a study in baro- (piezo-) physiology. Extremophiles 1998, 2:223-228.
2. Abe F., Horikoshi K. Tryptophan permease gene TAT2 confers high-pressure growth in Saccharomyces cerevisiae. Molecular Cell Biology 2000, 20:8093-8102.
3. Abe F., Minegishi H., Miura T., Nagahama T., Usami R., Horikoshi K. Characterization of cold- and high-pressure-active polygalacturonases from a deep-sea yeast, Cryptococcus liquefaciens strain N6. Bioscience, Biotechnology, Biochemistry 2006, 70:296-299.
4. Alain K., Marteinsson V.T., Miroshnichenko M.L., Bonch-Osmolovskaya E.A., Prieur D., Birrien J.L. Marinitoga piezophila sp. nov., a rod-shaped, thermo-piezophilic bacterium isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology 2002, 52:1331-1339.
5. Amaral Zettler L.A., Gómez F., Zettler E., Keenan B.G., Amils R., Sogin M.L. Microbiology: eukaryotic diversity in Spain's River of Fire. Nature 2002, 417:137.
6. Bale S.J., Goodman K., Rochelle P.A., Marchesi J.R., Fry J.C., Weightman A.J., Parkes R.J. Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. International Journal of Systematic Bacteriology 1997, 47:515-521.
7. Bass D., Howe A., Brown N., Barton H., Demidova M., Michelle H., Li L., Sanders H., Watkinson S.C., Willcock S., Richards T.A. Yeast forms dominate fungal diversity in the deep oceans. Proceedings of the Royal Society B Biological Sciences 2007, 274:3069-3077.
8. Birrien J.L., Zeng X., Jebbar M., Cambon-Bonavita M.A., Quérellou J., Oger P., Bienvenu N., Xiao X., Prieur D. Pyrococcus yayanosii sp. nov., the first obligate piezophilic hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology 2011.
9. Bridge P.D., Newsham K.K. Soil fungal community composition at Mars Oasis, a southern maritime Antarctic site, assessed by PCR amplification and cloning. Fungal Ecology 2009, 2:66-74.
10. Burgaud G., Arzur D., Durand L., Cambon-Bonavita M.A., Barbier G. Marine culturable yeasts in deep-sea hydrothermal vents: species richness and association with fauna. FEMS Microbiology Ecology 2010, 73:121-133.
11. Burgaud G., Le Calvez T., Arzur D., Vandenkoornhuyse P., Barbier G. Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents. Environmental Microbiology 2009, 11:1588-1600.
12. Cai S., Zhu T., Du L., Zhao B., Li D., Gu Q. Sterigmatocystins from the deep-sea-derived fungus Aspergillus versicolor. Journal of Antibiotics 2011, 64:193-196.
13. Cavanaugh C.M. Symbioses of chemoautotrophic bacteria and marine invertebrates from hydrothermal vents and reducing sediments. Bulletin of the Biological Society of Washington 1985, 6:373-388.
14. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., Thompson J.D. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research 2003, 31:3497-3500.
15. Connell L., Barrett A., Templeton A., Staudigel H. Fungal diversity associated with an active deep sea volcano: Vailulu'u seamount, Samoa. Geomicrobiology Journal 2009, 26:597-605.
16. Connell L., Redman R., Craig S., Scorzetti G., Iszard M., Rodriguez R. Diversity of soil yeasts isolated from South Victoria Land, Antarctica. Microbial Ecology 2008, 56:448-459.
17. Damare S., Raghukumar C. Fungi and macroaggregation in deep-sea sediments. Microbial Ecology 2008, 56:168-177.
18. Damare S., Raghukumar C., Raghukumar S. Fungi in deep-sea sediments of the Central Indian Basin. Deep-Sea Research I 2006, 53:14-27.
19. Dekas A.E., Poretsky R.S., Orphan V.J. Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. Science 2009, 326:422-426.
20. Dubilier N., Bergin C., Lott C. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nature Reviews Microbiology 2008, 6:725-740.
21. Edgcomb V.P., Beaudoin D., Gast R., Biddle J.F., Teske A. Marine subsurface eukaryotes: the fungal majority. Environmental Microbiology 2011, 13:172-183.
22. Eloe E.A., Shulse C.N., Fadrosh D.W., Williamson S.J., Allen E.E., Bartlett D.H. Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment. Environmental Microbiology Reports 2010, 3:449-458.
23. Fell J.W. Yeasts in oceanic regions. Recent Advances in Aquatic Mycology 1976, 93-124. Elek Science, London. E.B.G. Jones (Ed.).
24. Fernandes P.M.B., Domitrovic T., Kao C.M., Kurtenbach E. Genomic expression pattern in Saccharomyces cerevisiae cells in response to high hydrostatic pressure. FEBS Letters 2004, 556:153-160.
25. Freeman K.R., Martin A.P., Karki D., Lynch R.C., Mitter M.S., Meyer A.F., Longcore J.E., Simmons D.R., Schmidt S.K. Evidence that chytrids dominate fungal communities in high-elevation soils. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:18315-18320.
26. Gadanho M., Sampaio J.P. Occurrence and diversity of yeasts in the mid-atlantic ridge hydrothermal fields near the Azores Archipelago. Microbial Ecology 2005, 50:408-417.
27. Gleason F.H., Daynes C.N., McGee P.A. Some zoosporic fungi can grow and survive within a wide pH range. Fungal Ecology 2010, 3:31-37.
28. Gleason F.H., Lilje O. Structure and function of fungal zoospores: ecological implications. Fungal Ecology 2009, 2:53-59.
29. Gleason F.H., Marano A.V. The effects of antifungal substances on some zoosporic fungi (Kingdom Fungi). Hydrobiologia 2011, 659:81-92.
30. Grassle J.F. Hydrothermal vent animals: distribution and biology. Science 1985, 229:713-717.
31. Guillot J., Petit T., Degorce-Rubiales F., Guého E., Chermette R. Dermatitis caused by Malassezia pachydermatis in a California sea lion (Zalophus californianus). Veterinary Record 1998, 142:311-312.
32. Horikoshi K. Barophiles: deep-sea microorganisms adapted to an extreme environment. Current Opinion in Microbiology 1998, 1:291-295.
33. James T.Y., Kauff F., Schoch C.L., Matheny P.B., Hofstetter V., Cox C.J., Celio G., Gueidan C., Fraker E., Miadlikowska J., Lumbsch H.T., Rauhut A., Reeb V., Arnold A.E., Amtoft A., Stajich J.E., Hosaka K., Sung G.H., Johnson D., O'Rourke B., Crockett M., Binder M., Curtis J.M., Slot J.C., Wang Z., Wilson A.W., Schussler A., Longcore J.E., O'Donnell K., Mozley-Standridge S., Porter D., Letcher P.M., Powell M.J., Taylor J.W., White M.M., Griffith G.W., Davies D.R., Humber R.A., Morton J.B., Sugiyama J., Rossman A.Y., Rogers J.D., Pfister D.H., Hewitt D., Hansen K., Hambleton S., Shoemaker R.A., Kohlmeyer J., Volkmann-Kohlmeyer B., Spotts R.A., Serdani M., Crous P.W., Hughes K.W., Matsuura K., Langer E., Langer G., Untereiner W.A., Lucking R., Budel B., Geiser D.M., Aptroot A., Diederich P., Schmitt I., Schultz M., Yahr R., Hibbett D.S., Lutzoni F., McLaughlin D.J., Spatafora J.W., Vilgalys R. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 2006, 443:818-822.
34. Jebaraj C.S., Raghukumar C., Behnke A., Stoeck T. Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation. FEMS Microbiology Ecology 2010, 71:399-412.
35. Jones E.B.G., Sakayaroj J., Suetrong S., Somrithipol S., Pang K.L. Classification of marine Ascomycota, anamorphic taxa and Basidiomycota. Fungal Diversity 2009, 35:1-187.
36. Jones M.D., Forn I., Gadelha C., Egan M.J., Bass D., Massana R., Richards T.A. Discovery of novel intermediate forms redefines the fungal tree of life. Nature 2011, 474:200-203.
37. Jørgensen B.B., Boetius A. Feast and famine-microbial life in the deep-sea bed. Nature Reviews Microbiology 2007, 5:770-781.
38. Kato C., Li L., Nogi Y., Nakamura Y., Tamaoka J., Horikoshi K. Extremely barophilic bacteria isolated from the Mariana Trench, Challenger Deep, at a depth of 11,000 meters. Applied and Environmental Microbiology 1998, 64:1510-1513.
39. Kohlmeyer J., Volkmann-Kohlmeyer B. Illustrated key to the filamentous higher marine fungi. Botanica Marina 1991, 34:1-61.
40. Lai X., Cao L., Tan H., Fang S., Huang Y., Zhou S. Fungal communities from methane hydrate-bearing deep-sea marine sediments in South China Sea. The ISME Journal 2007, 1:756-762.
41. Lara E., Moreira D., López-García P. The environmental clade LKM11 and Rozella form the deepest branching clade of fungi. Protist 2010, 161:116-121.
42. Lauro F.M., Bartlett D.H. Prokaryotic lifestyles in deep sea habitats. Extremophiles 2008, 12:15-25.
43. Le Calvez T., Burgaud G., Mahe S., Barbier G., Vandenkoornhuyse P. Fungal diversity in deep sea hydrothermal ecosystems. Applied and Environmental Microbiology 2009, 75:6415-6421.
44. Li Y., Ye D., Chen X., Lu X., Shao Z., Zhang H., Che Y. Breviane spiroditerpenoids from an extreme-tolerant Penicillium sp. isolated from a deep sea sediment sample. Journal of Natural Products 2009, 72:912-916.
45. Lonsdale P. Clustering of suspension-feeding macrobenthos near abyssal hydrothermal vents at oceanic spreading centers. Deep-Sea Research 1977, 24:857-863.
46. Lopez-Garcia P., Vereshchaka A., Moreira D. Eukaryotic diversity associated with carbonates and fluid-seawater interface in Lost City hydrothermal field. Environmental Microbiology 2007, 9:546-554.
47. Lorenz R., Molitoris H.P. Cultivation of fungi under simulated deep sea conditions. Mycological Research 1997, 101:1355-1365.
48. Nagahama T., Abdel-Wahab M.A., Nogi Y., Miyazaki M., Uematsu K., Hamamoto M., Horikoshi K. Dipodascus tetrasporeus sp. nov., an ascosporogenous yeast isolated from deep-sea sediments in the Japan Trench. International Journal of Systematic and Evolutionary Microbiology 2008, 58:1040-1046.
49. Nagahama T., Hamamoto M., Horikoshi K. Rhodotorula pacifica sp. nov., a novel yeast species from sediment collected on the deep-sea floor of the north-west Pacific Ocean. International Journal of Systematic and Evolutionary Microbiology 2006, 56:295-299.
50. Nagahama T., Hamamoto M., Nakase T., Takami H., Horikoshi K. Distribution and identification of red yeasts in deep-sea environments around the northwest Pacific Ocean. Antonie Van Leeuwenhoek 2001, 80:101-110.
51. Nagahama T., Takahashi E., Nagano Y., Abdel-Wahab M.A., Miyazaki M. Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments. Environmental Microbiology 2011, 13:2359-2370.
52. Nagano Y., Nagahama T., Hatada Y., Nunoura T., Takami H., Miyazaki J., Takai K., Horikoshi K. Fungal diversity in deep-sea sediments - the presence of novel fungal groups. Fungal Ecology 2010, 3:316-325.
53. Nakagaki K., Hata K., Iwata E., Takeo K. Malassezia pachydermatis isolated from a South American sea lion (Otaria byronia) with dermatitis. The Journal of Veterinary Medical Science 2000, 62:901-903.
54. Nogi Y., Hosoya S., Kato C., Horikoshi K. Colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the Japan Trench. International Journal of Systematic and Evolutionary Microbiology 2004, 54:1627-1631.
55. Pollock C.G., Rohrbach B., Ramsay E.C. Fungal dermatitis in captive pinnipeds. Journal of Zoo and Wildlife Medicine 2000, 31:374-378.
56. Quaiser A., Zivanovic Y., Moreira D., López-García P. Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara. The ISME Journal 2011, 5:285-304.
57. Raghukumar C., Raghukumar S. Barotolerance of fungi isolated from deep-sea sediments of the Indian Ocean. Aquatic Microbial Ecology 1998, 15:153-163.
58. Raghukumar C., Raghukumar S., Sheelu G., Gupta S., Nagendernath B., Rao B. Buried in time: culturable fungi in a deep-sea sediment core from the Chagos Trench, Indian Ocean. Deep Sea Research Part I 2004, 51:1759-1768.
59. Renker C., Alphei J., Buscot F. Soil nematodes associated with the mammal pathogenic fungal genus Malassezia (Basidiomycota: Ustilaginomycetes) in Central European forests. Biology and Fertility of Soils 2003, 37:70-72.
60. Roth F.J., Orpurt P.A., Ahearn D.J. Occurrence and distribution of fungi in a subtropical marine environment. Canadian Journal of Botany 1964, 42:375-383.
61. Saito N., Nei M. The neighbor-joining method: a new method for constructing phylogenetic trees. Molecular Biology and Evolution 1987, 4:406-425.
62. Sauvadet A.L., Gobet A., Guillou L. Comparative analysis between protist communities from the deep-sea pelagic ecosystem and specific deep hydrothermal habitats. Environmental Microbiology 2010, 12:2946-2964.
63. Shimada S., Andou M., Naito N., Yamada N., Osumi M., Hayashi R. Effects of hydrostatic pressure on the ultrastructure and leakage of internal substances in the yeast Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 1993, 40:123-131.
64. Sime-Ngando T., Lefevre E., Gleason F.H. Hidden diversity among aquatic heterotrophic flagellates: ecological potentials of zoosporic fungi. Hydrobiologia 2011, 659:5-22.
65. Singh P., Raghukumar C., Verma P., Shouche Y. Phylogenetic diversity of culturable fungi from the deep-sea sediments of the Central Indian Basin and their growth characteristics. Fungal Diversity 2010, 40:89-102.
66. Singh P., Raghukumar C., Verma P., Shouche Y. Fungal community analysis in the deep-sea sediments of the central Indian basin by culture-independent approach. Microbial Ecology 2011, 61:507-517.
67. Takai K., Miyazaki M., Hirayama H., Nakagawa S., Querellou J., Godfroy A. Isolation and physiological characterization of two novel, piezophilic, thermophilic chemolithoautotrophs from a deep-sea hydrothermal vent chimney. Environmental Microbiology 2009, 11:1983-1997.
68. Takai K., Nakamura K. Archaeal diversity and community development in deep-sea hydrothermal vents. Current Opinion in Microbiology 2011, 14:282-291.
69. Takami H., Inoue A., Fuji F., Horikoshi K. Microbial flora in the deepest sea mud of the Mariana Trench. FEMS Microbiology Letters 1997, 152:279-285.
70. Takishita K., Miyake H., Kawato M., Maruyama T. Genetic diversity of microbial eukaryotes in anoxic sediment around fumaroles on a submarine caldera floor based on the small-subunit rDNA phylogeny. Extremophiles: Life Under Extreme Conditions 2005, 9:185-196.
71. Takishita K., Tsuchiya M., Kawato M., Oguri K., Kitazato H., Maruyama T. Genetic diversity of microbial eukaryotes in anoxic sediment of the saline meromictic Lake Namako-ike (Japan): on the detection of anaerobic or anoxic-tolerant lineages of eukaryotes. Protist 2007, 158:51-64.
72. Takishita K., Yubuki N., Kakizoe N., Inagaki Y., Maruyama T. Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures. Extremophiles: Life Under Extreme Conditions 2007, 11:563-576.
73. Tian F., Yu Y., Chen B., Li H., Yao Y.-F., Guo X.-K. Bacterial, archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis. Polar Biology 2008, 32:93-103.
74. Turchetti B., Buzzini P., Goretti M., Branda E., Diolaiuti G., D'Agata C., Smiraglia C., Vaughan-Martini A. Psychrophilic yeasts in glacial environments of Alpine glaciers. FEMS Microbiology Ecology 2008, 63:73-83.
75. van Hannen E.J., Mooij W., van Agterveld M.P., Gons H.J., Laanbroek H.J. Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis. Applied and Environmental Microbiology 1999, 65:2478-2484.
76. Wainright P.O., Hinkle G., Sogin M.L., Stickel S.K. Monophyletic origins of the metazoa: an evolutionary link with fungi. Science 1993, 260:340-342.
77. Wang F., Wang P., Chen M., Xiao X. Isolation of extremophiles with the detection and retrieval of Shewanella strains in deep-sea sediments from the west Pacific. Extremophiles 2004, 8:165-168.
78. Wolinska J., Giessler S., Koerner H. Molecular identification and hidden diversity of novel Daphnia parasites from European lakes. Applied and Environmental Microbiology 2009, 75:7051-7059.
79. Wurzbacher C.M., Barlocher F., Grossart H.P. Fungi in lake ecosystems. Aquatic Microbial Ecology 2010, 59:125-149.
80. Yayanos A.A., Dietz A.S., Van Boxtel R. Isolation of a deep-sea barophilic bacterium and some of its growth characteristics. Science 1979, 205:808-810.