Marine culturable yeasts in deep-sea hydrothermal vents: Species richness and association with fauna

FEMS Microbiology Ecology

Volumn 73, Issue 1, 2010, Pages 121-133

  Burgaud, Gaëtan ^a   Arzur, Danielle ^a   Durand, Lucile ^b   Cambon Bonavita, Marie Anne ^b   Barbier, Georges ^b  

^a UNIVERSITÉ DE BREST   (France)

^b IFREMER   (France)

Author keywords

26S rRNA gene; Fauna; FISH; Hydrothermal vents; Yeasts

Indexed keywords

FUNGAL DNA; RIBOSOME RNA; RNA, RIBOSOMAL, 26S; SEA WATER;

DEEP SEA; ENDEMIC SPECIES; HYDROTHERMAL VENT; MARICULTURE; MID-OCEAN RIDGE; NEW RECORD; PHYLOGENETICS; SPECIES RICHNESS; TAXONOMY; YEAST;

ANIMAL; ARTICLE; ASCOMYCETES; BASIDIOMYCETES; BIODIVERSITY; CLASSIFICATION; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; SEA;

ANIMALS; ASCOMYCOTA; BASIDIOMYCOTA; BIODIVERSITY; DNA, FUNGAL; IN SITU HYBRIDIZATION, FLUORESCENCE; OCEANS AND SEAS; PHYLOGENY; RNA, RIBOSOMAL; SEAWATER; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY;

ATLANTIC OCEAN; EAST PACIFIC RISE; PACIFIC OCEAN; PACIFIC OCEAN (SOUTH);

ANIMALIA; ASCOMYCOTA; BASIDIOMYCOTA; CANDIDA; CRYPTOCOCCUS (TREMELLOMYCETIDAE); CRYPTOCOCCUS (TRICHOSPORONALES); DEBARYOMYCES; RHODOSPORIDIUM; RHODOTORULA (AGARICOSTILBOMYCETIDAE); RHODOTORULA (ERYTHROBASIDIUM CLADE); RHODOTORULA (MICROBOTRYOMYCETIDAE); RHODOTORULA (MICROBOTRYUM CLADE); RHODOTORULA (MICROSTROMATALES); RHODOTORULA (SPORIDIOBOLACEAE); RHODOTORULA (USTILAGINALES);

EID: 77953192781     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2010.00881.x     Document Type: Article

References (60)

1. Altschul S, Gish W, Miller W, Myers E Lipman D (1990) Basic local alignment search tool. J Mol Biol 215 : 403 410.
2. Amann RI Fuchs BM (2008) Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 6 : 339 348.
3. Amann RI, Ludwig W Schleifer K (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59 : 143 169.
4. Ashelford KE, Weightman AJ Fry JC (2002) PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 30 : 3481 3489.
5. Bai F, Zhao JH, Takashima M, Jia JH, Boekhout T Nakase T (2002) Reclassification of the Sporobolomyces roseus and Sporidiobolus pararoseus complexes, with the description of Sporobolomyces phaffii sp. nov. Int J Syst Evol Micr 52 : 2309 2314.
6. Baschien C, Manz W, Neu T, Marvanova L Szewzyk U (2008) In situ detection of freshwater fungi in an alpine stream by new taxon-specific fluorescence in situ hybridization probes. Appl Environ Microb 74 : 6427 6436.
7. Bass D, Howe A, Brown N et al 2007) Yeast forms dominate fungal diversity in the deep oceans. P R Soc B 274 : 3069 3077.
8. Burgaud G, Le Calvez T, Arzur D, Vandenkoornhuyse P Barbier G (2009) Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents. Environ Microbiol 11 : 1588 1600.
9. Cancela da Fonseca JP (1966) L'outil statistique en biologie du sol. III. Indices d'intérêt écologique. Rev Ecol Biol Sol 3 : 381 407.
10. 4 vent fluids issuing from ultramafic rocks at the Rainbow hydrothermal field (36j14VN, MAR). Chem Geol 191 : 345 359.
11. Corbari L, Zbinden M, Cambon-Bonavita MA, Gaill F Compère P (2008) Bacterial symbionts and mineral deposits in the branchial chamber of the hydrothermal vent shrimp Rimicaris exoculata: relationship to moult cycle. Aquat Biol 1 : 225 238.
12. Daims H, Stoecker K Wagner M (2005) Fluorescence in situ hybridisation for the detection of prokaryotes. Advanced Methods in Molecular Microbial Ecology Osborn AM Smith CJ, eds), pp. 213 239. BIOS Scientific Publishers
13. Daims H, Lücker S Wagner M (2006) daime, a novel image analysis program for microbial ecology and biofilm research. Environ Microbiol 8 : 200 213.
14. Edgcomb VP, Kysela DT, Teske A de Vera Gomez A (2002) Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. P Natl Acad Sci USA 99 : 7658 7662.
15. Fell JW (1976) Yeasts in oceanic regions. Recent Advances in Aquatic Mycology (Jones EBG, ed), pp. 93 124. Elek Science
16. Gadanho M Sampaio JP (2004) Application of temperature gradient gel electrophoresis to the study of yeast diversity in the estuary of the Tagus river, Portugal. FEMS Yeast Res 5 : 253 261.
17. Gadanho M Sampaio J (2005) Occurrence and diversity of yeasts in the Mid-Atlantic Ridge hydrothermal fields near the Azores archipelago. Microb Ecol 50 : 408 417.
18. Gadanho M, Almeida JM Sampaio JP (2003) Assessment of yeast diversity in a marine environment in the south of Portugal by microsatellite-primed PCR. Antonie van Leeuwenhoek 84 : 217 227.
19. Gadd GM (2007) Geomycology: biogeochemical transformations of rocks, minerals and radionuclides by fungi, bioweathering and bioremediation. Mycol Res 111 : 3 49.
20. 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.
21. Gunde-Cimerman N, Zalar P, de Hoog S Plemenitas A (2000) Hypersaline waters in salterns - natural ecological niches for halophilic black yeasts. FEMS Microbiol Ecol 32 : 235 240.
22. Hawksworth DL (2002) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105 : 1422 1432.
23. Hernandez-Saavedra NY, Hernandez-Saavedra D Ochoa JL (1992) Distribution of Sporobolomyces (Kluyver et van Niel) genus in the western coast of Baja California Sur, Mexico. Syst Appl Microbiol 15 : 319 322.
24. Hoshino T, Yilmaz LS, Noguera DR, Daims H Wagner M (2008) Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH. Appl Environ Microb 74 : 5068 5077.
25. Joergensen BB Boetius A (2007) Feast and famine - microbial life in the deep-sea bed. Nat Rev Microbiol 5 : 770 781.
26. Kogej T, Ramos J, Plemenitas A Gunde-Cimerman N (2005) The halophilic fungus Hortaea werneckii and the halotolerant fungus Aureobasidium pullulans maintain low intracellular cation concentrations in hypersaline environments. Appl Environ Microb 71 : 6600 6605.
27. Kohlmeyer J Kohlmeyer E (1979) Marine Mycology: The Higher Fungi. Academic Press
28. Inacio J, Behrens S, Fuchs BM, Fonseca A, Spencer-Martins I Amann R (2003) In situ accessibility of Saccharomyces cerevisiae 26S rRNA to Cy3-labeled oligonucleotide probes comprising the D1 and D2 domains. Appl Environ Microb 69 : 2899 2905. (Pubitemid 36560372)
29. Kushner DJ (1978) Life in high salt and solute concentrations. Microbial Life in Extreme Environments (Kushner DJ, ed), pp. 317 368. Academic Press
30. Lachance MA Starmer WT (1998) Ecology and yeasts. The Yeasts, a Taxonomic Study, 4th edn (Kurtzman CP Fell JW, eds), pp. 21 30. Elsevier
31. Lai X, Cao L, Tan H, Fang S, Huang Y Zhou S (2007) Fungal communities from methane hydrate-bearing deep-sea marine sediments in South China Sea. ISME J 1 : 756 762.
32. Le Calvez T, Burgaud G, Mahe S, Barbier G Vandenkoornhuyse P (2009) Fungal diversity in deep sea hydrothermal ecosystems. Appl Environ Microb 75 : 6415 6421.
33. Libkind D, Brizzio S, Ruffini A, Gadanho M, van Broock M Sampaio JP (2003) Molecular characterization of carotenogenic yeasts from aquatic environments in Patagonia, Argentina. Antonie van Leeuwenhoek 84 : 313 322.
34. Lopez-Garcia P, Philippe H, Gail F Moreira D (2003) Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge. P Natl Acad Sci USA 100 : 697 702. (Pubitemid 36126115)
35. 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.
36. Margesin R Schinner F (2001) Potential of halotolerant and halophilic microorganisms for biotechnology. Extremophiles 5 : 73 83.
37. Maruyama A, Honda D, Yamamoto H, Kitamura K Higashihara T (2000) Phylogenetic analysis of psychrophilic bacteria from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov. Int J Syst Evol Micr 50 : 835 846.
38. Munn CB (2003) Marine Microbiology - Ecology and Applications. Bios-Garland Scientific
39. Nagahama T (2006) Yeast biodiversity in freshwater, marine and deep-sea environments. Biodiversity and Ecophysiology of Yeasts (The Yeast Handbook series) (Rosa CA Péter G, eds), pp. 241 262. Springer
40. Nagahama T, Hamamoto M, Nakase T Horikoshi K (1999) Kluyveromyces nonfermentans sp. nov., a new yeast species isolated from the deep sea. Int J Syst Evol Micr 49 : 1899 1905.
41. Nagahama T, Hamamoto M, Nakase T Horikoshi K (2001a) Rhodotorula lamellibrachii sp. nov., a new yeast species from a tubeworm collected at the deep-sea floor in Sagami Bay and its phylogenetic analysis. Antonie van Leeuwenhoek 80 : 317 323.
42. Nagahama T, Hamamoto M, Nakase T, Takami H Horikoshi K (2001b) Distribution and identification of red yeasts in deep-sea environments around the northwest Pacific Ocean. Antonie van Leeuwenhoek 80 : 101 110.
43. Nagahama T, Hamamoto M, Nakase T Horikoshi K (2003a) Rhodotorula benthica sp. nov. and Rhodotorula calyptogenae sp. nov., novel yeast species from animals collected from the deep-sea floor, and Rhodotorula lysiniphila sp. nov., which is related phylogenetically. Int J Syst Evol Micr 53 : 897 903.
44. Nagahama T, Hamamoto M, Nakase T, Takaki Y Horikoshi K (2003b) Cryptococcus surugaensis sp. nov., a novel yeast species from sediment collected on the floor of Suruga Bay. Int J Syst Evol Micr 53 : 2095 2098.
45. Nagahama T, Hamamoto M Horikoshi K (2006) Rhodotorula pacifica sp. nov., a novel yeast species from sediment collected on the deep-sea floor of the north-west Pacific Ocean. Int J Syst Evol Micr 56 : 295 299.
46. Nagahama T, Abdel-Wahab MA, Nogi Y, Miyazaki M, Uematsu K, Hamamoto M Horikoshi K (2008) Dipodascus tetrasporeus sp. nov., an ascosporogenous yeast isolated from deep-sea sediments in the Japan Trench. Int J Syst Evol Micr 58 : 1040 1046.
47. Nguyen H, Gaillardin C Neuvéglise C (2009) Differentiation of Debaryomyces hansenii and Candida famata by rRNA gene intergenic spacer fingerprinting and reassessment of phylogenetic relationships among D. hansenii, C. famata, D. fabryi, C. flareri (=D. subglobosus) and D. prosopidis: description of D. vietnamensis sp. nov. closely related to D. nepalensis. FEMS Yeast Res 9 : 641 662.
48. Posada D Crandall K (1998) Applications note. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 : 817 818.
49. Ronquist F Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 : 1572 1574.
50. Siepmann R Höhnk W (1962) Über Hefen und einige Pilze (Fungi imp., Hyphales) aus dem Nordatlantik. Veroeff Inst Meeresforsch Bremerhaven 8 : 79 97.
51. Stoecker K, Dorninger C, Daims H Wagner M (2010) Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility. Appl Environ Microb 76 : 922 926.
52. Takishita K, Tsuchiya M, Reimer JD Maruyama T (2006) Molecular evidence demonstrating the basidiomycetous fungus Cryptococcus curvatus is the dominant microbial eukaryote in sediment at the Kuroshima Knoll methane seep. Extremophiles 10 : 165 169.
53. Takishita K, Yubuki N, Kakizoe N, Inagaki Y Maruyama T (2007) 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 11 : 563 576.
54. 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.
55. Tivey MK (2007) Generation of seafloor hydrothermal vent fluids and associated mineral deposits. Oceanography 20 : 50 65.
56. Thompson JD, Higgins DG Gibson TJ (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.
57. Van Dover CL, Ward ME, Scott JL, Underdown J, Anderson B, Gustafson C, Whalen M Carnegie RA (2007) A fungal epizootic in mussels at a deep-sea hydrothermal vent. Mar Ecol 28 : 54 62.
58. Yang L, Haagensen JAJ, Jelsbak L, Johansen HK, Sternberg C, Hoiby N Molin S (2008) In situ growth rates and biofilm development of Pseudomonas aeruginosa populations in chronic lung infections. J Bacteriol 190 : 2767 2776.
59. Zalar P, de Hoog GS Gunde-Cimerman N (1999) Ecology of halotolerant dothideaceous black yeasts. Stud Mycol 43 : 38 48.
60. 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.