Isolation and identification of Rhodosporidium diobovatum DS-0205 from deep-sea sediment of eastern Pacific Ocean

Abstract

A facultative heterotrophic strain (DS-0205) was isolated from a deep-sea sediment sample collected at a depth of 5.2 km in the eastern Pacific Ocean, China. Strain DS-0205 is motile helmet-like single cell or pairs, forming hemisphere with the center sunken of variable size. It has a widespread carbon source and nitrogen source, including agarose, citric acid, salicin, D-glucitol nitrate, sodium nitrite and ethylamine. It can grow in the following environment: temperature 4–37 °C, pH 2.0–12.0, tolerance to NaCl⩽15%. Two phylogenetic trees, one based on the ITS and 5.8S rRNA sequences and the other based on the 18S rRNA sequences, unite strain DS-0205(=JCM 0205) to the type strain of Rhodosporidium diobovatum JCM 3787 through a considerable evolutionary distance. These results suggest that strain DS-0205 is a new strain of the Rhodosporidium diobovatum.

Keywords

deep-sea sediment / ITS and 5.8S rRNA sequences / 18S rRNA / isolation / identification

References

[1] ZhangJ.-w., ZengR.-ying.. Analysis and gene cloning of the S-adenosylhomocysteine hydrolase from antarctic psychrotrophilic pseudomonas sp. 7197 strain[J]. Progress in Modern Biomedicine, 2006, 6(4): 5-7

[2] HarmsenH., PrieurD., JeanthonC.. Distribution of microorganisms in deep-sea hydrothermal vent chimneys investigated by whole-cell hybridization and enrichment culture of thermophilic subpopulations[J]. Appl Environ Microbiol, 1997, 63(7): 2876-2883

[3] Pace NormanR.. A molecular view of microbial diversity and the biosphere[J]. Science, 1997, 276(5313): 734-740

[4] HuangJ.-f., ZengL.-p., ZhouH.-b., LiuX., LiuF.-f., ZhangRubing.. Effect of illumination to the growth of the culturable microorganisms from a deep-sea hydrothermal vent[J]. Biomagnetism, 2005, 5(4): 12-13

[5] NagahamaT., HamamotoM., NakaseT.. Rhodotorula benthica sp. nov. and Rhodotorula calyptogenae sp. nov., novel. International Journal of Systematic and Evolutionary Microbiology, 2003, 53(5): 897-903

[6] GadanhoM., AlmeidaJ. M., SampaioJ. P.. Assessment of yeast diversity in a marine environment in the south of portugal by microsatellite-primed PCR[J]. Antonie van Leeuwenhoek, 2003, 84(3): 217-227

[7] NewellS. Y., HunterI. L.. Rhodosporidium diobovatum sp. n., the perfect form of an asporogenous yeast (rhodotorula sp.)[J]. Journal of Bacteriology, 1970, 104(1): 503-508

[8] FellJ. W.Yeasts in oceanic regions. Recent advances in aquatic mycology[M], 1976, London, Elek Science

[9] van DoverC. L., HumphrisS. E., FornariD.. Biogeography and ecological setting of Indian Ocean hydrothermal vents[J]. Science, 2001, 294(5543): 818-823

[10] DamareS., RaghukumarC., MuraleedharanU. D.. Fungi in deep-sea sediments of the central indian basin[J]. Deep-Sea Research I, 2006, 53(1): 14-27

[11] KarstenZ., GerardoT., MichaelR., ElkinsJ., MathureJ., ShortJ. M., KellerM.. Cultivating the uncultured[J]. Proc Natl Acad Sci USA, 2002, 99(24): 15681-15686

[12] Seung Yeo Moon-vanD. S., RupertD. W., DanielV.. Oceanic 18S rRNA sequences from proplankton reveal unsuspected eukaryotic diversity[J]. Letters to Nature, 2001, 409: 606-608

[13] EmilieL., CorinneB., ChristopheN., CarriasJ. F., ViscogliosiE., AmblarD. C., TelesphoreS. N.. Unveiling fungal zoo flagellates as members of freshwater picoeukaryotes: Evidence from a molecular diversity study in a deep meromictic lake[J]. Environmental Microbiology, 2007, 9(1): 61-71

[14] HamamotoM., NagahamaT., TamuraM.. Systematic study of basidiomycetous yeasts-evaluation of the ITS regions of rRNA to delimit species of the genus Rhodosporidium[J]. FEMS Yeast Research, 2002, 2(3): 409-413

[15] KurtzmanC. P., FellJ. W.The yeasts: A taxonomic study[M], 19984th edNew York, Elsevier Amsterdam

[16] ZengL.-p., HuangJ.-f., ZhangY.-f., QiuG.-z., TongJ.-b., ChenD., LuoX.-gang.. An effective method of DNA extraction for bioleaching bacteria from acid mine drainage[J]. Applied Microbiology and Biotechnology, 2008, 79(5): 881-888

[17] CletusP. K., ChristieJ. R.. Phylogenetic relationships among yeasts of the ‘Saccharomyces complex’ determined from multigene sequence analyses[J]. FEMS Yeast Research, 2003, 3(4): 417-432

[18] ThompsonJ. D., GibsonT. J., PlewniakF., JeanmouginF., HigginsD. G.. The clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Research, 1997, 25(24): 4876-4882

[19] BarnettJ. A., PayneR. W., YarrowD.Yeasts: Characteristics and IDENTIFICATION[M], 19903rd edCambridge, Cambridge University Press

[20] WrightJ. A., PietrangeloC., MacnaughtonA.. Influence of simulated upper intestinal parameters on the efficiency of beta carotene micellarisation using an in vitro model of digestion[J]. Food Chemistry, 2008, 107(3): 1253-1260

[21] FellJ. W., BoekhoutT., FonsecaA., ScoriettiG., Statzell-TallmanA.. Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rRNA D1/D2 domain sequence analysis[J]. Int J Syst Evol Microbiol, 2000, 50: 1351-1371

[22] HamamotoM., NakaseT.. Phylogenetic analysis of the ballistoconidium-forming yeast genus Sporobolomyces based on 18S rRNA sequences[J]. Int J Syst Evol Microbiol, 2000, 50: 1373-1380