Advertisement

Eighteen new oleaginous yeast species

  • Luis A. Garay
  • Irnayuli R. Sitepu
  • Tomas Cajka
  • Idelia Chandra
  • Sandy Shi
  • Ting Lin
  • J. Bruce German
  • Oliver Fiehn
  • Kyria L. Boundy-Mills
Bioenergy/Biofuels/Biochemicals

Abstract

Of 1600 known species of yeasts, about 70 are known to be oleaginous, defined as being able to accumulate over 20 % intracellular lipids. These yeasts have value for fundamental and applied research. A survey of yeasts from the Phaff Yeast Culture Collection, University of California Davis was performed to identify additional oleaginous species within the Basidiomycota phylum. Fifty-nine strains belonging to 34 species were grown in lipid inducing media, and total cell mass, lipid yield and triacylglycerol profiles were determined. Thirty-two species accumulated at least 20 % lipid and 25 species accumulated over 40 % lipid by dry weight. Eighteen of these species were not previously reported to be oleaginous. Triacylglycerol profiles were suitable for biodiesel production. These results greatly expand the number of known oleaginous yeast species, and reveal the wealth of natural diversity of triacylglycerol profiles within wild-type oleaginous Basidiomycetes.

Keywords

Oleaginous yeast Triacylglycerol Basidiomycete Intracellular lipid Biodiesel 

Notes

Acknowledgments

The authors are grateful to Erin Cathcart, Jennifer Lincoln, Lauren Enriquez for technical assistance. This research was funded by Grant Number U01TW008160 from the NIH Fogarty International Center, the NIH Office of Dietary Supplements, the National Science Foundation and the Department of Energy. This project was supported by the USDA Agricultural Food Research Initiative of the National Food and Agriculture, USDA, Grant Number 35621-04750. The content is solely the responsibility of the authors and does not necessarily represent the official views of the Fogarty International Center or the National Institutes of Health, the Office of Dietary Supplements, the National Science Foundation, the Department of Energy, or the Department of Agriculture. This work was supported by the Science Translation and Innovation Research (STAIR) Grant Program of the University of California Davis, and by the Consejo Nacional de Ciencia y Tecnología (CONACYT) Grant Number 291795. Funding by NIH HL113452 and NIH DK097154 (to OF) is greatly appreciated. NIH instrument funding by NIH S10-RR031630 (to OF) is acknowledged. Strains UCDFST 10-421, 10-451, 12-776, 10-1058, 10-1109, 10-453, 11-470 and 10-441 were obtained through a collaboration between UC Davis and the Government of the Republic of Indonesia.Thanks to Sarah Faulina and Sira Silaban for isolating strain Rhodotorula mucilaginosa UCDFST 13-478. All authors have agreed to submit this manuscript to the “Journal of Industrial Microbiology and Biotechnology”.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10295_2016_1765_MOESM1_ESM.pdf (91 kb)
Supplementary material 1 (PDF 90 kb)
10295_2016_1765_MOESM2_ESM.pdf (205 kb)
Supplementary material 2 (PDF 204 kb)

References

  1. 1.
    Ageitos JM, Vallejo JA, Veiga-Crespo P, Villa TG (2011) Oily yeasts as oleaginous cell factories. Appl Microbiol Biotechnol 90:1219–1227CrossRefPubMedGoogle Scholar
  2. 2.
    Aggelis G, Komaitis M (1999) Enhancement of single cell oil production by Yarrowia lipolytica growing in the presence of Teucrium polium L. aqueous extract. Biotechnol Lett 21:747–749CrossRefGoogle Scholar
  3. 3.
    Alper H, Stephanopoulos G (2009) Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential? Nat Rev Microbiol 7:715–723CrossRefPubMedGoogle Scholar
  4. 4.
    Antoni D, Zverlov VV, Schwarz WH (2007) Biofuels from microbes. Appl Microbiol Biotechnol 77:23–35CrossRefPubMedGoogle Scholar
  5. 5.
    Aono R (1990) Taxonomic distribution of alkali-tolerant yeasts. Syst Appl Microbiol 13:394–397CrossRefGoogle Scholar
  6. 6.
    Baffi MA, Tobal T, Henrique J, Lago G, Leite RS, Boscolo M, Gomes E, Da-Silva R (2011) A novel β-glucosidase from Sporidiobolus pararoseus: characterization and application in winemaking. J Food Sci 76:C997–C1002CrossRefPubMedGoogle Scholar
  7. 7.
    Beopoulos A, Mrozova Z, Thevenieau F, Le Dall M-T, Hapala I, Papanikolaou S, Chardot T, Nicaud J-M (2008) Control of lipid accumulation in the yeast Yarrowia lipolytica. Appl Environ Microbiol 74:7779–7789CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Bickel P, Tansey J, Welte M (2009) PAT proteins, an ancient family of lipid droplet proteins that regulate cellular lipid stores. Biochim Biophys Acta (BBA) Mol Cell Biol Lipids 179:419–440CrossRefGoogle Scholar
  9. 9.
    Boundy-Mills K (2008) The phaff yeast culture collection has found its niche. Soc Ind Microbiol News 58:49–56Google Scholar
  10. 10.
    Brennan L, Owende P (2010) Biofuels from microlagae—a review of technologies for production, processing, and extractions of biofuels and co-products. Renew Sustain Energy Rev 14:557–577CrossRefGoogle Scholar
  11. 11.
    Cardenas F, De Castro M, Sanchez-Montero J, Sinisterra J, Valmaseda M, Elson S, Alvarez E (2001) Novel microbial lipases: catalytic activity in reactions in organic media. Enzyme Microbial Technol 28:145–154CrossRefGoogle Scholar
  12. 12.
    Chen Y, Daviet L, Schalk M, Siewers V, Nielsen J (2013) Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism. Metab Eng 15:48–54CrossRefPubMedGoogle Scholar
  13. 13.
    Choi J-H, Ryu Y-W, Seo J-H (2005) Biotechnological production and applications of coenzyme Q10. Appl Microbiol Biotechnol 68:9–15CrossRefPubMedGoogle Scholar
  14. 14.
    Cohen Z, Ratledge C (2005) Single Cell Oils. AOCS Press, ChampaignGoogle Scholar
  15. 15.
    Davis RW, Fishman D, Frank E, Wigmosta M (2012) Renewable diesel from algal lipids: an integrated baseline for cost, emissions, and resource potential from a harmonized model. Technical report ANL.ESD/12-4, NREL/TP-5100-55431, PNNL-21437. US Department of Energy Biomass ProgramGoogle Scholar
  16. 16.
    Garay L, Boundy-Mills K, German J (2014) Accumulation of high value lipids in single cell microorganisms: a mechanistic approach and future perspectives. J Agric Food Chem 62:2709–2727CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Golomb BL, Morales V, Jung A, Yau B, Boundy-Mills KL, Marco ML (2013) Effects of pectinolytic yeast on the microbial composition and spoilage of olive fermentations. Food Microbiol 33:97–106CrossRefPubMedGoogle Scholar
  18. 18.
    Guamán-Burneo C, Carvajal-Barriga J (2009) Caracterización e identificación de aislados de levaduras carotenogénicas de varias zonas naturales del Ecuador. Univ Sci 14:187–197CrossRefGoogle Scholar
  19. 19.
    Hamby KA, Hernández A, Boundy-Mills K, Zalom FG (2012) Associations of yeasts with spotted-wing Drosophila (Drosophila suzukii; Diptera: Drosophilidae) in cherries and raspberries. Appl Environ Microbiol 78:4869–4873CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Hanna M, Isom L, Campbell J (2005) Biodiesel: current perspectives and future. J Sci Ind Res 64:854Google Scholar
  21. 21.
    Huang R, Che H, Zhang J, Yang L, Jiang D, Li G (2012) Evaluation of Sporidiobolus pararoseus strain YCXT3 as biocontrol agent of Botrytis cinerea on post-harvest strawberry fruits. Biol Control 62:53–63CrossRefGoogle Scholar
  22. 22.
    Jacob Z (1993) Yeast lipid biotechnology. Adv Appl Microbiol 39:185CrossRefPubMedGoogle Scholar
  23. 23.
    Janderova B, Gášková D, Bendova O (1995) Consequences of Sporidiobolus pararoseus killer toxin action on sensitive cells. Folia Microbiol 40:165–167CrossRefGoogle Scholar
  24. 24.
    Katre G, Joshi C, Khot M, Zinjarde S, RaviKumar A (2012) Evaluation of single cell oil (SCO) from a tropical marine yeast Yarrowia lipolytica NCIM 3589 as a potential feedstock for biodiesel. AMB Express 2:1–14CrossRefGoogle Scholar
  25. 25.
    Kim JY (2009) Isolation of Sporidiobolus ruineniae CO-3 and characterization of its extracellular protease. J Korean Soc Appl Biol Chem 52:1–10CrossRefGoogle Scholar
  26. 26.
    Kind T, Liu K-H, Lee DY, DeFelice B, Meissen JK, Fiehn O (2013) LipidBlast in silico tandem mass spectrometry database for lipid identification. Nat Methods 10:755–758CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Knothe G (2005) Dependence of biodiesel fuel properties on the structure of fatty acid alkyl esters. Fuel Process Technol 86:1059–1070CrossRefGoogle Scholar
  28. 28.
    Knothe G (2008) “Designer” biodiesel: optimizing fatty ester composition to improve fuel properties. Energy Fuels 22:1358–1364CrossRefGoogle Scholar
  29. 29.
    Kosa M, Ragauskas AJ (2011) Lipids from heterotrophic microbes: advances in metabolism research. Trends Biotechnol 29:53–61CrossRefPubMedGoogle Scholar
  30. 30.
    Kumar S, Kushwaha H, Kumar Bachhawat A, Singh Raghava G, Ganesan K (2012) Genome sequence of the oleaginous red yeast Rhodosporidium toruloides MTCC 457. Eukaryot Cell 11:1083–1084CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Kurtzman C, Fell J, Boekhout T (2011) The yeasts: a taxonomic study, 5th edn. Elsevier, AmsterdamGoogle Scholar
  32. 32.
    Liu H, Zhao X, Wang F, Li Y, Jiang X, Ye M, Zhao ZK, Zou H (2009) Comparative proteomic analysis of Rhodosporidium toruloides during lipid accumulation. Yeast 26:553–566. doi: 10.1002/yea.1706 CrossRefPubMedGoogle Scholar
  33. 33.
    Liu H, Zhao X, Wang F, Jiang X, Zhang S, Ye M, Zhao Z, Zou H (2011) The proteome analysis of oleaginous yeast Lipomyces starkeyi. FEMS Yeast Res 11:42–51. doi: 10.1111/j.1567-1364.2010.00687.x CrossRefPubMedGoogle Scholar
  34. 34.
    Liu L, Redden H, Alper HS (2013) Frontiers of yeast metabolic engineering: diversifying beyond ethanol and Saccharomyces. Curr Opin Biotechnol 24:1023–1030CrossRefPubMedGoogle Scholar
  35. 35.
    Liu Y, Koh CMJ, Sun L, Hlaing MM, Du M, Peng N, Ji L (2013) Characterization of glyceraldehyde-3-phosphate dehydrogenase gene RtGPD1 and development of genetic transformation method by dominant selection in oleaginous yeast Rhodosporidium toruloides. Appl Microbiol Biotechnol 97:719–729CrossRefPubMedGoogle Scholar
  36. 36.
    Lundin H (1950) Fat synthesis by micro-organisms and its possible applications in industry. J Inst Brew 56:17–28CrossRefGoogle Scholar
  37. 37.
    Maharajh D, Roth R, Lalloo R, Simpson C, Mitra R, Görgens J, Ramchuran S (2008) Multi-copy expression and fed-batch production of Rhodotorula araucariae epoxide hydrolase in Yarrowia lipolytica. Appl Microbiol Biotechnol 79:235–244CrossRefPubMedGoogle Scholar
  38. 38.
    McCluskey K, Bates S, Boundy-Mills K, Broggiato A, Cova A, Desmeth P, DebRoy C, Fravel D, Garrity G, del Mar Jiménez Gasco M, Joseph L, Lindner D, Lomas M, Morton J, Nobles D, Turner J, Ward T, Wertz J, Wiest A, Geiser D (2014) Meeting report: 2nd workshop of the united states culture collection network. May 19–21, 2014, State College, PA, USA. Stand Genom Sci 9:27–31Google Scholar
  39. 39.
    McCluskey K, Wiest A, Boundy-Mills K (2014) Chapter 4: Genome data drives change at culture collections. In: Newrousian M (ed) Fungal genomics. Springer, Berlin, pp 81-96CrossRefGoogle Scholar
  40. 40.
    Moreton RS (1988) Physiology of lipid accumulating yeasts. In: Moreton RS (ed) Single Cell Oil. Longman, Harlow, UK, pp 1–32Google Scholar
  41. 41.
    Paddon CJ, Keasling JD (2014) Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 12:355–367CrossRefPubMedGoogle Scholar
  42. 42.
    Papanikolaou S, Aggelis G (2011) Lipids of oleaginous yeasts. Part II: Technology and potential applications. Eur J Lipid Sci Technol 113:1052–1073CrossRefGoogle Scholar
  43. 43.
    Patel A, Pravez M, Deeba F, Pruthi V, Singh RP, Pruthi PA (2014) Boosting accumulation of neutral lipids in Rhodosporidium kratochvilovae HIMPA1 grown on hemp (Cannabis sativa Linn) seed aqueous extract as feedstock for biodiesel production. Bioresour Technol 165:214–222CrossRefPubMedGoogle Scholar
  44. 44.
    Pereyra V, Martinez A, Rufo C, Vero S (2014) Oleaginous yeasts form Uruguay and Antarctica as renewable raw material for biodiesel production. Am J of Biosci 2:251–257CrossRefGoogle Scholar
  45. 45.
    Pfaller R, Leonhartsberger S (2004) Process for producing Sporidiobolus ruineniae strains with improved coenzyme Q10 production. Google PatentsGoogle Scholar
  46. 46.
    Qi F, Kitahara Y, Wang Z, Zhao X, Du W, Liu D (2013) Novel mutant strains of Rhodosporidium toruloides by plasma mutagenesis approach and their tolerance for inhibitors in lignocellulosic hydrolyzate. J Chem Technol Biotechnol 89:735–742CrossRefGoogle Scholar
  47. 47.
    Ratledge C (1987) Lipid biotechnology: a wonderland for the microbial physiologist. J Am Oil Chem Soc 64:1647–1656CrossRefGoogle Scholar
  48. 48.
    Ratledge C (1988) Yeasts for lipid production. Biochem Soc Trans 16:1088CrossRefPubMedGoogle Scholar
  49. 49.
    Ratledge C (1993) Single cell oils—have they a biotechnological future? Trends Biotechnol 11:278–284CrossRefPubMedGoogle Scholar
  50. 50.
    Ratledge C (2002) Regulation of lipid accumulation in oleaginous micro-organisms. Biochem Soc Trans 30:1047–1050CrossRefPubMedGoogle Scholar
  51. 51.
    Ratledge C, Wilkinson SG (1988) Microbial lipids, vol 1. Academic Press, LondonGoogle Scholar
  52. 52.
    Rattray J, Scheibeci A, Kidby D (1975) Lipids of yeasts. Bacteriol Rev 39:197–231PubMedPubMedCentralGoogle Scholar
  53. 53.
    Schulze I, Hansen S, Großhans S, Rudszuck T, Ochsenreither K, Syldatk C, Neumann A (2014) Characterization of newly isolated oleaginous yeasts—Cryptococcus podzolicus, Trichosporon porosum and Pichia segobiensis. AMB Express 4:1–11CrossRefGoogle Scholar
  54. 54.
    Schweizer M (2004) Lipids and membranes. The metabolism and molecular physiology of Saccharomyces cerevisiae. CRC Press, London, pp 140–223Google Scholar
  55. 55.
    Sitepu I, Ignatia L, Franz A, Wong D, Faulina S, Tsui M, Kanti A, Boundy-Mills K (2012) An improved high-throughput Nile red fluorescence assay for estimating intracellular lipids in a variety of yeast species. J Microbiol Methods 91:321–328CrossRefPubMedPubMedCentralGoogle Scholar
  56. 56.
    Sitepu IR, Sestric R, Ignatia L, Levin D, Bruce German J, Gillies LA, Almada LA, Boundy-Mills KL (2013) Manipulation of culture conditions alters lipid content and fatty acid profiles of a wide variety of known and new oleaginous yeasts species. Bioresour Technol 144:360–369CrossRefPubMedGoogle Scholar
  57. 57.
    Sitepu I, Garay L, Sestric R, Levin D, Block DE, German J, Boundy-Mills K (2014) Oleaginous yeasts for biodiesel: current and future trends in biology and production. J Biotechnol Adv 32:1336–1360. doi: 10.1016/j.biotechadv.2014.08.003 CrossRefGoogle Scholar
  58. 58.
    Sitepu I, Jin M, Fernandez J, Sousa L, Balan V, Boundy-Mills K (2014) Identification of oleaginous yeast strains able to accumulate high intracellular lipids when cultivated in alkaline pretreated corn stover. Appl Microbiol Biotechnol 98:7645–7657CrossRefPubMedPubMedCentralGoogle Scholar
  59. 59.
    Sitepu I, Selby T, Zhu S, Lin T, Boundy-Mills K (2014) Carbon source utilization and inhibitor tolerance of 45 oleaginous yeast species. J Ind Microbiol Biotechnol 41:1061–1070. doi: 10.1007/s10295-014-1447-y CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Sitepu I, Shi S, Simmons BA, Singer S, Boundy-Mills K, Simmons C (2014) Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate. FEMS Yeast Res 14:1286–1294CrossRefPubMedGoogle Scholar
  61. 61.
    Steen E, Kang Y, Bokinsky G, Hu Z, Schirmer A, McClure A, del Cardayre S, Keasling J (2010) Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463:559–562CrossRefPubMedGoogle Scholar
  62. 62.
    Sugiyama J, Fukagawa M, Chiu S-W, Komagata K (1985) Cellular carbohydrate composition, DNA base composition, ubiquinone systems, and Diazonium Blue B color test in the genera Rhodosporidium, Leucosporidium, Rhodotorula and related basidiomycetous yeasts. J Gen Appl Microbiol 31:519–550CrossRefGoogle Scholar
  63. 63.
    Suutari M, Priha P, Laakso S (1993) Temperature shifts in regulation of lipids accumulated by Lipomyces starkeyi. J Am Oil Chem Soc 70:891–894CrossRefGoogle Scholar
  64. 64.
    Turcotte G, Kosaric N (1988) Biosynthesis of lipids by Rhodosporidium toruloides ATCC 10788. J Biotechnol 8:221–237CrossRefGoogle Scholar
  65. 65.
    Valduga E, Ribeiro AHR, Cence K, Colet R, Tiggemann L, Zeni J, Toniazzo G (2014) Carotenoids production from a newly isolated Sporidiobolus pararoseus strain using agroindustrial substrates. Biocatal Agric Biotechnol 3:207–213Google Scholar
  66. 66.
    Wang C, Leger R (2007) The Metarhizium anisopliae perilipin homolog MPL1 regulates lipid metabolism, appressorial turgor pressure, and virulence. J Biol Chem 282:21110–21115CrossRefPubMedGoogle Scholar
  67. 67.
    Woodbine M (1959) Microbial fat: micro-organisms as potential fat producers. In: Hockenhull (ed) Progress in Industrial Microbiology, vol 1. Elsevier, London, UK, pp 181–245Google Scholar
  68. 68.
    Zhao X, Kong X, Hua Y, Feng N, Zhao Z (2008) Medium optimization for lipid production through co-fermentation of glucose and xylose by the oleaginous yeast Lipomyces starkeyi. Eur J Lipid Sci Technol 110:405–412CrossRefGoogle Scholar
  69. 69.
    Zhu Z, Zhang S, Liu H, Shen H, Lin X, Yang F, Zhou YJ, Jin G, Ye M, Zou H (2012) A multi-omic map of the lipid-producing yeast Rhodosporidium toruloides. Nat Commun 3:1112CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Society for Industrial Microbiology and Biotechnology 2016

Authors and Affiliations

  • Luis A. Garay
    • 1
  • Irnayuli R. Sitepu
    • 1
    • 2
  • Tomas Cajka
    • 3
  • Idelia Chandra
    • 1
  • Sandy Shi
    • 1
  • Ting Lin
    • 1
  • J. Bruce German
    • 4
  • Oliver Fiehn
    • 3
    • 5
  • Kyria L. Boundy-Mills
    • 1
  1. 1.Phaff Yeast Culture Collection, Department of Food Science and TechnologyUniversity of CaliforniaDavisUSA
  2. 2.Bioentrepreneurship DepartmentIndonesia International Institute for Life SciencesEast JakartaIndonesia
  3. 3.Metabolomics, UC Davis Genome CenterUniversity of California DavisDavisUSA
  4. 4.Department of Food Science and TechnologyUniversity of CaliforniaDavisUSA
  5. 5.Biochemistry Department, Faculty of ScienceKing Abdulaziz UniversityJeddahSaudi Arabia

Personalised recommendations