Yarrowia lipolytica: A Beneficial Yeast as a Biofactory for Biotechnological Applications

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 21482

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Guest Editor
Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, Warsaw, Poland
Interests: lipase-catalyzed ester synthesis; lipophilization; enzymatic (trans)esterification; whole-cell modification of phenolic compounds; microbiology; yarrowia lipolytica; lipases biosynthesis; antimicrobial and antioxidant activities of phenolic compounds; microbial enzymes
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Guest Editor
Department of Food Engineering and Process Management, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-776 Warsaw, Poland
Interests: drying; especially freeze-drying; chemical and physical changes of dried material during storage; food texture; biotechnological processes in bioreactors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Yeasts were used for fermentation processes long before their various properties were discovered and described. Among at least 1500 recognized yeast species, in addition to the most well-known baker’s yeasts, e.g., Saccharomyces cerevisiae, other yeasts also stand out, often characterized by unique features and capabilities.

Yarrowia lipolytica is one of the most studied “non-conventional” yeast species. A high secretory capacity and the capability of biosynthesis of many important secondary metabolites affect the growing scientific interest and biotechnological importance of this yeast. Y. lipolytica is considered non-pathogenic, and additionally, some commercial-scale processes with its participation have been granted GRAS (generally recognized as safe) status by the US Food and Drug Administration (FDA). The major advantages of using Y. lipolytica are its ability to grow and consumption of a wide range of substrates, such as alkanes, fatty acids, fats, and oils, as well as some waste substrates, namely, crude glycerol, waste cooking oils, sewage sludge, or olive mill wastewater, with simultaneous biosynthesis of varied metabolites.

This Special Issue will compile the current state-of-the-art research on Y. lipolytica and shed light on current research directions with the use of this yeast. Potential topics include but are not limited to:

  • Metabolic engineering of Y. lipolytica;
  • Biosynthesis of secondary metabolites, namely, enzymes, e.g., lipases or proteases, as well as organic acids, sugar alcohols, flavors, and aromas;
  • Whole-cell catalysis;
  • Lipid biosynthesis and accumulation;
  • Utilization of agri-food waste.

Dr. Bartłomiej Zieniuk
Dr. Dorota Nowak
Guest Editors

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Keywords

  • Yarrowia lipolytica
  • secondary metabolites
  • single-cell oils (SCO)
  • lipid accumulation
  • single-cell proteins (SCP)
  • enzymes biosynthesis
  • lipases production
  • metabolic engineering
  • organic acids synthesis
  • agri-food waste upgradation
  • whole-cell catalysis
  • biosynthesis of metal nanoparticles
  • bioreactor processes

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Published Papers (10 papers)

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Research

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14 pages, 3850 KiB  
Article
Effect of Elevated Oxygen Concentration on the Yeast Yarrowia lipolytica for the Production of γ-Decalactones in Solid State Fermentation
by Sophal Try, Andrée Voilley, Thavarith Chunhieng, Joëlle De-Coninck and Yves Waché
Fermentation 2023, 9(6), 532; https://doi.org/10.3390/fermentation9060532 - 30 May 2023
Cited by 1 | Viewed by 1369
Abstract
To study the effect of elevated oxygen concentrations on β-oxidation for the production of lactones by Yarrowia lipolytica W29 in solid state fermentation (SSF), experiments using oxygen-enriched air, with different initial concentrations of oxygen ratio, were carried out. Growth kinetics using an oxygen [...] Read more.
To study the effect of elevated oxygen concentrations on β-oxidation for the production of lactones by Yarrowia lipolytica W29 in solid state fermentation (SSF), experiments using oxygen-enriched air, with different initial concentrations of oxygen ratio, were carried out. Growth kinetics using an oxygen ratio of 30% reached the stationary phase earlier than other conditions used. In addition, the production of γ-decalactone and 3-hydroxy-γ-decalactone reached the maximal concentrations of 270 mg L−1 and 1190 mg L−1, respectively. Using higher initial oxygen ratios (40% and 50%), an incomplete growth inhibition occurred and resulted in a higher concentration of yeast at the stationary phase and a slightly higher 3-hydroxy-γ-decalactone accumulation. When oxygen-enriched air (oxygen ratio of 30%) was injected twice (at 0 and 20 h), 3-hydroxy-γ-decalactone reached a higher concentration (1620 mg L−1) and it reached a very high concentration of 4600 mg L−1 in the condition of oxygen-enriched air injected many times (at 0, 20, 35, 48 and 60 h). This study suggested that oxygen is required for the production of 3-hydroxy-γ-decalactone in SSF. Oxygen may be consumed preferentially for long-chain fatty acid oxidations rather than at C10-level. Furthermore, the production of γ-decalactone may be improved by optimizing the growth conditions to reach a very high specific growth rate. A low oxygen availability in the system at the stationary growth phase led to an inhibition of γ-decalactone degradation. From the present work, an alternative system is proposed as a novel model to study the effect of elevated oxygen concentration in SSF. Full article
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13 pages, 5580 KiB  
Article
Discovery and Functional Evaluation of Heat Tolerance Genes in the Nonconventional Yeast Yarrowia lipolytica
by Mengchan Liu and Hairong Cheng
Fermentation 2023, 9(6), 509; https://doi.org/10.3390/fermentation9060509 - 25 May 2023
Cited by 1 | Viewed by 1215
Abstract
Yarrowia lipolytica, a GRAS (generally recognized as safe) nonconventional yeast, has been used widely in industrial fermentation to produce chemicals, fuels, and functional sugars such as erythritol and mannitol. Although Y. lipolytica is a promising organism for bioconversion and has substantial potential [...] Read more.
Yarrowia lipolytica, a GRAS (generally recognized as safe) nonconventional yeast, has been used widely in industrial fermentation to produce chemicals, fuels, and functional sugars such as erythritol and mannitol. Although Y. lipolytica is a promising organism for bioconversion and has substantial potential in industrial production, its utilization is restricted by the high cost of cooling during the fermentation process; the optimum growth or fermentation temperature of Y. lipolytica is 28–30 °C, which is lower than that of some fermenting species. Therefore, it is necessary to breed a thermoresistant Y. lipolytica for use in a fermentation system. Here, we report a new thermoduric Y. lipolytica strain (a thermoresistant clone, HRC) that can grow at 35 °C—higher than the starting strain Y. lipolytica CGMCC7326 (maximum growth temperature at 33 °C)—by laboratory adaptive evolution. Based on the transcriptome analysis of the mutant strain HRC and the parental strain Y. lipolytica CGMCC7326 at different temperatures, 22 genes with increased expression at high temperatures were identified and 10 of them were overexpressed in Y. lipolytica CGMCC7326. HRC1, HRC2, and HRC3 (with YALI0B21582g, YALI0C13750g, and YALI0B10626g overexpressed, respectively) were assessed for growth at higher temperatures. This revealed that these three genes were related to thermotolerance. This study provides insights into the metabolic landscape of Y. lipolytica under heat stress, enabling future metabolic engineering endeavors to improve both thermoresistance and sugar alcohol production in the yeast Y. lipolytica. Full article
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12 pages, 3149 KiB  
Article
Homologous High-Level Lipase and Single-Cell Protein Production with Engineered Yarrowia lipolytica via Scale-Up Fermentation for Industrial Applications
by Dujie Pan, Shuhan Dai, Liangcheng Jiao, Qinghua Zhou, Genhan Zha, Jinyong Yan, Bingnan Han, Yunjun Yan and Li Xu
Fermentation 2023, 9(3), 268; https://doi.org/10.3390/fermentation9030268 - 9 Mar 2023
Cited by 2 | Viewed by 2004
Abstract
Yarrowia lipolytica is a promising feed additives. Here, we aimed to produce extracellular lipases and single-cell proteins (SCPs) at high levels simultaneously through fed-batch fermentation of engineered Y. lipolytica. The parameters for 500 mL shake flask cultures were optimized with a single [...] Read more.
Yarrowia lipolytica is a promising feed additives. Here, we aimed to produce extracellular lipases and single-cell proteins (SCPs) at high levels simultaneously through fed-batch fermentation of engineered Y. lipolytica. The parameters for 500 mL shake flask cultures were optimized with a single factorial design. The resultant activity of lipase reached 880.6 U/mL after 84 h of fermentation, and 32.0 g/L fermentation broth of dry SCP was obtained at 120 h. To attain high SCP and lipase productivity, the high-density fed-batch fermentation of Y. lipolytica was scaled up in 10 L, 30 L, and 100 L fermentors. Using glycerol as the sole carbon source, the lipase activity peaked to 8083.3 U/mL, and the final dry SCP weight was 183.1 g/L at 94.6 h in 10 L fermentors. The extracellular lipase activity and SCP weight reached 11,100.0 U/mL and 173.3 g of dry SCP/L at 136 h in 30 L fermentors, respectively. Following 136 h of fed-batch fermentation, the extracellular lipase activity and dry SCP weight reached 8532.0 U/mL and 170.3 g/L in 100 L fermentors, respectively. A balance between the lipase secretion and growth of Y. lipolytica recombinant strain was achieved, indicating that an efficient fermentation strategy could promote further scale-up for industrial SCP production from engineered Y. lipolytica. Full article
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18 pages, 2764 KiB  
Article
Dynamic Interplay between O2 Availability, Growth Rates, and the Transcriptome of Yarrowia lipolytica
by Abraham A. J. Kerssemakers, Süleyman Øzmerih, Gürkan Sin and Suresh Sudarsan
Fermentation 2023, 9(1), 74; https://doi.org/10.3390/fermentation9010074 - 16 Jan 2023
Viewed by 2478
Abstract
Industrial-sized fermenters differ from the laboratory environment in which bioprocess development initially took place. One of the issues that can lead to reduced productivity on a large scale or even early termination of the process is the presence of bioreactor heterogeneities. This work [...] Read more.
Industrial-sized fermenters differ from the laboratory environment in which bioprocess development initially took place. One of the issues that can lead to reduced productivity on a large scale or even early termination of the process is the presence of bioreactor heterogeneities. This work proposes and adopts a design–build–test–learn-type workflow that estimates the substrate, oxygen, and resulting growth heterogeneities through a compartmental modelling approach and maps Yarrowia lipolytica-specific behavior in this relevant range of conditions. The results indicate that at a growth rate of 0.1 h−1, the largest simulated volume (90 m3) reached partial oxygen limitation. Throughout the fed-batch, the cells experienced dissolved oxygen values from 0 to 75% and grew at rates of 0 to 0.2 h−1. These simulated large-scale conditions were tested in small-scale cultivations, which elucidated a transcriptome with a strong downregulation of various transporter and central carbon metabolism genes during oxygen limitation. The relation between oxygen availability and differential gene expression was dynamic and did not show a simple on–off behavior. This indicates that Y. lipolytica can differentiate between different available oxygen concentrations and adjust its transcription accordingly. The workflow presented can be used for Y. lipolytica-based strain engineering, thereby accelerating bioprocess development. Full article
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18 pages, 4530 KiB  
Article
Selection of Yarrowia lipolytica Strains as Possible Solution to Valorize Untreated Cheese Whey
by Davide Gottardi, Lorenzo Siroli, Giacomo Braschi, Samantha Rossi, Narinder Bains, Lucia Vannini, Francesca Patrignani and Rosalba Lanciotti
Fermentation 2023, 9(1), 51; https://doi.org/10.3390/fermentation9010051 - 7 Jan 2023
Cited by 3 | Viewed by 2140
Abstract
Cheese whey management and disposal is a major issue for dairy industries due to its high level of chemical and biochemical oxygen demand. However, it can still represent a source of nutrients (i.e., sugars, proteins and lipids) that can be applied, among other [...] Read more.
Cheese whey management and disposal is a major issue for dairy industries due to its high level of chemical and biochemical oxygen demand. However, it can still represent a source of nutrients (i.e., sugars, proteins and lipids) that can be applied, among other options, as substrate for microbial growth. Yarrowia lipolytica can grow in different environments, consuming both hydrophilic and hydrophobic substrates, and tolerates high salt concentrations. In this work, the lipolytic and proteolytic profile of 20 strains of Y. lipolytica were tested on caseins and butter. Then, their growth potential was evaluated in four types of whey (caciotta, ricotta, squacquerone and their mix). Y. lipolytica showed a very strain-dependent behavior for both hydrolytic profiles and growth capabilities on the different substrates. The best growers for all the types of whey tested were PO1, PO2, and RO2, with the first one reaching up to 8.77 log cfu/mL in caciotta whey after 72 h. The volatile molecule profile of the samples incubated with the best growers were characterized by higher amounts of esters, acids, ketones and alcohols. In this way, cheese whey can become a source of microbial cultures exploitable in the dairy sector. Full article
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14 pages, 3787 KiB  
Article
Biosurfactant Production from the Biodegradation of n-Paraffins, Isoprenoids and Aromatic Hydrocarbons from Crude Petroleum by Yarrowia lipolytica IMUFRJ 50682
by Tatiana Felix Ferreira, Fernanda Faria Martins, Caroline Alves Cayres, Priscilla F. F. Amaral, Débora de Almeida Azevedo and Maria Alice Zarur Coelho
Fermentation 2023, 9(1), 21; https://doi.org/10.3390/fermentation9010021 - 26 Dec 2022
Cited by 5 | Viewed by 2063
Abstract
Yarrowia lipolytica is a unique, strictly aerobic yeast with the ability to degrade efficiently hydrophobic substrates. In the present work, we evaluated the degrading potential of Yarrowia lipolytica IMUFRJ 50682, isolated from tropical estuarine water in Rio de Janeiro (Brazil), and the possible [...] Read more.
Yarrowia lipolytica is a unique, strictly aerobic yeast with the ability to degrade efficiently hydrophobic substrates. In the present work, we evaluated the degrading potential of Yarrowia lipolytica IMUFRJ 50682, isolated from tropical estuarine water in Rio de Janeiro (Brazil), and the possible biomolecules produced during this process. To investigate which crude oil compounds are degraded by Y. lipolytica IMUFRJ 50682, this microorganism was grown in a medium containing Marlim petroleum (19 °API, American Petroleum Institute gravity) at 28 °C and 160 rpm for 5 days. The residual petroleum was submitted to gas chromatograph-mass spectrometric analysis (GC-MS). The chromatographic fingerprints of the residual petroleum were compared with the abiotic control test incubated in the same conditions. Y. lipolytica assimilates high molecular weight hydrocarbons, such as n-alkanes (C11-C19), isoprenoids (pristane and phytane), aromatics with two or three aromatics rings (naphthalene, methylnaphthalenes, dimethylnaphthalenes, trimethylnaphthalenes, phenanthrene, methylphenanthrenes, dimethylphenanthrenes, anthracene). This strain was also capable of consuming more complex hydrocarbons, such as tricyclic terpanes. During this biodegradation, the emulsification index of the culture medium increased significantly, showing that biosurfactant molecules can be produced from this process. Therefore, Y. lipolytica IMUFRJ 50682 showed to be a potential crude oil degrading yeast, which can be used for bioremediation processes and simultaneously produce bioproducts of commercial interest. Full article
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11 pages, 1041 KiB  
Article
Citric Acid Production by Yarrowia lipolytica NRRL Y-1094: Optimization of pH, Fermentation Time and Glucose Concentration Using Response Surface Methodology
by Bilge Sayın Börekçi, Mükerrem Kaya and Güzin Kaban
Fermentation 2022, 8(12), 731; https://doi.org/10.3390/fermentation8120731 - 12 Dec 2022
Cited by 3 | Viewed by 1661
Abstract
In this study, three Yarrowia lipolytica strains (Y. lipolytica NRRL Y-1094, Y. lipolytica NRRL YB-423 and Y. lipolytica IFP29) were screened for acid-production capacity and the maximum zone-area was formed by Y. lipolytica NRRL Y-1094. The strain was then selected as a [...] Read more.
In this study, three Yarrowia lipolytica strains (Y. lipolytica NRRL Y-1094, Y. lipolytica NRRL YB-423 and Y. lipolytica IFP29) were screened for acid-production capacity and the maximum zone-area was formed by Y. lipolytica NRRL Y-1094. The strain was then selected as a potential citric-acid (CA) producer for further studies. The CA production by Y. lipolytica NRRL Y-1094 was optimized using response surface methodology (RSM) and considering three factors, comprising initial pH-value, fermentation time, and initial glucose-concentration. The highest CA-concentration was 30.31 g/L under optimum conditions (pH 5.5, 6 days, and 125 g/L glucose) in shake flasks. It has been reported that this result gives better results than many productions with shake flasks. According to estimated regression-coefficients for CA concentration, the fermentation time had the greatest impact on CA production, followed by the substrate concentration and initial pH-level, respectively. On the other hand, this study is a fundamental step in solving and optimizing the production mechanism of Y. lipolytica NRRL Y-1094, a microorganism that has not yet been used in CA production with a glucose-based medium. The results suggest that future studies can perform higher yields by optimizing other medium constituents and environmental factors. Full article
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10 pages, 941 KiB  
Article
Use of Pressurized and Airlift Bioreactors for Citric Acid Production by Yarrowia lipolytica from Crude Glycerol
by Patrícia Ferreira, Marlene Lopes and Isabel Belo
Fermentation 2022, 8(12), 700; https://doi.org/10.3390/fermentation8120700 - 2 Dec 2022
Cited by 5 | Viewed by 2493
Abstract
Citric acid production is generally carried out in an aqueous medium in stirred tank reactors (STR), where the solubility of oxygen is low and the oxygen demand of microbial cultures is high. Thus, for this bioprocess, providing adequate oxygen mass transfer rate (OTR) [...] Read more.
Citric acid production is generally carried out in an aqueous medium in stirred tank reactors (STR), where the solubility of oxygen is low and the oxygen demand of microbial cultures is high. Thus, for this bioprocess, providing adequate oxygen mass transfer rate (OTR) from the gas phase into the aqueous culture medium is the main challenge of bioreactor selection and operation. In this study, citric acid production by Yarrowia lipolytica W29 from crude glycerol, in batch cultures, was performed in two non-conventional bioreactors normally associated with high mass transfer efficiency: a pressurized STR and an airlift bioreactor. Increased OTR was obtained by raising the total air pressure in the pressurized STR and by increasing the aeration rate in the airlift bioreactor. An improvement of 40% in maximum citric acid titer was obtained by raising the air pressure from 1 bar to 2 bar, whereas, in the airlift bioreactor, a 30% improvement was attained by increasing the aeration rate from 1 vvm to 1.5 vvm. Both bioreactor types can be successfully applied for the citric acid production process using alternative ways of improving OTR than increasing mechanical stirring power input, thus leading to important operating saving costs. Full article
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13 pages, 1991 KiB  
Article
Simultaneous Production and Immobilization of Lipase Using Pomegranate-Seed Residue: A New Biocatalyst for Hydrolysis Reactions and Structured Lipids Synthesis
by Marianne M. Diniz, Adejanildo da S. Pereira, Gabriel Albagli and Priscilla F. F. Amaral
Fermentation 2022, 8(11), 651; https://doi.org/10.3390/fermentation8110651 - 18 Nov 2022
Viewed by 1375
Abstract
Pomegranate-seed residue (PSR) was used in a new strategy for the simultaneous production of Yarrowia lipolytica lipase by submerged fermentation and its immobilization by adsorption. This biocatalyst—the fermented solid residue containing the adsorbed lipase (fermPSR)—was evaluated in hydrolysis reactions and in structured lipid [...] Read more.
Pomegranate-seed residue (PSR) was used in a new strategy for the simultaneous production of Yarrowia lipolytica lipase by submerged fermentation and its immobilization by adsorption. This biocatalyst—the fermented solid residue containing the adsorbed lipase (fermPSR)—was evaluated in hydrolysis reactions and in structured lipid synthesis. In shake flasks, yeast extract and urea were the best nitrogen sources for lipase production with PSR and their simultaneous use increased the lipase production even further. This result was confirmed in a 3.5-liter bioreactor, with lipase activity in an extracellular medium of 40 U/mL. A maximum reaction rate (Vmax) of 49.5 µmol/min/g, a Michaelis–Menten constant (Km) of 207 µmol/L, and a turnover number (Kcat) of 130 s−1 were determined for the new biocatalyst, fermPSR, for the hydrolysis of p-nitrophenyl laurate (p-NPL) into p-nitrophenol. The conversion of p-NPL into p-nitrophenol in subsequent reactions confirmed fermPSR’s potential for industrial hydrolytic reactions. The production of structured lipids from vegetable oil and free fatty acids by fermPSR evidences the versatility of this new biocatalyst. Full article
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Review

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37 pages, 7084 KiB  
Review
Lipase from Yarrowia lipolytica: Prospects as an Industrial Biocatalyst for Biotechnological Applications
by Jessica Lopes da Silva, Misael Bessa Sales, Viviane de Castro Bizerra, Millena Mara Rabelo Nobre, Ana Kátia de Sousa Braz, Patrick da Silva Sousa, Antônio L. G. Cavalcante, Rafael L. F. Melo, Paulo Gonçalves De Sousa Junior, Francisco S. Neto, Aluísio Marques da Fonseca and José Cleiton Sousa dos Santos
Fermentation 2023, 9(7), 581; https://doi.org/10.3390/fermentation9070581 - 21 Jun 2023
Cited by 12 | Viewed by 2747
Abstract
This paper aims to present the advances related to the biotechnological application of lipases Y. lipolytica, presenting their properties and more efficient ways to use them in different industrial applications. Waste treatment and bioremediation highlight recent studies and advances and the interest [...] Read more.
This paper aims to present the advances related to the biotechnological application of lipases Y. lipolytica, presenting their properties and more efficient ways to use them in different industrial applications. Waste treatment and bioremediation highlight recent studies and advances and the interest in large-scale applications in the food sector and biofuel production. The USA and China, two major world powers in industy, are of utmost importance in the search for the improvement in the development and properties of a controlled system for the large-scale production of a significant number of applications of lipase from Y. lipolytica. Full article
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