Morphology and rheological behaviour of Yarrowia lipolytica: Impact of dissolved oxygen level on cell growth and lipid composition

Enhancement of lipid synthesis by the transcription factor Asg1 in Saitozyma podzolica zwy-2-3 under dissolved oxygen stress

Microbial oils have been of considerable interest as food additives and biofuel resources due to high lipid contents, but lipid accumulation of oleaginous microorganisms can be induced by environmental stresses, such as dissolved oxygen (DO), which limit large-scale lipid production. Here, DO stress gave rise to the endogenous nitric oxide (NO) level to mediate S-nitrosylation of SpAsg1, regulating the lipid accumulation in Saitozyma podzolica zwy-2-3. Notably, qRT-PCR, yeast one-hybrid, dual-luciferase reporter assays, and metabolomics analysis exhibited that overexpression of SpAsg1 promoted lipid synthesis by directly regulation of glucose metabolism, enhancing glucose uptake, ATP and NADPH contents under DO stress. Meanwhile, SpAsg1 improved the antioxidant capacity to reduce the intracellular reactive oxygen species (ROS) and NO levels. Overall, we systematically investigated the regulation of SpAsg1 on lipid metabolism of S. podzolica zwy-2-3 under DO stress, which sheds light on further studies for alleviating oxygen limitation of lipid production in microbial industry.

Molecular characterization and expression profiling of two flavohemoglobin genes play essential roles in dissolved oxygen and NO stress in Saitozyma podzolica zwy2-3

Flavohemoglobins (Fhbs) are key enzymes involved in microbial nitrosative stress resistance and nitric oxide degradation. However, the roles of Fhbs in fungi remain largely unknown. In this study, SpFhb1 and SpFhb2, two flavohemoglobin-encoding genes in Saitozyma podzolica zwy2-3 were characterized. Protein structure analysis and molecular docking showed that SpFhbs were conserved in bacteria and fungi. Phylogenetic analysis revealed that SpFhb2 may be acquired through the transfer event of independent horizontal genes from bacteria. The expression levels of SpFhb1 and SpFhb2 showed opposite trend under high/low dissolved oxygen, implying that they may exhibited different functions. Through deletion and overexpression of SpFhbs, we confirmed that SpFhbs were conducive to lipid accumulation under high stress. The sensitivities of ΔFhb mutants to NO stress were significantly increased compared with that in the WT, indicating that they were required for NO detoxification and nitrosative stress resistance in S. podzolica zwy2-3. Furthermore, SpAsg1 was identified that simultaneously regulates SpFhbs, which functions in the lipid accumulation under high/low dissolved oxygen and NO stress in S. podzolica zwy2-3. Overall, two different SpFhbs were identified in this study, providing new insights into the mechanism of lipid accumulation in fungi under high/low dissolved oxygen and NO stress.

Yarrowia lipolytica produces lipid-rich biomass in medium mimicking lignocellulosic biomass hydrolysate

In recent years, lignocellulosic biomass has become an attractive low-cost raw material for microbial bioprocesses aiming the production of biofuels and other valuable chemicals. However, these feedstocks require preliminary pretreatments to increase their utilization by microorganisms, which may lead to the formation of various compounds (acetic acid, formic acid, furfural, 5-hydroxymethylfurfural, p-coumaric acid, vanillin, or benzoic acid) with antimicrobial activity. Batch cultures in microplate wells demonstrated the ability of Yarrowia strains (three of Y. lipolytica and one of Y. divulgata) to grow in media containing each one of these compounds. Cellular growth of Yarrowia lipolytica W29 and NCYC 2904 (chosen strains) was proven in Erlenmeyer flasks and bioreactor experiments where an accumulation of intracellular lipids was also observed in culture medium mimicking lignocellulosic biomass hydrolysate containing glucose, xylose, acetic acid, formic acid, furfural, and 5-HMF. Lipid contents of 35% (w/w) and 42% (w/w) were obtained in bioreactor batch cultures with Y. lipolytica W29 and NCYC 2904, respectively, showing the potential of this oleaginous yeast to use lignocellulosic biomass hydrolysates as feedstock for obtaining valuable compounds, such as microbial lipids that have many industrial applications. KEY POINTS: • Yarrowia strains tolerate compounds found in lignocellulosic biomass hydrolysate • Y. lipolytica consumed compounds found in lignocellulosic biomass hydrolysate • 42% (w/w) of microbial lipids was attained in bioreactor batch cultures.

Isopropanol biosynthesis from crude glycerol using fatty acid precursors via engineered oleaginous yeast Yarrowia lipolytica

Background

Isopropanol is widely used as a biofuel and a disinfectant. Chemical preparation of isopropanol destroys the environment, which makes biological preparation of isopropanol necessary. Previous studies focused on the use of expensive glucose as raw material. Therefore, the microbial cell factory that ferments isopropanol with cheap raw materials will provide a greener way to produce isopropanol.

Results

This study converted crude glycerol into isopropanol using Y. lipolytica. As a microbial factory, the active natural lipid and fatty acid synthesis pathway endows Y. lipolytica with high malonyl-CoA production capacity. Acetoacetyl-CoA synthase (nphT7) and isopropanol synthesis genes are integrated into the Y. lipolytica genome. The nphT7 gene uses the accumulated malonyl-CoA to synthesize acetoacetyl-CoA, which increases isopropanol production. After medium optimization, the best glycerol medium was found and resulted in a 4.47-fold increase in isopropanol production. Fermenter cultivation with pure glycerol medium resulted in a maximum isopropanol production of 1.94 g/L. In a crude glycerol fermenter, 1.60 g/L isopropanol was obtained, 82.53% of that achieved with pure glycerol. The engineered Y. lipolytica in this study has the highest isopropanol titer reported.

Conclusions

The engineered Y. lipolytica successfully produced isopropanol by using crude glycerol as a cheap carbon source. This is the first study demonstrating the use of Y. lipolytica as a cell factory to produce isopropanol. In addition, this is also a new attempt to accumulate lipid synthesis precursors to synthesize other useful chemicals by integrating exogenous genes in Y. lipolytica.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01890-6.

Enhancing Red Yeast Biomass Yield and Lipid Biosynthesis by Using Waste Nitrogen Source by Glucose Fed-Batch at Low Temperature

This work reports the effect of simple feeding strategies and temperature to obtain high-cell-density cultures of Rhodotorula glutinis var. rubescens LOCKR13 maximizing the de novo lipid productivity using deproteinated potato wastewater (DPW) as a basic medium. Feeding DPW with glucose enables a high yield of Rhodotorula glutinis var. rubescens LOCKR13 biomass (52 g d.w. L−1) to be obtained. The highest values of lipid accumulation (34.15%, w/w), production (14.68 g L−1) and yield coefficients (YL/S: 0.242 g g−1), and volumetric productivity (PL: 0.1 g L−1 h−1) were reached by the strain in the two-stage fed-batch process at 20 °C. The lipid of yeast biomass was rich in oleic acid (Δ9C18:1) and palmitic acid (C16:0), and the lower temperature of incubation significantly increased the MUFA (especially oleic acid) content. For the first time, a unique set of thermal analyses of the microbial oil was performed. The isotherms of the oxidation kinetics (PDSC) showed that lipids extracted from the biomass of red yeast had high oxidative stability. This feature of the yeast oil can be useful for long-shelf-life food products and can be promising for the production of biodiesel.

Green route for recycling of low-cost waste resources for the biosynthesis of nanoparticles (NPs) and nanomaterials (NMs)-A review

Nowadays, nanoparticles (NPs) and nanomaterials (NMs) are used extensively in various streams such as medical science, solar energy, drug delivery, water treatment, and detection of persistent pollutants. Intensive synthesis of NPs/NMs carried out via physico-chemical technologies is deteriorating the environment globally. Therefore, an urgent need to adopt cost-effective and green technologies to synthesize NPs/NMs by recycling of secondary waste resources is highly required. Environmental wastes such as metallurgical slag, electronics (e-waste), and acid mine drainage (AMD) are rich sources of metals to produce NPs. This concept can remediate the environment on the one hand and the other hand, it can provide a future roadmap for economic benefits at industrial scale operations. The waste-derived NPs will reduce the industrial consumption of limited primary resources. In this review article, green emerging technologies involving lignocellulosic waste to synthesize the NPs from the waste streams and the role of potential microorganisms such as microalgae, fungi, yeast, bacteria for the synthesis of NPs have been discussed. A critical insight is also given on use of recycling technologies and the incorporation of NMs in the membrane bioreactors (MBRs) to improve membrane functioning and process performance. Finally, this study aims to mitigate various persisting scientific and technological challenges for the safe disposal and recycling of organic and inorganic waste for future use in the circular economy.

Evaluation of Lignocellulosic Wastewater Valorization with the Oleaginous Yeasts R. kratochvilovae EXF7516 and C. oleaginosum ATCC 20509

During the conversion of lignocellulose, phenolic wastewaters are generated. Therefore, researchers have investigated wastewater valorization processes in which these pollutants are converted to chemicals, i.e., lipids. However, wastewaters are lean feedstocks, so these valorization processes in research typically require the addition of large quantities of sugars and sterilization, which increase costs. This paper investigates a repeated batch fermentation strategy with Rhodotorula kratochvilovae EXF7516 and Cutaneotrichosporon oleaginosum ATCC 20509, without these requirements. The pollutant removal and its conversion to microbial oil were evaluated. Because of the presence of non-monomeric substrates, the ligninolytic enzyme activity was also investigated. The repeated batch fermentation strategy was successful, as more lipids accumulated every cycle, up to a total of 5.4 g/L (23% cell dry weight). In addition, the yeasts consumed up to 87% of monomeric substrates, i.e., sugars, aromatics, and organics acids, and up to 23% of non-monomeric substrates, i.e., partially degraded xylan, lignin, cellulose. Interestingly, lipid production was only observed during the harvest phase of each cycle, as the cells experienced stress, possibly due to oxygen limitation. This work presents the first results on the feasibility of valorizing non-sterilized lignocellulosic wastewater with R. kratochvilovae and C. oleaginosum using a cost-effective repeated batch strategy.

Novel approach for the management of acid mine drainage (AMD) for the recovery of heavy metals along with lipid production by Chlorella vulgaris

The treatment of acid mine drainage (AMD) is of paramount importance for environmental sustainability. A two-stage process involving AMD remediation and simultaneous lipid production represents a highly efficient approach with zero-waste generation. Alkaline (NaOH) treatment of AMD at pH 8.0, 10.0, and 12.0 had significantly reduced metal loads (copper (Cu), cobalt (Co), chromium (Cr), cadmium (Cd), nickel (Ni), and zinc (Zn)) compared to the acidic pH range (4.0 and 6.0). The concentration levels of sulfates (SO₄ = 4520 mg/L), iron (Fe = 788 mg/L), aluminum (Al = 310 mg/L), and manganese (Mn = 19.4) were reduced to 2971 mg/L, 10.3 mg/L, 16.4 mg/L, and 1.3 mg/L, respectively at pH value 8.0. AMD with a pH value of 8.0 was later chosen as an ideal medium to favor the lipid accumulation by Chlorella vulgaris. Algal biomass was increasing to 5.5 g/L from 0.6 g/L of AMD-based medium within 15 days of cultivation. The FTIR and SEM-EDS studies revealed significant morphological changes in the microbial cell wall. The metals might positively impact lipid production in microalgae, where lipid yield achieved 0.18 g/g of glucose with lipid content of 0.35 g/g of biomass. The fatty acid profile presented 53.4% of saturated fatty acid content with a cetane value of 60.7. Thus, the efficiency of C. vulgaris was demonstrated with AMD treatment proving it to be a good candidate for bioenergy production.

Bio-oil production for biodiesel industry by Yarrowia lipolytica from volatile fatty acids in two-stage batch culture

Microbial lipids-derived biodiesel is garnering much attention owing to its potential to substitute diesel fuel. In this study, lipid accumulation by Yarrowia lipolytica from volatile fatty acids (VFAs) was studied in a lab-scale stirred tank bioreactor. In batch cultures, Y. lipolytica NCYC 2904 was able to grow in 18 g·L^-1 of VFAs (acetate, propionate, and butyrate), and the addition of a co-substrate (glucose) led to a fivefold improvement in lipid concentration. Furthermore, the two-stage batch culture (growth phase in glucose (1st stage) followed by a lipogenic phase in VFAs (2nd stage)) was the best strategy to obtain the highest lipid content in the cells (37%, w/w), with aeration conditions that kept dissolved oxygen concentration between 40% and 50% of saturation during the lipogenic phase. The estimated fuel properties of biodiesel produced from Y. lipolytica NCYC 2904 lipids are comparable with those of the biodiesel produced from vegetable oils and are in accordance with the international standards (EN 14214 and ASTM D6751). The cultivation strategies herein devised enable a sustainable, eco-friendly, and economical production of microbial lipids, based on feedstocks such as VFAs that can be derived from the acidogenic fermentation of organic wastes. KEY POINTS: • Addition of glucose to VFAs enhances lipids in Y. lipolytica in batch cultures • Two-stage batch culture - growth in glucose followed by VFAs pulse - rises lipids • Dissolved oxygen of 40-50% of saturation is crucial at the lipogenic phase.

A review on contemporary approaches in enhancing the innate lipid content of yeast cell

For the past few decades, industrialization has made a huge environmental hazard to the world with its waste. The approach of waste to wealth in the recent era has made many Eco-economical suggestions for the industries. The valuable products in biorefinery aspects of the eco-economical suggestions include; energy products, high-value drugs and novel materials. Bio-lipids are found to be the major influencing eco-economical products in the process. Production of bio-lipid from microbial sources has paved the way for future research on lipid-bioproducts. The yeast cell is a unique organism with a large unicellular structure capable of accumulating a high amount of lipids. It constitutes 90% of neutral lipids. Various strategies enhance the lipid profile of yeast cells: usage of oleaginous yeast, usage of low cost (or) alternative substrates, developing stress conditions in the growth medium, using genetically modified yeast, altering metabolic pathways of yeast and by using the symbiotic cultures of yeast with other microbes. The metabolic alterations of lipid pathways such as lipid biosynthesis, lipid elongation, lipid accumulation and lipid degradation have been a striking feature of research in lipid-based microbial work. The lipid-bioproducts have also made a strong footprint in the history of alternative energy products. It includes partial acyl glycerol, oleochemicals, phospholipids and biofuels. This report comprises the recent approaches carried out in the yeast cell for enhancing its lipid content. The limitations, challenges and future scope of individual strategies were also highlighted in this article.

Agricultural waste materials for adsorptive removal of phenols, chromium (VI) and cadmium (II) from wastewater: A review

Management of basic natural resources and the spent industrial and domestic streams to provide a sustainable safe environment for healthy living is a magnum challenge to scientists and environmentalists. The present remedial approach to the wastewater focuses on recovering pure water for reuse and converting the contaminants into a solid matrix for permanent land disposal. However, the ground water aquifers, over a long period slowly leach the contaminants consequently polluting the ground water. Synthetic adsorbents, mainly consisting of polymeric resins, chelating agents, etc. are efficient and have high specificity, but ultimate disposal is a challenge as most of these materials are non-biodegradable. In this context, it is felt appropriate to review the utility of adsorbents based on natural green materials such as agricultural waste and restricted to few model contaminants: phenols, and heavy metals chromium(VI), and cadmium(II) in view of the vast amount of literature available. The article discusses the features of the agricultural waste material-based adsorbents including the mechanism. It is inferred that agricultural waste materials are some of the common renewable sources available across the globe and can be used as sustainable adsorbents. A discussion on challenges for industrial scale implementation and integration with advanced technologies like magnetic-based approaches and nanotechnology to improve the removal efficiency is included for future prospects.

Phosphorus and Nitrogen Limitation as a Part of the Strategy to Stimulate Microbial Lipid Biosynthesis

Microbial lipids called a sustainable alternative to traditional vegetable oils invariably capture the attention of researchers. In this study, the effect of limiting inorganic phosphorus (KH2PO4) and nitrogen ((NH4)2SO4) sources in lipid-rich culture medium on the efficiency of cellular lipid biosynthesis by Y. lipolytica yeast has been investigated. In batch cultures, the carbon source was rapeseed waste post-frying oil (50 g/dm3). A significant relationship between the concentration of KH2PO4 and the amount of lipids accumulated has been revealed. In the shake-flask cultures, storage lipid yield was correlated with lower doses of phosphorus source in the medium. In bioreactor culture in mineral medium with (g/dm3) 3.0 KH2PO4 and 3.0 (NH4)2SO4, the cellular lipid yield was 47.5% (w/w). Simultaneous limitation of both phosphorus and nitrogen sources promoted lipid accumulation in cells, but at the same time created unfavorable conditions for biomass growth (0.78 gd.m./dm3). Increased phosphorus availability with limited cellular access to nitrogen resulted in higher biomass yields (7.45 gd.m./dm3) than phosphorus limitation in a nitrogen-rich medium (4.56 gd.m./dm3), with comparable lipid yields (30% and 32%). Regardless of the medium composition, the yeast preferentially accumulated oleic and linoleic acids as well as linolenic acid up to 8.89%. Further, it is crucial to determine the correlation between N/P molar ratios, biomass growth and efficient lipid accumulation. In particular, considering the contribution of phosphorus as a component of coenzymes in many metabolic pathways, including lipid biosynthesis and respiration processes, its importance as a factor in the cultivation of the oleaginous microorganisms was highlighted.

Factors affecting microbial lipids production by Yarrowia lipolytica strains from volatile fatty acids: Effect of co-substrates, operation mode and oxygen

Volatile fatty acids (VFAs), which can be generated by acidogenesis of organic wastes, are important building blocks for chemicals production, and are intermediates in many bioprocesses such as microbial lipids production. Important factors affecting the bioconversion of VFAs (acetate, propionate and butyrate) by Yarrowia lipolytica W29 and NCYC 2904 for growth and lipids accumulation were studied. Yarrowia lipolytica grew efficiently in VFAs-based media, but lipids production was enhanced by the addition of co-substrates (glucose or glycerol) in batch cultures. A two-stage batch culture - growth phase on glucose, followed by VFAs addition, improved lipids accumulation. Lipids concentrations of 2.3 g·L^-1 and 3.5 g·L^-1 were obtained with this mode of operation, with addition of 18 g·L^-1 VFAs, for Y. lipolytica W29 and NCYC 2904, respectively. For the first time, it was demonstrated that oxygen mass transfer is a crucial factor for lipids production by Y. lipolytica from VFAs. Intracellular lipids produced by Y. lipolytica strains were mainly composed by oleic and linoleic acids, similar to common vegetable oils, making these lipids suitable for biodiesel production. Moreover, margaric acid, which may improve biodiesel properties, was only detected in propionate medium. The strategies studied herein will contribute to the feasibility of using VFAs as low-cost feedstock for microbial lipids production by Y. lipolytica strains.

Application of Stable Isotope Tracing to Elucidate Metabolic Dynamics During Yarrowia lipolytica α-Ionone Fermentation

Targeted metabolite analysis in combination with ¹³C-tracing is a convenient strategy to determine pathway activity in biological systems; however, metabolite analysis is limited by challenges in separating and detecting pathway intermediates with current chromatographic methods. Here, a hydrophilic interaction chromatography tandem mass spectrometry approach was developed for improved metabolite separation, isotopologue analysis, and quantification. The physiological responses of a Yarrowia lipolytica strain engineered to produce ∼400 mg/L α-ionone and temporal changes in metabolism were quantified (e.g., mevalonate secretion, then uptake) indicating bottleneck shifts in the engineered pathway over the course of fermentation. Dynamic labeling results indicated limited tricarboxylic acid cycle label incorporation and, combined with a measurable ATP shortage during the high ionone production phase, suggested that electron transport and oxidative phosphorylation may limit energy supply and strain performance. The results provide insights into terpenoid pathway metabolic dynamics of non-model yeasts and offer guidelines for sensor development and modular engineering.

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A HILIC method is demonstrated for efficient separation of 57 cellular metabolites

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Production of α-ionone was ∼400 mg/L in bench-top bioreactors

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Engineered Y. lipolytica secreted then consumed mevalonate during fermentation

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Oxidative phosphorylation may limit performance in high-cell-density fermentations

Dimorphism of Trichosporon cutaneum and impact on its lipid production

BACKGROUND

Compared to the oleaginous yeast Yarrowia lipolytica, Trichosporon cutaneum can metabolize pentose sugars more efficiently, and in the meantime is more tolerant to inhibitors, which is suitable for lipid production from lignocellulosic biomass. However, this species experiences dimorphic transition between yeast-form cells and hyphae during submerged fermentation, which consequently affects the rheology and mass transfer performance of the fermentation broth and its lipid production.

RESULTS

The strain T. cutaneum B3 was cultured with medium composed of yeast extract, glucose and basic minerals. The experimental results indicated that yeast-form morphology was developed when yeast extract was supplemented at 1 g/L, but hyphae were observed when yeast extract supplementation was increased to 3 g/L and 5 g/L, respectively. We speculated that difference in nitrogen supply to the medium might be a major reason for the dimorphic transition, which was confirmed by the culture with media supplemented with yeast extract at 1 g/L and urea at 0.5 g/L and 1.0 g/L to maintain total nitrogen at same levels as that detected in the media with yeast extract supplemented at 3 g/L and 5 g/L. The morphological change of T. cutaneum B3 affected not only the content of intracellular lipids but also their composition, due to its impact on the rheology and oxygen mass transfer performance of the fermentation broth, and more lipids with less polyunsaturated fatty acids such as linoleic acid (C18:2) were produced by the yeast-form cells. When T. cutaneum B3 was cultured at an aeration rate of 1.5 vvm for 72 h with the medium composed of 60 g/L glucose, 3 g/L yeast extract and basic minerals, 27.1 g (dry cell weight)/L biomass was accumulated with the lipid content of 46.2%, and lipid productivity and yield were calculated to be 0.174 g/L/h and 0.21 g/g, respectively. Comparative transcriptomics analysis identified differently expressed genes for sugar metabolism and lipid synthesis as well as signal transduction for the dimorphic transition of T. cutaneum B3.

CONCLUSIONS

Assimilable nitrogen was validated as one of the major reasons for the dimorphic transition between yeast-form morphology and hyphae with T. cutaneum, and the yeast-form morphology was more suitable for lipid production at high content with less polyunsaturated fatty acids as feedstock for biodiesel production.

Economical lipid production from Trichosporon oleaginosus via dissolved oxygen adjustment and crude glycerol addition

The effect of dissolved oxygen concentration on lipid accumulation in Trichosporon oleaginosus has been investigated. The experiment was performed in 15 L fermenters. The dissolved oxygen concentration varied by adjusting the agitation and aeration. High dissolved oxygen level at 50%-60% enhanced cell growth. Maintaining low dissolved oxygen concentration at 20%-30% during lipogenesis phase led to high final lipid content (51%) in Trichosporon oleaginosus. The consumptions of energy and cost of the process were evaluated. The energy consumption in the dissolved oxygen level optimized process was 41% less than that with dissolved oxygen level at 50%-60%. In addition, the cost was also reduced around one time in the dissolved oxygen level optimized process compared to the one with dissolved oxygen level at 50%-60%. The study provided a feasible way of enhancing lipid accumulation in Trichosporon oleaginosus and reducing the consumption of energy and cost of lipid production from Trichosporon oleaginosus.