Oleaginous yeastCryptococcus curvatusexhibits interplay between biosynthesis of intracellular sugars and lipids

A review of lipid accumulation by oleaginous yeasts: Culture mode

Microbial lipids have attracted considerable interest owing to their favorable environmental sustainability benefits. In laboratory-scale studies, the factors impacting lipid production in oleaginous yeasts, including culture conditions, nutrients, and low-cost substrates, have been extensively studied. However, there were several different modes of microbial lipid cultivation (batch culture, fed-batch culture, continuous culture, and other novel culture modes), making it difficult to comprehensively analyze impacting factors under different cultivation modes on a laboratory scale. And only few cases of microbial lipid production have been conducted at the pilot scale, which requires more technological reliability assessments and environmental benefit evaluations. Thus, this study summarized the different culture modes and cases of scale-up processes, highlighting the role of the nutrient element ratio in regulating culture mode selection and lipid accumulation. The cost distribution and environmental benefits of microbial lipid production by oleaginous yeasts were also investigated. Our results suggested that the continuous culture mode was recommended for the scale-up process because of its stable lipid accumulation. More importantly, exploring the continuous culture mode integrated with other efficient culture modes remained to be further investigated. In research on scale-up processes, low-cost substrate (organic waste) application and optimization of reactor operational parameters were key to increasing environmental benefits and reducing costs.

Challenges and prospects of yeast-based microbial oil production within a biorefinery concept

Biodiesel, unlike to its fossil-based homologue (diesel), is renewable. Its use contributes to greater sustainability in the energy sector, mainly by reducing greenhouse gas emissions. Current biodiesel production relies on plant- and animal-related feedstocks, resulting in high final costs to the prices of those raw materials. In addition, the production of those materials competes for arable land and has provoked a heated debate involving their use food vs. fuel. As an alternative, single-cell oils (SCOs) obtained from oleaginous microorganisms are attractive sources as a biofuel precursor due to their high lipid content, and composition similar to vegetable oils and animal fats. To make SCOs competitive from an economic point of view, the use of readily available low-cost substrates becomes essential. This work reviews the most recent advances in microbial oil production from non-synthetic sugar-rich media, particularly sugars from lignocellulosic wastes, highlighting the main challenges and prospects for deploying this technology fully in the framework of a Biorefinery concept.

Growth Response of Non-Conventional Yeasts on Sugar-Rich Media: Part 2: Citric Acid Production and Circular-Oriented Valorization of Glucose-Enriched Olive Mill Wastewaters Using Novel Yarrowia lipolytica Strains

The global market for citric acid (CA) is one of the biggest and fastest expanding markets in the food industry. The CA production employing microbial bioprocessing with efficient GRAS strains and renewable waste streams is in line with the European Union binding targets for resource efficiency, sustainable consumption-production, and low-carbon technologies. In this work, the potential of three novel wild-type Yarrowia lipolytica strains (namely LMBF Y-46, LMBF Y-47 and ACA-YC 5033) regarding the production of CA and other valuable metabolites was tested on glucose-based media, and the most promising amongst the screened strains (viz. the strain ACA-YC 5033) was cultured on glucose-based media, in which part of the fermentation water had been replaced by olive-mill wastewaters (OMWs) in a novel approach of simultaneous OMW valorization and bioremediation. In the first part of this study, the mentioned strains were cultured under nitrogen-limited conditions with commercial (low-cost) glucose employed as a sole carbon source in shake-flask cultures at an initial concentration (S0) ≈ of 50 g/L. Variable quantities of secreted citric acid (CA) and intra-cellular compounds (viz. polysaccharides and lipids) were produced. All strains did not accumulate significantly high lipid quantities (i.e., maximum lipid in dry cell weight [DCW] values ≈30% w/w were noted) but produced variable CA quantities. The most promising strain, namely ACA-YC 5033, produced CA up to c. 24 g/L, with a yield of CA produced on glucose consumed (YCA/S) ≈ 0.45 g/g. This strain in stirred tank bioreactor experiments, at remarkably higher S0 concentrations (≈110 g/L) and the same initial nitrogen quantity added into the medium, produced notably higher CA quantities, up to 57 g/L (YCA/S ≈ 0.52 g/g). The potential of the same strain (ACA-YC 5033) to bioremediate OMWs and to produce value-added compounds, i.e., yeast cells, CA, and intra-cellular metabolites, was also assessed; under nitrogen-limited conditions in which OMWs had partially replaced tap water and significant glucose concentrations had been added (S0 ≈ 100 g/L, simultaneous molar ratio C/N ≈ 285 g/g, initial phenolic compounds [Phen0] adjusted to ≈1.0 g/L; these media were similar to the OMWs generated from the traditional press extraction systems) the notable CA quantity of 60.2 g/L with simultaneous YCA/S = 0.66 g/g, was obtained in shake flasks, together with satisfactory phenolic compounds removal (up to 19.5% w/w) and waste decolorization (up to 47.0%). Carbon-limited conditions with Phen0 ≈ 1.0 g/L favored the production of yeast DCW (up to 25.3 g/L), with equally simultaneous interesting phenolic compounds and color removal. The fatty acid profile showed that cellular lipids were highly unsaturated with oleic, linoleic and palmitoleic acids, accounting for more than 80% w/w. This study proposed an interesting approach that could efficiently address the biotreatment of toxic effluents and further convert them into circular-oriented bioproducts.

A comprehensive review on microbial lipid production from wastes: research updates and tendencies

Microbial lipids have recently attracted attention as an intriguing alternative for the biodiesel and oleochemical industries to achieve sustainable energy generation. However, large-scale lipid production remains limited due to the high processing costs. As multiple variables affect lipid synthesis, an up-to-date overview that will benefit researchers studying microbial lipids is necessary. In this review, the most studied keywords from bibliometric studies are first reviewed. Based on the results, the hot topics in the field were identified to be associated with microbiology studies that aim to enhance lipid synthesis and reduce production costs, focusing on the biological and metabolic engineering involved. The research updates and tendencies of microbial lipids were then analyzed in depth. In particular, feedstock and associated microbes, as well as feedstock and corresponding products, were analyzed in detail. Strategies for lipid biomass enhancement were also discussed, including feedstock adoption, value-added product synthesis, selection of oleaginous microbes, cultivation mode optimization, and metabolic engineering strategies. Finally, the environmental implications of microbial lipid production and possible research directions were presented.

Redistributing Carbon Flux by Impairing Saccharide Synthesis to Enhance Lipid Yield in Oleaginous Fungus Mortierella alpina

Increasing carbon flux toward target metabolites is important in improving microbial productivity and economic value. To improve the efficiency of lipid production in Mortierella alpina, we knocked down genes for trehalose-6-phosphate synthetase (Matps) and phosphoenolpyruvate carboxykinase (Mapepck) in the major pathways for saccharide synthesis. The knockdown of Matps reduced trehalose content by an average of 31.87%, while the knockdown of Mapepck reduced the total saccharide content by 28.6%, and both recombinant strains showed more than 20% increased lipid yield. Trehalose plays a vital role in stress resistance, but a higher polyunsaturated fatty acid-rich lipid content was found to partly compensate for the loss of trehalose after Matps knockdown. As compared with Matps knockdown, the knockdown of Mapepck gave better lipid production by bringing forward the time to maximum lipid yield by three days in a scale-up test. The arachidonic acid yield after the Mapepck knockdown reached 1.23 g/L, which was 39.9% higher than that of the original strain. The present research provided an efficient strategy for redistributing carbon flux among different metabolites and therefore promoted microbial lipid yield in a shorter fermentation period.

Efficient use of discarded vegetal residues as cost-effective feedstocks for microbial oil production

BACKGROUND

Horticultural intensive type systems dedicated in producing greenhouse vegetables are one of the primary industries generating organic waste. Towards the implementation of a zero-waste strategy, this work aims to use discarded vegetables (tomato, pepper and watermelon) as feedstock for producing microbial oil using the oleaginous yeast Cryptococcus curvatus.

RESULTS

The soluble fraction, resulting after crushing and centrifuging these residues, showed C/N ratios of about 15, with a total carbohydrate content (mainly glucose, fructose and sucrose) ranging from 30 g/L to 65 g/L. Using these liquid fractions as substrate under a pulse-feeding strategy with a concentrated glucose solution resulted in an intracellular total lipid accumulation of about 30% (w/w) of the total dry cell weight (DCW). To increase this intracellular lipid content, the initial C/N content was increased from 15 to 30 and 50. Under these conditions, the process performance of the pulse-feeding strategy increased by 20-36%, resulting in a total intracellular lipid concentration of 35-40% DCW (w/w).

CONCLUSION

These results demonstrate the potential of discarded vegetables as a substrate for producing bio-based products such as microbial oil when proper cultivation strategies are available.

Yeast Lipid Produced through Glycerol Conversions and Its Use for Enzymatic Synthesis of Amino Acid-Based Biosurfactants

The aim of the present work was to obtain microbial lipids (single-cell oils and SCOs) from oleaginous yeast cultivated on biodiesel-derived glycerol and subsequently proceed to the enzymatic synthesis of high-value biosurfactant-type molecules in an aqueous medium, with SCOs implicated as acyl donors (ADs). Indeed, the initial screening of five non-conventional oleaginous yeasts revealed that the most important lipid producer was the microorganism Cryptococcus curvatus ATCC 20509. SCO production was optimised according to the nature of the nitrogen source and the initial concentration of glycerol (Glyc0) employed in the medium. Lipids up to 50% w/w in dry cell weight (DCW) (SCO_max = 6.1 g/L) occurred at Glyc0 ≈ 70 g/L (C/N ≈ 80 moles/moles). Thereafter, lipids were recovered and were subsequently used as ADs in the N-acylation reaction catalysed by aminoacylases produced from Streptomyces ambofaciens ATCC 23877 under aqueous conditions, while Candida antarctica lipase B (CALB) was used as a reference enzyme. Aminoacylases revealed excellent activity towards the synthesis of acyl-lysine only when free fatty acids (FAs) were used as the AD, and the rare regioselectivity in the α-amino group, which has a great impact on the preservation of the functional side chains of any amino acids or peptides. Aminoacylases presented higher α-oleoyl-lysine productivity and final titer (8.3 g/L) with hydrolysed SCO than with hydrolysed vegetable oil. The substrate specificity of both enzymes towards the three main FAs found in SCO was studied, and a new parameter was defined, viz., Specificity factor (Sf), which expresses the relative substrate specificity of an enzyme towards a FA present in a FA mixture. The Sf value of aminoacylases was the highest with palmitic acid in all cases tested, ranging from 2.0 to 3.0, while that of CALB was with linoleic acid (0.9-1.5). To the best of our knowledge, this is the first time that a microbial oil has been successfully used as AD for biosurfactant synthesis. This bio-refinery approach illustrates the concept of a state-of-the-art combination of enzyme and microbial technology to produce high-value biosurfactants through environmentally friendly and economically sound processes.

Enhancement production of lipid and unsaturation of fatty acids in Cryptococcus humicola via addition of calcium ion

Lipids synthesized by oleaginous yeasts are considered to be the best candidates for biodiesel production. Cryptococcus humicola as an oleaginous yeast accumulated lipid in cells. In order to optimize the conditions for lipid production, different carbon and nitrogen sources were used and metals were added into the medium. Ca²⁺ addition increased the lipid production greatly. Xylose and peptone were optimal carbon source and nitrogen source, respectively for lipid accumulation. Response surface experiment results revealed that the accumulation of lipid could be maximized when the xylose, peptone and Ca²⁺ concentration was 61 g/L, 4.31 g/L, 0.67 mmol/L. C16 and C18 fatty acid account for about 91% of the total fatty acids. The most abundant fatty acid was oleic acid (42.68%), followed by palmitic acid (29.7%) and stearic acid (13.87%). The addition of Ca²⁺ increased the content of unsaturated fatty acids (such as C16:1 and C18:1) and improved the unsaturation of fatty acids. Quantitative real time PCR analysis revealed that expression of genes related to lipid biosynthesis showed up-regulated by Ca²⁺ treatment. This study provided a strategy for increase in lipid production and content of unsaturated fatty acids.

Growth Potential of Selected Yeast Strains Cultivated on Xylose-Based Media Mimicking Lignocellulosic Wastewater Streams: High Production of Microbial Lipids by Rhodosporidium toruloides

The potential of Rhodosporidium toruloides, Candida oleophila, Metschnikowia pulcherima, and Cryptococcus curvatus species to produce single-cell-oil (SCO) and other valuable metabolites on low-cost media, based on commercial-type xylose, was investigated. Rhodosporidium strains were further evaluated in shake-flasks using different lignosulphonate (LS) concentrations, in media mimicking waste streams derived from the paper and pulp industry. Increasing the LS concentration up to 40 g/L resulted in enhanced dry cell weight (DCW) while SCO production increased up to ~5.0 g/L when R. toruloides NRRL Y-27012 and DSM 4444 were employed. The intra-cellular polysaccharide production ranged from 0.9 to 2.3 g/L in all fermentations. Subsequent fed-batch bioreactor experiments with R. toruloides NRRL Y-27012 using 20 g/L of LS and xylose, led to SCO production of 17.0 g/L with maximum lipids in DCW (YL/X) = 57.0% w/w. The fatty acid (FA) profile in cellular lipids showed that oleic (50.3–63.4% w/w) and palmitic acid (23.9–31.0%) were the major FAs. Only SCO from batch trials of R. toruloides strains contained α-linolenic acid. Media that was supplemented with various LS concentrations enhanced the unsaturation profile of SCO from R. toruloides NRRL Y-27012. SCO from R. toruloides strains could replace plant-based commodity oils in oleochemical-operations and/or it could be micro- and nano-encapsulated into novel food-based formulas offering healthier food-products.

Recycling industrial food wastes for lipid production by oleaginous yeasts Rhodosporidiobolus azoricus and Cutaneotrichosporon oleaginosum

BACKGROUND

Microbial lipids have been emerging as a sustainable alternative to vegetable oils and animal fat to produce biodiesel and industrial relevant chemicals. The use of wastes for microbial processes can represent a way for upgrading low value feedstock to high value products, addressing one of the main goals of circular economy, the reduction of wastes by recycling. Two oleaginous yeasts, Rhodosporidiobolus azoricus and Cutaneotrichosporon oleaginosum, were used in this study to demonstrate the feasibility of the proposed approach.

RESULTS

In this study wastes from industrial food processing, as pumpkin peels and syrup from candied fruits manufacture, were used for yeast cultivation and for lipids production. Evaluation of growth and sugar consumption revealed marked differences between the yeasts in capacity to utilize the main sugars present in the feedstock. In particular, we observed an unexpected limitation in glucose metabolism on mineral defined media by R. azoricus. Both species showed ability to grow and accumulate lipids on media exclusively composed by undiluted pumpkin peel hydrolysate, and R. azoricus was the best performing. By a two-stage process carried out in bioreactor, this species reached a biomass concentration of 45 g/L (dry weight) containing 55% of lipids, corresponding to a lipid concentration of 24 g/L, with a productivity of 0.26 g/L/h and yield of 0.24 g lipids per g of utilized sugar.

CONCLUSIONS

Wastes from industrial food processing were sufficient to completely support yeast growth and to induce lipid accumulation. This study provides strong evidence that the concept of valorisation through the production of lipids from the metabolism of nutrients present in agro-industrial wastes by oleaginous yeasts is promising for implementation of biotechnological processes in a circular economy contest.

In-situ transesterification of single-cell oil for biodiesel production: a review

In recent years, biodiesel synthesis and production demands have increased because of its high degradability, cleaner emissions, non-toxicity, and an alternative to petroleum diesel. In this context, Single Cell Oil (SCO) has been identified as an alternative feedstock, having the advantage of accumulating high intracellular lipid. SCO/microbial lipids are potential alternatives for sustainable biodiesel production. The traditional technique for biodiesel production from the oils obtained from microbes generally requires two steps: lipid extraction and transesterification. In-situ transesterification is an innovative and renewable process for biodiesel production. It rules out the need to isolate and refine the feedstock lipid, as it directly uses biomass in a single step, i.e., the pretreated biomass will be subjected to in-situ transesterification in the presence of catalysts. Hence, the production cost can be reduced by eliminating the lipid extraction procedure. The current review focuses on the basic features and advantages of in-situ transesterification of SCO for biodiesel production with the aid of short-chain alcohols along with different acid, base, and enzyme catalysts. In addition, a comparative study was carried out to highlight the merits of in-situ transesterification over conventional transesterification.

The history, state of the art and future prospects for oleaginous yeast research

Lipid-based biofuels, such as biodiesel and hydroprocessed esters, are a central part of the global initiative to reduce the environmental impact of the transport sector. The vast majority of production is currently from first-generation feedstocks, such as rapeseed oil, and waste cooking oils. However, the increased exploitation of soybean oil and palm oil has led to vast deforestation, smog emissions and heavily impacted on biodiversity in tropical regions. One promising alternative, potentially capable of meeting future demand sustainably, are oleaginous yeasts. Despite being known about for 143 years, there has been an increasing effort in the last decade to develop a viable industrial system, with currently around 100 research papers published annually. In the academic literature, approximately 160 native yeasts have been reported to produce over 20% of their dry weight in a glyceride-rich oil. The most intensively studied oleaginous yeast have been Cutaneotrichosporon oleaginosus (20% of publications), Rhodotorula toruloides (19%) and Yarrowia lipolytica (19%). Oleaginous yeasts have been primarily grown on single saccharides (60%), hydrolysates (26%) or glycerol (19%), and mainly on the mL scale (66%). Process development and genetic modification (7%) have been applied to alter yeast performance and the lipids, towards the production of biofuels (77%), food/supplements (24%), oleochemicals (19%) or animal feed (3%). Despite over a century of research and the recent application of advanced genetic engineering techniques, the industrial production of an economically viable commodity oil substitute remains elusive. This is mainly due to the estimated high production cost, however, over the course of the twenty-first century where climate change will drastically change global food supply networks and direct governmental action will likely be levied at more destructive crops, yeast lipids offer a flexible platform for localised, sustainable lipid production. Based on data from the large majority of oleaginous yeast academic publications, this review is a guide through the history of oleaginous yeast research, an assessment of the best growth and lipid production achieved to date, the various strategies employed towards industrial production and importantly, a critical discussion about what needs to be built on this huge body of work to make producing a yeast-derived, more sustainable, glyceride oil a commercial reality.

SNF1β-Modulated Glucose Uptake and the Balance between Polyunsaturated Fatty Acids and Carbohydrates in Mortierella alpina

A sucrose nonfermenting protein kinase 1 (SNF1) complex is an important metabolic regulator in fungi that is critical to cell metabolism and stress response. In this study, the role of an SNF1 β-subunit in the oleaginous fungus Mortierella alpina (MaSip2) was investigated. The MaSip2 contained a glycogen-binding domain and a conserved SNF1-complex interaction region; its transcriptional level during lipogenesis shared high consistency with a previously reported SNF1 γ-subunit (MaSnf4). Overexpression of MaSip2 in M. alpina significantly promoted glucose uptake and resulted in 34.1% increased total biomass, leading to 44.8% increased arachidonic acid yield after 7 day fermentation. MaSip2 also regulated the balance between polyunsaturated fatty acids and carbohydrates in M. alpina. Intracellular metabolite analysis revealed increased carbohydrate-related metabolite accumulation in MaSip2 overexpression strains. On the contrary, knockdown of MaSip2 increased the total fatty acid unsaturation degree, especially under low-temperature conditions. This research improved our knowledge of SNF1 complex in M. alpina and provided a target gene for enhancing glucose utilization and modulating fatty acid composition for better application of oleaginous fungi.

Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology

Background

The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysates. Currently, data related to molecular aspects of the metabolic utilisation of oligomeric carbohydrates are sparse. In addition, comprehensive proteomic information for C. oleaginosus focusing on carbohydrate metabolism is not available.

Results

In this study, we conducted a systematic analysis of carbohydrate intake and utilisation by C. oleaginosus and investigated the influence of different di- and trisaccharide as carbon sources. Changes in the cellular growth and morphology could be observed, depending on the selected carbon source. The greatest changes in morphology were observed in media containing trehalose. A comprehensive proteomic analysis of secreted, cell wall-associated, and cytoplasmatic proteins was performed, which highlighted differences in the composition and quantity of secreted proteins, when grown on different disaccharides. Based on the proteomic data, we performed a relative quantitative analysis of the identified proteins (using glucose as the reference carbon source) and observed carbohydrate-specific protein distributions. When using cellobiose or lactose as the carbon source, we detected three- and five-fold higher diversity in terms of the respective hydrolases released. Furthermore, the analysis of the secreted enzymes enabled identification of the motif with the consensus sequence LALL[LA]L[LA][LA]AAAAAAA as a potential signal peptide.

Conclusions

Relative quantification of spectral intensities from crude proteomic datasets enabled the identification of new enzymes and provided new insights into protein secretion, as well as the molecular mechanisms of carbo-hydrolases involved in the cleavage of the selected carbon oligomers. These insights can help unlock new substrate sources for C. oleaginosus, such as low-cost by-products containing difficult to utilize carbohydrates. In addition, information regarding the carbo-hydrolytic potential of C. oleaginosus facilitates a more precise engineering approach when using targeted genetic approaches. This information could be used to find new and more cost-effective carbon sources for microbial lipid production by the oleaginous yeast C. oleaginosus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01692-2.

Adaptive laboratory evolution principles and applications in industrial biotechnology

Adaptive laboratory evolution (ALE) is an innovative approach for the generation of evolved microbial strains with desired characteristics, by implementing the rules of natural selection as presented in the Darwinian Theory, on the laboratory bench. New as it might be, it has already been used by several researchers for the amelioration of a variety of characteristics of widely used microorganisms in biotechnology. ALE is used as a tool for the deeper understanding of the genetic and/or metabolic pathways of evolution. Another important field targeted by ALE is the manufacturing of products of (high) added value, such as ethanol, butanol and lipids. In the current review, we discuss the basic principles and techniques of ALE, and then we focus on studies where it has been applied to bacteria, fungi and microalgae, aiming to improve their performance to biotechnological procedures and/or inspect the genetic background of evolution. We conclude that ALE is a promising and efficacious method that has already led to the acquisition of useful new microbiological strains in biotechnology and could possibly offer even more interesting results in the future.

Rhodotorula kratochvilovae CCY 20-2-26-The Source of Multifunctional Metabolites

Multifunctional biomass is able to provide more than one valuable product, and thus, it is attractive in the field of microbial biotechnology due to its economic feasibility. Carotenogenic yeasts are effective microbial factories for the biosynthesis of a broad spectrum of biomolecules that can be used in the food and feed industry and the pharmaceutical industry, as well as a source of biofuels. In the study, we examined the effect of different nitrogen sources, carbon sources and CN ratios on the co-production of intracellular lipids, carotenoids, β-glucans and extracellular glycolipids. Yeast strain R. kratochvilovae CCY 20-2-26 was identified as the best co-producer of lipids (66.7 ± 1.5% of DCW), exoglycolipids (2.42 ± 0.08 g/L), β-glucan (11.33 ± 1.34% of DCW) and carotenoids (1.35 ± 0.11 mg/g), with a biomass content of 15.2 ± 0.8 g/L, by using the synthetic medium with potassium nitrate and mannose as a carbon source. It was shown that an increased C/N ratio positively affected the biomass yield and production of lipids and β-glucans.

Carbohydrate analysis of Mortierella alpina by colorimetry and HPLC-ELSD to reveal accumulation differences of sugar and lipid

OBJECTIVES

To establish reliable methods for the extraction and quantification of the total carbohydrate and intracellular saccharides from Mortierella alpina and study the changes between carbohydrate and lipid in fermentation process.

RESULTS

The extraction of mycelia with HCl following a photometric phenol-sulphuric acid reaction was identified as an optimal method for total carbohydrate analysis in Mortierella alpina, which the extraction efficiency performed 1.1-3.6 fold than other five methods. The total carbohydrate content increased from initial 19.26 to 25.86% during early fermentation process and declined gradually thereafter, while the fatty acid was increasing from 8.47 to 31.03%. For separation and qualitative estimation of intracellular saccharides, the acetonitrile/water freeze-thaw method for extraction and Sugar-Pak I column for separation proved to be possible. With the glucose rapidly decreasing at the beginning of growth, the trehalose accumulated rapidly from 1.63 to 5.04% and then decreased slightly but maintain above 4% of dry biomass.

CONCLUSIONS

This work established comprehensive carbohydrate extraction and analysis methods of Mortierella alpina and identified the main saccharide in fermentation process which indicated that the accumulation of fatty acids was related to the change of intracellular carbohydrate content.

Oleaginous Yeasts as Cell Factories for the Sustainable Production of Microbial Lipids by the Valorization of Agri-Food Wastes

The agri-food industry annually produces huge amounts of crops residues and wastes, the suitable management of these products is important to increase the sustainability of agro-industrial production by optimizing the entire value chain. This is also in line with the driving principles of the circular economy, according to which residues can become feedstocks for novel processes. Oleaginous yeasts represent a versatile tool to produce biobased chemicals and intermediates. They are flexible microbial factories able to grow on different side-stream carbon sources such as those deriving from agri-food wastes, and this characteristic makes them excellent candidates for integrated biorefinery processes through the production of microbial lipids, known as single cell oils (SCOs), for different applications. This review aims to present an extensive overview of research progress on the production and use of oleaginous yeasts and present discussions on the current bottlenecks and perspectives of their exploitation in different sectors, such as foods, biofuels and fine chemicals.

Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

BACKGROUND

Cutaneotrichosporon oleaginosus ATCC 20509 is a fast-growing oleaginous basidiomycete yeast that is able to grow in a wide range of low-cost carbon sources including crude glycerol, a byproduct of biodiesel production. When glycerol is used as a carbon source, this yeast can accumulate more than 50% lipids (w/w) with high concentrations of mono-unsaturated fatty acids.

RESULTS

To increase our understanding of this yeast and to provide a knowledge base for further industrial use, a FAIR re-annotated genome was used to build a genome-scale, constraint-based metabolic model containing 1553 reactions involving 1373 metabolites in 11 compartments. A new description of the biomass synthesis reaction was introduced to account for massive lipid accumulation in conditions with high carbon-to-nitrogen (C/N) ratio in the media. This condition-specific biomass objective function is shown to better predict conditions with high lipid accumulation using glucose, fructose, sucrose, xylose, and glycerol as sole carbon source.

CONCLUSION

Contributing to the economic viability of biodiesel as renewable fuel, C. oleaginosus ATCC 20509 can effectively convert crude glycerol waste streams in lipids as a potential bioenergy source. Performance simulations are essential to identify optimal production conditions and to develop and fine tune a cost-effective production process. Our model suggests ATP-citrate lyase as a possible target to further improve lipid production.

Lipid Production by Yeasts Growing on Commercial Xylose in Submerged Cultures with Process Water Being Partially Replaced by Olive Mill Wastewaters

Six yeast strains belonging to Rhodosporidium toruloides, Lipomyces starkeyi, Rhodotorula glutinis and Cryptococcus curvatus were shake-flask cultured on xylose (initial sugar—S0 = 70 ± 10 g/L) under nitrogen-limited conditions. C. curvatus ATCC 20509 and L. starkeyi DSM 70296 were further cultured in media where process waters were partially replaced by the phenol-containing olive mill wastewaters (OMWs). In flasks with S0 ≈ 100 g/L and OMWs added yielding to initial phenolic compounds concentration (PCC0) between 0.0 g/L (blank experiment) and 2.0 g/L, C. curvatus presented maximum total dry cell weight—TDCWmax ≈ 27 g/L, in all cases. The more the PCC0 increased, the fewer lipids were produced. In OMW-enriched media with PCC0 ≈ 1.2 g/L, TDCW = 20.9 g/L containing ≈ 40% w/w of lipids was recorded. In L. starkeyi cultures, when PCC0 ≈ 2.0 g/L, TDCW ≈ 25 g/L was synthesized, whereas lipids in TDCW = 24–28% w/w, similar to the experiments without OMWs, were recorded. Non-negligible dephenolization and species-dependent decolorization of the wastewater occurred. A batch-bioreactor trial by C. curvatus only with xylose (S0 ≈ 110 g/L) was performed and TDCW = 35.1 g/L (lipids in TDCW = 44.3% w/w) was produced. Yeast total lipids were composed of oleic and palmitic and to lesser extent linoleic and stearic acids. C. curvatus lipids were mainly composed of nonpolar fractions (i.e., triacylglycerols).

Production of added-value microbial metabolites during growth of yeast strains on media composed of biodiesel-derived crude glycerol and glycerol/xylose blends

A total of 11 yeast strains of Yarrowia lipolytica, Metschnikowia sp., Rhodotorula sp. and Rhodosporidium toruloides were grown under nitrogen-limited conditions with crude glycerol employed as substrate in shake flasks, presenting interesting dry cell weight (DCW) production. Three of these strains belonging to Metschnikowia sp. accumulated significant quantities of endopolysaccharides (i.e. the strain V.V.-D4 produced 11.0 g/L of endopolysaccharides, with polysaccharides in DCW ≈ 63% w/w). A total of six Y. lipolytica strains produced either citric acid or mannitol. Most of the screened yeasts presented somehow elevated lipid and polysaccharides in DCW values at the early steps of growth despite nitrogen appearance in the fermentation medium. Lipid in DCW values decreased as growth proceeded. R. toruloides DSM 4444 cultivated on media presenting higher glycerol concentrations presented interesting lipid-accumulating capacities (maximum lipid = 12.5 g/L, maximum lipid in DCW = 43.0–46.0% w/w, conversion yield on glycerol = 0.16 g/g). Replacement of crude glycerol by xylose resulted in somehow decreased lipid accumulation. In xylose/glycerol mixtures, xylose was more rapidly assimilated from glycerol. R. toruloides total lipids were mainly composed of triacylglycerols. Total cellular fatty acid composition on xylose presented some differences compared with that on glycerol. Cellular lipids contained mainly oleic and palmitic acid.

Orange peel waste-based liquid medium for biodiesel production by oleaginous yeasts

Orange peel waste (OPW), the primary byproduct of the juice extraction process, is annually generated in massive amounts (21 Mton), and its aqueous extraction in biorefining operations yields a liquid fraction, referred to as orange peel extract (OPE). Although OPE contains significant amounts of easily assimilable carbohydrates, such as fructose, glucose, and sucrose, no investigations have been conducted yet to assess its possible use in biodiesel production by oleaginous yeasts. Consequently, the objective of the present study was to assess whether OPE might act as the basis of a liquid medium for microbial lipid production. A screening conducted with 18 strains of oleaginous yeasts in shaken flask on the OPE-based medium showed that Rhodosporidium toruloides NRRL 1091 and Cryptococcus laurentii UCD 68-201 gave the best results in terms of lipid production (5.8 and 4.5 g L^-1, respectively) and accumulation (77 and 47% on a dry matter basis, respectively). The subsequent scale transfer of the process to a 3-L STR operated in batch mode halved the time required to reach the lipid peak with the ensuing increase in volumetric productivities in R. toruloides NRRL 1091 (3646 mg L^-1 day^-1) and C. laurentii UCD 68-201 (2970.7 mg L^-1 day^-1). The biodiesel yields from the lipids of the former and the latter strain were 36.9 and 31.9%, respectively. Based on multivariate analysis of fatty acid methyl ester compositions, the lipids from the former and the latter strain were highly resembling those of Jatropha and palm oils, two commonly used feedstocks for biodiesel manufacturing.

An Overview of Potential Oleaginous Microorganisms and Their Role in Biodiesel and Omega-3 Fatty Acid-Based Industries

Microorganisms are known to be natural oil producers in their cellular compartments. Microorganisms that accumulate more than 20% w/w of lipids on a cell dry weight basis are considered as oleaginous microorganisms. These are capable of synthesizing vast majority of fatty acids from short hydrocarbonated chain (C6) to long hydrocarbonated chain (C36), which may be saturated (SFA), monounsaturated (MUFA), or polyunsaturated fatty acids (PUFA), depending on the presence and number of double bonds in hydrocarbonated chains. Depending on the fatty acid profile, the oils obtained from oleaginous microorganisms are utilized as feedstock for either biodiesel production or as nutraceuticals. Mainly microalgae, bacteria, and yeasts are involved in the production of biodiesel, whereas thraustochytrids, fungi, and some of the microalgae are well known to be producers of very long-chain PUFA (omega-3 fatty acids). In this review article, the type of oleaginous microorganisms and their expertise in the field of biodiesel or omega-3 fatty acids, advances in metabolic engineering tools for enhanced lipid accumulation, upstream and downstream processing of lipids, including purification of biodiesel and concentration of omega-3 fatty acids are reviewed.

Sources of microbial oils with emphasis to Mortierella (Umbelopsis) isabellina fungus

The last years a constantly rising number of publications have appeared in the literature in relation to the production of oils and fats deriving from microbial sources (the "single cell oils"-SCOs). SCOs can be used as precursors for the synthesis of lipid-based biofuels or employed as substitutes of expensive oils rarely found in the plant or animal kingdom. In the present review-article, aspects concerning SCOs (economics, biochemistry, substrates, technology, scale-up), with emphasis on the potential of Mortierella isabellina were presented. Fats and hydrophilic substrates have been used as carbon sources for cultivating Zygomycetes. Among them, wild-type M. isabellina strains have been reported as excellent SCO-producers, with conversion yields on sugar consumed and lipid in DCW values reported comparable to the maximum ones achieved for genetically engineered SCO-producing strains. Lipids produced on glucose contain γ-linolenic acid (GLA), a polyunsaturated fatty acid (PUFA) of high dietary and pharmaceutical importance, though in low concentrations. Nevertheless, due to their abundance in oleic acid, these lipids are perfect precursors for the synthesis of 2nd generation biodiesel, while GLA can be recovered and directed to other usages. Genetic engineering focusing on over-expression of Δ6 and Δ12 desaturases and of C16 elongase may improve the fatty acid composition (viz. increasing the concentration of GLA or other nutritionally important PUFAs) of these lipids.

Multi-Factorial-Guided Media Optimization for Enhanced Biomass and Lipid Formation by the Oleaginous Yeast Cutaneotrichosporon oleaginosus

The non-conventional, oleaginous yeast Cutaneotrichosporon oleaginosus is flagged as an industrial cell factory for generation of oleochemicals and biofuels due to its substrate flexibility and high triglyceride yields. In this study, we employed a computational Response Surface Methodology to guide and streamline the experimental media optimization matrix with 12 nitrogen and 10 carbon sources in order to provide for high biomass and lipid accumulation toward an industrially relevant fermentation process. The resulting data provide new insights into C. oleaginosus physiology under variable nutritional states. Accordingly, the lipid content % (lipid weight/yeast dry weight) is controlled by a defined interplay between carbon and nitrogen. In our experimental setup, the highest biomass (18.4 ± 2.20 g/L) and lipid yield (9 ± 0.34 g/L; 49.74 ± 5.16% g lipid weight/g yeast dry cell weight) were obtained with lactose and yeast extract as carbon and nitrogen sources at an elemental weight ratio of 120:1, respectively. Interestingly, with ammonium salts as a N-source, the intracellularly accumulated triglycerides increasingly contain saturated fatty acids, which provides a new route to generate tailored fatty acid profiles for specific oleochemicals or food applications. Our data indicate that a metabolic ceiling for lipid accumulation in C. oleaginosus is obtained with the correct carbon and nitrogen source mixture.

N. de Moura Bell JM. Bioconversion of cheese whey permeate into fungal oil by Mucor circinelloides

BACKGROUND

Oleaginous fungi are efficient tools to convert agricultural waste streams into valuable components. The filamentous fungus Mucor circinelloides was cultivated in whey permeate, a byproduct from cheese production, to produce an oil-rich fungal biomass. Response surface methodology was used to optimize the fermentation conditions such as pH and temperature for increased biomass yield and lipid accumulation. Quantification and characterization of the fungal biomass oil was conducted.

RESULTS

Upstream lactose hydrolysis of the whey permeate increased the biomass yield from 2.4 to 7.8 (g dry biomass/L) compared to that of non-hydrolyzed whey permeate. The combination of low pH (4.5) and pasteurization minimized microbial competition, thus favoring fungal growth. A central composite rotatable design was used to evaluate the effects of temperature (22.4-33.6 °C) and a lower pH range (3.6-4.7) on biomass yield and composition. The highest biomass yield and oil content was observed at high temperature (33.6 °C), while the pH range evaluated had a less pronounced effect. The predictive model was validated at the optimal conditions of 33.6 °C and pH 4.5. The fungal biomass yield plateaued at 9 g dry cell weight per liter, while the oil content and lipid yield reached a maximum of 24% dry biomass and 2.20 g/L, respectively, at 168 h. Triacylglycerides were the major lipid class (92%), which contained predominantly oleic (41%), palmitic (23%), linoleic (11%), and γ-linolenic acid (9%).

CONCLUSIONS

This study provided an alternative way of valorization of cheese whey permeate by using it as a substrate for the production of value-added compounds by fungal fermentation. The fatty acid profile indicates the suitability of M. circinelloides oil as a potential feedstock for biofuel production and nutraceutical applications.

Lipid production and characterization by Mortierella (Umbelopsis) isabellina cultivated on lignocellulosic sugars

AIMS

To study and characterize the lipids produced by Mortierella (Umbelopsis) isabellina, during its growth on mixtures of glucose and xylose.

METHODS AND RESULTS

Glucose and xylose were utilized as carbon sources, solely or in blends, under nitrogen-limited conditions, in batch-flask trials (initial sugars at 80 g l^-1 ). Significant lipid production (maximum lipid 17·8 g l^-1 ; lipid in DCW 61·0% w/w; lipid on glucose consumed 0·23 g g^-1 ) occurred on glucose employed solely, while xylose concentration in the growth medium was conversely correlated with lipid accumulation. With increasing xylose concentrations into the blend, lipid storage decreased while xylitol in significant concentrations (up to 24 g l^-1 ) was produced. Irrespective of the sugar blend employed, significant quantities of endopolysaccharides were detected in the first growth steps (in the presence of nitrogen into the medium or barely after its disappearance) while lipids were stored thereafter. Neutral lipids, mainly composed of triacylglycerols, were the main microbial lipid fraction. Phospholipids were quantified both through fractionation and subsequent gravimetric determination and also through determination of phosphorus, and it seemed that the second method was more accurate. Phospholipids were mainly composed of phosphatidylcholine and another nonidentified compound presumably being phosphatidyldimethylethanolamine.

CONCLUSIONS

Mortierella isabellina is suitable to convert lignocellulosic sugars into lipids.

SIGNIFICANCE AND IMPACT OF THE STUDY

Differentiations between metabolism on xylose and glucose were reported. Moreover, this is one of the first reports indicating extensive analysis of microbial lipids produced by M. isabellina.

Corn bran bioprocessing: Development of an integrated process for microbial lipids production

This study investigated the potential of corn bran as a feedstock for microbial lipid production using oleaginous yeast, Trichosporon oleaginosus ATCC20509. Different conditions (solid loading of biomass, acid loading, and pretreatment duration) were applied to optimize pretreatment processes using the Box-Behnken design. The highest sugar yield of 0.53g/g was obtained from corn bran hydrolysates at a pretreatment condition of 5% solid loading and 1% acid loading for 30min. Compared with synthetic media, up to 50% higher lipid accumulations in T. oleaginosus were achieved using corn bran hydrolysates during fermentation. Also, the direct effect of pretreatment condition on the lipid accumulation of T. oleaginosus was investigated using response surface methodology (RSM). Solid loading of biomass during the pretreatment process significantly affected the fermentation process for lipid accumulation of T. oleaginosus. The RSM model can provide useful information to design an integrated bioconversion platform.

Opportunities and challenges in the development of Cutaneotrichosporon oleaginosus ATCC 20509 as a new cell factory for custom tailored microbial oils

Cutaneotrichosporon oleaginosus ATCC 20509, previously known as Trichosporon oleaginosus, Cryptococcus curvatus, Apiotrichum curvatum or Candida curvata D is an oleaginous yeast with several favorable qualities: it is fast growing, accumulates high amounts of lipid and has a very broad substrate spectrum. Its resistance to hydrolysis byproducts and genetic accessibility make it a promising cell factory for custom tailored microbial oils. However, literature about this organism is of varying degree of quality. Moreover, due to numerous changes of the species name, reports are highly scattered and poorly cited. This led to a poor integration of the findings into a unified body of knowledge. Particularly, errors in strain name usage and consequently citation are found even in most recent literature. To simplify future work, this review provides an overview of published studies and main findings regarding the metabolic capacities of C. oleaginosus.

Nutritional Requirements and Their Importance for Virulence of Pathogenic Cryptococcus Species

Cryptococcus sp. are basidiomycete yeasts which can be found widely, free-living in the environment. Interactions with natural predators, such as amoebae in the soil, are thought to have promoted the development of adaptations enabling the organism to survive inside human macrophages. Infection with Cryptococcus in humans occurs following inhalation of desiccated yeast cells or spore particles and may result in fatal meningoencephalitis. Human disease is caused almost exclusively by the Cryptococcus neoformans species complex, which predominantly infects immunocompromised patients, and the Cryptococcus gattii species complex, which is capable of infecting immunocompetent individuals. The nutritional requirements of Cryptococcus are critical for its virulence in animals. Cryptococcus has evolved a broad range of nutrient acquisition strategies, many if not most of which also appear to contribute to its virulence, enabling infection of animal hosts. In this review, we summarise the current understanding of nutritional requirements and acquisition in Cryptococcus and offer perspectives to its evolution as a significant pathogen of humans.

Substrates and oxygen dependent citric acid production by Yarrowia lipolytica: insights through transcriptome and fluxome analyses

BACKGROUND

Unlike the well-studied backer yeast where catabolite repression represents a burden for mixed substrate fermentation, Yarrowia lipolytica, an oleaginous yeast, is recognized for its potential to produce single cell oils and citric acid from different feedstocks. These versatilities of Y. lipolytica with regards to substrate utilization make it an attractive host for biorefinery application. However, to develop a commercial process for the production of citric acid by Y. lipolytica, it is necessary to better understand the primary metabolism and its regulation, especially for growth on mixed substrate.

RESULTS

Controlling the dissolved oxygen concentration (pO2) in Y. lipolytica cultures enhanced citric acid production significantly in cultures grown on glucose in mono- or dual substrate fermentations, whereas with glycerol as mono-substrate no significant effect of pO2 was found on citrate production. Growth on mixed substrate with glucose and glycerol revealed a relative preference of glycerol utilization by Y. lipolytica. Under optimized conditions with pO2 control, the citric acid titer on glucose in mono- or in dual substrate cultures was 55 and 50 g/L (with productivity of 0.6 g/L*h in both cultures), respectively, compared to a maximum of 18 g/L (0.2 g/L*h) with glycerol in monosubstrate culture. Additionally, in dual substrate fermentation, glycerol limitation was found to trigger citrate consumption despite the presence of enough glucose in pO2-limited culture. The metabolic behavior of this yeast on different substrates was investigated at transcriptomic and 13C-based fluxomics levels.

CONCLUSION

Upregulation of most of the genes of the pentose phosphate pathway was found in cultures with highest citrate production with glucose in mono- or in dual substrate fermentation with pO2 control. The activation of the glyoxylate cycle in the oxygen limited cultures and the imbalance caused by glycerol limitation might be the reason for the re-consumption of citrate in dual substrate fermentations. This study provides interesting targets for metabolic engineering of this industrial yeast.

High lipid accumulation in Yarrowia lipolytica cultivated under double limitation of nitrogen and magnesium

Yarrowia lipolytica cultivated under double nitrogen and magnesium limitation, but not under single nitrogen or single magnesium limitation, produced 12.2g/l biomass containing 47.5% lipids, which corresponds to a lipid production 5.8g/l. These yields are the higher described in the literature for wild strains of Y. lipolytica. Transcription of ACL1 and ACL2, encoding for ATP-citrate lyase (ATP:CL) was observed even under non-oleaginous conditions but high activity of ATP:CL was only detected under oleaginous conditions induced by low or zero activity of NAD(+) dependent isocitrate dehydrogenase. The low activity of malic enzyme (ME), a NADPH donor in typical oleaginous microorganisms, indicated that ME may not be implicated in lipid biosynthesis in this yeast, and NADPH may be provided by the pentose phosphate pathway (PPP). These findings underline the essential role of magnesium in lipogenesis, which is currently quite unexplored. The presence of organic nitrogen in low concentrations during lipogenesis was also required, and this peculiarity was probably related with the PPP functioning, being the NADPH donor of lipogenic machinery in Y. lipolytica.

Glucose-mediated regulation of glycerol uptake in Rhodosporidium toruloides: Insights through transcriptomic analysis on dual substrate fermentation

Rhodosporidium toruloides is a robust oleaginous yeast that can accumulate lipids to more than 70% of its dry cell mass. Even though it is extensively studied for its fermentation of substrates like glucose and glycerol, limited information is available about its metabolism of mixture of glucose and glycerol. During growth on mixture of glucose and glycerol a typical diauxic growth and higher lipid yields were observed. To understand this phenomenon, RNA-seq analysis was implemented to study the gene expression profiles during growth on mixtures mainly to elucidate regulation of glycerol metabolism. Insights into lipid biosynthesis on mixed substrates are provided at a systems level. Among others, transcriptional profiles showed that glycerol might be produced intracellularly and glycerol kinase (GUT1) and glycerol 3-phosphate dehydrogenase (GUT2) enzymes were not downregulated in the presence of glucose. Transcriptional analysis also showed that the regulation of glycerol uptake in the presence of glucose at transcriptional level is different from that observed in Saccharomyces cerevisiae.

Conversion of biodiesel-derived glycerol into biotechnological products of industrial significance by yeast and fungal strains

Oleochemical activities (e.g. biodiesel production, fat saponification) generate annually very high amounts of concentrated glycerol-containing waters (called crude glycerol) as the principal residues of these processes. Crude glycerol is an industrial residue the valorization of which attracts remarkable and constantly increasing interest. In the current investigation, biodiesel-derived glycerol was employed as substrate for yeast and fungal strains cultivated under nitrogen-limited conditions in shake flasks. Glucose was employed as reference substrate. Several yeasts (Candida diddensiae, Candida tropicalis, Pichia ciferrii, Williopsis saturnus, Candida boidinii, and Candida oleophila) rapidly assimilated glucose and converted it into ethanol, despite aerobic conditions imposed, and were Crabtree-positive. None of these yeasts produced ethanol during growth on glycerol or accumulated significant quantities of lipid during growth on glucose or glycerol. Only Rhodosporidium toruloides produced notable lipid quantities from glucose and to lesser extent from glycerol. Yarrowia lipolytica LFMB 20 produced citrate ≈58 g/L growing on high-glucose media, while on high-glycerol media ≈42 g/L citrate and ≈18 g/L mannitol. During growth on glucose/glycerol blends, glycerol was assimilated first and thereafter glucose was consumed. Fungi produced higher lipid quantities compared with yeasts. High lipid quantities were produced by Mortierella ramanniana, Mucor sp., and mainly Mortierella isabellina, with glycerol being more adequate for M. ramanniana and glucose for Mucor sp. and M. isabellina. M. isabellina ATHUM 2935 produced lipids of 8.5 g/L, 83.3% w/w in dry cell weight (DCW) and conversion yield per unit of glucose consumed ≈0.25 g/g. The respective values on glycerol were 5.4 g/L, 66.6% w/w in DCW and ≈0.22 g/g. Lipids of all microorganisms were analyzed with regards to their fatty acid composition, and M. isabellina presented the closest similitude with rapeseed oil. Crude lipids produced by this fungus and extracted with chloroform/methanol blend, were composed mostly of triacylglycerols, thus indicating that these solvents are adequate for triacylglycerol extraction.

Production of Palmitoleic and Linoleic Acid in Oleaginous and Nonoleaginous Yeast Biomass

We investigated the possibility of utilizing both oleaginous yeast species accumulating large amounts of lipids (Yarrowia lipolytica, Rhodotorula glutinis, Trichosporon cutaneum, and Candida sp.) and traditional biotechnological nonoleaginous ones (Kluyveromyces polysporus, Torulaspora delbrueckii, and Saccharomyces cerevisiae) as potential producers of dietetically important major fatty acids. The main objective was to examine the cultivation conditions that would induce a high ratio of dietary fatty acids and biomass. Though genus-dependent, the type of nitrogen source had a higher influence on biomass yield than the C/N ratio. The nitrogen source leading to the highest lipid accumulation was potassium nitrate, followed by ammonium sulfate, which is an ideal nitrogen source supporting, in both oleaginous and nonoleaginous species, sufficient biomass growth with concomitantly increased lipid accumulation. All yeast strains displayed high (70–90%) content of unsaturated fatty acids in total cell lipids. The content of dietary fatty acids of interest, namely, palmitoleic acid and linoleic acid, reached in Kluyveromyces and Trichosporon strains over 50% of total fatty acids and the highest yield, over 280 mg per g of dry cell weight of these fatty acids, was observed in Trichosporon with ammonium sulfate as nitrogen source at C/N ratio 70.