Conversion of raw glycerol to microbial lipids by new Metschnikowia and Yarrowia lipolytica strains

Engineering Strategies for Efficient Bioconversion of Glycerol to Value-Added Products by Yarrowia lipolytica

Yarrowia lipolytica has been a valuable biotechnological workhorse for the production of commercially important biochemicals for over 70 years. The knowledge gained so far on the native biosynthetic pathways, as well as the availability of numerous systems and synthetic biology tools, enabled not only the regulation and the redesign of the existing metabolic pathways, but also the introduction of novel synthetic ones; further consolidating the position of the yeast in industrial biotechnology. However, for the development of competitive and sustainable biotechnological production processes, bioengineering should be reinforced by bioprocess optimization strategies. Although there are many published reviews on the bioconversion of various carbon sources to value-added products by Yarrowia lipolytica, fewer works have focused on reviewing up-to-date strain, medium, and process engineering strategies with an aim to emphasize the significance of integrated engineering approaches. The ultimate goal of this work is to summarize the necessary knowledge and inspire novel routes to manipulate at a systems level the yeast biosynthetic machineries by combining strain and bioprocess engineering. Due to the increasing surplus of biodiesel-derived waste glycerol and the favored glycerol-utilization metabolic pathways of Y. lipolytica over other carbon sources, the present review focuses on pure and crude glycerol-based biomanufacturing.

Tailoring and optimizing fatty acid production by oleaginous yeasts through the systematic exploration of their physiological fitness

Background

The use of palm oil for our current needs is unsustainable. Replacing palm oil with oils produced by microbes through the conversion of sustainable feedstocks is a promising alternative. However, there are major technical challenges that must be overcome to enable this transition. Foremost among these challenges is the stark increase in lipid accumulation and production of higher content of specific fatty acids. Therefore, there is a need for more in-depth knowledge and systematic exploration of the oil productivity of the oleaginous yeasts. In this study, we cultivated Cutaneotrichosporon oleaginosus and Yarrowia lipolytica at various C/N ratios and temperatures in a defined medium with glycerol as carbon source and urea as nitrogen source. We ascertained the synergistic effect between various C/N ratios of a defined medium at different temperatures with Response Surface Methodology (RSM) and explored the variation in fatty acid composition through Principal Component Analysis.

Results

By applying RSM, we determined a temperature of 30 °C and a C/N ratio of 175 g/g to enable maximal oil production by C. oleaginosus and a temperature of 21 °C and a C/N ratio of 140 g/g for Y. lipolytica. We increased production by 71% and 66% respectively for each yeast compared to the average lipid accumulation in all tested conditions. Modulating temperature enabled us to steer the fatty acid compositions. Accordingly, switching from higher temperature to lower cultivation temperature shifted the production of oils from more saturated to unsaturated by 14% in C. oleaginosus and 31% in Y. lipolytica. Higher cultivation temperatures resulted in production of even longer saturated fatty acids, 3% in C. oleaginosus and 1.5% in Y. lipolytica.

Conclusions

In this study, we provided the optimum C/N ratio and temperature for C. oleaginosus and Y. lipolytica by RSM. Additionally, we demonstrated that lipid accumulation of both oleaginous yeasts was significantly affected by the C/N ratio and temperature. Furthermore, we systematically analyzed the variation in fatty acids composition and proved that changing the C/N ratio and temperature steer the composition. We have further established these oleaginous yeasts as platforms for production of tailored fatty acids.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01956-5.

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.

Use of Waste Substrates for the Lipid Production by Yeasts of the Genus Metschnikowia-Screening Study

Oleogenic yeasts are characterized by the ability to accumulate increased amounts of lipids under certain conditions. These microbial lipids differ in their fatty acid composition, which allows them to be widely used in the biotechnology industry. The interest of biotechnologists is closely linked to the rising prices of fossil fuels in recent years. Their negative environmental impact is caused by significantly increased demand for biodiesel. The composition of microbial lipids is very similar to vegetable oils, which provides great potential for use in the production of biodiesel. In addition, some oleogenic microorganisms are capable of producing lipids with a high proportion of unsaturated fatty acids. The presented paper’s main aim was to study the production of lipids and lipid substances by yeasts of the genus Metschnikowia, to cultivate crude waste animal fat to study its utilization by yeasts, and to apply the idea of circular economy in the biotechnology of Metschnikowia yeasts. The work focuses on the influence of various stress factors in the cultivation process, such as reduced temperature or nutritional stress through the use of various waste substrates, together with manipulating the ratio of carbon and nitrogen sources in the medium. Yeast production properties were monitored by several instrumental techniques, including gas chromatography and Raman spectroscopy. The amount of lipids and in particular the fatty acid composition varied depending on the strains studied and the culture conditions used. The ability of yeast to produce significant amounts of unsaturated fatty acids was also demonstrated in the work. The most suitable substrate for lipid production was a medium containing glycerol, where the amount of accumulated lipids in the yeast M. pulcherrima 1232 was up to 36%. In our work, the crude animal fat was used for the production of high-value lipids, which to the best of our knowledge is a new result. Moreover, quantitative screening of lipase enzyme activity cultivated on animal fat substrate on selected yeasts of the genus Metschnikowia was performed. We found that for the yeast utilizing glycerol, animal fat seems to be an excellent source of carbon. Therefore, the yeast conversion of crude processed animal fat to value-added products is a valuable process for the biotechnology and food industry.

Possible Dietary Effects of Insect-Based Diets across Zebrafish (Danio rerio) Generations: A Multidisciplinary Study on the Larval Phase

Insects represent a valuable and sustainable alternative ingredient for aquafeed formulation. However, insect-based diets have often highlighted controversial results in different fish species, especially when high inclusion levels were used. Several studies have demonstrated that nutritional programming through parental feeding may allow the production of fish better adapted to use sub-optimal aquafeed ingredients. To date, this approach has never been explored on insect-based diets. In the present study, five experimental diets characterized by increasing fish meal substitution levels with full-fat Black Soldier Fly (Hermetia illucens; BSF) prepupae meal (0%, 25%, 50%, 75% and 100%) were used to investigate the effects of programming via broodstock nutrition on F1 zebrafish larvae development. The responses of offspring were assayed through biometric, gas chromatographic, histological, and molecular analyses. The results evidenced that the same BSF-based diets provided to adults were able to affect F1 zebrafish larvae fatty acid composition without impairing growth performances, hepatic lipid accumulation and gut health. Groups challenged with higher BSF inclusion with respect to fish meal (50%, 75% and 100%) showed a significant downregulation of stress response markers and a positive modulation of inflammatory cytokines gene expression. The present study evidences that nutritional programming through parental feeding may make it possible to extend the fish meal substitution level with BSF prepupae meal in the diet up to almost 100% without incurring the well-known negative side effects of BSF-based diets.

The Use of Raman Spectroscopy to Monitor Metabolic Changes in Stressed Metschnikowia sp. Yeasts

Raman spectroscopy is a universal method designed for the analysis of a wide range of physical, chemical and biological systems or various surfaces. This technique is suitable to monitor various components of cells, tissues or microorganisms. The advantages include very fast non-contact and non-destructive analysis and no or minimal need for sample treatment. The yeasts Metschnikowia can be considered as industrially usable producers of pulcherrimin or single-cell lipids, depending on cultivation conditions and external stress. In the present study, Raman spectroscopy was used as an effective tool to identify both pulcherrimin and lipids in single yeast cells. The analysis of pulcherrimin is very demanding; so far, there is no optimal procedure to analyze or identify this pigment. Based on results, the strong dependence of pulcherrimin production on the ferric ion concentration was found with the highest yield in media containing 0.1 g/L iron. Further, production of lipids in Metschnikowia cells was studied at different temperatures and C:N ratios, using Raman spectroscopy to follow fatty acids composition, under different regimes, by monitoring the iodine number. The results of Raman spectroscopy were comparable with the fatty acid analysis obtained by gas chromatography. This study therefore supported use of Raman spectroscopy for biotechnological applications as a simple tool in the identification and analysis both the pulcherrimin and microbial lipids. This method provides a quick and relatively accurate estimation of targeted metabolites with minimal sample modification and allows to monitor metabolic changes over time of cultivation.

Physiological responses of Siberian sturgeon (Acipenser baerii) juveniles fed on full-fat insect-based diet in an aquaponic system

Over the last years, the potential use of Black Soldier Fly meal (BSF) as a new and sustainable aquafeed ingredient has been largely explored in several fish species. However, only fragmentary information is available about the use of BSF meal-based diets in sturgeon nutrition. In consideration of a circular economy concept and a more sustainable aquaculture development, the present research represents the first comprehensive multidisciplinary study on the physiological effects of a BSF diet during sturgeon culture in an aquaponic system. Siberian sturgeon (Acipenser baerii) juveniles were fed over a 60-days feeding trial on a control diet (Hi0) and a diet containing 50% of full-fat BSF meal respect to fish meal (Hi50). Physiological responses of fish were investigated using several analytical approaches, such as gas chromatography-mass spectrometry, histology, Fourier Transformed Infrared Spectroscopy (FTIR), microbiome sequencing and Real-time PCR. While aquaponic systems performed optimally during the trial, Hi50 group fish showed lower diet acceptance that resulted in growth and survival reduction, a decrease in hepatic lipids and glycogen content (FTIR), a higher hepatic hsp70.1 gene expression and a worsening in gut histological morphometric parameters. The low feed acceptance showed by Hi50 group sturgeon highlighted the necessity to improve the palatability of BSF-based diet designed for sturgeon culture.

Can Insect-Based Diets Affect Zebrafish (Danio rerio) Reproduction? A Multidisciplinary Study

Black Soldier Fly (BSF) meal is considered an alternative, emerging, and sustainable ingredient for aquafeed formulation. However, results on fish physiological responses are still fragmentary and often controversial, and no data are available on the effect of insect meal-based diets on fish reproduction. On this regard, zebrafish, with its relatively short life cycle, represents an ideal experimental model to explore this topic. In this study, female zebrafish were fed for 12 months on a control diet based on fish meal (FM) and fish oil and two experimental diets with full-fat BSF (Hermetia illucens) prepupae meal inclusion, to replace 25% and 50% of FM (BSF25 and BSF50). All diets were isonitrogenous, isolipidic, and isoenergetic. The effects of these two experimental diets on female's reproduction were investigated through a multidisciplinary approach, including the evaluation of growth, gonadosomatic index, spawned/fertilized eggs and hatching rate, adult female carcass and fertilized egg fatty acid composition, histological analysis of the ovary, spectroscopic macromolecular composition of class IV oocytes, and expression of genes involved in fish lipid metabolism in the liver. Results showed that while fish were perfectly able to cope with a 25% insect meal dietary inclusion, a 50% inclusion level caused the overexpression of genes involved in lipid metabolism, a general reduction in the number of spawned eggs, and differences in the frequency rate of previtellogenic oocytes, class III, IV, oocytes and postovulatory follicles and atretic oocytes, in the macromolecular composition of class IV oocytes, and in the fatty acid composition of the fertilized eggs, respect to control and 25% group.

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).

Zebrafish (Danio rerio) physiological and behavioural responses to insect-based diets: a multidisciplinary approach

Black Soldier Fly (BSF) meal is considered as an alternative, emerging and sustainable ingredient for aquafeed production. However, results on fish physiological responses are still fragmentary and often controversial, while no studies are available on fish behavior in response to these new diets. The present work represents the first comprehensive multidisciplinary study aimed to investigate zebrafish physiological and behavioural responses to BSF-based diets. Five experimental diets characterized by increasing inclusion levels (0, 25, 50, 75 and 100% respect to fish meal) of full fat BSF prepupae meal were tested during a 2-months feeding trial. Prepupae were cultured on coffee silverskin growth substrate enriched with a 10% Schizochytrium sp. to improve insects’ fatty acids profile. The responses of zebrafish were assayed through biometric, histological, gas chromatographic, microbiological, spectroscopic, molecular and behavioural analyses. Results evidenced that BSF-based diets affected fish fatty acid composition, while behavioural tests did not show differences among groups. Specifically, a 50% BSF inclusion level diet represented the best compromise between ingredient sustainability and proper fish growth and welfare. Fish fed with higher BSF inclusions (75 and 100%) showed hepatic steatosis, microbiota modification, higher lipid content, fatty acid modification and higher expression of immune response markers.

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.

Evaluation of synthetic formaldehyde and methanol assimilation pathways in Yarrowia lipolytica

Background

Crude glycerol coming from biodiesel production is an attractive carbon source for biological production of chemicals. The major impurity in preparations of crude glycerol is methanol, which is toxic for most microbes. Development of microbes, which would not only tolerate the methanol, but also use it as co-substrate, would increase the feasibility of bioprocesses using crude glycerol as substrate.

Results

To prevent methanol conversion to CO₂ via formaldehyde and formate, the formaldehyde dehydrogenase (FLD) gene was identified in and deleted from Yarrowia lipolytica. The deletion strain was able to convert methanol to formaldehyde without expression of heterologous methanol dehydrogenases. Further, it was shown that expression of heterologous formaldehyde assimilating enzymes could complement the deletion of FLD. The expression of either 3-hexulose-6-phosphate synthase (HPS) enzyme of ribulose monosphosphate pathway or dihydroxyacetone synthase (DHAS) enzyme of xylulose monosphosphate pathway restored the formaldehyde tolerance of the formaldehyde sensitive Δfld1 strain.

Conclusions

In silico, the expression of heterologous formaldehyde assimilation pathways enable Y. lipolytica to use methanol as substrate for growth and metabolite production. In vivo, methanol was shown to be converted to formaldehyde and the enzymes of formaldehyde assimilation were actively expressed in this yeast. However, further development is required to enable Y. lipolytica to efficiently use methanol as co-substrate with glycerol.

Achieving a high-density oleaginous yeast culture: Comparison of four processing strategies using Metschnikowia pulcherrima

Microbial lipids have the potential to displace terrestrial oils for fuel, value chemical, and food production, curbing the growth in tropical oil plantations and helping to reduce deforestation. However, commercialization remains elusive partly due to the lack of suitably robust organisms and their low lipid productivity. Extremely high cell densities in oleaginous cultures are needed to increase reaction rates, reduce reactor volume, and facilitate downstream processing. In this investigation, the oleaginous yeast Metschnikowia pulcherrima, a known antimicrobial producer, was cultured using four different processing strategies to achieve high cell densities and gain suitable lipid productivity. In batch mode, the yeast demonstrated lipid contents more than 40% (w/w) under high osmotic pressure. In fed-batch mode, however, high-lipid titers were prevented through inhibition above 70.0 g L^-1 yeast biomass. Highly promising were a semi-continuous and continuous mode with cell recycle where cell densities of up to 122.6 g L^-1 and maximum lipid production rates of 0.37 g L^-1  h^-1 (daily average), a nearly two-fold increase from the batch, were achieved. The findings demonstrate the importance of considering multiple fermentation modes to achieve high-density oleaginous yeast cultures generally and indicate the limitations of processing these organisms under the extreme conditions necessary for economic lipid production.

Comparison of Three Deoxidation Agents for Ozonated Broths Used in Anaerobic Biotechnological Processes

Anaerobic fermentation of organic compounds is used in many biotechnological processes and has been the subject of much research. A variety of process conditions and different growth media can be used to obtain microbial metabolites. The media must be free from contamination before fermentation. Sterilization is most often achieved by applying heat or other treatments, such as ozonation. Sterilization of liquid media using ozone can be very beneficial, but this method introduces high concentrations of residual oxygen, which inhibit anaerobic processes. Deoxidation is therefore necessary to remove the oxygen from ozonated broths. This study evaluates the effectiveness of three deoxidation agents for two kinds of fermentation media based on malt or molasses: ultrasound, iron(II) sulfate, and Metschnikowia sp. yeast. The time needed for deoxidation varied, depending on the kind of broth and the deoxidation agent. In general, the dynamics of oxygen removal were faster in malt broth. A comparative analysis showed that yeast biomass was the most effective agent, achieving deoxidation in the shortest time. Moreover, the fully deoxidated broth was supplemented with yeast biomass, which is rich in biogenic substrates, expressed as a protein content of 0.13–0.73 g/L. Application of Metschnikowia sp. may therefore be considered as an effective strategy for simultaneous deoxidation and nutrient supplementation of broths used in anaerobic biotechnological processes.

Heat shock influences the fatty acid composition of the muscle of the Antarctic fish Trematomus bernacchii

In the Ross Sea region (average temperature of -1.87 °C), shelf water warming up to +0.8-+1.4 °C is predicted by 2200, so there is an urgent need to understand how organisms can respond to rising temperatures. In this study, we analyzed the effect of a heat shock on the fatty acid (FAs) composition of muscle of the Antarctic teleost Trematomus bernacchii, caught in Terra Nova Bay (Ross Sea), and held in fish tanks at 0, +1 or +2 °C, for 1, 5 and 10 days. In general, heat shock produced, beyond a reduction in total lipid content correlated to the temperature, an increase in the percentage of saturated FAs, and a decrease in mono-unsaturated FAs; however, the level of poly-unsaturated FAs did not seem to directly correlate with temperature. Principal component analysis indicated that both temperature and exposure time affect the composition of FAs in the muscle probably through an alteration of the metabolic pathways of FAs. In this study, we demonstrated that T. bernacchii was capable to rapidly acclimatize to a heat shock. This study contributes to increasing knowledge on the effect of temperature on the lipid composition of T. bernacchii and is complementary to previous studies on the gene expression and biochemistry of this species face multiple stressors.

A multidisciplinary approach to study the reproductive biology of wild prawns

This work aims to provide deeper knowledge on reproductive biology of P. kerathurus in a multidisciplinary way. Upon 789 examined females, 285 were found inseminated. The logistic equation enabled to estimate the size at first maturity at 30.7 mm CL for female. The Gono-Somatic Index (GSI) showed a pronounced seasonality, ranged from 0.80 ± 0.34 to 11.24 ± 5.72. Histological analysis highlighted five stages of ovarian development. Gonadal fatty acids analysis performed with gas chromatograph evidenced a pronounced seasonal variation; total lipids varied from 1.7% dry weight (dw) in Winter, to 7.2% dw in Summer. For the first time, a chemometric approach (Principal Component Analysis) was applied to relate GSI with total lipid content and fatty acid composition of gonads. The first two components (PC1 and PC2) showed that seasonality explained about 84% of the variability of all data set. In particular, in the period February-May, lipids were characterized by high PUFAs content, that were probably utilized during embryogenesis as energy source and as constituent of the cell membranes. During the summer season, gonads accumulated saturated FAs, that will be used during embryogenesis and early larval stages, while in the cold season total lipids decreased drastically and the gonad reached a quiescent state.

From low-cost substrates to Single Cell Oils synthesized by oleaginous yeasts

As new feedstock for biofuels, microbial oils have received worldwide attentions due to their environmentally-friendly characters. Microbial oil production based on low-cost raw materials is significantly attractive to the current biodiesel refinery industry. In terms of SCOs production, oleaginous yeast has numerous advantages over bacteria, molds and microalgae based on their high growth rate and lipid yield. Numerous efforts have been made on the competitive lipid production combining the use of cheap raw materials as substrates by yeasts. In this paper, we provided an overview of lipid metabolism in yeast cells. New advances using oleaginous yeast as a cell factory for high-value lipid production from various low-cost substrates are also reviewed, and the enhanced strategies based on synergistic effects of oleaginous yeast and microalgae in co-culture are discussed in details.