Lipid and carotenoid production by Rhodotorula glutinis under irradiation/high-temperature and dark/low-temperature cultivation

Research progress on carotenoid production by Rhodosporidium toruloides

Carotenoids are natural lipophilic pigments, which have been proven to provide significant health benefits to humans, relying on their capacity to efficiently scavenge singlet oxygen and peroxyl radicals as antioxidants. Strains belonging to the genus Rhodosporidium represent a heterogeneous group known for a number of phenotypic traits including accumulation of carotenoids and lipids and tolerance to heavy metals and oxidative stress. As a representative of these yeasts, Rhodosporidium toruloides naturally produces carotenoids with high antioxidant activity and grows on a wide variety of carbon sources. As a result, R. toruloides is a promising host for the efficient production of more value-added lipophilic compound carotenoids, e.g., torulene and torularhodin. This review provides a comprehensive summary of the research progress on carotenoid biosynthesis in R. toruloides, focusing on the understanding of biosynthetic pathways and the regulation of key enzymes and genes involved in the process. Moreover, the relationship between the accumulation of carotenoids and lipid biosynthesis, as well as the stress from diverse abiotic factors, has also been discussed for the first time. Finally, several feasible strategies have been proposed to promote carotenoid production by R. toruloides. It is possible that R. toruloides may become a critical strain in the production of carotenoids or high-value terpenoids by genetic technologies and optimal fermentation processes. KEY POINTS: • Biosynthetic pathway and its regulation of carotenoids in Rhodosporidium toruloides were concluded • Stimulation of abiotic factors for carotenoid biosynthesis in R. toruloides was summarized • Feasible strategies for increasing carotenoid production by R. toruloides were proposed.

A chromosome-scale genome provides new insights into the typical carotenoid biosynthesis in the important red yeast Rhodotorula glutinis QYH-2023 with anti-inflammatory effects

Rhodotorula spp. has been studied as one powerful source for a novel cell factory with fast growth and its high added-value biomolecules. However, its inadequate genome and genomic annotation have hindered its widespread use in cosmetics and food industries. Rhodotorula glutinis QYH-2023, was isolated from rice rhizosphere soil, and the highest quality of the genome of the strain was obtained at chromosome level (18 chromosomes) than ever before in red yeast in this study. Comparative genomics analysis revealed that there are more key gene copies of carotenoids biosynthesis in R. glutinis QYH-2023 than other species of Rhodotorula spp. Integrated transcriptome and metabolome analysis revealed that lipids and carotenoids biosynthesis was significantly enriched during fermentation. Subsequent investigation revealed that the over-expression of the strain three genes related to carotenoids biosynthesis in Komagataella phaffii significantly promoted the carotenoid production. Furthermore, in vitro tests initially confirmed that the longer the fermentation period, the synthesized metabolites controlled by R. glutinis QYH-2023 genome had the stronger anti-inflammatory properties. All of the findings revealed a high-quality reference genome which highlight the potential of R. glutinis strains to be employed as chassis cells for biosynthesizing carotenoids and other active chemicals.

Integrated Transcriptomics and Metabolomics Analysis Reveal the Regulatory Mechanisms Underlying Sodium Butyrate-Induced Carotenoid Biosynthesis in Rhodotorula glutinis

Sodium butyrate (SB) is a histone deacetylase inhibitor that can induce changes in gene expression and secondary metabolite titers by inhibiting histone deacetylation. Our preliminary analysis also indicated that SB significantly enhanced the biosynthesis of carotenoids in the Rhodotorula glutinis strain YM25079, although the underlying regulatory mechanisms remained unclear. Based on an integrated analysis of transcriptomics and metabolomics, this study revealed changes in cell membrane stability, DNA and protein methylation levels, amino acid metabolism, and oxidative stress in the strain YM25079 under SB exposure. Among them, the upregulation of oxidative stress may be a contributing factor for the increase in carotenoid biosynthesis, subsequently enhancing the strain resistance to oxidative stress and maintaining the membrane fluidity and function for normal cell growth. To summarize, our results showed that SB promoted carotenoid synthesis in the Rhodotorula glutinis strain YM25079 and increased the levels of the key metabolites and regulators involved in the stress response of yeast cells. Additionally, epigenetic modifiers were applied to produce fungal carotenoid, providing a novel and promising strategy for the biosynthesis of yeast-based carotenoids.

Dissecting Holistic Metabolic Acclimatization of Mucor circinelloides WJ11 Defective in Carotenoid Biosynthesis

Mucor circinelloides WJ11 is a lipid-producing strain with industrial potential. A holistic approach using gene manipulation and bioprocessing development has improved lipid production and the strain's economic viability. However, the systematic regulation of lipid accumulation and carotenoid biosynthesis in M. circinelloides remains unknown. To dissect the metabolic mechanism underlying lipid and carotenoid biosynthesis, transcriptome analysis and reporter metabolites identification were implemented between the wild-type (WJ11) and ΔcarRP WJ11 strains of M. circinelloides. As a result, transcriptome analysis revealed 10,287 expressed genes, with 657 differentially expressed genes (DEGs) primarily involved in amino acid, carbohydrate, and energy metabolism. Integration with a genome-scale metabolic model (GSMM) identified reporter metabolites in the ΔcarRP WJ11 strain, highlighting metabolic pathways crucial for amino acid, energy, and nitrogen metabolism. Notably, the downregulation of genes associated with carotenoid biosynthesis and acetyl-CoA generation suggests a coordinated relationship between the carotenoid and fatty acid biosynthesis pathways. Despite disruptions in the carotenoid pathway, lipid production remains stagnant due to reduced acetyl-CoA availability, emphasizing the intricate metabolic interplay. These findings provide insights into the coordinated relationship between carotenoid and fatty acid biosynthesis in M. circinelloides that are valuable in applied research to design optimized strains for producing desired bioproducts through emerging technology.

Culturable yeast diversity in urban topsoil influenced by various anthropogenic impacts

In urban ecosystems, processes associated with anthropogenic influences almost always lead to changes in soil micromycete complexes. The taxonomic structure of soil micromycete complexes is an important informative parameter of soil bioindication in the ecological control of urban environments. Unicellular fungi, such as culturable yeasts, are a very suitable and promising object of microbiological research for monitoring urban topsoil. This review aims to give an overview of the yeast communities in urban topsoil in different areas of Moscow (heating main area, household waste storage and disposal area, highway area) and to discuss the changes in the taxonomic structure of culturable yeast complexes depending on the type and intensity of anthropogenic impact.

Production of single cell protein rich in potassium by Nectaromyces rattus using biogas slurry and molasses

Single-cell protein (SCP) is a vital supplement for animal protein feed. This study utilized biogas slurry and sugarcane molasses to ferment Nectaromyces rattus for the production of SCP. The optimal batch fermentation conditions were obtained in a 5L jar with a tank pressure of 0.1 MPa, an initial speed of 300 rpm, and an inoculum volume of 30%. The highest cell dry weight concentrations of the fed-batch fermentation without reflux and the fed-batch fermentation with reflux were 46.33 g/L and 29.71 g/L, respectively. The nitrogen conversion rates (47.05% and 44.12%) and the cell yields of total organic carbon (1 g/g and 1.17 g/g) of both fermentation modes were compared. The SCP contained 42.32% amino acids. Its high concentrations of potassium (19859.96 mg/kg) and phosphorus (7310.44 mg/kg) present a novel approach for the extraction of these essential nutrients from biogas slurry. The enrichment of K was related to the H+ efflux and sugar transport.

Utilization of olive mill wastewater for selective production of lipids and carotenoids by Rhodotorula glutinis

Olive mill wastewater (OMW) is a zero-cost substrate for numerous value-added compounds. Although several studies on the production of lipids and carotenoids by Rhodotorula glutinis in OMW exist, none of them has specifically focused on the conditions for a target lipid or carotenoid. This study presents cultivation conditions that selectively stimulate the cell biomass, individual carotenoids and lipids. It was found that supplemental carbon and nitrogen sources as well as illumination affected cell biomass the most. High temperature, low initial pH, illumination, lack of urea and presence of glycerol stimulated the lipid synthesis. The highest total lipid content obtained in undiluted OMW supplemented with urea was 11.08 ± 0.17% (w/w) whilst it was 41.40 ± 0.21% (w/w) when supplemented with glycerol. Moreover, the main fatty acid produced by R. glutinis in all media was oleic acid, whose fraction reached 63.94 ± 0.58%. Total carotenoid yield was significantly increased with low initial pH, high temperature, illumination, certain amounts of urea, glycerol and cultivation time. Up to 192.09 ± 0.16 μg/g cell carotenoid yield was achieved. Torularhodin could be selectively produced at high pH, low temperature and with urea and glycerol supplementation. To selectively induce torulene synthesis, cultivation conditions should have low pH, high temperature and illumination. In addition, low pH, high temperature and urea supplementation served high production of β-carotene. Up to 85.40 ± 0.76, 80.67 ± 1.40 and 39.45 ± 0.69% of torulene, torularhodin and β-carotene, respectively, were obtained under selected conditions. KEY POINTS: • Cultivation conditions selectively induced target carotenoids and lipids • 41.40 ± 0.21% (w/w) lipid content and 192.09 ± 0.16 μg/g cell carotenoid yield were achieved • Markedly high selectivity values for torularhodin and torulene were achieved.

Multi-omics analysis reveals the mechanism of torularhodin accumulation in the mutant Rhodosporidium toruloides A1-15 under nitrogen-limited conditions

A carotenoid production strain Rhodosporidium toruloides NP11 and its mutant strain R. toruloides A1-15 were studied under chemostat nitrogen-limited cultivation. Multi-omics analysis (metabolomics, lipidomics and transcriptomics) was used to investigate the different mechanisms of torularhodin accumulation between NP11 and A1-15. The results showed that the carotenoid synthesis pathway was significantly enhanced in A1-15 compared to NP11 under nitrogen limitation, due to the significant increase of torularhodin. Under nitrogen-limited conditions, higher levels of β-oxidation were present in A1-15 compared to those in NP11, which provided sufficient precursors for carotenoid synthesis. In addition, ROS stress accelerated the intracellular transport of iron ions, promoted the expression of CRTI and CRTY genes, and reduced the transcript levels of FNTB1 and FNTB2 in the bypass pathway, and these factors may be responsible for the regulation of high torularhodin production in A1-15. This study provided insights into the selective production of torularhodin.

Microalgae, Seaweeds and Aquatic Bacteria, Archaea, and Yeasts: Sources of Carotenoids with Potential Antioxidant and Anti-Inflammatory Health-Promoting Actions in the Sustainability Era

Carotenoids are a large group of health-promoting compounds used in many industrial sectors, such as foods, feeds, pharmaceuticals, cosmetics, nutraceuticals, and colorants. Considering the global population growth and environmental challenges, it is essential to find new sustainable sources of carotenoids beyond those obtained from agriculture. This review focuses on the potential use of marine archaea, bacteria, algae, and yeast as biological factories of carotenoids. A wide variety of carotenoids, including novel ones, were identified in these organisms. The role of carotenoids in marine organisms and their potential health-promoting actions have also been discussed. Marine organisms have a great capacity to synthesize a wide variety of carotenoids, which can be obtained in a renewable manner without depleting natural resources. Thus, it is concluded that they represent a key sustainable source of carotenoids that could help Europe achieve its Green Deal and Recovery Plan. Additionally, the lack of standards, clinical studies, and toxicity analysis reduces the use of marine organisms as sources of traditional and novel carotenoids. Therefore, further research on the processing of marine organisms, the biosynthetic pathways, extraction procedures, and examination of their content is needed to increase carotenoid productivity, document their safety, and decrease costs for their industrial implementation.

From Aquaculture to Aquaculture: Production of the Fish Feed Additive Astaxanthin by Corynebacterium glutamicum Using Aquaculture Sidestream

Circular economy holds great potential to minimize the use of finite resources, and reduce waste formation by the creation of closed-loop systems. This also pertains to the utilization of sidestreams in large-scale biotechnological processes. A flexible feedstock concept has been established for the industrially relevant Corynebacterium glutamicum, which naturally synthesizes the yellow C50 carotenoid decaprenoxanthin. In this study, we aimed to use a preprocessed aquaculture sidestream for production of carotenoids, including the fish feed ingredient astaxanthin by C. glutamicum. The addition of a preprocessed aquaculture sidestream to the culture medium did not inhibit growth, obviated the need for addition of several components of the mineral salt's medium, and notably enhanced production of astaxanthin by an engineered C. glutamicum producer strain. Improved astaxanthin production was scaled to 2 L bioreactor fermentations. This strategy to improve astaxanthin production was shown to be transferable to production of several native and non-native carotenoids. Thus, this study provides a proof-of-principle for improving carotenoid production by C. glutamicum upon supplementation of a preprocessed aquaculture sidestream. Moreover, in the case of astaxanthin production it may be a potential component of a circular economy in aquaculture.

Use of environmentally safe micromycetes of the genus <i>Rhodotorula</i> to obtain fodder carotene‐containing concentrate

Aim. The aim of the work was to study the possibility of using an environmentally friendly strain of yeast of the genus Rhodotorula for the bioconversion into fodder carotenoid‐containing biomass of the secondary product of processing pea flour into a protein concentrate (whey).

Material and Methods. We used a new strain of Rhodotorula mucilaginosa 111 and by‐products of processing pea and chickpea flour into protein concentrates and potatoes into starch (whey). We used standard and special methods for the analysis of serum and microbial‐vegetable concentrate (FMVC) namely: chemical; biochemical; microbiological; and the determination of toxicity with ciliates.

Results. Optimal conditions for growing R. mucilaginosa 111 on pea whey were determined (temperature 16.9°C, pH 7.8, amount of inoculum 1.85%). More biomass was synthesized on pea whey than on chickpea and potato whey – 81 g/dm3. The mass fraction of protein in the biomass is 58.90±3.03% on dry matter and the rate of essential amino acids is 119– 243%. Lipids included 20% saturated and 78% unsaturated fatty acids, linoleic acid – 45.26±0.70%, oleic – 24.04±0.76%, palmitoleic – 6.46±0.31%, palmitic – 13.70±0.81%. The yeast produced phytoin derivatives, torulene, β‐carotene, torularodin and phytoin. FMVC from pea whey stimulated the growth of ciliates Tetrahymena pyriformis by 29.1%, from chickpea whey (by 18.6% more intensively than distilled water), while potato whey reduced its growth rate.

Conclusion. The dry biomass of the ecologically safe new yeast strain R. mucilaginosa 111 contained complete proteins, lipids, minerals, and carotenoids necessary for feeding animals. Thus liquid pea whey can be used for its biokonversions, while avoiding environmental pollution.

Carotenoid biosynthesis is associated with low-temperature adaptation in Rhodosporidium kratochvilovae

BACKGROUND

Low temperatures greatly limit the growth of microorganisms. Low-temperature adaptation in microorganisms involves multiple mechanisms. Carotenoids are naturally occurring lipid-soluble pigments that act as antioxidants and protect cells and tissues from the harmful effects of free radicals and singlet oxygen. However, studies on the regulation of carotenoid biosynthesis at low temperatures in microorganisms are limited. In this study, we investigated the correlation between carotenoids and low-temperature adaptation in the cold-adapted strain of Rhodosporidium kratochvilovae YM25235.

RESULTS

Carotenoid biosynthesis in YM25235 was inhibited by knocking out the bifunctional lycopene cyclase/phytoene synthase gene (RKCrtYB) using the established CRISPR/Cas9 gene-editing system based on endogenous U6 promoters. The carotenoids were extracted with acetone, and the content and composition of the carotenoids were analyzed by spectrophotometry and HPLC. Then, the levels of reactive oxygen species (ROS) and the growth rate in YM25235 were determined at a low temperature. The results indicated that the carotenoid biosynthesis and ROS levels were increased in the YM25235 strain at a low temperature and inhibition of carotenoid biosynthesis was associated with higher ROS levels and a significant decrease in the growth rate of YM25235 at a low temperature.

CONCLUSIONS

The regulation of carotenoid biosynthesis was associated with low-temperature adaptation in YM25235. Our findings provided a strong foundation for conducting further studies on the mechanism by which YM25235 can adapt to low-temperature stress.

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.

Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues

Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.

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.

Yeasts Inhabiting Extreme Environments and Their Biotechnological Applications

Yeasts are microscopic fungi inhabiting all Earth environments, including those inhospitable for most life forms, considered extreme environments. According to their habitats, yeasts could be extremotolerant or extremophiles. Some are polyextremophiles, depending on their growth capacity, tolerance, and survival in the face of their habitat’s physical and chemical constitution. The extreme yeasts are relevant for the industrial production of value-added compounds, such as biofuels, lipids, carotenoids, recombinant proteins, enzymes, among others. This review calls attention to the importance of yeasts inhabiting extreme environments, including metabolic and adaptive aspects to tolerate conditions of cold, heat, water availability, pH, salinity, osmolarity, UV radiation, and metal toxicity, which are relevant for biotechnological applications. We explore the habitats of extreme yeasts, highlighting key species, physiology, adaptations, and molecular identification. Finally, we summarize several findings related to the industrially-important extremophilic yeasts and describe current trends in biotechnological applications that will impact the bioeconomy.

Culturing rhodotorula glutinis in fermentation-friendly deep eutectic solvent extraction liquor of lignin for producing microbial lipid

Currently, deep eutectic solvents (DES) have attracted increasing attention due to their excellent performance in delignification. However, few studies focused on the treatment of DES waste liquid after extraction of lignin. In this work, the fermentation-friendly DES comprised of glycerol, choline chloride (ChCl) and acetic acid (AA) was applied for delignification of lignocellulose. Subsequently, the extraction effects of different DES were investigated, and the DES extraction liquor was used for lipid production. Results shows ChCl made little difference to lipid synthesis, while excessive AA exerted inhibitory effect on the growth of cells. Following pretreatment, the delignification exceeded 63%. When the DES liquid obtained after lignin extraction was used to produce lipid, the delay period was obvious, while the lipid yield and content were unaffected. Not only is the DES prepared in this study effective in delignification of lignocellulose, it is also applicable as raw material to produce lipid.

Biotechnological Production of Carotenoids Using Low Cost-Substrates Is Influenced by Cultivation Parameters: A Review

Carotenoids are natural lipophilic pigments mainly found in plants, but also found in some animals and can be synthesized by fungi, some bacteria, algae, and aphids. These pigments are used in food industries as natural replacements for artificial colors. Carotenoids are also known for their benefits to human health as antioxidants and some compounds have provitamin A activity. The production of carotenoids by biotechnological approaches might exceed yields obtained by extraction from plants or chemical synthesis. Many microorganisms are carotenoid producers; however, not all are industrially feasible. Therefore, in this review, we provide an overview regarding fungi that are potentially interesting to industry because of their capacity to produce carotenoids in response to stresses on the cultivation medium, focusing on low-cost substrates.

Analysis of the light regulatory mechanism in carotenoid production in Rhodosporidium toruloides NBRC 10032

Light stimulates carotenoid production in an oleaginous yeast Rhodosporidium toruloides NBRC 10032 by promoting carotenoid biosynthesis genes. These genes undergo two-step transcriptional activation. The potential light regulator, Cryptochrome DASH (CRY1), has been suggested to contribute to this mechanism. In this study, based on KU70 (a component of nonhomologous end joining (NHEJ)) disrupting background, CRY1 disruptant was constructed to clarify CRY1 function. From analysis of CRY1 disruptant, it was suggested that CRY1 has the activation role of the carotenogenic gene expression. To obtain further insights into the light response, mutants varying carotenoid production were generated. Through analysis of mutants, the existence of the control two-step gene activation was proposed. In addition, our data analysis showed the strong possibility that R. toruloides NBRC 10032 is a homo-diploid strain.

Carotenoids and Some Other Pigments from Fungi and Yeasts

Carotenoids are an essential group of compounds that may be obtained by microbiological synthesis. They are instrumental in various areas of industry, medicine, agriculture, and ecology. The increase of carotenoids' demand at the global market is now essential. At the moment, the production of natural carotenoids is more expensive than obtaining their synthetic forms, but several new approaches/directions on how to decrease this difference were developed during the last decades. This review briefly describes the information accumulated until now about the beneficial effects of carotenoids on human health protection, their possible application in the treatments of various diseases, and their use in the food and feed industry. This review also describes some issues that are linked with biotechnological production of fungal and yeasts carotenoids, as well as new approaches/directions to make their biotechnological production more efficient.

Genomics and lipidomics analysis of the biotechnologically important oleaginous red yeast Rhodotorula glutinis ZHK provides new insights into its lipid and carotenoid metabolism

Background

Rhodotorula glutinis is recognized as a biotechnologically important oleaginous red yeast, which synthesizes numerous meritorious compounds with wide industrial usages. One of the most notable properties of R. glutinis is the formation of intracellular lipid droplets full of carotenoids. However, the basic genomic features that underlie the biosynthesis of these valuable compounds in R. glutinis have not been fully documented. To reveal the biotechnological potential of R. glutinis, the genomics and lipidomics analysis was performed through the Next-Generation Sequencing and HPLC-MS-based metabolomics technologies.

Results

Here, we firstly assemble the genome of R. glutinis ZHK into 21.8 Mb, containing 30 scaffolds and 6774 predicted genes with a N50 length of 14, 66,672 bp and GC content of 67.8%. Genome completeness assessment (BUSCO alignment: 95.3%) indicated the genome assembly with a high-quality features. According to the functional annotation of the genome, we predicted several key genes involved in lipids and carotenoids metabolism as well as certain industrial enzymes biosynthesis. Comparative genomics results suggested that most of orthologous genes have underwent the strong purifying selection within the five Rhodotorula species, especially genes responsible for carotenoids biosynthesis. Furthermore, a total of 982 lipids were identified using the lipidomics approaches, mainly including triacylglycerols, diacylglyceryltrimethylhomo-ser and phosphatidylethanolamine.

Conclusion

Using whole genome shotgun sequencing, we comprehensively analyzed the genome of R. glutinis and predicted several key genes involved in lipids and carotenoids metabolism. By performing comparative genomic analysis, we show that most of the ortholog genes have undergone strong purifying selection within the five Rhodotorula species. Furthermore, we identified 982 lipid species using lipidomic approaches. These results provided valuable resources to further advance biotechnological applications of R .glutinis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07244-z.

Modeling and optimization of microbial lipid fermentation from cellulosic ethanol wastewater by Rhodotorula glutinis based on the support vector machine

To establish the models of microbial lipid production from cellulosic ethanol wastewater by R. glutinis, the biomass, lipid yield, and COD removal rate were investigated under different conditions. Subsequently, the genetic algorithm based on SVM was adopted to optimize parameters for obtaining the maximum biomass. The results demonstrated that the initial COD and glucose content had a significant effect on lipids synthesis. Most of the organic matter in the wastewater was consumed with the production of lipid. Compared with BP-ANN, SVM had better fitting and generalization ability for small amount of experimental data. By genetic algorithm optimization based on SVM, the maximum biomass and lipid yield could reach 11.87 g/L and 2.18 g/L, respectively. The results suggest that the SVM model could be used as an effective tool to optimize fermentation conditions.

Lipid Production from Sugarcane Top Hydrolysate and Crude Glycerol with Rhodosporidiobolus fluvialis using a Two-Stage Batch-Cultivation Strategy with Separate Optimization of Each Stage

Lipids from oleaginous microorganisms, including oleaginous yeasts, are recognized as feedstock for biodiesel production. A production process development of these organisms is necessary to bring lipid feedstock production up to the industrial scale. This study aimed to enhance lipid production of low-cost substrates, namely sugarcane top and biodiesel-derived crude glycerol, by using a two-stage cultivation process with Rhodosporidiobolus fluvialis DMKU-SP314. In the first stage, sugarcane top hydrolysate was used for cell propagation, and in the second stage, cells were suspended in a crude glycerol solution for lipid production. Optimization for high cell mass production in the first stage, and for high lipid production in the second stage, were performed separately using a one-factor-at-a-time methodology together with response surface methodology. Under optimum conditions in the first stage (sugarcane top hydrolysate broth containing; 43.18 g/L total reducing sugars, 2.58 g/L soy bean powder, 0.94 g/L (NH₄)₂SO₄, 0.39 g/L KH₂PO₄ and 2.5 g/L MgSO₄ 7H₂O, pH 6, 200 rpm, 28 °C and 48 h) and second stage (81.54 g/L crude glycerol, pH 5, 180 rpm, 27 °C and 196 h), a high lipid concentration of 15.85 g/L, a high cell mass of 21.07 g/L and a high lipid content of 73.04% dry cell mass were obtained.

Effect of light on carotenoid and lipid production in the oleaginous yeast Rhodosporidium toruloides

The oleaginous yeast Rhodosporodium toruloides is receiving widespread attention as an alternative energy source for biofuels due to its unicellular nature, high growth rate and because it can be fermented on a large-scale. In this study, R. toruloides was cultured under both light and dark conditions in order to understand the light response involved in lipid and carotenoid biosynthesis. Our results from phenotype and gene expression analysis showed that R. toruloides responded to light by producing darker pigmentation with an associated increase in carotenoid production. Whilst there was no observable difference in lipid production, slight changes in the fatty acid composition were recorded. Furthermore, a two-step response was found in three genes (GGPSI, CAR1, and CAR2) under light conditions and the expression of the gene encoding the photoreceptor CRY1 was similarly affected.

C/N ratio and carbon source-dependent lipid production profiling in Rhodotorula toruloides

Microbial oils are lipids produced by oleaginous microorganisms, which can be used as a potential feedstock for oleochemical production. The oleaginous yeast Rhodotorula toruloides can co-produce microbial oils and high-value compounds from low-cost substrates, such as xylose and acetic acid (from hemicellulosic hydrolysates) and raw glycerol (a byproduct of biodiesel production). One step towards economic viability is identifying the best conditions for lipid production, primarily the most suitable carbon-to-nitrogen ratio (C/N). Here, we aimed to identify the best conditions and cultivation mode for lipid production by R. toruloides using various low-cost substrates and a range of C/N ratios (60, 80, 100, and 120). Turbidostat mode was used to achieve a steady state at the maximal specific growth rate and to avoid continuously changing environmental conditions (i.e., C/N ratio) that inherently occur in batch mode. Regardless of the carbon source, higher C/N ratios increased lipid yields (up to 60% on xylose at a C/N of 120) but decreased the specific growth rate. Growth on glycerol resulted in the highest specific growth and lipid production (0.085 g lipids/gDW*h) rates at C/Ns between 60 and 100. We went on to study lipid production using glycerol in both batch and fed-batch modes, which resulted in lower specific lipid production rates compared with turbisdostat, however, fed batch is superior in terms of biomass production and lipid titers. By combining the data we obtained in these experiments with a genome-scale metabolic model of R. toruloides, we identified targets for improvements in lipid production that could be carried out either by metabolic engineering or process optimization.

Manipulation of Culture Conditions: Tool for Correlating/Improving Lipid and Carotenoid Production by Rhodotorula glutinis

The coproduction of lipid and carotenoid by red yeasts in one cycle is more convenient and economical for the industrial sectors, while the kinetics correlation between both products under different culture conditions has been scarcely studied. This study is aiming to correlate the impact of different carbon sources, carbon to phosphorus ratio (C/P), temperature, aeration, pH, and metals on dry cell weight, lipid (GC and fluorescence microscope), and carotenoid (HPLC) production by Rhodotorula glutinis, and applying a novel feeding approach using a 5 L bioreactor to enhance carotenoid and unsaturated fatty acid production by R. glutinis. Whatever the culture condition is, the reversible correlation between lipid and carotenoid production was detected. Remarkably, when adding 0.1 mM BaCl2, cellular lipid was significantly increased 14% more than the control, with 79.3% unsaturated fatty acid (46% C18:2 and C18:3) and 50% γ-carotene, while adding 1 mM NiSO4, cellular carotenoid was enhanced around 53% than the control (torulene 88%) with 81% unsaturated fatty acid (61% oleic acid). Excitingly, 68.8 g/l biomass with 41% cellular lipid (79% unsaturated fatty acid) and 426 µgpigment/gdcw cellular carotenoid (29.3 mg/L) (71% torulene) were obtained, when the pH-temperature dual controlled process combined with metallo-sulfo-phospho-glucose feeding approach in the 5 L bioreactor during the accumulation phase was conducted. This is the first study on the kinetic correlation between lipid and carotenoid under different C/P ratio and the dual effect of different metals like NiSO4 on lipid and carotenoid production by red oleaginous yeasts, which in turn significant for enhancing the coproduction of lipid and carotenoid by R. glutinis.

Comparative Analysis of β-Carotene Production by Mucor circinelloides Strains CBS 277.49 and WJ11 under Light and Dark Conditions

Carotenoids are natural potent antioxidants and free radical scavengers which are able to modulate the pathogenesis of some cancers and heart diseases in human, indicating their importance in being provided through the diet. Mucor circinelloides accumulates β-carotene as the main carotenoid compound and has been used as a model organism in carotenogenic studies. In the present study, the potential of two M. circinelloides strains to accumulate β-carotene was investigated under light and dark conditions. The results, which were quantitated by HPLC, showed that CBS 277.49 accumulated higher pigment in comparison to WJ11 under both conditions. Continuous illumination triggered the pigment accumulation up to 2.7-fold in strain CBS 277.49 and 2.2-fold in strain WJ11 in comparison to dark. The mRNA analysis of the four key genes involved in isoprenoid pathway by RT-qPCR showed higher transcriptional levels in CBS 277.49 as compared to WJ11, indicating that the pigment production metabolic machinery is more active in CBS 277.49 strain. A new scope for further research was established by this work for improved β-carotene production in the high producing strain CBS 277.49.

Light irradiation can regulate the growth characteristics and metabolites compositions of Rhodotorula mucilaginosa

Light is an important factor that can induce the growth of varieties of organisms including fungi and their secondary metabolites. The evolutions of biomass, carotenoids, lipid production, compositions and contents of fatty acid and amino acid in Rhodotorula mucilaginosa were investigated under different light irradiation conditions. The results indicated that irradiation with 1700 lx could promote the growth and glucose assimilation of R. mucilaginosa, compared to the dark control, while the trial with 3500 lx had certain inhibiting effects. The carotenoids concentrations and percentages of unsaturated fatty acid (USFA, C16:1 and C18:1) increased with the improvement of irradiation intensity. Conversely, the proportions of saturated fatty acids (C16:0, C18:0 and C20:0) were decreased. The relative contents of amino acid and total protein were reduced under illumination compared to dark control. Conclusively, irradiation could change the cell growth and metabolites of the pigmented fungus, which implied that there may be a photoinduced mode exists in R. mucilaginosa similar to that of Neurospora crassa, and it also could be applied to regulate the biosynthesis and production of valuable components such as carotenoids and USFA.

Effect of exogenous stress factors on the biosynthesis of carotenoids and lipids by Rhodotorula yeast strains in media containing agro-industrial waste

In this study, we aimed to determine the effect of exogenous stress factors (sodium chloride as osmotic stressor, hydrogen peroxide as an inducer of oxidative stress, white light irradiation, and low temperature) on the biosynthesis of carotenoids and lipids by red yeast (Rhodotorula glutinis, R. mucilaginosa, and R. gracilis) during cultivation in media containing potato wastewater and glycerol. According to our results, the yeast were able to grow and biosynthesize lipids and carotenoids in the presence of the applied stress factors. Low temperature caused an increase in the biosynthesis of intracellular lipids and carotenoids. R. gracilis synthesized lipids (21.1 g/100 g_d.w.) and carotenoids (360.4 µg/g_d.w.) in greater quantities than that of other strains. Under these conditions, there was also an increase in the content of unsaturated fatty acids, especially linoleic and linolenic acids. The highest percentage of polyunsaturated fatty acid (PUFA) (30.4%) was synthesized by the R. gracilis yeast after cultivation at 20°C. Their quantity was 2.5-fold greater than that of the biomass grown in control conditions. The contribution of individual carotenoid fractions depended both on the yeast strain and the culture conditions. Induction of osmotic stress and low temperature intensified the biosynthesis of β-carotene (up to 73.9% of the total carotenoid content). In oxidative stress conditions, yeast synthesized torulene (up to 82.2%) more efficiently than under other conditions, whereas white light irradiation increased the production of torularhodin (up to 20.0%).

Comparative evaluation of different carbon sources supply on simultaneous production of lipid and carotene of Rhodotorula glutinis with irradiation and the assessment of key gene transcription

To investigate the feasibility of simultaneously enhancing lipid and carotene production by irradiation with different carbon sources, a strategy by controlling the carbon sources supply were selected to culture Rhodotorula glutinis under the irradiation condition. The results demonstrated that the irradiation indeed enhanced cell growth, lipid and carotene production with different carbon sources supply. Besides, the fatty acids profiling as revealed by more unsaturated fatty acids (mainly C16:1, C18:2 and C18:3) and less saturated fatty acids (C18:0, C22:0 and C24:0) were found during the process of irradiation. Compared with the control, the increase of the transcription levels in genes connected with substrates assimilation, lipid production and carotene accumulation were observed under the irradiation condition. The results suggest the possibility of using irradiation as an effective strategy to increase the production of both lipid and carotene with the controlled carbon sources supply.

Lipid and Carotenoid Production by Rhodotorula glutinis with a Combined Cultivation Mode of Nitrogen, Sulfur, and Aluminium Stress

Torulene is a promising pink pigment, produced only by yeasts and fungi, and its production is still in a developing stage due to the low production rate. Accordingly, this study focuses on maximizing torulene production by Rhodotorula glutinis using shaken flask fermentation. The effect of different nitrogen sources, and C/N and C/S ratios on lipid and carotenoid production by R. glutinis was studied using 60 g/L glucose. The largest cells filled with golden fluorescence lipid bodies were observed using fluorescence microscopy when peptone was used as a nitrogen source. The highest total pigment (0.947 mg/L) and carotenoid relative productivity (Car-RP) (89.04 µg/g) were obtained at C/N 146 and C/S 120, and with ammonium sulfate as a nitrogen source, with 62% torulene domination using High Performance Liquid Chromatography (HPLC) for identification. Under a high C/N ratio, regardless of the C/S ratio, the carotenoid synthesis rate decreased after three days while the lipid synthesis rate kept increasing to the sixth day. Interestingly, after adding 0.7 mM Al2(SO4)3 to the optimized medium, the total pigment and Car-RP (2.2 mg/L and 212.9 µg/g) sharply increased, producing around 2.16 mg/L torulene (98%) with around 50% decrease in lipid yield. This is the first report on the role of Al2(SO4)3 for enhancing torulene production under lipogenesis condition, which could be used as a potential tool for torulene production.

Enhancement of Torularhodin Production in Rhodosporidium toruloides by Agrobacterium tumefaciens-Mediated Transformation and Culture Condition Optimization

Nine transformants of Rhodosporidium toruloides with significant changes in the carotenoid profile were obtained by Agrobacterium tumefaciens-mediated transformation, including a white, three red, and four yellow mutants. A red mutant A1-15-BRQ that showed a high torularhodin production was selected for culture condition optimization. Results indicated that the torularhodin yield was boosted with glucose as the carbon source, at a carbon/nitrogen ratio of 22, a loading volume of 75 mL, and 28 °C. The torularhodin yield of 21.3 mg/L consisting of 94.4% total carotenoids was obtained by Box-Behnken design experiments. The torularhodin yield was 17.0-fold higher than that of the wild type, with time shortened from 9 to 3 days. This study reports an effective strategy for improving torularhodin production and provides a candidate R. toruloides strain for highly selective production of torularhodin.

Development of an Improved Carotenoid Extraction Method to Characterize the Carotenoid Composition under Oxidative Stress and Cold Temperature in the Rock Inhabiting Fungus Knufia petricola A95

Black yeasts are a highly specified group of fungi, which are characterized by a high resistance against stress factors. There are several factors enabling the cells to survive harsh environmental conditions. One aspect is the pigmentation, the melanin black yeasts often display a highly diverse carotenoid spectrum. Determination and characterization of carotenoids depend on an efficient extraction and separation, especially for black yeast, which is characterized by thick cell walls. Therefore, specific protocols are needed to ensure reliable analyses regarding stress responses in these fungi. Here we present both. First, we present a method to extract and analyze carotenoids and secondly we present the unusual carotenoid composition of the black yeast Knufia petricola A95. Mechanical treatment combined with an acetonitrile extraction gave us very good extraction rates with a high reproducibility. The presented extraction and elution protocol separates the main carotenoids (7) in K. petricola A95 and can be extended for the detection of additional carotenoids in other species. K. petricola A95 displays an unusual carotenoid composition, with mainly didehydrolycopene, torulene, and lycopene. The pigment composition varied in dependency to oxidative stress but remained relatively constant if the cells were cultivated under low temperature. Future experiments have to be carried out to determine if didehydrolycopene functions as a protective agent itself or if it serves as a precursor for antioxidative pigments like torulene and torularhodin, which could be produced after induction under stress conditions. Black yeasts are a promising source for carotenoid production and other substances. To unravel the potential of these fungi, new methods and studies are needed. The established protocol allows the determination of carotenoid composition in black yeasts.

Microbial lipid production and organic matters removal from cellulosic ethanol wastewater through coupling oleaginous yeasts and activated sludge biological method

In this paper, a novel strategy for lipid production through coupling oleaginous yeasts and activated sludge biological methods by cultivation of Rhodotorula glutinis in cellulosic ethanol wastewater was studied. Under optimal conditions in wastewater medium (dilution ratio of 1:2 and glucose supplement of 40 g/L), the maximum biomass and lipid content as well as the lipid yield reached 11.31 g/L, 18.35% and 2.08 g/L, with the associated removal rates of COD, TOC, NH₄⁺-N, TN and TP reaching 83.15%, 81.81%, 85.49%, 70.52% and 67.46%, respectively. Cellulosic ethanol wastewater treated by the anaerobic-aerobic biological process resulted in removal of COD, NH₄⁺-N, TP and TN reaching 67.55%, 94.17%, 90.16% and 48.89%, respectively. The reused water was used to dilute medium of R. glutinis for microbial lipid production reaching 2.38 g/L and caused positive effects on the accumulation of biomass and lipid.

Multi-omics metabolism analysis on irradiation-induced oxidative stress to Rhodotorula glutinis

Oxidative stress is induced in many organisms by various natural abiotic factors including irradiation. It has been demonstrated that it significantly improves growth rate and lipid production of Rhodotorula glutinis. However, the specific mechanism of how irradiation influences the metabolism of R. glutinis remains still unavailable. To investigate and better understand the mechanisms involved in irradiation-induced stress resistance in R. glutinis, a multi-omics metabolism analysis was implemented. The results confirmed that irradiation indeed not only improved cell biomass but also accelerated the production of carotenoids and lipids, especially neutral lipid. Compared with the control, metabolome profiling in the group exposed to irradiation exhibited an obvious difference in the activation of the tricarboxylic acid cycle and triglyceride (TAG) production. The results of proteome analysis (data are available via ProteomeXchange with identifier PXD009678) showed that 423 proteins were changed significantly, and proteins associated with protein folding and transport, the Hsp40 and Sec12, were obviously upregulated, indicating that cells responded to irradiation by accelerating the protein folding and transport of correctly folded proteins as well as enhanced the degradation of misfolded proteins. A significant upregulation of the carotenoid biosynthetic pathway was observed which revealed that increased carotenoid content is a cellular defense mechanism against oxidative stress generated by irradiation. Therefore, the results of comprehensive omics analysis provide intensive insights on the response mechanism of R. glutinis to irradiation-induced oxidative stress which could be helpful for using irradiation as an effective strategy to enhance the joint production of the neutral lipid and carotene.

Lipid and carotenoid synthesis by Rhodosporidium diobovatum, grown on glucose versus glycerol, and its biodiesel properties

Relationships between lipid and carotenoid synthesis by Rhodosporidium diobovatum were investigated for cell cultures in nitrogen-limited medium (GMY) containing equimolar amounts of carbon of glucose or glycerol. The cultures were also supplemented with additional substrate at 120 h postinoculation (pi) and during a fed-batch experiment. Growth of R. diobovatum on glucose resulted in higher yields of triacyglycerides (TAGs) and carotenoid than when grown on glycerol, even though the cultures contained equimolar amounts of carbon. After the addition of fresh substrate at 120 h pi, total carotenoid concentrations were significantly different from the concentrations measured at 120 h pi in both glucose and glycerol cultures, with no concomitant increase in lipid concentrations, suggesting that carotenoid synthesis is linked to exponential-phase growth, while lipid synthesis is linked to stationary phase. We also compared the calculated properties of biodiesel that could be made with TAGs derived from R. diobovatum with properties of biodiesel made from TAGs of other oleaginous yeasts, microalgae, vegetable oils, and animal fats. This study shows that R. diobovatum can be an effective strain for production of neutral lipids containing high percentages of oleic acid, palmitic acid, and linoleic acid, as well as carotenoids.

Torulene and torularhodin: "new" fungal carotenoids for industry?

Torulene and torularhodin represent the group of carotenoids and are synthesized by yeasts and fungi. The most important producers of these two compounds include yeasts of Rhodotorula and Sporobolomyces genera. The first reports confirming the presence of torulene and torularhodin in the cells of microorganisms date to the 1930s and 1940s; however, only in the past few years, the number of works describing the properties of these compounds increased. These compounds have strong anti-oxidative and anti-microbial properties, and thus may be successfully used as food, feedstock, and cosmetics additives. In addition, tests performed on rats and mice showed that both torulene and torularhodin have anti-cancerous properties. In order to commercialize the production of these two carotenoids, it is necessary to obtain highly efficient yeast strains, for example, via mutagenization and optimization of cultivation conditions. Further studies on the activity of torulene and torularhodin on the human body are also needed.

Growth and carotenogenesis in Rhodosporidium diobovatum IMB Y-5023: effects of culture medium and illumination intensity

The oleaginous yeast Rhodosporidium diobovatum is a poorly described producer of carotenoids and may be of interest in biotechnology. This study investigated the effects of culture medium and illumination on effective carotenoid production by R. diobovatum IMB Y-5023. Yeast was cultured on carrot, bran extract, and modified yeast malt (YM) medium at illuminations in the 0-5000 lx range. Biomass, total carotenoids and their profile were assessed after cultivation. In order to compare samples, cluster analysis and principal component analysis were used to visualize the relationships between the variables and samples. Results show that it is not illumination but culture medium that is the main factor determining the quantity and proportions of carotenoids produced by R. diobovatum IMB Y-5023. The yeast grew and produced pigments throughout the tested range of illumination intensity. The modified YM medium was optimal for carotenogenesis. In cultures on that medium, the highest carotenoid yields of 24.98 mg g-1 dry cell weight and 77 mg L-1 were recorded. It was found that this yeast is capable of assimilating oligosaccharides and can grow and produce carotenoids in low-glucose media containing DP3 and DP4. Moreover R. diobovatum IMB Y-5023 produced lycopene as the main pigment independently of the culture conditions.

Bioconversion of biodiesel-derived crude glycerol into lipids and carotenoids by an oleaginous red yeast Sporidiobolus pararoseus KM281507 in an airlift bioreactor

Here we tested the bioconversion of biodiesel-derived crude glycerol by the oleaginous red yeast Sporidiobolus pararoseus KM281507 in two bioreactors types (stirred-tank and airlift). High production yields (biomass, 10.62 ± 0.21 g/L; lipids, 3.26 ± 0.13 g/L; β-carotene, 30.64 ± 0.05 mg/L; total carotenoids, 46.59 ± 0.07 mg/L) were achieved in a 3.0 L airlift bioreactor under uncontrolled pH regimes (initial pH 5.63). Under optimized conditions (6.0 vvm aeration rate; 60 ± 5% constant dissolved oxygen [DO] maintained by flushing pure oxygen [O₂] into the vessel; 10,000 Lux light irradiation) volumetric production in the airlift bioreactor was further increased (biomass, 19.30 ± 1.07 g/L; lipids, 6.61 ± 0.04 g/L, β-carotene, 109.75 ± 0.21 mg/L; total carotenoids 151.00 ± 2.71 mg/L). Production was also recorded at a S. pararoseus KM281507 growth rate of 0.16 ± 0.00 h^-1 (lipids, 0.94 ± 0.04 g/L/d; β-carotene, 15.68 ± 0.40 mg/L/d; total carotenoids, 21.56 ± 0.20 mg/L/d). Lipids from S. pararoseus KM281507 had a high unsaturated fatty acid content, with oleic acid (C18:1) accounting for 80% of all fatty acids. This high oleic acid content makes S. pararoseus KM281507 well-suited as a third generation biodiesel feedstock. Our findings show that airlift bioreactors are suitable for bioconversion of crude glycerol into lipids and carotenoids using S. pararoseus KM281507. This approach is advantageous because of its ease of operation, cost efficiency, and low energy consumption.