Efficient simultaneous production of extracellular polyol esters of fatty acids and intracellular lipids from inulin by a deep-sea yeast Rhodotorula paludigena P4R5

Engineering oleaginous red yeasts as versatile chassis for the production of oleochemicals and valuable compounds: Current advances and perspectives

Enabling the transition towards a future circular bioeconomy based on industrial biomanufacturing necessitates the development of efficient and versatile microbial platforms for sustainable chemical and fuel production. Recently, there has been growing interest in engineering non-model microbes as superior biomanufacturing platforms due to their broad substrate range and high resistance to stress conditions. Among these non-conventional microbes, red yeasts belonging to the genus Rhodotorula have emerged as promising industrial chassis for the production of specialty chemicals such as oleochemicals, organic acids, fatty acid derivatives, terpenoids, and other valuable compounds. Advancements in genetic and metabolic engineering techniques, coupled with systems biology analysis, have significantly enhanced the production capacity of red yeasts. These developments have also expanded the range of substrates and products that can be utilized or synthesized by these yeast species. This review comprehensively examines the current efforts and recent progress made in red yeast research. It encompasses the exploration of available substrates, systems analysis using multi-omics data, establishment of genome-scale models, development of efficient molecular tools, identification of genetic elements, and engineering approaches for the production of various industrially relevant bioproducts. Furthermore, strategies to improve substrate conversion and product formation both with systematic and synthetic biology approaches are discussed, along with future directions and perspectives in improving red yeasts as more versatile biotechnological chassis in contributing to a circular bioeconomy. The review aims to provide insights and directions for further research in this rapidly evolving field. Ultimately, harnessing the capabilities of red yeasts will play a crucial role in paving the way towards next-generation sustainable bioeconomy.

Diversity and Antifungal Susceptibilities of Yeasts from Mangroves in Hong Kong, China-A One Health Aspect

While mangrove ecosystems are rich in biodiversity, they are increasingly impacted by climate change and urban pollutants. The current study provides first insights into the emergence of potentially pathogenic yeasts in Hong Kong's mangroves. Sediment and water samples were collected from ten urban and rural mangroves sites. Initial CHROMagarTM Candida Plus screening, representing the first application of this differential medium for water and soil samples collected from a non-clinical environment, enabled the rapid, preliminary phenotypic identification of yeast isolates from mangroves. Subsequent molecular profiling (ITS and/or 28S nrDNA sequencing) and antifungal drug susceptibility tests were conducted to further elucidate yeast diversity and drug resistance. A diversity of yeasts, including 45 isolates of 18 distinct species across 13 genera/clades, was isolated from sediments and waters from Hong Kong mangroves. Molecular profiling revealed a dominance of the Candida/Lodderomyces clade (44.4%), a group of notorious opportunistic pathogens. The findings also reveal a rich biodiversity of non-Candida/Lodderomyces yeasts in mangroves, including the first reported presence of Apiotrichum domesticum and Crinitomyces flavificans. A potentially novel Yamadazyma species was also discovered. Remarkably, 14.3% of the ubiquitous Candida parapsilosis isolates displayed resistance to multiple antifungal drugs, suggesting that mangroves may be reservoirs of multi-drug resistance. Wildlife, especially migratory birds, may disseminate these hidden threats. With significant knowledge gaps regarding the environmental origins, drug resistance, and public health impacts of pathogenic yeasts, urgent surveillance is needed from a One Health perspective. This study provides an early warning that unrestrained urbanization can unleash resistant pathogens from coastal ecosystems globally. It underscores the necessity for enhanced surveillance studies and interdisciplinary collaboration between clinicians, ornithologists, and environmental microbiologists to effectively monitor and manage this environmental health risk, ensuring the maintenance of 'One Health'.

Draft genome sequence of Rhodotorula sp. BUB8, an oleaginous yeast isolated from Mt. Makiling Forest Reserve, Laguna, Philippines

This paper reports the draft genome sequence of Rhodotorula sp. BUB8, an oleaginous yeast isolated from the forest canopy of Mt. Makiling Forest Reserve in the Philippines. The draft genome is 20,394,133 bp with 64.3% guanine-cytosine (GC) content, 6,604 coding genes, 109 tRNA coding, and 6 snRNA-coding genes.

Comparative genomic analysis and optimization of astaxanthin production of Rhodotorula paludigena TL35-5 and Rhodotorula sampaioana PL61-2

Astaxanthin is a powerful antioxidant known to enhance skin, cardiovascular, eye, and brain health. In this study, the genome insights and astaxanthin production of two newly isolated astaxanthin-producing yeasts (TL35-5 and PL61-2) were evaluated and compared. Based on their phenotypic and genotypic characteristics, TL35-5 and PL61-2 were identified as basidiomycetous yeasts belonging to Rhodotorula paludigena and Rhodotorula sampaioana, respectively. To optimize astaxanthin production, the effects of cultural medium composition and cultivation conditions were examined. The optimal conditions for astaxanthin production in R. paludigena TL35-5 involved cultivation in AP medium containing 10 g/L glucose as the sole carbon source, supplemented with 1.92 g/L potassium nitrate, pH 6.5, and incubation at 20°C for 3 days with shaking at 200 rpm. For R. sampaioana PL61-2, the optimal medium composition for astaxanthin production consisted of AP medium with 40 g/L glucose, supplemented with 0.67 g/L urea, pH 7.5, and the fermentation was carried out at 20°C for 3 days with agitating at 200 rpm. Under their optimal conditions, R. paludigena TL35-5 and R. sampaioana PL61-2 gave the highest astaxanthin yields of 3.689 ± 0.031 and 4.680 ± 0.019 mg/L, respectively. The genome of TL35-5 was 20,982,417 bp in length, with a GC content of 64.20%. A total of 6,789 protein-encoding genes were predicted. Similarly, the genome of PL61-2 was 21,374,169 bp long, with a GC content of 64.88%. It contained 6,802 predicted protein-encoding genes. Furthermore, all essential genes involved in astaxanthin biosynthesis, including CrtE, CrtYB, CrtI, CrtS, and CrtR, were identified in both R. paludigena TL35-5 and R. sampaioana PL61-2, providing evidence for their ability to produce astaxanthin.

Exploring fungal bioemulsifiers: insights into chemical composition, microbial sources, and cross-field applications

The demand for emulsion-based products is crucial for economic development and societal well-being, spanning diverse industries such as food, cosmetics, pharmaceuticals, and oil extraction. Formulating these products relies on emulsifiers, a distinct class of surfactants. However, many conventional emulsifiers are derived from petrochemicals or synthetic sources, posing potential environmental and human health risks. In this context, fungal bioemulsifiers emerge as a compelling and sustainable alternative, demonstrating superior performance, enhanced biodegradability, and safety for human consumption. From this perspective, the present work provides the first comprehensive review of fungal bioemulsifiers, categorizing them based on their chemical nature and microbial origin. This includes polysaccharides, proteins, glycoproteins, polymeric glycolipids, and carbohydrate-lipid-protein complexes. Examples of particular interest are scleroglucan, a polysaccharide produced by Sclerotium rolfsii, and mannoproteins present in the cell walls of various yeasts, including Saccharomyces cerevisiae. Furthermore, this study examines the feasibility of incorporating fungal bioemulsifiers in the food and oil industries and their potential role in bioremediation events for oil-polluted marine environments. Finally, this exploration encourages further research on fungal bioemulsifier bioprospecting, with far-reaching implications for advancing sustainable and eco-friendly practices across various industrial sectors.

Genomic analysis of the marine yeast Rhodotorula sphaerocarpa ETNP2018 reveals adaptation to the open ocean

BACKGROUND

Despite a rising interest in the diversity and ecology of fungi in marine environments, there are few published genomes of fungi isolated from the ocean. The basidiomycetous yeast (unicellular fungus) genus Rhodotorula are prevalent and abundant in the open ocean, and they have been isolated from a wide range of other environments. Many of these environments are nutrient poor, such as the Antarctica and the Atacama deserts, raising the question as to how Rhodotorula yeasts may have adapted their metabolic strategies to optimize survival under low nutrient conditions. In order to understand their adaptive strategies in the ocean, the genome of R. sphaerocarpa ETNP2018 was compared to that of fourteen representative Rhodotorula yeasts, isolated from a variety of environments.

RESULTS

Rhodotorula sphaerocarpa ETNP2018, a strain isolated from the oligotrophic part of the eastern tropical North Pacific (ETNP) oxygen minimum zone (OMZ), hosts the smallest of the fifteen genomes and yet the number of protein-coding genes it possesses is on par with the other strains. Its genome exhibits a distinct reduction in genes dedicated to Major Facilitator Superfamily transporters as well as biosynthetic enzymes. However, its core metabolic pathways are fully conserved. Our research indicates that the selective pressures of the ETNP OMZ favor a streamlined genome with reduced overall biosynthetic potential balanced by a stable set of core metabolisms and an expansion of mechanisms for nutrient acquisition.

CONCLUSIONS

In summary, this study offers insights into the adaptation of fungi to the oligotrophic ocean and provides valuable information for understanding the ecological roles of fungi in the ocean.

Are all yeast biosurfactants really capable of lowering surface tension below 30 mN/m ?

The study discusses pitfalls in attempts to determine reliable surface tension values for the culture media and their extracts for two biosurfactant-producing yeast strains: Rhodotorula graminis and Rhodotorula babjevae. The values obtained from an Axisymmetric Drop Shape Analysis (ADSA) tensiometer showed systematically more and more shallow dynamic surface tension decays, suggesting a deterioration of their surface activity. The rate of this apparent surface activity loss was shown to depend on the sample history, with slower changes observed in vigorously shaken samples. On the other hand, the force-based Wilhelmy plate method provided apparently stable surface tension values of the order of 30 mN/m, in accordance with numerous previous literature reports on similar yeast biosurfactants. Both observations can be justified by the presence of an oil emulsified by biosurfactants produced by the yeast. We show that the odd (apparent) surface tension results are in fact the measurement artifacts resulting from slow demulsification and subsequent oil-spreading assisted by the yeast biosurfactants. The apparent surface tension reduction is thus indeed caused by the presence of biosurfactants, but its value does not represent their real adsorption in a thermodynamic sense. Consequently, the often reported in the literature very low surface tension values for the yeast culture media, of the order of 30 ± 5 mN/m, should be treated with caution, especially if the emulsion stabilized with the biosurfactant had not been fully destabilized prior to the measurement.

Effect of fed dietary yeast (Rhodotorula paludigena CM33) on shrimp growth, gene expression, intestinal microbial, disease resistance, and meat composition of Litopenaeus vannamei

Yeast is a health-promoting and bio-therapeutic probiotic that is commonly used in aquaculture. Rhodotorula paludigena CM33 can accumulate amounts of intracellular carotenoids and lipid, which are regarded as nutritionally beneficial compounds in various aspects. The aim of this study was to evaluate the impact of different levels of R. paludigena CM33 (RD) incorporated in a dietary composition at 0% (control), 1% (1% RD), 2% (2% RD), and 5% (5% RD) on the growth of shrimp (Litopenaeus vannamei), their immune-related gene expression, intestinal health, resistance to Vibrio parahaemolyticus (VPAHPND) infection, and meat composition. The results showed significant improvements in the specific growth rate, weight gain, and survival of shrimp fed with 1% RD, 2% RD, and 5% RD, which were higher than the control group after 4 weeks of administration. The administration of 5% RD group resulted in a decrease in cumulative mortality upon VPAHPND challenge when compared to the control group. Furthermore, the expression levels of immune-responsive genes, including proPO system (prophenoloxidase-2: PO2), antioxidant enzyme (superoxide dismutase: SOD, glutathione peroxidase: GPX, and catalase: CAT), JAK/STAT pathway (signal transducer and activator of transcription: STAT, gamma interferon inducible lysosomal thiol reductase: GILT), IMD pathway (inhibitor of nuclear factor kappa-B kinase subunit beta and epsilon: IKKb and IKKe), and Toll pathway (Lysozyme) genes, were up-regulated in the 5% RD group. In the context of microbiota, microbiome analysis revealed that the main phyla in shrimp intestines were Proteobacteria, Firmicutes, Bacteroidota, Campilobacterota, Actinobacteriota, and Verrucomicrobiota. At the genus level, Vibrio was found to be reduced in the 5% RD group, whereas the abundance of potentially beneficial bacteria Bifidobacterium was increased. The 5% RD group showed a significant increase in the levels of crude protein and crude lipid, both of which are essential nutritious components. Our results show the capability of R. paludigena CM33 as a probiotic supplement in shrimp feed in improving growth, antimicrobial responses against VPAHPND, and meat quality by increasing protein and lipid content in shrimp.

Fungal bioproducts for petroleum hydrocarbons and toxic metals remediation: recent advances and emerging technologies

Petroleum hydrocarbons and toxic metals are sources of environmental contamination and are harmful to all ecosystems. Fungi have metabolic and morphological plasticity that turn them into potential prototypes for technological development in biological remediation of these contaminants due to their ability to interact with a specific contaminant and/or produced metabolites. Although fungal bioinoculants producing enzymes, biosurfactants, polymers, pigments and organic acids have potential to be protagonists in mycoremediation of hydrocarbons and toxic metals, they can still be only adjuvants together with bacteria, microalgae, plants or animals in such processes. However, the sudden accelerated development of emerging technologies related to the use of potential fungal bioproducts such as bioinoculants, enzymes and biosurfactants in the remediation of these contaminants, has boosted fungal bioprocesses to achieve higher performance and possible real application. In this review, we explore scientific and technological advances in bioprocesses related to the production and/or application of these potential fungal bioproducts when used in remediation of hydrocarbons and toxic metals from an integral perspective of biotechnological process development. In turn, it sheds light to overcome existing technological limitations or enable new experimental designs in the remediation of these and other emerging contaminants.

Bioconversion of non-food corn biomass to polyol esters of fatty acid and single-cell oils

BACKGROUND

Lignocellulose is a valuable carbon source for the production of biofuels and biochemicals, thus having the potential to substitute fossil resources. Consolidated bio-saccharification (CBS) is a whole-cell-based catalytic technology previously developed to produce fermentable sugars from lignocellulosic agricultural wastes. The deep-sea yeast strain Rhodotorula paludigena P4R5 can produce extracellular polyol esters of fatty acids (PEFA) and intracellular single-cell oils (SCO) simultaneously. Therefore, the integration of CBS and P4R5 fermentation processes would achieve high-value-added conversion of lignocellulosic biomass.

RESULTS

The strain P4R5 could co-utilize glucose and xylose, the main monosaccharides from lignocellulose, and also use fructose and arabinose for PEFA and SCO production at high levels. By regulating the sugar metabolism pathways for different monosaccharides, the strain could produce PEFA with a single type of polyol head. The potential use of PEFA as functional micelles was also determined. Most importantly, when sugar-rich CBS hydrolysates derived from corn stover or corncob residues were used to replace grain-derived pure sugars for P4R5 fermentation, similar PEFA and SCO productions were obtained, indicating the robust conversion of non-food corn plant wastes to high-value-added glycolipids and lipids. Since the produced PEFA could be easily collected from the culture via short-time standing, we further developed a semi-continuous process for PEFA production from corncob residue-derived CBS hydrolysate, and the PEFA titer and productivity were enhanced up to 41.1 g/L and 8.22 g/L/day, respectively.

CONCLUSIONS

Here, we integrated the CBS process and the P4R5 fermentation for the robust production of high-value-added PEFA and SCO from non-food corn plant wastes. Therefore, this study suggests a feasible way for lignocellulosic agro-waste utilization and the potential application of P4R5 in industrial PEFA production.

Efficient production of mannosylerythritol lipids by a marine yeast Moesziomyces aphidis XM01 and their application as self-assembly nanomicelles

Mannosylerythritol lipids (MELs) are one of the most promising biosurfactants because of their excellent physicochemical properties, high environmental compatibility, and various biological functions. In this study, a mangrove yeast strain Moesziomyces aphidis XM01 was identified and used for efficient extracellular MEL production. The MEL titer reached 64.5 ± 0.7 g/L at flask level within 7 days with the optimized nitrogen and carbon source of 2.0 g/L NaNO₃ and 70 g/L soybean oil. Furthermore, during a 10-L two-stage fed-batch fermentation, the final MEL titer reached 113.6 ± 3.1 g/L within 8 days, with prominent productivity and yield of 14.2 g·L^-1·day^-1 and 94.6 g/g_{(glucose and soybean oil)}. Structural analysis indicated that the produced MELs were mainly MEL-A and its fatty acid profile was composed of only medium-chain fatty acids (C8-C12), especially C10 acids (77.81%). Further applications of this compound were evaluated as one-step self-assembly nanomicelles. The obtained MEL nanomicelles showed good physicochemical stability and antibacterial activity. In addition, using clarithromycin as a model hydrophobic drug, the MEL nanomicelles exhibited high loading capacity and could be used for the controlled and sustained drug release in low-pH environments. Therefore, M. aphidis XM01 is an excellent candidate for efficient MEL production, and the prepared MEL nanomicelles have broad application prospects in the pharmaceutical and cosmetic fields.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00135-0.

Fungal biosurfactants, from nature to biotechnological product: bioprospection, production and potential applications

Biosurfactants are in demand by the global market as natural commodities that can be added to commercial products or use in environmental applications. These biomolecules reduce the surface/interfacial tension between fluid phases and exhibit superior stability to chemical surfactants under different physico-chemical conditions. Biotechnological production of biosurfactants is still emerging. Fungi are promising producers of these molecules with unique chemical structures, such as sophorolipids, mannosylerythritol lipids, cellobiose lipids, xylolipids, polyol lipids and hydrophobins. In this review, we aimed to contextualize concepts related to fungal biosurfactant production and its application in industry and the environment. Concepts related to the thermodynamic and physico-chemical properties of biosurfactants are presented, which allows detailed analysis of their structural and application. Promising niches for isolating biosurfactant-producing fungi are presented, as well as screening methodologies are discussed. Finally, strategies related to process parameters and variables, simultaneous production, process optimization through statistical and genetic tools, downstream processing and some aspects of commercial products formulations are presented.

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.

Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B

Red yeasts of the genus Rhodotorula are of great interest to the biotechnological industry due to their ability to produce valuable natural products, such as lipids and carotenoids with potential applications as surfactants, food additives, and pharmaceuticals. Herein, we explored the biosynthetic potential of R. mucilaginosa 50-3-19/20B collected from the Mid-Atlantic Ridge using modern genomics and untargeted metabolomics tools. R. mucilaginosa 50-3-19/20B exhibited anticancer activity when grown on PDA medium, while antimicrobial activity was observed when cultured on WSP-30 medium. Applying the bioactive molecular networking approach, the anticancer activity was linked to glycolipids, namely polyol esters of fatty acid (PEFA) derivatives. We purified four PEFAs (1–4) and the known methyl-2-hydroxy-3-(1H-indol-2-yl)propanoate (5). Their structures were deduced from NMR and HR-MS/MS spectra, but 1–5 showed no anticancer activity in their pure form. Illumina-based genome sequencing, de novo assembly and standard biosynthetic gene cluster (BGC) analyses were used to illustrate key components of the PEFA biosynthetic pathway. The fatty acid producing BGC3 was identified to be capable of producing precursors of PEFAs. Some Rhodotorula strains are able to convert inulin into high-yielding PEFA and cell lipid using a native exo-inulinase enzyme. The genomic locus for an exo-inulinase enzyme (g1629.t1), which plays an instrumental role in the PEFA production via the mannitol biosynthesis pathway, was identified. This is the first untargeted metabolomics study on R. mucilaginosa providing new genomic insights into PEFA biosynthesis.