Triauxic growth of an oleaginous red yeast Rhodosporidium toruloides on waste 'extract' for enhanced and concomitant lipid and β-carotene production

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.

Methylation Modification in Ornamental Plants: Impact on Floral Aroma and Color

Methylation represents a crucial class of modification that orchestrates a spectrum of regulatory roles in plants, impacting ornamental characteristics, growth, development, and responses to abiotic stress. The establishment and maintenance of methylation involve the coordinated actions of multiple regulatory factors. Methyltransferases play a pivotal role by specifically recognizing and methylating targeted sites, which induces alterations in chromatin structure and gene expression, subsequently influencing the release of volatile aromatic substances and the accumulation of pigments in plant petals. In this paper, we review the regulatory mechanisms of methylation modification reactions and their effects on the changes in aromatic substances and pigments in plant petals. We also explore the potential of methylation modifications to unravel the regulatory mechanisms underlying aroma and color in plant petals. This aims to further elucidate the synthesis, metabolism, and regulatory mechanisms of various methylation modifications related to the aroma and color substances in plant petals, thereby providing a theoretical reference for improving the aroma and color of plant petals.

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.

Potential of Rhodosporidium toruloides for Fatty Acids Production Using Lignocellulose Biomass

Microbial lipids are ideal for developing liquid biofuels because of their sustainability and no dependence on food crops. Especially the bioprocess for microbial lipids may be made economical by using sustainable approaches, e.g., lignocellulose-based carbon sources. This demand led to a search for ideal microorganisms with the ability to utilize efficiently biomass into value-added products. Rhodosporidium toruloides species belongs to the family of oleaginous (OG) yeast, which aggregates up to 70% of its biomass to produce fatty acids which can be converted to a variety of biofuels. R. toruloides is extremely adaptable to different types of feedstocks. Among all feedstock, a lot of effort is going on to develop a bioprocess of fatty acid production from lignocellulose biomass. The lignocellulose biomass is pretreated using harsh conditions of acid, alkali, and other which leads to the generation of a variety of sugars and toxic compounds. Thus, so obtained lignocellulose hydrolysate may have conditions of different pH, variable carbon and nitrogen ratios, and other non-optimum conditions. Accordingly, a detailed investigation is required for molecular level metabolism of R. toruloides in response to the hydrolysate for producing desired biochemicals like fatty acids. The present review focuses on numerous elements and obstacles, including metabolism, biofuel production, cultivation parameters, and genetic alteration of mutants in extracting fatty acids from lignocellulosic materials utilizing Rhodosporidium spp. This review provides useful information on the research working to develop processes for lignocellulose biomass using oleaginous yeast.

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

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

Yeast Carotenoids: Cost-Effective Fermentation Strategies for Health Care Applications

Carotenoid production from oleaginous red yeast has been considered as a safe alternative to chemically synthesized carotenoids commonly used in the food industry, since plant-based carotenoids are expensive and an irregular source for obtaining pigments. This is a summative review on the factors affecting carotenoid production, cost-effective production strategies using various inexpensive feedstock, metabolic engineering, and strain improvisation. The review specially highlights the various potential applications of carotenoids as anti-microbial, anti-viral, antioxidant, anti-cancerous, anti-malarial agents, etc. The importance of such natural and easily available resources for prevention, evasion, or cure of emerging diseases and their plausible nutraceutical effect demands exhaustive research in this area.

Development and Perspective of Rhodotorula toruloides as an Efficient Cell Factory

Rhodotorula toruloides is receiving significant attention as a novel cell factory because of its high production of lipids and carotenoids, fast growth and high cell density, as well as the ability to utilize a wide variety of substrates. These attractive traits of R. toruloides make it possible to become a low-cost producer that can be engineered for the production of various fuels and chemicals. However, the lack of understanding and genetic engineering tools impedes its metabolic engineering applications. A number of research efforts have been devoted to filling these gaps. This review focuses on recent developments in genetic engineering tools, advances in systems biology for improved understandings, and emerging engineered strains for metabolic engineering applications. Finally, future trends and barriers in developing R. toruloides as a cell factory are also discussed.

Anti-microbial, anti-oxidant, and anti-breast cancer properties unraveled in yeast carotenoids produced via cost-effective fermentation technique utilizing waste hydrolysate

Introduction

Natural carotenoids are well known for their anti-oxidant property and also shown to have antimicrobial and anticancer efficacy. Production of carotenoids from microbial resources mainly from yeast has attracted commercial interest. Breast cancer has the highest incidence among women, and therapy resistance and lack of effective therapeutic strategies are major treatment bottlenecks, particularly for triple-negative subtypes. Yeast carotenoids are recently being evaluated for affordable, non-toxic, natural product-based therapies. In the present study, we have shown an environment-friendly and inexpensive method for carotenoid production from yeasts, utilizing "mandi" wastes, and investigated the biomedical properties of carotenoids, particularly antineoplastic properties.

Methods

Vegetable "mandi" waste was used to prepare waste hydrolysate, a culture medium, in which oleaginous red yeast Rhodosporidium sp. was grown. Carotenoid pigments were extracted using the solvent extraction method and analyzed by UV spectroscopy, thin-layer chromatography (TLC), and high-performance liquid chromatography (HPLC). Antimicrobial, antioxidant, and anticancer activities of the extract were evaluated, followed by in silico docking and absorption, distribution, metabolism, and excretion/toxicity (ADME/T) studies.

Results

Carotenoid extract was found to be composed of three main pigments-β-carotene, torulene, and torularhodin. Extract exhibited significant antioxidant, antimicrobial, and anti-breast cancer activities in vitro while being biocompatible. Interestingly, carotenoids have shown better efficacy in triple-negative breast cancer (TNBC) cells than ER+PR+ cells. In silico evaluation predicted binding with breast cancer-specific molecular targets, specifically the three components showed good binding energy toward VEGF receptors and good drug likeliness properties, as well as less toxicity.

Discussion

This is the first report on anti-breast cancer activities, particularly targeting TNBC cells by red yeast carotenoids (β-carotene, torulene, and torularhodin) produced via a sustainable environment-friendly bioprocess utilizing waste hydrolysate.

Red yeasts and their carotenogenic enzymes for microbial carotenoid production

Carotenoids are C40 isoprene-based compounds with significant commercial interests that harbor diverse bioactivities. Prominent examples of carotenoids are beta-carotene, a precursor to vitamin A essential for proper eye health, and lycopene and astaxanthin, powerful antioxidants implicated in preventing cancers and atherosclerosis. Due to their benefits to human health, the market value for carotenoids is rapidly increasing and is projected to reach USD 1.7 billion by 2025. However, their production now relies on chemical synthesis and extraction from plants that pose risks to food management and numerous biological safety issues. Thus, carotenoid production from microbes is considered a promising strategy for achieving a healthy society with more sustainability. Red yeast is a heterogeneous group of basidiomycetous fungi capable of producing carotenoids. It is a critical source of microbial carotenoids from low-cost substrates. Carotenogenic enzymes from red yeasts have also been highly efficient, invaluable biological resources for biotechnological applications. In this minireview, we focus on red yeast as a promising source for microbial carotenoids, strain engineering strategies for improving carotenoid production in red yeasts, and potential applications of carotenogenic enzymes from red yeasts in conventional and nonconventional yeasts.

Valorization of phenol contaminated wastewater for lipid production by Rhodosporidium toruloides 9564T

Phenol is one of the most common hazardous organic compound presents in several industrial effluents which directly affects the aquatic environment. The present study envisaged the phenol biodegradation and simultaneous lipid production along with its underlying mechanism by oleaginous yeast Rhodosporidium toruloides 9564^T. Experiments were designed using simulated wastewater by varying phenol concentration in the range of 0.25-1.5 g/L and inoculum size of 1, 5, and 10% with and without glucose. The oleaginous yeast was found to completely degrade up to 0.75 g/L phenol with lipid accumulation of 26.3%. Phenol at > 0.5 g/L severely inhibited the growth of R. toruloides 9564^T at 1% and 5% inoculum size. Phenol toxicity up to 0.75 g/L can be overcome by increasing inoculum size to 10%. The maximum specific growth rate (μ_max) and phenol degradation rate (q_max) were found to be 0.0717 h^-1 and 0.01523 h^-1, respectively. The enzymatic pathway study suggested that R. toruloides 9564^T follows an ortho cleavage pathway for phenol degradation and lipid accumulation. Phytotoxicty and cytotoxicity tests for treated and untreated samples clearly demonstrated a decline in toxicity of the treated wastewater. R. toruloides brought about an important paradigm shift toward a circular economy in which industrial wastewater is considered a valuable resource for bioenergy production.

Bioprospecting lipid-producing microorganisms: From metagenomic-assisted isolation techniques to industrial application and innovations

Traditionally, lipid-producing microorganisms have been obtained via conventional bioprospecting based on isolation and screening techniques, demanding time and effort. Thus, high-throughput sequencing combined with conventional microbiological approaches has emerged as an advanced and rapid strategy for recovering novel oleaginous microorganisms from target environments. This review highlights recent developments in lipid-producing microorganism bioprospecting, following (i) from traditional cultivation techniques to state-of-the-art metagenomics approaches; (ii) related topics on workflow, next-generation sequencing platforms, and knowledge bioinformatics; and (iii) biotechnological potential of the production of docosahexaenoic acid (DHA) by Aurantiochytrium limacinum, arachidonic acid (ARA) by Mortierella alpina and biodiesel by Rhodosporidium toruloides. These three species have been shown to be highly promising and studied in research articles, patents and commercialized products. Trends, innovations and future perspectives of these microorganisms are also addressed. Thus, these microbial lipids allow the development of food, feed and biofuels as alternative solutions to animal and vegetable oils.

Rhodotorula toruloides: an ideal microbial cell factory to produce oleochemicals, carotenoids, and other products

Requirement of clean energy sources urges us to find substitutes for fossil fuels. Microorganisms provide an option to produce feedstock for biofuel production by utilizing inexpensive, renewable biomass. Rhodotorula toruloides (Rhodosporidium toruloides), a non-conventional oleaginous yeast, can accumulate intracellular lipids (single cell oil, SCO) more than 70% of its cell dry weight. At present, the SCO-based biodiesel is not a price-competitive fuel to the petroleum diesel. Many efforts are made to cut the cost of SCO by strengthening the performance of genetically modified R. toruloides strains and by valorization of low-cost biomass, including crude glycerol, lignocellulosic hydrolysates, food and agro waste, wastewater, and volatile fatty acids. Besides, optimization of fermentation and SCO recovery processes are carefully studied as well. Recently, new R. toruloides strains are developed via metabolic engineering and synthetic biology methods to produce value-added chemicals, such as sesquiterpenes, fatty acid esters, fatty alcohols, carotenoids, and building block chemicals. This review summarizes recent advances in the main aspects of R. toruloides studies, namely, construction of strains with new traits, valorization of low-cost biomass, process detection and optimization, and product recovery. In general, R. toruloides is a promising microbial cell factory for production of biochemicals.

Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14

Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in R. toruloides and to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft of R. toruloides CBS 14, using a hybrid assembly approach, consisting of short and long reads generated by Illumina and Nanopore sequencing, respectively. The genome draft consists of 23 contigs and 3 scaffolds, with a N50 length of 1,529,952 bp, thus largely representing chromosomal organization. The total size of the genome is 20,534,857 bp and the overall GC content is 61.83%. Transcriptomic data from different growth conditions was used to aid species-specific gene annotation. We annotated 9464 genes and identified 11,691 transcripts. Furthermore, we demonstrated the presence of a potential plasmid, an extrachromosomal circular structure of about 11 kb with a copy number about three times as high as the other chromosomes.

Optimization of Carotenoids Production from Camelina sativa Meal Hydrolysate by Rhodosporidium toruloides

Several compounds on the market derive from petrochemical synthesis, and carotenoids are no exception. Nonetheless, since their applications in the food, feed and cosmetic sectors, and because of sustainability issues, carotenoids of natural origin are desirable. Carotenoids can be extracted from several plants but also from carotenogenic microorganisms, among which are yeasts. Nonetheless, to meet sustainability criteria, the substrate used for yeast cultivation has to be formulated from residual biomasses. For these reasons, we deploy the yeast, Rhodosporidium toruloides, to obtain carotenoids from Camelina sativa meal, an underrated lignocellulosic biomass. Its enzymatic hydrolysis ensures the release of the sugars, as well as of the other nutrients necessary to sustain the process. We therefore separately optimized enzymatic and biomass loadings, and calculated the yields and productivities of the obtained carotenoids. The best conditions (9% w/v biomass, 0.56% w/wbiomass enzymes) were tested in different settings, in which the fermentation was performed separately or simultaneously with hydrolysis, resulting in a similar production of carotenoids. In order to collect quantitative data under controlled chemo-physical parameters, the process was implemented in stirred-tank bioreactors, obtaining 3.6 ± 0.69 mg/L of carotenoids; despite the volumetric and geometric change, the outcomes were consistent with results from the fermentation of shake flasks. Therefore, these data pave the way to evaluate a potential future industrialization of this bioprocess, considering the opportunity to optimize the use of different amounts of biomass and enzyme loading, as well as the robustness of the process in the bioreactor.

Isolation and identification of carotenoid-producing yeast and evaluation of antimalarial activity of the extracted carotenoid(s) against P. falciparum

Plasmodial resistance to a variety of plant-based antimalarial drugs has led toward the discovery of more effective antimalarial compounds having chemical or biological origin. Since natural compounds are considered as safer drugs, in this study, yeast strains were identified and compared for the production of carotenoids that are well-known antioxidants and this metabolite was tested for its antiparasitic activity. Plasmodium falciparum 3D7 strain was selected as the target parasite for evaluation of antimalarial activity of yeast carotenoids using in vitro studies. Data were analyzed by FACS (fluorescence-activated cell sorter) and counted via gold standard Giemsa-stained smears. The extracted yeast carotenoids showed a profound inhibitory effect at a concentration of 10^-3 µg/µl and 10^-4 µg/µl when compared to β- carotene as control. SYBR Green1 fluorescent dye was used to confirm the decrease in parasitaemia at given range of concentration. Egress assay results suggested that treated parasite remained stalled at schizont stage with constricted morphology and were darkly stained. Non-toxicity of carotenoids on erythrocytes and on human liver hepatocellular carcinoma cells (HepG2 cells) was shown at a given concentration. This report provides strong evidence for antimalarial effects of extracted yeast carotenoids, which can be produced via a sustainable and cost-effective strategy and may be scaled up for industrial application.

Evaluation of red-colored carotenoids in yeasts by the biomass color

Production of carotenoids with red yeasts is a promising area of industrial biotechnology. All spectrophotometrical ("classic") analyses of carotenoids are based on preliminary extraction of the water-insoluble carotenoids; thus, these analyses are precise but complicated and time consuming. This paper presents a simple method to evaluate the red-colored carotenoids in yeast biomass by its color, without extraction. The method is based on digital characteristics of the biomass whole coloring, and it has already been successfully applied in other areas of biology: to compare plant and animal objects. In contrast to spectrophotometry measuring the amount of light that can pass through a solution, the biomass photo is a reflected color of the insoluble compounds. Application of this method to microorganisms permitted to compare the yeast strains and the effects of substrates or culturing regimes for any change in the red-colored pigments. The proposed rapid method was compared with the classic analyses of the carotenoids and showed that evaluation of red-colored carotenoids by the whole coloring of biomass can be used to discover changes in the yeast carotenoid production. In whole, the paper contributes method which is new for pigmented microorganisms and has a potential application in biotechnology.

Rhodosporidium sp. DR37: a novel strain for production of squalene in optimized cultivation conditions

BACKGROUND

Rhodosporidium strain, a well-known oleaginous yeast, has been widely used as a platform for lipid and carotenoid production. However, the production of squalene for application in lipid-based biofuels is not reported in this strain. Here, a new strain of Rhodosporidium sp. was isolated and identified, and its potential was investigated for production of squalene under various cultivation conditions.

RESULTS

In the present study, Rhodosporidium sp. DR37 was isolated from mangrove ecosystem and its potential for squalene production was assessed. When Rhodosporidium sp. DR37 was cultivated on modified YEPD medium (20 g/L glucose, 5 g/L peptone, 5 g/L YE, seawater (50% v/v), pH 7, 30 °C), 64 mg/L of squalene was produced. Also, squalene content was obtained as 13.9% of total lipid. Significantly, use of optimized medium (20 g/L sucrose, 5 g/L peptone, seawater (20% v/v), pH 7, 25 °C) allowed highest squalene accumulation (619 mg/L) and content (21.6% of total lipid) in Rhodosporidium sp. DR37. Moreover, kinetic parameters including maximum specific cell growth rate (μ_max, h^-1), specific lipid accumulation rate (q_p, h^-1), specific squalene accumulation rate (q_sq, h^-1) and specific sucrose consumption rate (q_s, h^-1) were determined in optimized medium as 0.092, 0.226, 0.036 and 0.010, respectively.

CONCLUSIONS

This study is the first report to employ marine oleaginous Rhodosporidium sp. DR37 for accumulation of squalene in optimized medium. These findings provide the potential of Rhodosporidium sp. DR37 for production of squalene as well as lipid and carotenoids for biofuel applications in large scale.

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

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

Current Pretreatment/Cell Disruption and Extraction Methods Used to Improve Intracellular Lipid Recovery from Oleaginous Yeasts

The production of lipids from oleaginous yeasts involves several stages starting from cultivation and lipid accumulation, biomass harvesting and finally lipids extraction. However, the complex and relatively resistant cell wall of yeasts limits the full recovery of intracellular lipids and usually solvent extraction is not sufficient to effectively extract the lipid bodies. A pretreatment or cell disruption method is hence a prerequisite prior to solvent extraction. In general, there are no recovery methods that are equally efficient for different species of oleaginous yeasts. Each method adopts different mechanisms to disrupt cells and extract the lipids, thus a systematic evaluation is essential before choosing a particular method. In this review, mechanical (bead mill, ultrasonication, homogenization and microwave) and nonmechanical (enzyme, acid, base digestions and osmotic shock) methods that are currently used for the disruption or permeabilization of oleaginous yeasts are discussed based on their principle, application and feasibility, including their effects on the lipid yield. The attempts of using conventional and “green” solvents to selectively extract lipids are compared. Other emerging methods such as automated pressurized liquid extraction, supercritical fluid extraction and simultaneous in situ lipid recovery using capturing agents are also reviewed to facilitate the choice of more effective lipid recovery methods.

Engineering xylose metabolism in yeasts to produce biofuels and chemicals

Xylose is the second most abundant sugar in lignocellulosic biomass. Efficient and rapid xylose utilization is essential for the economic bioconversion of lignocellulosic biomass into value-added products. Building on previous pathway engineering efforts to enable xylose fermentation in Saccharomyces cerevisiae, recent work has focused on reprogramming regulatory networks to enhance xylose utilization by engineered S. cerevisiae. Also, potential benefits of using xylose for the production of various value-added products have been demonstrated. With increasing needs of lipid-derived bioproducts, activation and enhancement of xylose metabolism in oleaginous yeasts have been attempted. This review highlights recent progress of metabolic engineering to achieve efficient and rapid xylose utilization by S. cerevisiae and oleaginous yeasts, such as Yarrowia lipolytica, Rhodosporidium toruloides, and Lipomyces starkeyi.

Rhodosporidium toruloides - A potential red yeast chassis for lipids and beyond

The red yeast Rhodosporidium toruloides naturally produces microbial lipids and carotenoids. In the past decade or so, many studies demonstrated R. toruloides as a promising platform for lipid production owing to its diverse substrate appetites, robust stress resistance and other favorable features. Also, significant progresses have been made in genome sequencing, multi-omic analysis and genome-scale modeling, thus illuminating the molecular basis behind its physiology, metabolism and response to environmental stresses. At the same time, genetic parts and tools are continuously being developed to manipulate this distinctive organism. Engineered R. toruloides strains are emerging for enhanced production of conventional lipids, functional lipids as well as other interesting metabolites. This review updates those progresses and highlights future directions for advanced biotechnological applications.

Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges

Pectin-rich agro-industrial residues are feedstocks with potential for sustainable biorefineries. They are generated in high amounts worldwide from the industrial processing of fruits and vegetables. The challenges posed to the industrial implementation of efficient bioprocesses are however manyfold and thoroughly discussed in this review paper, mainly at the biological level. The most important yeast cell factory platform for advanced biorefineries is currently Saccharomyces cerevisiae, but this yeast species cannot naturally catabolise the main sugars present in pectin-rich agro-industrial residues hydrolysates, in particular D-galacturonic acid and L-arabinose. However, there are non-Saccharomyces species (non-conventional yeasts) considered advantageous alternatives whenever they can express highly interesting metabolic pathways, natively assimilate a wider range of carbon sources or exhibit higher tolerance to relevant bioprocess-related stresses. For this reason, the interest in non-conventional yeasts for biomass-based biorefineries is gaining momentum. This review paper focuses on the valorisation of pectin-rich residues by exploring the potential of yeasts that exhibit vast metabolic versatility for the efficient use of the carbon substrates present in their hydrolysates and high robustness to cope with the multiple stresses encountered. The major challenges and the progresses made related with the isolation, selection, sugar catabolism, metabolic engineering and use of non-conventional yeasts and S. cerevisiae-derived strains for the bioconversion of pectin-rich residue hydrolysates are discussed. The reported examples of value-added products synthesised by different yeasts using pectin-rich residues are reviewed. Key Points • Review of the challenges and progresses made on the bioconversion of pectin-rich residues by yeasts. • Catabolic pathways for the main carbon sources present in pectin-rich residues hydrolysates. • Multiple stresses with potential to affect bioconversion productivity. • Yeast metabolic engineering to improve pectin-rich residues bioconversion. Graphical abstract.

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.

Camelina sativa meal hydrolysate as sustainable biomass for the production of carotenoids by Rhodosporidium toruloides

BACKGROUND

As the circular economy advocates a near total waste reduction, the industry has shown an increased interest toward the exploitation of various residual biomasses. The origin and availability of biomass used as feedstock strongly affect the sustainability of biorefineries, where it is converted in energy and chemicals. Here, we explored the valorization of Camelina meal, the leftover residue from Camelina sativa oil extraction. In fact, in addition to Camelina meal use as animal feed, there is an increasing interest in further valorizing its macromolecular content or its nutritional value.

RESULTS

Camelina meal hydrolysates were used as nutrient and energy sources for the fermentation of the carotenoid-producing yeast Rhodosporidium toruloides in shake flasks. Total acid hydrolysis revealed that carbohydrates accounted for a maximum of 31 ± 1.0% of Camelina meal. However, because acid hydrolysis is not optimal for subsequent microbial fermentation, an enzymatic hydrolysis protocol was assessed, yielding a maximum sugar recovery of 53.3%. Separate hydrolysis and fermentation (SHF), simultaneous saccharification and fermentation (SSF), and SSF preceded by presaccharification of Camelina meal hydrolysate produced 5 ± 0.7, 16 ± 1.9, and 13 ± 2.6 mg/L of carotenoids, respectively. Importantly, the presence of water-insoluble solids, which normally inhibit microbial growth, correlated with a higher titer of carotenoids, suggesting that the latter could act as scavengers.

CONCLUSIONS

This study paves the way for the exploitation of Camelina meal as feedstock in biorefinery processes. The process under development provides an example of how different final products can be obtained from this side stream, such as pure carotenoids and carotenoid-enriched Camelina meal, can potentially increase the initial value of the source material. The obtained data will help assess the feasibility of using Camelina meal to generate high value-added products.

Analysis of nicotine-induced metabolic changes in Blakeslea trispora by GC-MS

Blakeslea trispora is a natural source of carotenoids, including β-carotene and lycopene, which have industrial applications. Therefore, classical selective breeding techniques have been applied to generate strains with increased productivity, and microencapsulated β-carotene preparation has been used in food industry (Li et al., 2019). In B. trispora, lycopene is synthesized via the mevalonate pathway (Venkateshwaran et al., 2015). Lycopene cyclase, which is one of the key enzymes in this pathway, is a bifunctional enzyme that can catalyze the cyclization of lycopene to produce β-carotene and exhibit phytoene synthase activity (He et al., 2017).

Comparative Metabolic Responses Induced by Pyridine and Imidazole in Blakeslea trispora

Lycopene cyclase needs to be inhibited by the blockers like pyridine or imidazole in the lycopene accumulation of Blakeslea trispora. This work investigated how pyridine and imidazole impacted the basal metabolism of B. trispora, the results helped us understand how they could affect the lycopene production and application, and see the metabolic risks from different inhibitors. In this study, the highest yield of lycopene with pyridine was obtained at 176 mg/L without amino acids supplement, and got more lycopene at 237 mg/L adding tyrosine, lysine, proline all together as 0.01 mol/L each in fermented broth. GC-MS and Principal Component Analysis (PCA) were used to find that amino acids, fatty acids, organic acids including phosphoric acid, carbon source and imidazole derivatives played the most important roles in lycopene fermentation with imidazole, differently, fatty acids, carbon source, and pyridine derivatives were more significant in the pyridine process and it was remarkable that the residual of both blockers' derivatives would bring the potential risks on applications of lycopene products. Predominantly, durene met 0.35 mg/g DCW with imidazole and piperidine formaldehyde attained 0.24 mg/g DCW with pyridine after the end of lycopene fermentations.

Correction to: Triauxic growth of an oleaginous red yeast Rhodosporidium toruloides on waste 'extract' for enhanced and concomitant lipid and β‑carotene production

Upon publication of this article [1], the authors realized that one of the coauthor name was accedentally deleted during the review process and not presented in the original version of the article. The coauthor Dr. Ram Prasad should be listed as fifth author. The corrected author group is published with this erratum.