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

A comparative assessment of microbial biodiesel and its life cycle analysis

Biodiesel is a type of sustainable, biodegradable energy made from natural sources like vegetable oils, animal fat, and from microbes. Unlike traditional diesel, it has a lower carbon footprint and produces fewer harmful emissions when burned. Biodiesel has gained popularity as a more sustainable substitute for hydrocarbon-based diesel and may be utilized in diesel engines without any modification. In this review, biodiesel from microorganisms such as algae, yeast, and fungi and advantages over another feedstock were discussed. The life cycle evaluation of biodiesel is a thorough assessment of the ecological and economic effects of biodiesel production and use, from the extraction of raw ingredients to the waste disposal process. The life cycle analysis considers the entire process, including the production of feedstocks, the production of biodiesel, and the use of biodiesel in vehicles and other applications. Life cycle analysis of biodiesel produced from microorganisms takes into consideration the environmental impact and sustainability of each step in the production process, including the impact on land use, water use, greenhouse gas emissions, and the availability of resources. In this section, biodiesel produced from microorganisms and other raw materials, its comparisons, and also steps involved in the life cycle such as the cultivation of microorganisms, harvesting of biomass, and conversion to biodiesel were discussed. The processes like extraction and purification, hydrothermal liquefaction, and their environmental impacts were examined by using various LCA software from the previously mentioned process.

Molecular phylogenetics of the Umbelopsis genus-identification of new species and evaluation of their oil application value

AIMS

The aim of this study was to reconstruct the evolutionary framework of the genus Umbelopsis by using modern taxonomic strategies and evaluating the quality of oil and prospective uses of three distinct species.

METHODS AND RESULTS

Three species of Umbelopsis were identified based on morphological characteristics and phylogenetic evidence obtained from three genes (ITS, LSU, and ACT). A new species of Umbelopsis was described and illustrated, and subsequently named U. ophiocordycipiticola. The characteristics of U. ophiocordycipiticola exhibited sporangia with a diameter ranging from 8 to 17 µm. and sporangiospores that were oval to ellipsoidal in shape, irregularly angular, with dimensions of ∼1.9-2.9 × 1.7-3.0 µm. Gas chromatography and mass spectrometry (GC-MS) were used to examine the composition of fatty acids. Notably, U. ophiocordycipiticola showed a significantly higher oil content of 50.89% in dry cell weight (DCW) compared to U. vinacea and U. ramanniana. The mean proportion of polyunsaturated fatty acids (PUFAs) in U. ophiocordycipiticola was 32.38%, and the maximum levels of γ-linolenic acid (GLA), arachidonic acid (ARA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) in U. ophiocordycipiticola were found to be 14.51, 0.24, 0.54, and 0.53%, respectively. The biodiesel quality from all three species complied with applicable standards set by the American Association for Testing and Materials (ASTM 6751) and the Brazilian National Petroleum Agency (ANP 255).

CONCLUSIONS

The establishment of a novel species, U. ophiocordycipiticola, was strongly supported by morphological and molecular evidence. Umbelopsis ophiocordycipiticola exhibited a high-value PUFA content. Additionally, three Umbelopsis species demonstrated good quality for biodiesel production.

Poly-Unsaturated Fatty Acids (PUFAs) from Cunninghamella elegans Grown on Glycerol Induce Cell Death and Increase Intracellular Reactive Oxygen Species

Cunninghamella elegans NRRL-1393 is an oleaginous fungus able to synthesize and accumulate unsaturated fatty acids, amongst which the bioactive gamma-linolenic acid (GLA) has potential anti-cancer activities. C. elegans was cultured in shake-flask nitrogen-limited media with either glycerol or glucose (both at ≈60 g/L) employed as the sole substrate. The assimilation rate of both substrates was similar, as the total biomass production reached 13.0-13.5 g/L, c. 350 h after inoculation (for both instances, c. 27-29 g/L of substrate were consumed). Lipid production was slightly higher on glycerol-based media, compared to the growth on glucose (≈8.4 g/L vs. ≈7.0 g/L). Lipids from C. elegans grown on glycerol, containing c. 9.5% w/w of GLA, were transformed into fatty acid lithium salts (FALS), and their effects were assessed on both human normal and cancerous cell lines. The FALS exhibited cytotoxic effects within a 48 h interval with an IC50 of about 60 μg/mL. Additionally, a suppression of migration was shown, as a significant elevation of oxidative stress levels, and the induction of cell death. Elementary differences between normal and cancer cells were not shown, indicating a generic mode of action; however, oxidative stress level augmentation may increase susceptibility to anticancer drugs, improving chemotherapy effectiveness.

Hormesis and Low Toxic Effects of Three Lanthanides in Microfungi Isolated from Rare Earth Mining Waste in Northwestern Russia

The low-dose toxicity of chloride and nitrate salts of three lanthanides (La, Ce and Nd) was tested on six microfungal species. Five of them (Geomyces vinaceus, Aspergillus niveoglaucus, Pseudogymnoascus pannorum, Penicillium simplicissimum and Umbelopsis isabellina) were isolated from the loparite ore tailings on the Kola Peninsula, northwestern Russia. Sydowia polyspora was a control strain. In the case of nitrate salts, the toxicity of REEs to four of six microorganisms was significantly (p < 0.5) lower compared to chloride salts. In this case, nitrates can play the role of exogenous nutrients, compensating for the toxic effect of REEs. Interestingly, U. isabellina only showed an opposite response, indicating the highest toxicity of nitrate (IC5 = 9-20 mg/L) REEs' salts compared to chlorides (IC5 = 80-195 mg/L) at low concentration levels. In addition, treatment with lanthanides showed a "hormesis effect" on fungal growth with stimulation at low doses and inhibition at high doses. However, U. isabellina and S. polyspora demonstrated the absence of hormetic response under the treatment of REEs' nitrate salt. Taking into account the specific hormetic responses and high tolerance of P. simplicissimum and U. isabellina to lanthanides, our findings may be useful in the assessment of the potential application of the selected fungi to bioremediation and REE bioleaching.

Unveiling the anticancer potentiality of single cell oils produced by marine oleaginous Paradendryphiella sp. under optimized economic growth conditions

Bioprospecting about new marine oleaginous fungi that produce advantageous bioproducts in a green sustainable process is the key of blue bioeconomy. Herein, the marine Paradendryphiella sp. was utilized for single cell oils (SCOs) production economically, via central composite design, the lipid content enhanced 2.2-fold by 5.5 g/L lipid yeild on seawater-based media supplemented with molasses concentration 50 g/L, yeast extract, 2.25 g/L at initial pH value (5.3) and 8 days of static incubation. Subsequently, the fatty acid methyl esters profiles of SCOs produced on optimized media under different abiotic conditions were determined; signifying qualitative and quantitative variations. Interestingly, the psychrophilic-prolonged incubation increased the unsaturation level of fatty acids to 59.34%, while ω-6 and ω-3 contents representing 23.53% and 0.67% respectively. Remarkably, it exhibited the highest EC100 dose by 677.03 µg/mL on normal human lung fibroblast Wi-38 cells. Meanwhile, it showed the highest inhibiting proliferation potential on cancer cell lines of A549, MDA-MB 231 and HepG-2 cells by 372.37, 417.48 and 365.00 µg/mL, respectively. Besides, it elevated the oxidative stress, the expression of key apoptotic genes and suppressed the expression of key oncogenes (NF-κB, BCL2 and cyclin D); implying its promising efficacy in cancer treatment as adjuvant drug. This study denoted the lipogenesis capacity of Paradendryphiella sp. under acidic/alkaline and psychrophilic/mesophilic conditions. Hereby attaining efficient and economic process under seasonal variation with different Egyptian marine sources to fill the gap of freshwater crisis and simultaneously preserve energy.

What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota

Mucoromycota is a phylum of early diverging fungal (EDF) lineages, of mostly plant-associated terrestrial fungi. Some strains have been selected as promising biotechnological organisms due to their ability to produce polyunsaturated fatty acids and efficient conversion of nutrients into lipids. Others get their lipids from the host plant and are unable to produce even the essential ones on their own. Following the advancement in EDF genome sequencing, we carried out a systematic survey of lipid metabolism protein families across different EDF lineages. This enabled us to explore the genomic basis of the previously documented ability to produce several types of lipids within the fungal tree of life. The core lipid metabolism genes showed no significant diversity in distribution, however specialized lipid metabolic pathways differed in this regard among different fungal lineages. In total 165 out of 202 genes involved in lipid metabolism were present in all tested fungal lineages, while remaining 37 genes were found to be absent in some of fungal lineages. Duplications were observed for 69 genes. For the first time we demonstrate that ergosterol is not being produced by several independent groups of plant-associated fungi due to the losses of different ERG genes. Instead, they possess an ancestral pathway leading to the synthesis of cholesterol, which is absent in other fungal lineages. The lack of diacylglycerol kinase in both Mortierellomycotina and Blastocladiomycota opens the question on sterol equilibrium regulation in these organisms. Early diverging fungi retained most of beta oxidation components common with animals including Nudt7, Nudt12 and Nudt19 pointing at peroxisome divergence in Dikarya. Finally, Glomeromycotina and Mortierellomycotina representatives have a similar set of desaturases and elongases related to the synthesis of complex, polyunsaturated fatty acids pointing at an ancient expansion of fatty acid metabolism currently being explored by biotechnological studies.

Production of Single-Cell Oil from a Local Isolate Bacillus subtilis Using Palm Fronds

This study, conducted at the Department of Biology, University of Anbar, Iraq, focuses on addressing the escalating issue of contamination and aims to acquire microbial oils to alleviate the global shortage in plant and animal oil production, utilizing environmental waste as a carbon source to reduce global pollution and select efficient local bacterial isolates of Bacillus subtilis for the production of single-cell oil (SCO) using local soil and environmental waste as a carbon source. Four isolates were selected as the best in producing single-cell oil, with the isolate with code C4 standing out as it recorded the highest production. It is worth noting that all these isolates belong to the bacteria type Bacillus subtilis. Palm fronds were found to be the most suitable environmental residue for SCO production compared to other waste materials (wheat straw and wheat bran). Submerged cultures were used to improve SCO production, with optimal conditions determined as pH 7, a temperature of 30°C, carbon source concentration of 3 g/100 ml, inoculum volume of 3 ml/100 ml, inoculum density of 20 × 107 cells, and an incubation period of 72 hours. The Soxhlet extraction method was used to obtain the oil, which was found to contain high percentages of unsaturated fatty acids, particularly linoleic acid (46.030%) and palmitoleic acid (16.579%). The oil was highly soluble in chloroform and ethanol but insoluble in water. The saponification test indicated the potential for soap production from the oil. This comprehensive research addresses the need for locally sourced and sustainable SCO production, offering insights into the selection of efficient bacterial isolates, the optimization of cultivation conditions, and the valuable properties of the resulting SCO. The significance of this study lies in the production of single-cell oil from soil-isolated Bacillus subtilis bacteria for use in food applications.

Tolerance of Rare-Earth Elements in Extremophile Fungus Umbelopsis isabellina from Polar Loparite Ore Tailings in Northwestern Russia

In this study, extremophile fungal species isolated from pure loparite-containing sands and their tolerance/resistance to the lanthanides Ce and Nd were investigated. The loparite-containing sands were collected at the tailing dumps of an enterprise developing a unique polar deposit of niobium, tantalum and rare-earth elements (REEs) of the cerium group: the Lovozersky Mining and Processing Plant (MPP), located in the center of the Kola Peninsula (northwestern Russia). From the 15 fungal species found at the site, one of the most dominant isolates was identified by molecular analysis as the zygomycete fungus Umbelopsis isabellina (GenBank accession no. OQ165236). Fungal tolerance/resistance was evaluated using different concentrations of CeCl₃ and NdCl₃. Umbelopsis isabellina exhibited a higher degree of tolerance/resistance to cerium and neodymium than did the other dominant isolates (Aspergillus niveoglaucus, Geomyces vinaceus and Penicillium simplicissimum). The fungus began to be inhibited only after being exposed to 100 mg L^-1 of NdCl₃. The toxic effects of Ce were not observed in fungus growth until it was subjected to 500 mg∙L^-1 of CeCl₃. Moreover, only U. isabellina started to grow after extreme treatment with 1000 mg∙L^-1 of CeCl₃ one month after inoculation. This work indicates, for the first time, the potential of Umbelopsis isabellina to remove REEs from the loparite ore tailings, making it a suitable candidate for the development of bioleaching methods.

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

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

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

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

Comparative Genomics of Mortierellaceae Provides Insights into Lipid Metabolism: Two Novel Types of Fatty Acid Synthase

Fungal species in the family Mortierellaceae are important for their remarkable capability to synthesize large amounts of polyunsaturated fatty acids, especially arachidonic acid (ARA). Although many genomes have been published, the quality of these data is not satisfactory, resulting in an incomplete understanding of the lipid pathway in Mortierellaceae. We provide herein two novel and high-quality genomes with 55.32% of syntenic gene pairs for Mortierella alpina CGMCC 20262 and M. schmuckeri CGMCC 20261, spanning 28 scaffolds of 40.22 Mb and 25 scaffolds of 49.24 Mb, respectively. The relative smaller genome for the former is due to fewer protein-coding gene models (11,761 vs. 13,051). The former yields 45.57% of ARA in total fatty acids, while the latter 6.95%. The accumulation of ARA is speculated to be associated with delta-5 desaturase (Delta5) and elongation of very long chain fatty acids protein 3 (ELOVL3). A further genomic comparison of 19 strains in 10 species in three genera in the Mortierellaceae reveals three types of fatty acid synthase (FAS), two of which are new to science. The most common type I exists in 16 strains of eight species of three genera, and was discovered previously and consists of a single unit with eight active sites. The newly revealed type II exists only in M. antarctica KOD 1030 where the unit is separated into two subunits α and β comprised of three and five active sites, respectively. Another newly revealed type III exists in M. alpina AD071 and Dissophora globulifera REB-010B, similar to type II but different in having one more acyl carrier protein domain in the α subunit. This study provides novel insights into the enzymes related to the lipid metabolism, especially the ARA-related Delta5, ELOVL3, and FAS, laying a foundation for genetic engineering of Mortierellaceae to modulate yield in polyunsaturated fatty acids.

Valorization of lipid-rich wastewaters: A theoretical analysis to tackle the competition between polyhydroxyalkanoate and triacylglyceride-storing populations

The lipid fraction of the effluents generated in several food-processing activities can be transformed into polyhydroxyalkanoates (PHAs) and triacylglycerides (TAGs), through open culture biotechnologies. Although competition between storing and non-storing populations in mixed microbial cultures (MMCs) has been widely studied, the right selective environment allowing for the robust enrichment of a community when different types of accumulators coexist is still not clear. In this research, comprehensive metabolic analyses of PHA and TAG synthesis and degradation, and concomitant respiration of external carbon, were used to understand and explain the changes observed in a laboratory-scale bioreactor fed with the lipid-rich fraction (mainly oleic acid) of a wastewater stream produced in the fish-canning industry. It was concluded that the mode of oxygen, carbon, and nitrogen supply determines the enrichment of the culture in specific populations, and hence the type of intracellular compounds preferentially accumulated. Coupled carbon and nitrogen feeding regime mainly selects for TAG producers whereas uncoupled feeding leads to PHA or TAG production function of the rate of carbon supply under specific aeration rates and feast and famine phases lengths.

Strategies for Improvement of Lipid Production by Yeast Trichosporon oleaginosus from Lignocellulosic Biomass

Microbial lipids have similar fatty acid composition to plant oils, and therefore, are considered as an alternative feedstock for biodiesel production. Oleaginous yeasts accumulate considerable amounts of lipids intracellularly during growth on low-cost renewable feedstocks such as lignocellulosic biomass. In this study, we cultivated yeast Trichosporon oleaginosus on hydrolysate of alkaline pretreated corn cobs. Different process configurations were evaluated and compared, including separate hydrolysis and fermentation (SHF) with cellulase recycle and simultaneous saccharification and fermentation (SSF) in batch and fed-batch mode. At low enzyme loading, the highest lipid concentration of 26.74 g L⁻¹ was reached in fed-batch SSF fed with 2.5% (g g⁻¹) substrate. Batch SHF was conducted for four rounds with recycling the cellulase adsorbed on unhydrolyzed lignocellulosic biomass. Thirty percent of cellulase saving was achieved for rounds 2–4 without compromising productivity and lipid yield. The addition of Tween 80 to lignocellulosic slurry improved the hydrolysis rate of structural carbohydrates in pretreated lignocellulosic biomass. Furthermore, supplementing the growth medium with Tween 80 improved lipid yield and productivity without affecting yeast growth. Oleaginous yeast T. oleaginosus is a promising strain for the sustainable and efficient production of lipids from renewable lignocellulosic feedstock.

Biosynthesis of polyunsaturated fatty acids by two newly cold-adapted Egyptian marine yeast

The widespread awareness of polyunsaturated fatty acids (PUFAs) benefits for human health has increased the need for their commercial production. Two oleaginous yeast were isolated from the Mediterranean Sea fish and Red Sea fish Epinephelus aeneus and E. areolatus, respectively. These marine candidates were identified by MALDI-TOF/MS biotyper^® as Lodderomyces elongisporus and Rhodotorula mucilaginosa. The effect of incubation temperature (7, 15, and 26 °C) and glucose concentration (3% and 8%) on their lipids content were investigated using Sulfo-Phospho-Vanillin (SPV) assay. Their intercellular lipids were visualized by fluorescence microscope using Nile-Red dye. L. elongisporus and R. mucilaginosa produced 20.04% and 26.79% of Linoleic acid, respectively, on normal Basal-Defatted Medium (BDM). Linoleic acid (21.4-22.7%) and α-Linolenic acid (7.5-10.8%) were produced by R. mucilaginosa and L. elongisporus, on normal BDM at 15 °C. High-Glucose BDM induced a positive effect on the total lipids production that reached its maximum of 48% and 54% by R. mucilaginosa and L. elongisporus, respectively, grown at 15 °C. Remarkably, 12.12% of long-chain 15-Docosenoic acid (C_22:1) and 21.49% of Tricosanoic acid (C_23:0) were detected in the FAs profile of L. elongisporus, when grown on normal BDM at 26 °C. The present study is the first one reporting the FAs profile of the Egyptian Marine L. elongisporus, and its capability to accumulate high amounts of lipids under appropriate fermentation conditions; thus, it could be considered for scaling up production.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03010-4.

Customizing lipids from oleaginous microbes: leveraging exogenous and endogenous approaches

To meet the growing demands of the oleochemical industry, tailored lipid sources are expanding to oleaginous microbes. To control the fatty acid composition of microbial lipids, ground-breaking exogenous and endogenous approaches are being developed. Exogenous approaches employ extracellular tools such as product-specific feedstocks, process optimization, elicitors, and magnetic and mechanical energy, whereas endogenous approaches leverage biology through the use of product-specific microbes, adaptive laboratory evolution (ALE), and the creation of custom strains via random and targeted cellular engineering. We consolidate recent advances from both fields into a review that will serve as a resource for those striving to fulfill the vision of microbial cell factories for tailored lipid production.

Biodiesel Production From Lignocellulosic Biomass Using Oleaginous Microbes: Prospects for Integrated Biofuel Production

Biodiesel is an eco-friendly, renewable, and potential liquid biofuel mitigating greenhouse gas emissions. Biodiesel has been produced initially from vegetable oils, non-edible oils, and waste oils. However, these feedstocks have several disadvantages such as requirement of land and labor and remain expensive. Similarly, in reference to waste oils, the feedstock content is succinct in supply and unable to meet the demand. Recent studies demonstrated utilization of lignocellulosic substrates for biodiesel production using oleaginous microorganisms. These microbes accumulate higher lipid content under stress conditions, whose lipid composition is similar to vegetable oils. In this paper, feedstocks used for biodiesel production such as vegetable oils, non-edible oils, oleaginous microalgae, fungi, yeast, and bacteria have been illustrated. Thereafter, steps enumerated in biodiesel production from lignocellulosic substrates through pretreatment, saccharification and oleaginous microbe-mediated fermentation, lipid extraction, transesterification, and purification of biodiesel are discussed. Besides, the importance of metabolic engineering in ensuring biofuels and biorefinery and a brief note on integration of liquid biofuels have been included that have significant importance in terms of circular economy aspects.

Adaptive laboratory evolution principles and applications in industrial biotechnology

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

Transcriptome Analysis of Oleaginous Fungus Mucor circinelloides WJ11 in Response to Exogenous Soybean Oil as Carbon Source

Mucor circinelloides is an oleaginous fungus that utilizes a wide variety of carbon substrates for its growth. The different sources of carbon strongly influence the total lipid content of the fungus. These different carbon substrates are assimilated and dissimilated through different metabolic pathways before entering into the TAG synthesis pathway. In the present study, we attempted to explore the mechanism of ex-novo lipid biosynthesis in M. circinelloides WJ11 in response to exogenous plant oil as a carbon source through transcriptomic analysis. The lipid content of WJ11 grown in a media containing mixed soybean oil with glucose as a carbon source was up to 43.8%, an increase of 13.9% as compared to glucose alone as the carbon source. RNA-Seq analysis was performed to investigate global gene expression patterns in the oil-treated WJ11. Based on RNA-seq analysis, among the 4646 differentially expressed genes (DEGs), 2379 were up-regulated and 2267 down-regulated. The expression of acetyl-CoA synthetase, 6-phosphofructokinase, alcohol dehydrogenase (NADP+), fructose-bisphosphate aldolase, and pyruvate kinase was down-regulated while genes related to triglyceride synthesis were up-regulated. The majority of genes and pathways related to lipid biosynthesis were up-regulated indicating a diversion of metabolic pathways towards lipid biosynthesis. The data generated advance the genomic resources and provide insights into the mechanisms of ex-novo lipid accumulation in fungi that use exogenous oil as a carbon source.

Advances in production of high-value lipids by oleaginous yeasts

The global market for high-value fatty acids production, mainly omega-3/6, hydroxy fatty-acids, waxes and their derivatives, has seen strong development in the last decade. The reason for this growth was the increasing utilization of these lipids as significant ingredients for cosmetics, food and the oleochemical industries. The large demand for these compounds resulted in a greater scientific interest in research focused on alternative sources of oil production - among which microorganisms attracted the most attention. Microbial oil production offers the possibility to engineer the pathways and store lipids enriched with the desired fatty acids. Moreover, costly chemical steps are avoided and direct commercial use of these fatty acids is available. Among all microorganisms, the oleaginous yeasts have become the most promising hosts for lipid production - their efficient lipogenesis, ability to use various (often highly affordable) carbon sources, feasible large-scale cultivations and wide range of available genetic engineering tools turns them into powerful micro-factories. This review is an in-depth description of the recent developments in the engineering of the lipid biosynthetic pathway with oleaginous yeasts. The different classes of valuable lipid compounds with their derivatives are described and their importance for human health and industry is presented. The emphasis is also placed on the optimization of culture conditions in order to improve the yield and titer of these valuable compounds. Furthermore, the important economic aspects of the current microbial oil production are discussed.

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.

Enzymatic Synthesis of Glucose Fatty Acid Esters Using SCOs as Acyl Group-Donors and Their Biological Activities

Sugar fatty acid esters, especially glucose fatty acid esters (GEs), have broad applications in food, cosmetic and pharmaceutical industries. In this research, the fatty acid moieties derived from polyunsaturated fatty acids containing single-cell oils (SCOs) (i.e., those produced from Cunninghamella echinulata, Umbelopsis isabellina and Nannochloropsis gaditana, as well as from olive oil and an eicosapentaenoic acid (EPA) concentrate) were converted into GEs by enzymatic synthesis, using lipases as biocatalysts. The GE synthesis was monitored using thin-layer chromatography, FTIR and in situ NMR. It was found that GE synthesis carried out using immobilized Candida antarctica B lipase was very effective, reaching total conversion of reactants. It was shown that EPA-GEs were very effective against several pathogenic bacteria and their activity can be attributed to their high EPA content. Furthermore, C. echinulata-GEs were more effective against pathogens compared with U. isabellina-GEs, probably due to the presence of gamma linolenic acid (GLA) in the lipids of C. echinulata, which is known for its antimicrobial activity, in higher concentrations. C. echinulata-GEs also showed strong insecticidal activity against Aedes aegypti larvae, followed by EPA-GEs, olive oil-GEs and N. gaditana-GEs. All synthesized GEs induced apoptosis of the SKOV-3 ovarian cancer cell line, with the apoptotic rate increasing significantly after 48 h. A higher percentage of apoptosis was observed in the cells treated with EPA-GEs, followed by C. echinulata-GEs, U. isabellina-GEs and olive oil-GEs. We conclude that SCOs can be used in the synthesis of GEs with interesting biological properties.

Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina

Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.

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.

Animal Fat as a Substrate for Production of n-6 Fatty Acids by Fungal Solid-State Fermentation

The method of solid-state fermentation (SSF) represents a powerful technology for the fortification of animal-based by-products. Oleaginous Zygomycetes fungi are efficient microbial cell factories used in SSF to valorize a wide range of waste and rest cereal materials. The application of this fermentation technique for utilization and biotransformation of animal-based materials represents a distinguished step in their treatment. In this study, for the first time, the strain Umbelopsis isabellina CCF2412 was used for the bioconversion of animal fat by-products to the fermented bioproducts enriched with n-6 polyunsaturated fatty acids, mainly γ-linolenic acid (GLA). Bioconversion of both cereals and the animal fat by-product resulted in the production of fermented bioproducts enriched with not just GLA (maximal yield was 6.4 mg GLA/g of fermented bioproduct), but also with high yields of glucosamine. Moreover, the fermentation on the cornmeal matrix led to obtaining bioproduct enriched with β-carotene. An increased amount of β-carotene content improved the antioxidant stability of obtained fermented bioproducts. Furthermore, the application of Fourier-transform infrared spectroscopy for rapid analysis and characterization of the biochemical profile of obtained SSF bioproducts was also studied.

Single Cell Oil Production by Oleaginous Yeasts Grown in Synthetic and Waste-Derived Volatile Fatty Acids

Four yeast isolates from the species—Apiotrichum brassicae, Candida tropicalis, Metschnikowia pulcherrima, and Pichia kudriavzevii—previously selected by their oleaginous character and growth flexibility in different carbon sources, were tested for their capacity to convert volatile fatty acids into lipids, in the form of single cell oils. Growth, lipid yields, volatile fatty acids consumption, and long-chain fatty acid profiles were evaluated in media supplemented with seven different volatile fatty acids (acetic, butyric, propionic, isobutyric, valeric, isovaleric, and caproic), and also in a dark fermentation effluent filtrate. Yeasts A. brassicae and P. kudriavzevii attained lipid productivities of more than 40% (w/w), mainly composed of oleic (>40%), palmitic (20%), and stearic (20%) acids, both in synthetic media and in the waste-derived effluent filtrate. These isolates may be potential candidates for single cell oil production in larger scale applications by using alternative carbon sources, combining economic and environmental benefits.

Single Cell Oil (SCO)-Based Bioactive Compounds: I-Enzymatic Synthesis of Fatty Acid Amides Using SCOs as Acyl Group Donors and Their Biological Activities

Fatty acid amides (FAAs) are of great interest due to their broad industrial applications. They can be synthesized enzymatically with many advantages over chemical synthesis. In this study, the fatty acid moieties of lipids of Cunninghamella echinulata ATHUM 4411, Umbelopsis isabellina ATHUM 2935, Nannochloropsis gaditana CCAP 849/5, olive oil, and an eicosapentaenoic acid (EPA) concentrate were converted into their fatty acid methyl esters and used in the FAA (i.e., ethylene diamine amides) enzymatic synthesis, using lipases as biocatalysts. The FAA synthesis, monitored using in situ NMR, FT-IR, and thin-layer chromatography, was catalyzed efficiently by the immobilized Candida rugosa lipase. The synthesized FAAs exhibited a significant antimicrobial activity, especially those containing oleic acid in high proportions (i.e., derived from olive oil and U. isabellina oil), against several human pathogenic microorganisms, insecticidal activity against yellow fever mosquito, especially those of C. echinulata containing gamma-linolenic acid, and anticancer properties against SKOV-3 ovarian cancer cell line, especially those containing EPA in their structures (i.e., EPA concentrate and N. gaditana oil). We conclude that FAAs can be efficiently synthesized using microbial oils of different fatty acid composition and used in specific biological applications.

Lignocellulosic Biomass as a Substrate for Oleaginous Microorganisms: A Review

Microorganisms capable of accumulating lipids in high percentages, known as oleaginous microorganisms, have been widely studied as an alternative for producing oleochemicals and biofuels. Microbial lipid, so-called Single Cell Oil (SCO), production depends on several growth parameters, including the nature of the carbon substrate, which must be efficiently taken up and converted into storage lipid. On the other hand, substrates considered for large scale applications must be abundant and of low acquisition cost. Among others, lignocellulosic biomass is a promising renewable substrate containing high percentages of assimilable sugars (hexoses and pentoses). However, it is also highly recalcitrant, and therefore it requires specific pretreatments in order to release its assimilable components. The main drawback of lignocellulose pretreatment is the generation of several by-products that can inhibit the microbial metabolism. In this review, we discuss the main aspects related to the cultivation of oleaginous microorganisms using lignocellulosic biomass as substrate, hoping to contribute to the development of a sustainable process for SCO production in the near future.

Physiological Characterization of a Novel Wild-Type Yarrowia lipolytica Strain Grown on Glycerol: Effects of Cultivation Conditions and Mode on Polyols and Citric Acid Production

A new yeast wild-type Yarrowia lipolytica isolate presented efficient growth on glycerol. During flask cultures, nitrogen limitation led to the secretion of sugar-alcohols as the major metabolites of the process (mannitol, arabitol and erythritol), whereas insignificant quantities of citrate were synthesized. Although in some instances high initial glycerol concentrations were employed (≈150 g/L), remarkable glycerol assimilation and polyol secretion was observed. Total polyols ≈ 52 g/L (conversion yield on glycerol consumed = 0.43 g/g) was recorded in the flask experiments. The sugar-alcohol production bioprocess was successfully simulated with the aid of a modified Velhlust–Aggelis model that fitted very well with the experimental data, while optimized parameter values seemed to be quite consistent. In bioreactor trials, a noticeable metabolic shift towards citric acid production was observed, while simultaneously insignificant polyol quantities were produced. In fed-batch bioreactor experiments, a total citric acid quantity ≈ 102 g/L was recorded—one of the highest in the literature for wild-type Y. lipolytica strains. This metabolic transition was due to higher oxygen saturation into the medium that occurred in the bioreactor experiments compared with the flasks. Cellular lipids produced in the bioreactor trial contained higher concentrations of unsaturated fatty acids compared with those produced in flasks.

Microbial sources of polyunsaturated fatty acids (PUFAs) and the prospect of organic residues and wastes as growth media for PUFA-producing microorganisms

The discovery of non-fish sources of polyunsaturated fatty acids (PUFAs) is of great biotechnological importance. Although various oleaginous microalgae and fungi are able of accumulating storage lipids (single cell oils - SCOs) containing PUFAs, the industrial applications utilizing these organisms are rather limited due to the high-fermentation cost. However, combining SCO production with other biotechnological applications, including waste and by-product valorization, can overcome this difficulty. In the current review, we present the major sources of fungi (i.e. members of Mucoromycota, fungoid-like Thraustochytrids and genetically modified strains of Yarrowia lipolytica) and microalgae (e.g. Isochrysis, NannochloropsisandTetraselmis) that have come recently to the forefront due to their ability to produce PUFAs. Approaches adopted in order to increase PUFA productivity and the potential of using various residues, such as agro-industrial, food and aquaculture wastes as fermentation substrates for SCO production have been considered and discussed. We concluded that several organic residues can be utilized as feedstock in the SCO production increasing the competitiveness of oleaginous organisms against conventional PUFA producers.

Single-cell oil production by Mortierella isabellina DSM 1414 using different sugars as carbon source

Pure carbon sources, especially carbohydrates which are raw materials deriving from agro-industrial processes, are often used for small-scale single-cell oil production by fermentation. The aim of this study was to investigate the effects of different pure carbon sources on cell growth, lipid accumulation, and γ-linolenic acid (GLA) production by the filamentous fungus Mortierella isabellina DSM 1414 (Deutsche Sammlung von Mikroorganismen). The sugars utilized in this study are found extensively and abundantly in nature, especially in food raw materials and, in consequence, in agro-food industry wastes or surpluses. Thus, the potential of many waste materials containing these sugars to be used in the production of single-cell oil by fermentation could also be evaluated. The effects of the sugars utilized on cell growth, biomass production, and lipid production were investigated. Fatty acids were also analysed in the lipids produced at the end of the fermentations. Results showed that the maximum biomass production was 10.80 g/L in lactose-based media, while the maximum oil production was 5.44 g/L in maltose-based media. Oleic (20.42%-42.94%), palmitic (14.96%-22.19%), and stearic (9.00%-26.92%) acids were the major fatty acids along with linoleic acid (11.35%-18.67%) and GLA (3.56%-8.04%). The production of GLA as the target fatty acid was remarkable. This study indicates that agro-industrial waste including most of the sugars utilized (except for arabinose and sucrose with lipid production of 0.81 and 0.28 g/L, respectively) can be employed for production of single-cell oil by M. isabellina DSM 1414 which contains a high amount of GLA.

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

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

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

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

Effect of Salt Addition upon the Production of Metabolic Compounds by Yarrowia lipolytica Cultivated on Biodiesel-Derived Glycerol Diluted with Olive-Mill Wastewaters

One of the major environmental problems is the highly toxic agro-industrial waste called olive mill wastewater (OMW), deriving from olive oil production. On the other hand, the continuous development of the biological liquid fuel industry (biodiesel and bioethanol) makes it mandatory the process and exploitation of their main by-products, crude glycerol. This study dealt with the biotechnological conversions of biodiesel-derived crude glycerol with the use of the non-conventional yeast Yarrowia lipolytica in media that had been diluted with OMWs. OMWs, employed as simultaneous liquid medium and substrate, is a new trend recently appearing in Industrial Biotechnology, where value-added metabolites could be produced with simultaneous partial detoxification (i.e. decolorization and phenol removal) of the used residue. In the present study, diluted OMWs (containing 2.0 g/L of total phenolic compounds) blended with 70.0 g/L crude glycerol were employed as substrates. Production of value-added compounds by Y. lipolytica strain ACA-YC 5031 was studied in nitrogen-limited media favoring the production of secondary metabolites (i.e. citric acid, polyols, microbial lipids, polysaccharides). Batch-flask cultures were carried out and the impact of the addition of different NaCl concentrations (1.0%, 3.0%, 5.0% w/w) added upon the biochemical behavior of the strain was studied. Remarkable biomass production was observed in all trials, while in the “blank” experiment (no OMWs and no salt added), the metabolism was shifted toward the synthesis of polyols (Σpolyols = mannitol + arabitol + erythritol > 20 g/L and maximum total citric acid-Cit (sum of citric and isocitric acid) = 10.5 g/L). Addition of OMWs resulted in Citmax = 32.7 g/L, while Σpolyols concentration dropped to <15 g/L. Addition of salt in the OMW-based media slightly reduced the produced biomass, while Cit production drastically increased, reaching a final value of 54.0 g/L (conversion yield of Cit produced per unit of glycerol consumed = 0.82 g/g) in the trial with addition of 5.0% NaCl. Finally, significant color and phenols removal were observed, evaluating the yeast as a decontamination medium for the OMW and a great candidate for the production of value-added compounds.