Microbial lipid-based lignocellulosic biorefinery: feasibility and challenges

Organosolv-derived lipids from hemicellulose and cellulose, and pre-extracted tannins as additives upon hydrothermal liquefaction (HTL) of spruce bark lignins to bio-oil

The rise in global temperature and accumulation of petroleum-based wastes in the environment forces the scientific focus towards renewable alternatives. In the present work, an under-exploited resource - spruce bark - is investigated as a raw material for production of bio-oil as a liquid energy carrier. To enhance the energy-content of the produced bio-crude, ultimately being produced through hydrothermal liquefaction, the polysaccharides were extracted through organosolv fractionation and converted to lipids by oleaginous microorganisms. The effect originating from tannins was also investigated by performing a pre-extraction before the organosolv fractionation. It was found that performing the organosolv fractionation and upgrading the isolated organosolv lignin to bio-oil greatly reduced the oxygen content of the oil fraction thereby improving its energy content, and introducing upgraded polysaccharides in the form of lipids, as well as pre-extracted tannins, caused clear changes in the product distribution of the final bio-oil and kept a final product with low oxygen content. The other factor largely influencing the product distribution originated from the various heating rates tested by altering operational mode of the HTL process between batch and semi-continuous. Ultimately, performing the organosolv fractionation and individual upgrading of the polysaccharides had a beneficial effect on reducing the final solids content and enhancing the liquid oil yield.

Hydrothermal conditioning of oleaginous yeast cells to enable recovery of lipids as potential drop-in fuel precursors

BACKGROUND

Lipids produced using oleaginous yeast cells are an emerging feedstock to manufacture commercially valuable oleochemicals ranging from pharmaceuticals to lipid-derived biofuels. Production of biofuels using oleaginous yeast is a multistep procedure that requires yeast cultivation and harvesting, lipid recovery, and conversion of the lipids to biofuels. The quantitative recovery of the total intracellular lipid from the yeast cells is a critical step during the development of a bioprocess. Their rigid cell walls often make them resistant to lysis. The existing methods include mechanical, chemical, biological and thermochemical lysis of yeast cell walls followed by solvent extraction. In this study, an aqueous thermal pretreatment was explored as a method for lysing the cell wall of the oleaginous yeast Rhodotorula toruloides for lipid recovery.

RESULTS

Hydrothermal pretreatment for 60 min at 121 °C with a dry cell weight of 7% (w/v) in the yeast slurry led to a recovery of 84.6 ± 3.2% (w/w) of the total lipids when extracted with organic solvents. The conventional sonication and acid-assisted thermal cell lysis led to a lipid recovery yield of 99.8 ± 0.03% (w/w) and 109.5 ± 1.9% (w/w), respectively. The fatty acid profiles of the hydrothermally pretreated cells and freeze-dried control were similar, suggesting that the thermal lysis of the cells did not degrade the lipids.

CONCLUSION

This work demonstrates that hydrothermal pretreatment of yeast cell slurry at 121 °C for 60 min is a robust and sustainable method for cell conditioning to extract intracellular microbial lipids for biofuel production and provides a baseline for further scale-up and process integration.

Lipid production from corn straw by cellobiohydrolase and delta-6 desaturase engineered Mucor circinelloides strains under solid state fermentation

Previously, we constructed engineered M. circinelloides strains that can not only utilize cellulose, but also increase the yield of γ-linolenic acid (GLA). In the present study, an in-depth analysis of lipid accumulation by engineered M. circinelloides strains using corn straw was to be explored. When a two-stage temperature control strategy was adopted with adding 1.5% cellulase and 15% inoculum, the engineered strains led to increases in the lipid yield (up to 1.56 g per 100 g dry medium) and GLA yield (up to 274 mg per 100 g dry medium) of 1.8- and 2.3-fold, respectively, compared with the control strain. This study proved the engineered M. circinelloides strains, especially for Mc-C2PD6, possess advantages in using corn straw to produce GLA. This work provided a reference for transformation from agricultural cellulosic waste to functional lipid in one step, which might play a positive role in promoting the sustainable development of biological industry.

Turning waste into treasure: A new direction for low-cost production of lipid chemicals from Thraustochytrids

Thraustochytrids are marine microorganisms known for their fast growth and ability to store lipids, making them useful for producing polyunsaturated fatty acids (PUFAs), biodiesel, squalene, and carotenoids. However, the high cost of production, mainly due to expensive fermentation components, limits their wider use. A significant challenge in this context is the need to balance production costs with the value of the end products. This review focuses on integrating the efficient utilization of waste with Thraustochytrids fermentation, including the economic substitution of carbon sources, nitrogen sources, and fermentation water. This approach aligns with the 3Rs principles (reduction, recycling, and reuse). Furthermore, it emphasizes the role of Thraustochytrids in converting waste into lipid chemicals and promoting sustainable circular production models. The aim of this review is to emphasize the value of Thraustochytrids in converting waste into treasure, providing precise cost reduction strategies for future commercial production.

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.

Making the biochemical conversion of lignocellulose more robust

Lignocellulose is an alternative to fossil resources, but its biochemical conversion is not economically competitive. While decentralized processing can reduce logistical cost for this feedstock, sugar platforms need to be developed with energy-saving pretreatment technologies and cost-effective cellulases, and products must be selected correctly. Anaerobic fermentation with less energy consumption and lower contamination risk is preferred, particularly for producing biofuels. Great effort has been devoted to producing cellulosic ethanol, but CO2 released with large quantities during ethanol fermentation must be utilized in situ for credit. Unless titer and yield are improved substantially, butanol cannot be produced as an advanced biofuel. Microbial lipids produced through aerobic fermentation with low yield and intensive energy consumption are not affordable as feedstocks for biodiesel production.

Combination of alkaline biodiesel-derived crude glycerol pretreated corn stover with dilute acid pretreated water hyacinth for highly-efficient single cell oil production by oleaginous yeast Cutaneotrichosporon oleaginosum

Single cell oil (SCO) prepared from biodiesel-derived crude glycerol (BCG) and lignocellulosic biomass (LCB) via oleaginous yeasts is an intriguing alternative precursor of biodiesel. Here, a novel strategy combining alkaline BCG pretreated corn stover and dilute acid pretreated water hyacinth for SCO overproduction was developed. The mixed pretreatment liquors (MPLs) were naturally neutralized and adjusted to a proper carbon-to-nitrogen ratio beneficial for SCO overproduction by Cutaneotrichosporon oleaginosum. The toxicity of inhibitors was relieved by dilution detoxification. The enzymatic hydrolysate of solid fractions was suitable for SCO production either separately or simultaneously with MPLs. Fed-batch fermentation of the MPLs resulted in high cell mass, SCO content, and SCO titer of 80.7 g/L, 75.7 %, and 61.1 g/L, respectively. The fatty acid profiles of SCOs implied high-quality biodiesel characteristics. This study offers a novel BCG&LCB-to-SCO route integrating BCG-based pretreatment and BCG/LCB hydrolysates co-utilization, which provides a cost-effective technical route for micro-biodiesel production.

Highly-efficient lipid production from hydrolysate of Radix paeoniae alba residue by oleaginous yeast Cutaneotrichosporon oleaginosum

Valorization of herbal extraction residues (HERs) into value-added products is pivotal for the sustainability of Chinese medicine industry. Here, seven different enzymatic hydrolysates of dilute acid pretreated HERs were evaluated for lipid production by Cutaneotrichosporon oleaginosum. Among them, the highest sugar yield via hydrolysis and the maximum lipid production were obtained from Radix paeoniae alba residue (RPAR). More interestingly, high proportion of sugar polymers was disintegrated into fermentable sugars during the pretreatment step, allowing a cheap non-enzymatic route for producing sugars from RPAR. A repeated dilute acid pretreatment gained a high sugar concentration of 241.6 g/L through reusing the pretreatment liquor (PL) for four times. Biomass, lipid concentration, and lipid content achieved 49.5 g/L, 35.7 g/L and 72.2 %, respectively, using fed-batch culture of PL. The biodiesel parameters indicated lipids produced from HERs were suitable for biodiesel production. This study offers a cost-effective way to upgrade the HERs waste into micro-biodiesel.

Computational assessment of lipid production in Rhodosporidium toruloides in two-stage and one-stage batch bioprocesses

Oleaginous yeasts are promising platforms for microbial lipids production as a renewable and sustainable alternative to vegetable oils in biodiesel production. In this paper, a thorough in silico assessment of lipid production in batch cultivation by Rhodosporidium toruloides was developed. By means of dynamic flux balance analysis, the traditional two-stage bioprocess (TSB) performed by the native strain was contrasted with one-stage bioprocess (OSB) using four designed strains obtained by gene knockout strategies. Lipid titer, yield, content, and productivity were analyzed at different initial C/N ratios as relevant performance indicators used in bioprocesses. By weighting these indicators, a global lipid efficiency metric (GLEM) was defined to consider different scenarios. Under simulated conditions, designed strains for lipid overproduction in OSB outperformed the TSB in terms of lipid title (up to threefold), lipid yield (up to 2.4-fold), lipid content (up to 2.8-fold, with a maximum of 76%), and productivity (up to 1.3-fold), depending on C/N ratios. Using these efficiency parameters and the proposed GLEM, the process of selecting the most suitable candidates for lipid production could be carried out before experimental assays. This methodology holds the potential to be extended to other oleaginous microorganisms and diverse strain design techniques.

Lipid Accumulation by Snf-β Engineered Mucor circinelloides Strains on Glucose and Xylose

Sucrose non-fermenting 1 (SNF1) protein kinase plays the regulatory roles in the utilization of selective carbon sources and lipid metabolism. Previously, the role of β subunit of SNF1 in lipid accumulation was evaluated by overexpression and knockout of Snf-β in oleaginous fungus M. circinelloides. In the present study, the growth and lipid accumulation of Snf-β overexpression and knockout strains were further analyzed and compared with glucose or xylose as a single or mixed carbon sources. The results showed that the lipid contents in Snf-β knockout strain improved by 23.2% (for glucose), 28.4% (for xylose), and 30.5% (for mixed glucose and xylose) compared with that of the control strain, respectively. The deletion of Snf-β subunit also altered the transcriptional level of acetyl-CoA carboxylase (ACC). The highest transcriptional levels of ACC1 in Snf-β knockout strain at 24 h were increased by 2.4-fold (for glucose), 2.8-fold (for xylose), and 3.1-fold (for mixed glucose and xylose) compared with that of the control strain, respectively. Our results indicated that Snf-β subunit enhanced lipid accumulation through the regulation of ACC1 in response to xylose or mixed sugars of glucose and xylose more significantly than that of response to glucose. This is the first study to explore the effect of Snf-β subunit of M. circinelloides in regulating lipid accumulation responding to different carbon nutrient signals of glucose and xylose. This study provides a foundation for the future application of the Snf-β engineered strains in lipid production from lignocellulose.

Application of adaptive laboratory evolution for Yarrowia lipolytica: A comprehensive review

Adaptive laboratory evolution is an innovative approach utilized by researchers to enhance the characteristics of microorganisms in the field of biology. With the advancement of this technology, it is now being extended to non-model strains. Yarrowia lipolytica, an oleaginous yeast with significant industrial potential, stands out among the non-conventional fungi. However, the activity of Yarrowia lipolytica is frequently affected by specific substances and environmental factors, necessitating the development of techniques to address these challenges. This manuscript provides an overview of adaptive laboratory evolution experiments conducted on Yarrowia lipolytica, and categorizes the contents into two aspects including improving lignocellulose utilization and enhancing the production in Yarrowia lipolytica. Additionally, we selected several representative examples to illustrate how adaptive laboratory evolution can be combined with other techniques to elucidate the potential mechanisms underlying strain evolution. Lastly, we anticipate a promising future for adaptive laboratory evolution technology and Yarrowia lipolytica in tandem.

Lignocellulosic biorefineries as a platform for the production of high-value yeast derived pigments - A review

Lignocellulosic byproducts, mainly generated by the agro-industrial sector, have great potential as cost-effective feedstocks for bioprocesses because of their abundant availability and high content of sugar-rich and nutrient-rich elements. This biomass can be employed as a carbon source to produce various molecules using several microorganisms. Yeast strains have shown their capability to metabolize diverse C5 and C6 carbon sources, thereby facilitating their use in the bioprocessing of lignocellulosic biomass. Furthermore, yeasts can produce a wide range of valuable products, including biofuels, enzymes, proteins, and pigments, making them attractive for use in integrated biorefineries. Yeast-derived pigments have versatile applications and are environmentally friendly alternatives to their synthetic counterparts. This review emphasizes the potential of lignocellulosic biomass as a feedstock for producing yeast-derived products with a focus on pigments as valuable molecules. It also proposes a yeast-derived pigment platform utilizing lignocellulosic byproducts and explores its potential integration in biorefineries.

From straw to salmon: a technical design and energy balance for production of yeast oil for fish feed from wheat straw

BACKGROUND

Aquaculture is a major user of plant-derived feed ingredients, such as vegetable oil. Production of vegetable oil and protein is generally more energy-intensive than production of the marine ingredients they replace, so increasing inclusion of vegetable ingredients increases the energy demand of the feed. Microbial oils, such as yeast oil made by fermentation of lignocellulosic hydrolysate, have been proposed as a complement to plant oils, but energy assessments of microbial oil production are needed. This study presents a mass and energy balance for a biorefinery producing yeast oil through conversion of wheat straw hydrolysate, with co-production of biomethane and power.

RESULTS

The results showed that 1 tonne of yeast oil (37 GJ) would require 9.2 tonnes of straw, 14.7 GJ in fossil primary energy demand, 14.6 GJ of process electricity and 13.3 GJ of process heat, while 21.5 GJ of biomethane (430 kg) and 6 GJ of excess power would be generated simultaneously. By applying economic allocation, the fossil primary energy demand was estimated to 11.9 GJ per tonne oil.

CONCLUSIONS

Fossil primary energy demand for yeast oil in the four scenarios studied was estimated to be 10-38% lower than for the commonly used rapeseed oil and process energy demand could be met by parallel combustion of lignin residues. Therefore, feed oil can be produced from existing non-food biomass without causing agricultural expansion.

A comprehensive review on microbial lipid production from wastes: research updates and tendencies

Microbial lipids have recently attracted attention as an intriguing alternative for the biodiesel and oleochemical industries to achieve sustainable energy generation. However, large-scale lipid production remains limited due to the high processing costs. As multiple variables affect lipid synthesis, an up-to-date overview that will benefit researchers studying microbial lipids is necessary. In this review, the most studied keywords from bibliometric studies are first reviewed. Based on the results, the hot topics in the field were identified to be associated with microbiology studies that aim to enhance lipid synthesis and reduce production costs, focusing on the biological and metabolic engineering involved. The research updates and tendencies of microbial lipids were then analyzed in depth. In particular, feedstock and associated microbes, as well as feedstock and corresponding products, were analyzed in detail. Strategies for lipid biomass enhancement were also discussed, including feedstock adoption, value-added product synthesis, selection of oleaginous microbes, cultivation mode optimization, and metabolic engineering strategies. Finally, the environmental implications of microbial lipid production and possible research directions were presented.

Coproduction of single cell protein and lipid from lignocellulose derived carbohydrates and inorganic ammonia salt with soluble ammonia recycling

Co-production of single cell protein (SCP) and lipid from lignocellulose-derived carbohydrates and inorganic ammonia offers a promising alternative for poultry or aquaculture feeds. An engineered oleaginous yeast Trichosporon cutaneum MP11 showed great potential for producing SCP and lipid from wheat straw and ammonia sulfate with minimum nutrient input. Trichosporon cutaneum MP11 showed stronger SCP and lipid fermentability using dry acid pretreated and biodetoxified wheat straw than using pure sugars. The residual ammonium sulfate in fermentation broth was recycled up to five times, resulting in ∼70% of nitrogen fixation into SCP. The overall yield of SCP and lipid from lignocellulose-derived sugars was 0.15 g/g and 0.11 g/g, respectively. This translates to the production of one ton of SCP (0.56 ton) and lipid (0.44 ton) from 6.6 tons of wheat straw, or one ton of SCP and lipid containing yeast cells (dry) from 4.8 tons of wheat straw.

Microbial Lipid Based Biorefinery Concepts: A Review of Status and Prospects

The use of lignocellulosic biomass as a raw material for the production of lipids has gained increasing attention, especially in recent years when the use of food in the production of biofuels has become a current technology. Thus, the competition for raw materials for both uses has brought the need to create technological alternatives to reduce this competition that could generate a reduction in the volume of food offered and a consequent commercial increase in the value of food. Furthermore, the use of microbial oils has been studied in many industrial branches, from the generation of renewable energy to the obtainment of several value-added products in the pharmaceutical and food industries. Thus, this review provides an overview of the feasibility and challenges observed in the production of microbial lipids through the use of lignocellulosic biomass in a biorefinery. Topics covered include biorefining technology, the microbial oil market, oily microorganisms, mechanisms involved in lipid-producing microbial metabolism, strain development, processes, lignocellulosic lipids, technical drawbacks, and lipid recovery.

Lipid accumulation and SNF1 transcriptional analysis of Mucor circinelloides on xylose under nitrogen limitation

Sucrose non-fermenting 1 (SNF1) plays a crucial role in utilizing non-glucose carbon sources and regulating lipid metabolism. However, the mechanism by which SNF1 regulates lipid accumulation in oleaginous filamentous fungi in response to nutrient signals remains unclear. In the present study, by analysing the growth and lipid accumulation of M. circinelloides on xylose under nitrogen limitation, combined with the transcriptional changes of each subunit of SNF1, the regulation of SNF1 between nutrient signal and lipid accumulation was explored. The results showed that with the increase of carbon/nitrogen (C/N) ratio, the xylose consumption and cell growth of M. circinelloides decreased, and the lipid accumulation increased gradually. The optimal C/N ratio was 160:1, and the maximum lipid yield was 4.1 g/L. Two subunits of SNF1, Snf-α1 and Snf-β, are related to the regulation of lipid metabolism in response to nutrient signals from different external nitrogen sources. This is the first report on the transcriptional analysis of SNF1 subunits on xylose metabolism under nitrogen limitation. This study provides a basis for further understanding of lipid synthesis mechanism on xylose in oleaginous fungi, and it also lays a foundation for the genetic engineering of high-lipid strain.

Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates

Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of the recently isolated P. hubeiensis BOT-O strain was sequenced using MinION long-read sequencing and resulted in the most contiguous P. hubeiensis assembly to date with 18.95 Mb in 31 contigs. Using transcriptome data as experimental support, we generated the first mRNA-supported P. hubeiensis genome annotation and identified 6540 genes. 80% of the predicted genes were assigned functional annotations based on protein homology to other yeasts. Based on the annotation, key metabolic pathways in BOT-O were reconstructed, including pathways for storage lipids, mannosylerythritol lipids and xylose assimilation. BOT-O was confirmed to consume glucose and xylose at equal rates, but during mixed glucose-xylose cultivation glucose was found to be taken up faster. Differential expression analysis revealed that only a total of 122 genes were significantly differentially expressed at a cut-off of |log₂ fold change| ≥ 2 when comparing cultivation on xylose with glucose, during exponential growth and during nitrogen-starvation. Of these 122 genes, a core-set of 24 genes was identified that were differentially expressed at all time points. Nitrogen-starvation resulted in a larger transcriptional effect, with a total of 1179 genes with significant expression changes at the designated fold change cut-off compared with exponential growth on either glucose or xylose.

Determining mating type and ploidy in Rhodotorula toruloides and its effect on growth on sugars from lignocellulosic biomass

Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating type was determined using a novel polymerase chain reaction (PCR)-based assay, which was validated using the classical microscopic test. Three of the strains were heterozygous for mating type (A1/A2). Ploidy analysis revealed a complex pattern. Two strains were triploid, eight haploid, and eight either diploid or aneuploid. Two of the A1/A2 strains were compared to their parents for growth on 75%v/v concentrated SGH. The A1/A2 strains were much more robust than the parental strains, which either did not grow or had extended lag times. The entire set was evaluated in 60%v/v SGH batch cultures for growth kinetics and biomass and lipid production. Lipid titers were 2.33-9.40 g/L with a median of 6.12 g/L, excluding the two strains that did not grow. Lipid yields were 0.032-0.131 (g/g) and lipid contents were 13.5-53.7% (g/g). Four strains had significantly higher lipid yields and contents. One of these strains, which had among the highest lipid yield in this study (0.131 ± 0.007 g/g), has not been previously described in the literature.

SUMMARY

The yeast Rhodotorula toruloides was used to produce oil using sugars extracted from a bioenergy grass.

New Papiliotrema laurentii UFV-1 strains with improved acetic acid tolerance selected by adaptive laboratory evolution

The production of yeast oil from lignocellulosic biomasses is impaired by inhibitors formed during the pretreatment step, mainly acetic acid. Herein, we applied Adaptive Laboratory Evolution (ALE) to select three Acetic acid Tolerant Strains (ATS) of P. laurentii UFV-1. Different phenotypes emerged alongside evolution. The ATS II presented trade-offs in the absence of acetic acid, suggesting that it displays a specialized phenotype of tolerance to growth on organic acids. On the other hand, ATS I and ATS III presented phenotypes associated with the behavior of generalists. ATS I was considered the most promising evolved strain as it displayed the oleaginous phenotype in all conditions tested. Thus, we applied whole-genome sequencing to detect the mutations that emerged in this strain during the ALE. We found alterations in genes encoding proteins involved in different cellular functions, including multidrug resistance (MDR) transporters, energy metabolism, detoxification, coenzyme recycling, and cell envelope remodeling. To evaluate acetic acid stress responses, both parental and ATS I strains were cultivated in chemostat mode in the absence and presence of acetic acid. In contrast to ATS I, the parental strain presented alterations in the cell envelope and cell size under acetic acid stress conditions. Furthermore, the parental strain and the ATS I presented differences regarding acetic acid assimilation. Contrary to the parental strain, the ATS I displayed an increase in unsaturated fatty acid content irrespective of acetic acid stress, which might be related to improved tolerance to acetic acid. Altogether, these results provided insights into the mechanisms involved with the acetic acid tolerance displayed by ATS I and the responses of P. laurentii to this stressful condition.

A Chemical-Free Pretreatment for Biosynthesis of Bioethanol and Lipids from Lignocellulosic Biomass: An Industrially Relevant 2G Biorefinery Approach

A wide range of inorganic and organic chemicals are used during the pretreatment and enzymatic hydrolysis of lignocellulosic biomass to produce biofuels. Developing an industrially relevant 2G biorefinery process using such chemicals is challenging and requires more unit operations for downstream processing. A sustainable process has been developed to achieve industrially relevant titers of bioethanol with significant ethanol yield. The pretreatment of sorghum biomass was performed by a continuous pilot-scale hydrothermal reactor followed by disk milling. Enzymatic hydrolysis was performed without washing the pretreated biomass. Moreover, citrate buffer strength was reduced to 100-fold (50 mM to 0.5 mM) during the enzymatic hydrolysis. Enzymatic hydrolysis at 0.5 mM citrate buffer strength showed that significant sugar concentrations of 222 ± 2.3 to 241 ± 2.3 g/L (glucose + xylose) were attained at higher solids loadings of 50 to 60% (w/v). Furthermore, hydrolysates were fermented to produce bioethanol using two different xylose-fermenting Saccharomyces cerevisiae strains and a co-culture of xylose-fermenting and non-GMO yeast cultures. Bioethanol titer of 81.7 g/L was achieved with an ethanol yield of 0.48 gp/gs. Additionally, lipids were produced using the oleaginous yeast Rhodosporidium toruloides, yielding 13.2 g/L lipids with cellular lipid accumulation of 38.5% w/w from 100 g/L of sugar concentration. In summary, reducing the strength of the citrate buffer during enzymatic hydrolysis and omitting inorganic chemicals from the pretreatment process enhances the fermentability of hydrolysates and can also reduce operating costs.

Combination of simultaneous saccharification and fermentation of corn stover with consolidated bioprocessing of cassava starch enhances lipid production by the amylolytic oleaginous yeast Lipomyces starkeyi

Highly integrated processes are crucial for the commercial success of microbial lipid production from low-cost substrates. Here, combination of simultaneous saccharification and fermentation (SSF) of corn stover with consolidated bioprocessing (CBP) of cassava starch by Lipomyces starkeyi was firstly developed as a novel strategy for lipid production. Starch was quickly hydrolyzed within 24 h by the amylolytic enzymes secreted by L. starkeyi to provide adequate fermentable sugars at the initial stage of culture, which eliminated the pre-hydrolysis step. More interestingly, synergistic effect for achieving higher lipid production by combined utilization of corn stover and cassava starch at relatively low enzyme dosage was realized, in comparison with the separate utilization of these two substrates. The fatty acid profiles indicated that lipid prepared by the combination strategy was suitable precursor for biodiesel production. The combined SSF&CBP strategy offers a simplified, highly-efficient, and economical route for co-valorization of low-cost substrates into lipids.

An Approach for Incorporating Glycerol as a Co-Substrate into Unconcentrated Sugarcane Bagasse Hydrolysate for Improved Lipid Production in Rhodotorula glutinis

Sugarcane bagasse is a potential raw material for microbial lipid production by oleaginous yeasts. Due to the limited sugar concentrations in bagasse hydrolysate, increasing carbon the concentration is necessary in order to improve lipid production. We aimed to increase carbon concentration by incorporating glycerol as a co-substrate into unconcentrated bagasse hydrolysate in the cultivation of Rhodotorula glutinis TISTR 5159. Cultivation in hydrolysate without nitrogen supplementation (C/N = 42) resulted in 60.31% lipid accumulation with 11.45 ± 0.75 g/L biomass. Nitrogen source supplementation increased biomass to 26.29 ± 2.05 g/L without losing lipid accumulation at a C/N of 25. Yeast extract improved lipid production in the hydrolysate due to high growth without altering the lipid content of the cells. Mixing glycerol up to 10% v/v into the unconcentrated hydrolysate improved biomass and lipid production. A further increase in glycerol concentrations drastically decreased growth and lipid accumulation by the yeast. By maintaining C/N at 27 using yeast extract as the sole nitrogen source, hydrolysate mixed with 10% v/v glycerol resulted in the highest lipid yield, at 19.57 ± 0.53 g/L with 50.55% lipid content, which was a 2.8-fold increase compared to using the hydrolysate alone. In addition, yeast extracts were superior for promoting growth and lipid production compared to inorganic nitrogen sources.

GATA-type transcriptional factor SpGAT1 interacts with SpMIG1 and promotes lipid accumulation in the oleaginous yeast [Formula: see text] zwy-2-3

BACKGROUND

In oleaginous yeast, nitrogen limitation is a critical parameter for lipid synthesis. GATA-family transcriptional factor GAT1, a member of the target of rapamycin (TOR) pathway and nitrogen catabolite repression (NCR), regulates nitrogen uptake and utilization. Therefore, it is significant to study the SpGAT1 regulatory mechanism of lipid metabolism for conversion of biomass to microbial oil in [Formula: see text] zwy-2-3.

RESULTS

Compared with WT, [Formula: see text], and OE::gat1, the lipid yield of OE::gat1 increased markedly in the low carbon and nitrogen ratio (C/N ratio) mediums, while the lipid yield and residual sugar of [Formula: see text] decreased in the high C/N ratio medium. According to yeast two-hybrid assays, SpGAT1 interacted with SpMIG1, and its deletion drastically lowered SpMIG1 expression on the high C/N ratio medium. MIG1 deletion has been found in earlier research to affect glucose metabolic capacity, resulting in a prolonged lag period. Therefore, we speculated that SpGAT1 influenced glucose consumption rate across SpMIG1. Based on yeast one-hybrid assays and qRT-PCR analyses, SpGAT1 regulated the glyoxylate cycle genes ICL1, ICL2, and pyruvate bypass pathway gene ACS, irrespective of the C/N ratio. SpGAT1 also could bind to the ACAT2 promoter in the low C/N medium and induce sterol ester (SE) accumulation.

CONCLUSION

Our findings indicated that SpGAT1 positively regulated lipid metabolism in S.podzolica zwy-2-3, but that its regulatory patterns varied depending on the C/N ratio. When the C/N ratio was high, SpGAT1 interacted with SpMIG1 to affect carbon absorption and utilization. SpGAT1 also stimulated lipid accumulation by regulating essential lipid anabolism genes. Our insights might spur more research into how nitrogen and carbon metabolism interact to regulate lipid metabolism.

Life cycle assessment of microalgal biorefinery: A state-of-the-art review

Microalgal biorefineries represent an opportunity to economically and environmentally justify the production of bioproducts. The generation of bioproducts within a biorefinery system must quantitatively demonstrate its viability in displacing traditional fossil-based refineries. To this end, several works have conducted life cycle analyses on microalgal biorefineries and have shown technological bottlenecks due to energy-intensive processes. This state-of-the-art review covers different studies that examined microalgal biorefineries through life cycle assessments and has identified strategic technologies for the sustainable production of microalgal biofuels through biorefineries. Different metrics were introduced to supplement life cycle assessment studies for the sustainable production of microalgal biofuel. Challenges in the comparison of various life cycle assessment studies were identified, and the future design choices for microalgal biorefineries were established.

Microorganisms as New Sources of Energy

The use of fossil energy sources has a negative impact on the economic and socio-political stability of specific regions and countries, causing environmental changes due to the emission of greenhouse gases. Moreover, the stocks of mineral energy are limited, causing the demand for new types and forms of energy. Biomass is a renewable energy source and represents an alternative to fossil energy sources. Microorganisms produce energy from the substrate and biomass, i.e., from substances in the microenvironment, to maintain their metabolism and life. However, specialized microorganisms also produce specific metabolites under almost abiotic circumstances that often do not have the immediate task of sustaining their own lives. This paper presents the action of biogenic and biogenic–thermogenic microorganisms, which produce methane, alcohols, lipids, triglycerides, and hydrogen, thus often creating renewable energy from waste biomass. Furthermore, some microorganisms acquire new or improved properties through genetic interventions for producing significant amounts of energy. In this way, they clean the environment and can consume greenhouse gases. Particularly suitable are blue-green algae or cyanobacteria but also some otherwise pathogenic microorganisms (E. coli, Klebsiella, and others), as well as many other specialized microorganisms that show an incredible ability to adapt. Microorganisms can change the current paradigm, energy–environment, and open up countless opportunities for producing new energy sources, especially hydrogen, which is an ideal energy source for all systems (biological, physical, technological). Developing such energy production technologies can significantly change the already achieved critical level of greenhouse gases that significantly affect the climate.

Dissecting carbon metabolism of Yarrowia lipolytica type strain W29 using genome-scale metabolic modelling

Yarrowia lipolytica is a widely-used chassis cell in biotechnological applications. It has recently gained extensive research interest owing to its extraordinary ability of producing industrially valuable biochemicals from a variety of carbon sources. Genome-scale metabolic models (GSMMs) enable analyses of cellular metabolism for engineering various industrial hosts. In the present study, we developed a high-quality GSMM iYli21 for Y. lipolytica type strain W29 by extensive manual curation with Biolog experimental data. The model showed a high accuracy of 85.7% in predicting nutrient utilization. Transcriptomics data were integrated to delineate cellular metabolism of utilizing six individual metabolites as sole carbon sources. Comparisons showed that 302 reactions were commonly used, including those from TCA cycle, oxidative phosphorylation, and purine metabolism for energy and material supply. Whereas glycolytic reactions were employed only when glucose and glycerol used as sole carbon sources, gluconeogenesis and fatty acid oxidation reactions were specifically employed when fatty acid, alkane and glycerolipid were the sole carbon sources. Further test of 46 substrates for generating 5 products showed that hexanoate outcompeted other compounds in terms of maximum theoretical yield owing to the lowest carbon loss for energy supply. This newly generated model iYli21 will be a valuable tool in dissecting metabolic mechanism and guiding metabolic engineering of this important industrial cell factory.

Improved γ-Linolenic Acid Production from Cellulose in Mucor circinelloides via Coexpression of Cellobiohydrolase and Delta-6 Desaturase

The present study was aimed at facilitating the production of γ-linolenic acid (GLA) from the cellulosic substrate with the engineered oleaginous fungus Mucor circinelloides WJ11. Here, the homologous recombination technology was used to overexpress the cellobiohydrolase (CBH2) derived from Trichoderma longibrachiatum and the original delta-6 fatty acid desaturase (D6) in M. circinelloides to construct genetically engineered strains capable of effectively using cellulose to enhance GLA synthesis. When cultivated in modified K&R medium supplemented with microcrystalline cellulose, the CBH2 and D6 coexpressing strains led to increases in the biomass (up to 12.8 g/L) and lipid yield (up to 3.7 g/L) of 87% and 2.4-fold, respectively, compared to that of the control strain. Notably, when CBH2 and D6 were coexpressed in M. circinelloides, the yield of GLA reached 608 mg/L, which was a dramatic increase of 3.9-fold compared to that of the control strain. This is the first report on promoting the GLA production from the cellulosic substrate via coexpression of CBH2 and delta-6 desaturase. This work provides a theoretical basis for efficient transformation from the cellulosic substrate to functional GLA by CBH2 and D6 coexpressing strains, which might play a positive role in promoting the sustainable development of biological industry.

Engineering the Oleaginous Yeast Rhodosporidium toruloides for Improved Resistance Against Inhibitors in Biomass Hydrolysates

Conversion of lignocellulosic biomass into lipids and related chemicals has attracted much attention in the past two decades, and the oleaginous yeast Rhodosporidiumtoruloides has been widely used in this area. While R. toruloides species naturally have physiological advantages in terms of substrate utilization, lipid accumulation, and inhibitor resistance, reduced lipid production and cell growth are noticed when biomass hydrolysates are used as feedstocks. To improve the robustness of R. toruloides, here, we devised engineered strains by overexpressing genes responsible for phenolic compound degradation. Specifically, gene expression cassettes of the manganese peroxidase gene (MNP) and versatile peroxidase gene (VP) were constructed and integrated into the genome of R. toruloides NP11. A series of engineered strains were evaluated for lipid production in the presence of typical phenolic inhibitors. The results showed that R. toruloides strains with proper expression of MNP or VP indeed grew faster in the presence of vanillin and 5-hydroxymethylfurfural than the parental strain. When cultivated in concentrated mode biomass hydrolysates, the strain VP18 had improved performance as the cell mass and lipid content increased by 30% and 25%, respectively. This study provides more robust oleaginous yeast strains for microbial lipid production from lignocellulosic biomass, and similar efforts may be used to devise more advanced lipid producers.

The history, state of the art and future prospects for oleaginous yeast research

Lipid-based biofuels, such as biodiesel and hydroprocessed esters, are a central part of the global initiative to reduce the environmental impact of the transport sector. The vast majority of production is currently from first-generation feedstocks, such as rapeseed oil, and waste cooking oils. However, the increased exploitation of soybean oil and palm oil has led to vast deforestation, smog emissions and heavily impacted on biodiversity in tropical regions. One promising alternative, potentially capable of meeting future demand sustainably, are oleaginous yeasts. Despite being known about for 143 years, there has been an increasing effort in the last decade to develop a viable industrial system, with currently around 100 research papers published annually. In the academic literature, approximately 160 native yeasts have been reported to produce over 20% of their dry weight in a glyceride-rich oil. The most intensively studied oleaginous yeast have been Cutaneotrichosporon oleaginosus (20% of publications), Rhodotorula toruloides (19%) and Yarrowia lipolytica (19%). Oleaginous yeasts have been primarily grown on single saccharides (60%), hydrolysates (26%) or glycerol (19%), and mainly on the mL scale (66%). Process development and genetic modification (7%) have been applied to alter yeast performance and the lipids, towards the production of biofuels (77%), food/supplements (24%), oleochemicals (19%) or animal feed (3%). Despite over a century of research and the recent application of advanced genetic engineering techniques, the industrial production of an economically viable commodity oil substitute remains elusive. This is mainly due to the estimated high production cost, however, over the course of the twenty-first century where climate change will drastically change global food supply networks and direct governmental action will likely be levied at more destructive crops, yeast lipids offer a flexible platform for localised, sustainable lipid production. Based on data from the large majority of oleaginous yeast academic publications, this review is a guide through the history of oleaginous yeast research, an assessment of the best growth and lipid production achieved to date, the various strategies employed towards industrial production and importantly, a critical discussion about what needs to be built on this huge body of work to make producing a yeast-derived, more sustainable, glyceride oil a commercial reality.

Engineering Yarrowia lipolytica to produce advanced biofuels: Current status and perspectives

Energy security and global climate change have necessitated the development of renewable energy with net-zero emissions. As alternatives to traditional fuels used in heavy-duty vehicles, advanced biofuels derived from fatty acids and terpenes have similar properties to current petroleum-based fuels, which makes them compatible with existing storage and transportation infrastructures. The fast development of metabolic engineering and synthetic biology has shown that microorganisms can be engineered to convert renewable feedstocks into these advanced biofuels. The oleaginous yeast Yarrowia lipolytica is rapidly emerging as a valuable chassis for the sustainable production of advanced biofuels derived from fatty acids and terpenes. Here, we provide a summary of the strategies developed in recent years for engineering Y. lipolytica to synthesize advanced biofuels. Finally, efficient biotechnological strategies for the production of these advanced biofuels and perspectives for future research are also discussed.

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

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

The effect of volatile fatty acids on the growth and lipid properties of two microalgae strains during batch heterotrophic cultivation

To overcome the bottlenecks of waste resource utilization and energy shortage that restrict the commercial production of microalgae biodiesel, volatile fatty acids (VFAs) derived from activated sludge were used as the sole carbon source to culture oleaginous microalgae Chlorella pyrenoidosa FACHB-1216 and Scenedesmus quadricauda FACHB-1297 under the mixotrophic and heterotrophic cultivation. Four VFAs ratios (acetic acids (AA): propionic acids (PA): butyric acids (BA)) were tested to determine the effects and mechanisms of the VFAs on the two microalgae. The highest lipid content (29.54%) and lipid production (71.10 mg L^-1) were achieved by S. quadricauda at the VFAs ratio of 6: 1: 3 under heterotrophic condition, with 46.27% and 67.52% removal efficiencies of total nitrogen and phosphorus, respectively. The assimilation efficiency of AA was the highest at 73.37%, followed by that of PA and BA. For C. pyrenoidosa, VFAs promoted the rapid reproduction within 2 days under the heterotrophic condition at different initial inoculation densities. At the optimal VFA ratio, algae achieved the highest biomass concentration (0.14 ± 0.02 g L^-1), with a specific growth rate of 0.91 d^-1 and biomass productivity of 125.17 mg L^-1 d^-1. The removal rates of total nitrogen and phosphorus were 47.03% and 74.40%, respectively, and the assimilation efficiency of AA was the best (61.06%). High AA assimilation efficiency under the heterotrophic condition was beneficial for the algal growth and lipid accumulation. These results simultaneously produced microalgae-based bioenergy and recycled VFAs in anaerobically digested effluent.

Single-Cell Oils from Oleaginous Microorganisms as Green Bio-Lubricants: Studies on Their Tribological Performance

Biolubricants refer to eco-friendly, biodegradable, and non-toxic lubricants. Their applications are still limited compared to mineral oils; however, their sustainable credentials are making them increasingly attractive. Vegetable oils are frequently used for this purpose. However, vegetable oils have issues of low lipid productivity, dependence on climatic conditions, and need for agricultural land. Microbial oils represent a more sustainable alternative. To ensure their widespread applicability, the suitability of microbial oils from a physicochemical point of view needs to be determined first. In this study, oils obtained from various oleagenic microbes—such as microalgae, thraustochytrids, and yeasts—were characterized in terms of their fatty acid profile, viscosity, friction coefficient, wear, and thermal stability. Oleaginous microalgal strains (Auxenochlorella protothecoides and Chlorella sorokiniana), thraustochytrids strains (Aurantiochytrium limacinum SR21 and Aurantiochytrium sp. T66), and yeast strains (Rhodosporidium toruloides and Cryptococcus curvatus) synthesized 64.5%, 35.15%, 47.89%, 47.93%, 56.42%, and 52.66% of lipid content, respectively. Oils from oleaginous microalgae (A. protothecoides and C. sorokiniana) and yeasts (R. toruloides and C. curvatus) possess excellent physicochemical and tribological qualities due to high amount of monounsaturated fatty acids (oleic acid C18:1 content, 56.38%, 58.82%, 46.67%, 38.81%) than those from oleaginous thraustochytrids (A. limacinum SR21 and Aurantiochytrium sp. T66; 0.96%, 0.08%, respectively) supporting their use as renewable and biodegradable alternatives to traditional mineral oil-based lubricants. Oil obtained from microalgae showed a lower friction coefficient than oils obtained from yeasts and thraustochytrids.

Tolerance of Trichosporon cutaneum to lignin derived phenolic aldehydes facilitate the cell growth and cellulosic lipid accumulation

Phenolic aldehydes are the major inhibitors from lignocellulose pretreatment. Previous studies show that oleaginous yeasts are difficult to survive in lignocellulosic hydrolysates even after the removal of furan aldehydes and organic acids inhibitors. This study investigated the cell viability, sugar consumption and lipid accumulation of the major oleaginous yeasts including Trichosporon cutaneum, Rhodosporidium toruloides, Rhodotorula glutinis, Yarrowia lipolytica in wheat straw hydrolysate containing only phenolic aldehydes after furan aldehydes and organic acids were selectively degraded by microorganisms. The results confirmed that the existence of residual phenolic aldehydes was the major reason for poor cell growth and metabolism of oleaginous yeasts. Only T. cutaneum demonstrated the higher tolerance by biodegrading phenolic aldehydes and the satisfactory cell growth and lipid production were obtained. This study revealed that T. cutaneum might be one of the promising cell factories for microbial lipid production from lignocellulosic feedstock.

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.

The Role of Metabolic Engineering Technologies for the Production of Fatty Acids in Yeast

Simple Summary

Metabolic engineering involves the sustainable production of high-value products. E. coli and yeast, in particular, are used for such processes. Using metabolic engineering, the biosynthetic pathways of these cells are altered to obtain a high production of desired products. Fatty acids (FAs) and their derivatives are products produced using metabolic engineering. However, classical methods used for engineering yeast metabolic pathways for the production of fatty acids and their derivatives face problems such as the low supply of key precursors and product tolerance. This review introduces the different ways FAs are being produced in E. coli and yeast and the genetic manipulations for enhanced production of FAs. The review also summarizes the latest techniques (i.e., CRISPR–Cas and synthetic biology) for developing FA-producing yeast cell factories.

Abstract

Metabolic engineering is a cutting-edge field that aims to produce simple, readily available, and inexpensive biomolecules by applying different genetic engineering and molecular biology techniques. Fatty acids (FAs) play an important role in determining the physicochemical properties of membrane lipids and are precursors of biofuels. Microbial production of FAs and FA-derived biofuels has several advantages in terms of sustainability and cost. Conventional yeast Saccharomyces cerevisiae is one of the models used for FA synthesis. Several genetic manipulations have been performed to enhance the citrate accumulation and its conversation into acetyl-CoA, a precursor for FA synthesis. Success has been achieved in producing different chemicals, including FAs and their derivatives, through metabolic engineering. However, several hurdles such as slow growth rate, low oleaginicity, and cytotoxicity are still need to be resolved. More robust research needs to be conducted on developing microbes capable of resisting diverse environments, chemicals, and cost-effective feed requirements. Redesigning microbes to produce FAs with cutting-edge synthetic biology and CRISPR techniques can solve these problems. Here, we reviewed the technological progression of metabolic engineering techniques and genetic studies conducted on S. cerevisiae, making it suitable as a model organism and a great candidate for the production of biomolecules, especially FAs.

Improved glucose and xylose co-utilization by overexpression of xylose isomerase and/or xylulokinase genes in oleaginous fungus Mucor circinelloides

Most of the oleaginous microorganisms cannot assimilate xylose in the presence of glucose, which is the major bottleneck in the bioconversion of lignocellulose to biodiesel. Our present study revealed that overexpression of xylose isomerase (XI) gene xylA or xylulokinase (XK) gene xks1 increased the xylose consumption by 25 to 37% and enhanced the lipid content by 8 to 28% during co-fermentation of glucose and xylose. In xylA overexpressing strain Mc-XI, the activity of XI was 1.8-fold higher and the mRNA level of xylA at 24 h and 48 h was 11- and 13-fold higher than that of the control, respectively. In xks1 overexpressing strain Mc-XK, the mRNA level of xks1 was 4- to 11-fold of that of the control strain and the highest XK activity of 950 nmol min^-1 mg^-1 at 72 h which was 2-fold higher than that of the control. Additionally, expression of a translational fusion of xylA and xks1 further enhanced the xylose utilization rate by 45%. Our results indicated that overexpression of xylA and/or xks1 is a promising strategy to improve the xylose and glucose co-utilization, alleviate the glucose repression, and produce lipid from lignocellulosic biomass in the oleaginous fungus M. circinelloides. KEY POINTS: • Overexpressing xylA or xks1 increased the xylose consumption and the lipid content. • The xylose isomerase activity and the xylA mRNA level were enhanced in strain Mc-XI. • Co-expression of xylA and xks1 further enhanced the xylose utilization rate by 45%.

Microbial lipid biosynthesis from lignocellulosic biomass pyrolysis products

Lipids are a biorefinery platform to prepare fuel, food and health products. They are traditionally obtained from plants, but those of microbial origin allow for a better use of land and C resources, among other benefits. Several (thermo)chemical and biochemical strategies are used for the conversion of C contained in lignocellulosic biomass into lipids. In particular, pyrolysis can process virtually any biomass and is easy to scale up. Products offer cost-effective, renewable C in the form of readily fermentable molecules and other upgradable intermediates. Although the production of microbial lipids has been studied for 30 years, their incorporation into biorefineries was only described a few years ago. As pyrolysis becomes a profitable technology to depolymerize lignocellulosic biomass into assimilable C, the number of investigations on it raises significantly. This article describes the challenges and opportunities resulting from the combination of lignocellulosic biomass pyrolysis and lipid biosynthesis with oleaginous microorganisms. First, this work presents the basics of the individual processes, and then it shows state-of-the-art processes for the preparation of microbial lipids from biomass pyrolysis products. Advanced knowledge on separation techniques, structure analysis, and fermentability is detailed for each biomass pyrolysis fraction. Finally, the microbial fatty acid platform comprising biofuel, human food and animal feed products, and others, is presented. Literature shows that the microbial lipid production from anhydrosugars, like levoglucosan, and short-chain organic acids, like acetic acid, is straightforward. Indeed, processes achieving nearly theoretical yields form the latter have been described. Some authors have shown that lipid biosynthesis from different lignin sources is biochemically feasible. However, it still imposes major challenges regarding strain performance. No report on the fermentation of pyrolytic lignin is yet available. Research on the microbial uptake of pyrolytic humins remains vacant. Microorganisms that make use of methane show promising results at the proof-of-concept level. Overall, despite some issues need to be tackled, it is now possible to conceive new versatile biorefinery models by combining lignocellulosic biomass pyrolysis products and robust oleaginous microbial cell factories.

Enhanced lipid production by addition of malic acid in fermentation of recombinant Mucor circinelloides Mc-MT-2

In our previous work, we reported a novel approach for increasing lipid production in an oleaginous fungus Mucor circinelloides by overexpression of mitochondrial malate transporter protein. This transporter plays a vital role in fatty acid biosynthesis during malate and citrate transport systems in oleaginous fungi. In this study, the controlling metabolic supplementation strategy was used to improve the lipid production by overexpression of malate transporter protein in M. circinelloides strain coded as Mc-MT-2. The effects of different metabolic intermediates on lipid production in batch fermentation by Mc-MT-2 were investigated. The optimal lipid production was obtained at 0.8% malic acid after 24 h of fermentation. Furthermore, in fed-batch bioreactors containing glucose as a carbon source supplemented with malic acid, the highest cell growth, and lipid production were achieved. The resulting strain showed the fungal dry biomass of 16 g/L, a lipid content of 32%, lipid yield of 5.12 g/L in a controlled bench-top bioreactor, with 1.60-, 1.60- and 2.56-fold improvement, respectively, compared with the batch control without supplementation of malic acid. Our findings revealed that the addition of malic acid during fermentation might play an important role in lipid accumulation in the recombinant M. circinelloides Mc-MT-2. This study provides valuable insights for enhanced microbial lipid production through metabolic supplementation strategy in large scale and industrial applications.

Socio-Economic and Environmental Impacts of Biomass Valorisation: A Strategic Drive for Sustainable Bioeconomy

In the late twentieth century, the only cost-effective opportunity for waste removal cost at least several thousand dollars, but nowadays, a lot of improvement has occurred. The biomass and waste generation problems attracted concerned authorities to identify and provide environmentally friendly sustainable solutions that possess environmental and economic benefits. The present study emphasises the valorisation of biomass and waste produced by domestic and industrial sectors. Therefore, substantial research is ongoing to replace the traditional treatment methods that potentially acquire less detrimental effects. Synthetic biology can be a unique platform that invites all the relevant characters for designing and assembling an efficient program that could be useful to handle the increasing threat for human beings. In the future, these engineered methods will not only revolutionise our lives but practically lead us to get cheaper biofuels, producing bioenergy, pharmaceutics, and various biochemicals. The bioaugmentation approach concomitant with microbial fuel cells (MFC) is an example that is used to produce electricity from municipal waste, which is directly associated with the loading of waste. Beyond the traditional opportunities, herein, we have spotlighted the new advances in pertinent technology closely related to production and reduction approaches. Various integrated modern techniques and aspects related to the industrial sector are also discussed with suitable examples, including green energy and other industrially relevant products. However, many problems persist in present-day technology that requires essential efforts to handle thoroughly because significant valorisation of biomass and waste involves integrated methods for timely detection, classification, and separation. We reviewed and proposed the anticipated dispensation methods to overcome the growing stream of biomass and waste at a distinct and organisational 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.

Coupling azo dye degradation and biodiesel production by manganese-dependent peroxidase producing oleaginous yeasts isolated from wood-feeding termite gut symbionts

BACKGROUND

Textile industry represents one prevalent activity worldwide, generating large amounts of highly contaminated and rich in azo dyes wastewater, with severe effects on natural ecosystems and public health. However, an effective and environmentally friendly treatment method has not yet been implemented, while concurrently, the increasing demand of modern societies for adequate and sustainable energy supply still remains a global challenge. Under this scope, the purpose of the present study was to isolate promising species of yeasts inhabiting wood-feeding termite guts, for combined azo dyes and textile wastewater bioremediation, along with biodiesel production.

RESULTS

Thirty-eight yeast strains were isolated, molecularly identified and subsequently tested for desired enzymatic activity, lipid accumulation, and tolerance to lignin-derived metabolites. The most promising species were then used for construction of a novel yeast consortium, which was further evaluated for azo dyes degradation, under various culture conditions, dye levels, as well as upon the addition of heavy metals, different carbon and nitrogen sources, and lastly agro-waste as an inexpensive and environmentally friendly substrate alternative. The novel yeast consortium, NYC-1, which was constructed included the manganese-dependent peroxidase producing oleaginous strains Meyerozyma caribbica, Meyerozyma guilliermondii, Debaryomyces hansenii, and Vanrija humicola, and showed efficient azo dyes decolorization, which was further enhanced depending on the incubation conditions. Furthermore, enzymatic activity, fatty acid profile and biodiesel properties were thoroughly investigated. Lastly, a dye degradation pathway coupled to biodiesel production was proposed, including the formation of phenol-based products, instead of toxic aromatic amines.

CONCLUSION

In total, this study might be the first to explore the application of MnP and lipid-accumulating yeasts for coupling dye degradation and biodiesel production.

Microbial lipids from organic wastes: Outlook and challenges

Microbial lipids have recently drawn a lot of attention as renewable sources for biochemicals production. Strong research efforts have been addressed to efficiently use organic wastes as carbon source for microbial lipids, which would definitively increase the profitability of the production process and boost a bio-based economy. This review compiles interesting traits of oleaginous microorganisms and highlights current trends on microbial- and process-oriented approaches to maximize microbial oil production from inexpensive substrates like lignocellulosic sugars, volatile fatty acids and glycerol. Furthermore, downstream processes such as cell harvesting or lipid extraction, that are decisive for the cost-effectiveness of the process, are discussed. To underpin microbial oils within the so demanded circular economy, associated challenges, recent advances and possible industrial applications that are also identified in this review.

Adaptive laboratory evolution of Yarrowia lipolytica improves ferulic acid tolerance

Yarrowia lipolytica strain is a promising cell factory for the conversion of lignocellulose to biofuels and bioproducts. Despite the inherent robustness of this strain, further improvements to lignocellulose-derived inhibitors toxicity tolerance of Y. lipolytica are also required to achieve industrial application. Here, adaptive laboratory evolution was employed with increasing concentrations of ferulic acid. The adaptive laboratory evolution experiments led to evolve Y. lipolytica strain yl-XYL + *FA*4 with increased tolerance to ferulic acid as compared to the parental strain. Specifically, the evolved strain could tolerate 1.5 g/L ferulic acid, whereas 0.5 g/L ferulic acid could cause about 90% lethality of the parental strain. Transcriptome analysis of the evolved strain revealed several targets underlying toxicity tolerance enhancements. YALI0_E25201g, YALI0_F05984g, YALI0_B18854g, and YALI0_F16731g were among the highest upregulated genes, and the beneficial contributions of these genes were verified via reverse engineering. Recombinant strains with overexpressing each of these four genes obtained enhanced tolerance to ferulic acid as compared to the control strain. Fortunately, recombinant strains with overexpression of YALI0_E25201g, YALI0_B18854g, and YALI0_F16731g individually also obtained enhanced tolerance to vanillic acid. Overall, this work demonstrated a whole strain improvement cycle by "non-rational" metabolic engineering and presented new targets to modify Y. lipolytica for microbial lignocellulose valorization. KEY POINTS: • Adaptive evolution improved the ferulic acid tolerance of Yarrowia lipolytica • Transcriptome sequence was applied to analyze the ferulic acid tolerate strain • Three genes were demonstrated for both ferulic acid and vanillic acid tolerance.

The Potential of Single-Cell Oils Derived From Filamentous Fungi as Alternative Feedstock Sources for Biodiesel Production

Microbial lipids, also known as single-cell oils (SCOs), are highly attractive feedstocks for biodiesel production due to their fast production rates, minimal labor requirements, independence from seasonal and climatic changes, and ease of scale-up for industrial processing. Among the SCO producers, the less explored filamentous fungi (molds) exhibit desirable features such as a repertoire of hydrolyzing enzymes and a unique pellet morphology that facilitates downstream harvesting. Although several oleaginous filamentous fungi have been identified and explored for SCO production, high production costs and technical difficulties still make the process less attractive compared to conventional lipid sources for biodiesel production. This review aims to highlight the ability of filamentous fungi to hydrolyze various organic wastes for SCO production and explore current strategies to enhance the efficiency and cost-effectiveness of the SCO production and recovery process. The review also highlights the mechanisms and components governing lipogenic pathways, which can inform the rational designs of processing conditions and metabolic engineering efforts for increasing the quality and accumulation of lipids in filamentous fungi. Furthermore, we describe other process integration strategies such as the co-production with hydrogen using advanced fermentation processes as a step toward a biorefinery process. These innovative approaches allow for integrating upstream and downstream processing units, thus resulting in an efficient and cost-effective method of simultaneous SCO production and utilization for biodiesel production.

L-asparaginase Production by Leucosporidium scottii in a Bench-Scale Bioreactor With Co-production of Lipids

L-asparaginase (ASNase) is a therapeutical enzyme used for treatment of acute lymphoblastic leukemia. ASNase products available in the market are produced by bacteria and usually present allergic response and important toxicity effects to the patients. Production of ASNase by yeasts could be an alternative to overcome these problems since yeasts have better compatibility with the human system. Recently, it was found that Leucosporidium scottii, a psychrotolerant yeast, produces ASNase. In order to advance the production of ASNase by this yeast, the present study aimed to select suitable process conditions able to maximize the production of this enzyme in a bench-scale bioreactor. Additionally, the accumulation of lipids during the enzyme production process was also determined and quantified. Experiments were carried out with the aim of selecting the most appropriate conditions of initial cell concentration (1.0, 3.5, and 5.6 g L^–1), carbon source (sucrose and glycerol, individually or in mixture) and oxygen transfer rate (k_La in the range of 1.42–123 h^–1) to be used on the production of ASNase by this yeast. Results revealed that the enzyme production increased when using an initial cell concentration of 5.6 g L^–1, mixture of sucrose and glycerol as carbon source, and k_La of 91.72 h^–1. Under these conditions, the enzyme productivity was maximized, reaching 35.11 U L^–1 h^–1, which is already suitable for the development of scale-up studies. Additionally, accumulation of lipids was observed in all the cultivations, corresponding to 2–7 g L^–1 (32–40% of the cell dry mass), with oleic acid (C_18:1) being the predominant compound (50.15%). Since the L-asparaginase biopharmaceuticals on the market are highly priced, the co-production of lipids as a secondary high-value product during the ASNase production, as observed in the present study, is an interesting finding that opens up perspectives to increase the economic feasibility of the enzyme production process.

Immobilization of Laccase on Magnetic Nanoparticles and Application in the Detoxification of Rice Straw Hydrolysate for the Lipid Production of Rhodotorula glutinis

The production of microbial lipid using lignocellulosic agroforestry residues has attracted much attention. But, various inhibitors such as phenols and furans, which are produced during lignocellulosic hydrolysate preparation, are harmful to microbial lipid accumulation. Herein, we developed a novel detoxification strategy of rice straw hydrolysate using immobilized laccase on magnetic Fe₃O₄ nanoparticles for improving lipid production of Rhodotorula glutinis. Compared with free laccase, the immobilized laccase on magnetic nanoparticles showed better stability, which still retained 76% of original activity at 70 °C and 56% at pH 2 for 6 h. This immobilized laccase was reused to remove inhibitors in acid-pretreated rice straw hydrolysate through recycling with external magnetic field. The results showed that most of phenols, parts of furans, and formic acids could be removed by immobilized laccase after the first batch. Notably, the immobilized laccase exhibited good reusability in repeated batch detoxification. 78.2% phenols, 43.8% furfural, 30.4% HMF, and 16.5% formic acid in the hydrolysate were removed after the fourth batch. Furthermore, these detoxified rice straw hydrolysates, as substrates, were applied to the lipid production of Rhodotorula glutinis. The lipid yield in detoxified hydrolysate was significantly higher than that in undetoxified hydrolysate. These findings suggest that the immobilized laccase on magnetic nanoparticles has a potential to detoxify lignocellusic hydrolysate for improving microbial lipid production.

Lipid Accumulation by Xylose Metabolism Engineered Mucor circinelloides Strains on Corn Straw Hydrolysate

Previously, we presented a novel approach for increasing the consumption of xylose and the lipid yield by overexpressing the genes coding for xylose isomerase (XI) and xylulokinase (XK) in Mucor circinelloides. In the present study, an in-depth analysis of lipid accumulation by xylose metabolism engineered M. circinelloides strains (namely Mc-XI and Mc-XK) using corn straw hydrolysate was to be explored. The results showed that the fatty acid contents of the engineered M. circinelloides strains were, respectively, increased by 19.8% (in Mc-XI) and 22.3% (in Mc-XK) when compared with the control strain, even though a slightly decreased biomass in these engineered strains was detected. Moreover, the xylose uptake rates of engineered strains in the corn straw hydrolysate were improved significantly by 71.5% (in Mc-XI) and 68.8% (in Mc-XK), respectively, when compared with the control strain. Maybe the increased utilization of xylose led to an increase in lipid synthesis. When the recombinant M. circinelloides strains were cultured in corn straw hydrolysate medium with the carbon-to-nitrogen ratio (C/N ratio) of 50 and initial pH of 6.0, at 30 °C and 500 rpm for 144 h, a total biomass of 12.6-12.9 g/L with a lipid content of 17.2-17.7% (corresponding to a lipid yield of 2.17-2.28 g/L) was achieved. Our study provides a foundation for the further application of the engineered M. circinelloides strains to produce lipid from lignocelluloses.