The influence of different carbon sources on growth and single cell oil production in oleaginous yeasts Apiotrichum brassicae and Pichia kudriavzevii

Microbial production of food lipids using the oleaginous yeast Apiotrichum brassicae

Oleaginous yeasts offer a promising sustainable alternative for producing edible lipids, potentially replacing animal and unsustainable plant fats and oils. In this study, we screened 11 oleaginous yeast species for their lipid profiles and identified Apiotrichum brassicae as the most promising candidate due to its versatility across different growth media. A. brassicae grown in a dairy side stream produced lipids with a composition most similar to cocoa butter, but the stearic acid and linoleic acid content varied greatly when grown on different substrates. We visualised the formation of lipid droplets by digital holotomography. Pilot-scale production was followed by enzymatic and ultrasonic treatment of biomass and heptane/ethanol extraction. The fatty acid (FA) and triacylglycerol (TAG) composition, thermal behaviour, and solid fat content of A. brassicae lipids was compared to benchmarks such as beef fat, cocoa butter, palm oil and milk fat. The FA profile of the A. brassicae lipids shares the same types of fatty acids with cocoa butter, beef fat and palm oil, however concentrations differ resulting in a lower content of saturated FAs. This increased the proportion of unsaturated TAGs, reducing the melting and crystallisation temperatures and the solid fat content. The microbial lipids contained the major TAGs of cocoa butter at similar ratios, resulting in a comparable melting peak and crystallisation peaks similar to the low-melting groups of beef fat and palm oil. Fractionation has the potential to produce beef fat, cocoa butter or palm oil equivalents with desired techno-functional properties. This study demonstrates the potential of A. brassicae to produce tailored lipid profiles for various food applications through strain and process engineering or downstream processing.

Enhanced degradation of exogenetic citrinin by glycosyltransferases in the oleaginous yeast Saitozyma podzolica zwy-2-3

The contamination by the toxin citrinin (CIT), produced by fungi, has been reported in agricultural foods and is known to be nephrotoxic to humans. In this study, we found that CIT could be effectively degraded by the oleaginous yeast Saitozyma podzolica zwy-2-3. Four genes encoding glycosyltransferases (GTs) in S. podzolica zwy-2-3 (SPGTs) were identified by evolutionary and structural analyses. The overexpression of SPGTs enhanced CIT degradation to 0.56 mg/L/h in S. podzolica zwy-2-3 by increasing ATP and glutathione (GSH) contents to oxidize CIT and scavenge reactive oxygen species (ROS). Besides, SPGTs promoted lipid synthesis by 9.3 % of S. podzolica zwy-2-3 under CIT stress. These results suggest that SPGTs in oleaginous yeast play a pivotal role in enhancing CIT degradation and lipid accumulation. These findings provide a valuable basis for the application of GTs in oleaginous yeast to alleviate CIT contamination in agricultural production, which may contribute to food safety.

Clostridium carboxidivorans and Rhodosporidium toruloides as a platform for the valorization of carbon dioxide to microbial oils

There is growing scientific interest in oleaginous yeasts producing microbial oils as precursors of biofuels and potential substitutes for fossil fuels. Due to the high cost of substrates commonly metabolized by yeasts, volatile fatty acids (VFAs) are gaining interest as alternative cheap and sustainable carbon sources, which can be obtained from solid, liquid and gas pollutants. In this research, Rhodosporidium toruloides was proven to be able to accumulate microbial oils from VFAs obtained from the fermentation of syngas by Clostridium carboxidivorans. Using CO2 and CO as carbon sources from the syngas mixture and H2 as energy source, this acetogen produced, via the Wood-Ljungdahl pathway, a mixture of acetic, butyric and caproic acids. It was first revealed that R. toruloides exhibited minimal inhibition at concentrations below 12 g/L when exposed to a mixture of VFAs, which included acetic, butyric and even hexanoic acids. The yeast was then grown on the culture medium derived from the acetogenic fermentation of syngas. Between the two yeast strains tested of the same species, R. toruloides DSM 4444 reached a total VFAs consumption of 69.1 g/L, supplied by successive additions of acids to the reactor, yielding a maximum lipid content of 29.7% w/w cell. The lipid profile obtained in this case, in terms of abundance followed the order C18:1 > C16:0 ≥ C18:0 > C18:2>others; in which the dominant compound (C18:1), represented approximately 50% of the total. This research opens new possibilities in the cultivation of oleaginous yeasts for the production of biofuels and bioproducts from C1 gases.

Oleaginous fungi: a promising source of biofuels and nutraceuticals with enhanced lipid production strategies

Oleaginous fungi have attracted a great deal of interest for their potency to accumulate high amounts of lipids (more than 20% of biomass dry weight) and polyunsaturated fatty acids (PUFAs), which have a variety of industrial and biological applications. Lipids of plant and animal origin are related to some restrictions and thus lead to attention towards oleaginous microorganisms as reliable substitute resources. Lipids are traditionally biosynthesized intra-cellularly and involved in the building structure of a variety of cellular compartments. In oleaginous fungi, under certain conditions of elevated carbon ratio and decreased nitrogen in the growth medium, a change in metabolic pathway occurred by switching the whole central carbon metabolism to fatty acid anabolism, which subsequently resulted in high lipid accumulation. The present review illustrates the bio-lipid structure, fatty acid classes and biosynthesis within oleaginous fungi with certain key enzymes, and the advantages of oleaginous fungi over other lipid bio-sources. Qualitative and quantitative techniques for detecting the lipid accumulation capability of oleaginous microbes including visual, and analytical (convenient and non-convenient) were debated. Factors affecting lipid production, and different approaches followed to enhance the lipid content in oleaginous yeasts and fungi, including optimization, utilization of cost-effective wastes, co-culturing, as well as metabolic and genetic engineering, were discussed. A better understanding of the oleaginous fungi regarding screening, detection, and maximization of lipid content using different strategies could help to discover new potent oleaginous isolates, exploit and recycle low-cost wastes, and improve the efficiency of bio-lipids cumulation with biotechnological significance.

High-throughput screening of non-conventional yeasts for conversion of organic waste to microbial oils via carboxylate platform

Converting waste into high-value products promotes sustainability by reducing waste and creating new revenue streams. This study investigates the potential of diverse yeasts for microbial oil production by utilizing short-chain fatty acids (SCFAs) that can be produced from organic waste and focuses on identifying strains with the best SCFA utilisation, tolerance and lipid production. A collection of 1434 yeast strains was cultivated with SCFAs as the sole carbon source. Eleven strains emerged as candidates with promising growth rates and high lipid accumulation. Subsequent fermentation experiments in liquid SCFA-rich media, which focused on optimizing lipid accumulation by adjusting the carbon to nitrogen (C/N) ratio, showed an increase in lipid content at a C/N ratio of 200:1, but with a concurrent reduction in biomass. Two strains were characterized by their superior ability to produce lipids compared to the reference strain Yarrowia lipolytica CECT124: Y. lipolytica EXF-17398 and Pichia manshurica EXF-7849. Characterization of these two strains indicated that they exhibit a biotechnologically relevant balance between maximizing lipid yield and maintaining growth at high SCFA concentrations. These results emphasize the potential of using SCFAs as a sustainable feedstock for oleochemical production, offering a dual benefit of waste valorisation and microbial oil production.

Physiological evaluation of yeast strains under anaerobic conditions using glucose, fructose, or sucrose as the carbon source

The aim of this study was to evaluate the physiology of 13 yeast strains by assessing their kinetic parameters under anaerobic conditions. They included Saccharomyces cerevisiae CAT-1 and 12 isolated yeasts from different regions in Brazil. The study aimed to enhance understanding of the metabolism of these strains for more effective applications. Measurements included quantification of sugars, ethanol, glycerol, and organic acids. Various kinetic parameters were analyzed, such as specific substrate utilization rate (qS), maximum specific growth rate (μmax), doubling time, biomass yield, product yield, maximum cell concentration, ethanol productivity (PEth), biomass productivity, and CO2 concentration. S. cerevisiae CAT-1 exhibited the highest values in glucose for μmax (0.35 h-1), qS (3.06 h-1), and PEth (0.69 gEth L-1 h-1). Candida parapsilosis Recol 37 did not fully consume the substrate. In fructose, S. cerevisiae CAT-1 stood out with higher values for μmax (0.25 h-1), qS (2.24 h-1), and PEth (0.60 gEth L-1 h-1). Meyerozyma guilliermondii Recol 09 and C. parapsilosis Recol 37 had prolonged fermentation times and residual substrate. In sucrose, only S. cerevisiae CAT-1, S. cerevisiae BB9, and Pichia kudriavzevii Recol 39 consumed all the substrate, displaying higher PEth (0.72, 0.51, and 0.44 gEth L-1 h-1, respectively) compared to other carbon sources.

Shared and more specific genetic determinants and pathways underlying yeast tolerance to acetic, butyric, and octanoic acids

BACKGROUND

The improvement of yeast tolerance to acetic, butyric, and octanoic acids is an important step for the implementation of economically and technologically sustainable bioprocesses for the bioconversion of renewable biomass resources and wastes. To guide genome engineering of promising yeast cell factories toward highly robust superior strains, it is instrumental to identify molecular targets and understand the mechanisms underlying tolerance to those monocarboxylic fatty acids. A chemogenomic analysis was performed, complemented with physiological studies, to unveil genetic tolerance determinants in the model yeast and cell factory Saccharomyces cerevisiae exposed to equivalent moderate inhibitory concentrations of acetic, butyric, or octanoic acids.

RESULTS

Results indicate the existence of multiple shared genetic determinants and pathways underlying tolerance to these short- and medium-chain fatty acids, such as vacuolar acidification, intracellular trafficking, autophagy, and protein synthesis. The number of tolerance genes identified increased with the linear chain length and the datasets for butyric and octanoic acids include the highest number of genes in common suggesting the existence of more similar toxicity and tolerance mechanisms. Results of this analysis, at the systems level, point to a more marked deleterious effect of an equivalent inhibitory concentration of the more lipophilic octanoic acid, followed by butyric acid, on the cell envelope and on cellular membranes function and lipid remodeling. The importance of mitochondrial genome maintenance and functional mitochondria to obtain ATP for energy-dependent detoxification processes also emerged from this chemogenomic analysis, especially for octanoic acid.

CONCLUSIONS

This study provides new biological knowledge of interest to gain further mechanistic insights into toxicity and tolerance to linear-chain monocarboxylic acids of increasing liposolubility and reports the first lists of tolerance genes, at the genome scale, for butyric and octanoic acids. These genes and biological functions are potential targets for synthetic biology approaches applied to promising yeast cell factories, toward more robust superior strains, a highly desirable phenotype to increase the economic viability of bioprocesses based on mixtures of volatiles/medium-chain fatty acids derived from low-cost biodegradable substrates or lignocellulose hydrolysates.

Engineering low-salt growth Halomonas Bluephagenesis for cost-effective bioproduction combined with adaptive evolution

Halophilic Halomonas bluephagenesis has been engineered to produce various added-value bio-compounds with reduced costs. However, the salt-stress regulatory mechanism remained unclear. H. bluephagenesis was randomly mutated to obtain low-salt growing mutants via atmospheric and room temperature plasma (ARTP). The resulted H. bluephagenesis TDH4A1B5 was constructed with the chromosomal integration of polyhydroxyalkanoates (PHA) synthesis operon phaCAB and deletion of phaP1 gene encoding PHA synthesis associated protein phasin, forming H. bluephagenesis TDH4A1B5P, which led to increased production of poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-4-hydrobutyrate) (P34HB) by over 1.4-fold. H. bluephagenesis TDH4A1B5P also enhanced production of ectoine and threonine by 50% and 77%, respectively. A total 101 genes related to salinity tolerance was identified and verified via comparative genomic analysis among four ARTP mutated H. bluephagenesis strains. Recombinant H. bluephagenesis TDH4A1B5P was further engineered for PHA production utilizing sodium acetate or gluconate as sole carbon source. Over 33% cost reduction of PHA production could be achieved using recombinant H. bluephagenesis TDH4A1B5P. This study successfully developed a low-salt tolerant chassis H. bluephagenesis TDH4A1B5P and revealed salt-stress related genes of halophilic host strains.

Molecular mechanisms through which different carbon sources affect denitrification by Thauera linaloolentis: Electron generation, transfer, and competition

Characterizing the molecular mechanism through which different carbon sources affect the denitrification process would provide a basis for the proper selection of carbon sources, thus avoiding excessive carbon source dosing and secondary pollution while also improving denitrification efficiency. Here, we selected Thauera linaloolentis as a model organism of denitrification, whose genomic information was elucidated by draft genome sequencing and KEGG annotations, to investigate the growth kinetics, denitrification performances and characteristics of metabolic pathways under diverse carbon source conditions. We reconstructed a metabolic network of Thauera linaloolentis based on genomic analysis to help develop a systematic method of researching electron pathways. Our findings indicated that carbon sources with simple metabolic pathways (e.g., ethanol and sodium acetate) promoted the reproduction of Thauera linaloolentis, and its maximum growth density reached OD₆₀₀ = 0.36 and maximum specific growth rate reached 0.145 h^-1. These carbon sources also accelerated the denitrification process without the accumulation of intermediates. Nitrate could be reduced completely under any carbon source condition; but in the "glucose group", the maximum accumulation of nitrite was 117.00 mg/L (1.51 times more than that in the "ethanol group", which was 77.41 mg/L), the maximum accumulation of nitric oxide was 363.02 μg/L (7.35 times more than that in the "ethanol group", which was 49.40 μg/L), and the maximum accumulation of nitrous oxide was 22.58 mg/L (26.56 times more than that in the "ethanol group", which was 0.85 mg/L). Molecular biological analyses demonstrated that diverse types of carbon sources directly induced different carbon metabolic activities, resulting in variations in electron generation efficiency. Furthermore, the activities of the electron transport system were positively correlated with different carbon metabolic activities. Finally, these differences were reflected in the phenomenon of electronic competition between denitrifying reductases. Thus we concluded that this was the main molecular mechanism through which the carbon source type affected the denitrification process. In brief, carbon sources with simple metabolic pathways induced higher efficiency of electron generation, transfer, and competition, which promoted rapid proliferation and complete denitrification; otherwise Thauera linaloolentis would grow slowly and intermediate products would accumulate seriously. Our study established a method to evaluate and optimize carbon source utilization efficiency based on confirmed molecular mechanisms.

Investigation of stress tolerance of Pichia kudriavzevii for high gravity bioethanol production from steam-exploded wheat straw hydrolysate

This study investigated a newly isolated thermotolerant strain of Pichia kudriavzevii with respect to its stress tolerance and fermentation performance. Response surface methodology was applied to evaluate the combined effects of furfural, osmotic and thermal stress on ethanol yield. The proposed model shows that P. kudriavzevii has a natural resistance against multiple stress factors. Further evolutionary adaptation of the isolated strain in lignocellulosic hydrolysates improved the ethanol yield by ≥ 24 %. The adapted strain HYPK213_ELA was able to produce ethanol from wheat straw hydrolysates at a high solid loading of 37 %ww-1 at 40 °C and anaerobic conditions. The highest ethanol concentration of 56.8 ± 1.0 gL-1 was reached at 40°C with an inoculum size of 2.5 × 106cellsmL-1. The results show that Pichia kudriavzevii has the potential to enable high gravity bioethanol production under conditions where most yeast strains are unable to grow.

Growth ability, carbon source utilization and biochemical features of the new specie Zalaria obscura

This research investigated the characteristics of Zalaria obscura LS31012019 in terms of growth ability in different media (SDB, YPD and TSB) and temperatures (22, 25 and 37 °C), utilization of several carbon sources (Glucose, Fructose, Lactose, Sucrose, Xylose, Glycerol and Mannitol at 5, 2 and 1%) and several biochemical features (total protein content, Glutathione, pigments), in comparison with those of the phylogenetically related Aureobasidium pullulans ATCC 15233. The best growth of Z. obscura LS31012019 was obtained in YPD at 25 °C with the highest OD value (0.45) after 144 h of incubation, similar to that of A. pullulans ATCC 15233 (0.48). Glucose resulted the preferred carbon source for both the considered yeasts but also sucrose resulted in efficacy supporting the growth of Z. obscura LS31012019 and A. pullulans ATCC 15233, for their ability in converting sucrose to glucose and fructose and the latter into glucose. Interestingly, Z. obscura LS31012019 utilized also glycerol and mannitol. The biochemical analysis showed the similarity of protein profile in Z. obscura LS31012019 and A. pullulans ATCC 15233 (from 90 to 20 kDa) and a reduced GSH content (0.321 and 0.233 µmol/mg). The pigments extraction with hexane generated a yellow oleaginous pellet in both the strains, while a yellow solid matrix more intensely coloured in A. pullulans ATTC 15233 was visible with the following solvent extractions. Overall, our data showed that Z. obscura LS31012019 can grow in different media and temperatures and utilize carbon sources apart from glucose and sucrose, shifting to a non-fermentative metabolism. These results improve the information regarding the characteristics of Z. obscura, opening a new field of investigation for the possible application of new species of black yeasts in human application.