Development of a scale-up strategy for fermentative production of docosahexaenoic acid by Schizochytrium sp

Mid-Long Chain Dicarboxylic Acid Production via Systems Metabolic Engineering: Progress and Prospects

Mid-to-long-chain dicarboxylic acids (DCAi, i ≥ 6) are organic compounds in which two carboxylic acid functional groups are present at the terminal position of the carbon chain. These acids find important applications as structural components and intermediates across various industrial sectors, including organic compound synthesis, food production, pharmaceutical development, and agricultural manufacturing. However, conventional petroleum-based DCA production methods cause environmental pollution, making sustainable development challenging. Hence, the demand for eco-friendly processes and renewable raw materials for DCA production is rising. Owing to advances in systems metabolic engineering, new tools from systems biology, synthetic biology, and evolutionary engineering can now be used for the sustainable production of energy-dense biofuels. Here, we explore systems metabolic engineering strategies for DCA synthesis in various chassis via the conversion of different raw materials into mid-to-long-chain DCAs. Subsequently, we discuss the future challenges in this field and propose synthetic biology approaches for the efficient production and successful commercialization of these acids.

Development of a green fermentation strategy with resource cycle for the docosahexaenoic acid production by Schizochytrium sp

The fermentation production of docosahexaenoic acid (DHA) is an industrial process with huge consumption of freshwater resource and nutrient, such as carbon sources and nitrogen sources. In this study, seawater and fermentation wastewater were introduced into the fermentation production of DHA, which could solve the problem of fermentation industry competing with humans for freshwater. In addition, a green fermentation strategy with pH control using waste ammonia, NaOH and citric acid as well as FW recycling was proposed. It could provide a stable external environment for cell growth and lipid synthesis while alleviating the dependence on organic nitrogen sources of Schizochytrium sp. It was proved that this strategy has good industrialization potential for DHA production, and the biomass, lipid and DHA yield reached to 195.8 g/L, 74.4 g/L and 46.4 g/L in 50 L bioreactor, respectively. This study provides a green and economic bioprocess technology for DHA production by Schizochytrium sp.

Economical downstream processing of microbial polyunsaturated fatty acids

Polyunsaturated fatty acids (PUFAs) are important nutrients for humans and animals. Microorganisms, such as yeast, filamentous fungi, and microalgae, have successfully been modified to produce PUFAs. Apart from strain improvement and fermentation optimization, efficient and cost-effective downstream processing will determine whether production can advance from the laboratory to the factory.

Identification and Functional Analysis of Two Novel Genes-Geranylgeranyl Pyrophosphate Synthase Gene (AlGGPPS) and Isopentenyl Pyrophosphate Isomerase Gene (AlIDI)-from Aurantiochytrium limacinum Significantly Enhance De Novo β-Carotene Biosynthesis in Escherichia coli

Precursor regulation has been an effective strategy to improve carotenoid production and the availability of novel precursor synthases facilitates engineering improvements. In this work, the putative geranylgeranyl pyrophosphate synthase encoding gene (AlGGPPS) and isopentenyl pyrophosphate isomerase encoding gene (AlIDI) from Aurantiochytrium limacinum MYA-1381 were isolated. We applied the excavated AlGGPPS and AlIDI to the de novo β-carotene biosynthetic pathway in Escherichia coli for functional identification and engineering application. Results showed that the two novel genes both functioned in the synthesis of β-carotene. Furthermore, AlGGPPS and AlIDI performed better than the original or endogenous one, with 39.7% and 80.9% increases in β-carotene production, respectively. Due to the coordinated expression of the 2 functional genes, β-carotene content of the modified carotenoid-producing E. coli accumulated a 2.99-fold yield of the initial EBIY strain in 12 h, reaching 10.99 mg/L in flask culture. This study helped to broaden current understanding of the carotenoid biosynthetic pathway in Aurantiochytrium and provided novel functional elements for carotenoid engineering improvements.

The Potential of Marine Microalgae for the Production of Food, Feed, and Fuel (3F)

Whole-cell microalgae biomass and their specific metabolites are excellent sources of renewable and alternative feedstock for various products. In most cases, the content and quality of whole-cell biomass or specific microalgal metabolites could be produced by both fresh and marine microalgae strains. However, a large water footprint for freshwater microalgae strain is a big concern, especially if the biomass is intended for non-food applications. Therefore, if any marine microalgae could produce biomass of desired quality, it would have a competitive edge over freshwater microalgae. Apart from biofuels, recently, microalgal biomass has gained considerable attention as food ingredients for both humans and animals and feedstock for different bulk chemicals. In this regard, several technologies are being developed to utilize marine microalgae in the production of food, feed, and biofuels. Nevertheless, the production of suitable and cheap biomass feedstock using marine microalgae has faced several challenges associated with cultivation and downstream processing. This review will explore the potential pathways, associated challenges, and future directions of developing marine microalgae biomass-based food, feed, and fuels (3F).

Effects of glycerol and glucose on docosahexaenoic acid synthesis in Aurantiochyrium limacinum SFD-1502 by transcriptome analysis

Docosahexaenoic acid (DHA) has numerous functions in adjusting the organic health and pragmatic value in medicine and food field. In this study, we compared glycerol and glucose as the only carbon source for DHA production by Aurantiochytrium. When the glycerol concentration was 120 g/L, the maximum DHA yield was 11.08 g/L, and the DHA yield increased significantly, reaching 47.67% of the total lipid content. When the cells grew in glucose, the DHA proportion was 37.39%. Transcriptome data showed that the glycolysis pathway and tricarboxylic acid cycle in Aurantiochytrium were significantly inhibited during glycerol culture, which promoted the tricarboxylic acid transport system and was conducive to the synthesis of fatty acids by acetyl coenzyme A; glucose as substrate activated fatty acid synthesis (FAS)pathway and produced more saturated fatty acids, while glycerol as substrate activated polyketide synthase (PKS)pathway and produced more long-chain polyunsaturated fatty acids. This laid a foundation for fermentation metabolism regulation and molecular transformation.

Production of polyunsaturated fatty acids by Schizochytrium (Aurantiochytrium) spp

Diverse health benefits are associated with dietary consumption of omega-3 long-chain polyunsaturated fatty acids (ω-3 LC-PUFA), particularly docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Traditionally, these fatty acids have been obtained from fish oil, but limited supply, variably quality, and an inability to sustainably increase production for a rapidly growing market, are driving the quest for alternative sources. DHA derived from certain marine protists (heterotrophic thraustochytrids) already has an established history of commercial production for high-value dietary use, but is too expensive for use in aquaculture feeds, a much larger potential market for ω-3 LC-PUFA. Sustainable expansion of aquaculture is prevented by its current dependence on wild-caught fish oil as the source of ω-3 LC-PUFA nutrients required in the diet of aquacultured animals. Although several thraustochytrids have been shown to produce DHA and EPA, there is a particular interest in Schizochytrium spp. (now Aurantiochytrium spp.), as some of the better producers. The need for larger scale production has resulted in development of many strategies for improving productivity and production economics of ω-3 PUFA in Schizochytrium spp. Developments in fermentation technology and metabolic engineering for enhancing LC-PUFA production in Schizochytrium spp. are reviewed.

Exogenous Antioxidants Improve the Accumulation of Saturated and Polyunsaturated Fatty Acids in Schizochytrium sp. PKU#Mn4

Species of Schizochytrium are well known for their remarkable ability to produce lipids intracellularly. However, during their lipid accumulation, reactive oxygen species (ROS) are generated inevitably as byproducts, which if in excess results in lipid peroxidation. To alleviate such ROS-induced damage, seven different natural antioxidants (ascorbic acid, α-tocopherol, tea extract, melatonin, mannitol, sesamol, and butylated hydroxytoluene) were evaluated for their effects on the lipid accumulation in Schizochytrium sp. PKU#Mn4 using a fractional factorial design. Among the tested antioxidants, mannitol showed the best increment (44.98%) in total fatty acids concentration. However, the interaction effects of mannitol (1 g/L) and ascorbic acid (1 g/L) resulted in 2.26 ± 0.27 g/L and 1.45 ± 0.04 g/L of saturated and polyunsaturated fatty acids (SFA and PUFA), respectively, in batch fermentation. These concentrations were further increased to 7.68 ± 0.37 g/L (SFA) and 5.86 ± 0.03 g/L (PUFA) through fed-batch fermentation. Notably, the interaction effects yielded 103.7% and 49.6% increment in SFA and PUFA concentrations in batch fermentation. The possible mechanisms underlining those increments were an increased maximum growth rate of strain PKU#Mn4, alleviated ROS level, and the differential expression of lipid biosynthetic genes andupregulated catalase gene. This study provides an applicable strategy for improving the accumulation of SFA and PUFA in thraustochytrids by exogenous antioxidants and the underlying mechanisms.

A non-canonical Δ9-desaturase synthesizing palmitoleic acid identified in the thraustochytrid Aurantiochytrium sp. T66

Abstract

Thraustochytrids are oleaginous marine eukaryotic microbes currently used to produce the essential omega-3 fatty acid docosahexaenoic acid (DHA, C22:6 n-3). To improve the production of this essential fatty acid by strain engineering, it is important to deeply understand how thraustochytrids synthesize fatty acids. While DHA is synthesized by a dedicated enzyme complex, other fatty acids are probably synthesized by the fatty acid synthase, followed by desaturases and elongases. Which unsaturated fatty acids are produced differs between different thraustochytrid genera and species; for example, Aurantiochytrium sp. T66, but not Aurantiochytrium limacinum SR21, synthesizes palmitoleic acid (C16:1 n-7) and vaccenic acid (C18:1 n-7). How strain T66 can produce these fatty acids has not been known, because BLAST analyses suggest that strain T66 does not encode any Δ9-desaturase-like enzyme. However, it does encode one Δ12-desaturase-like enzyme. In this study, the latter enzyme was expressed in A. limacinum SR21, and both C16:1 n-7 and C18:1 n-7 could be detected in the transgenic cells. Our results show that this desaturase, annotated T66Des9, is a Δ9-desaturase accepting C16:0 as a substrate. Phylogenetic studies indicate that the corresponding gene probably has evolved from a Δ12-desaturase-encoding gene. This possibility has not been reported earlier and is important to consider when one tries to deduce the potential a given organism has for producing unsaturated fatty acids based on its genome sequence alone.

Key points

• In thraustochytrids, automatic gene annotation does not always explain the fatty acids produced.

• T66Des9 is shown to synthesize palmitoleic acid (C16:1 n-7).

• T66des9 has probably evolved from Δ12-desaturase-encoding genes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11425-5.

Integration of continuous-high cell density-fed-batch fermentation for Aurantiochytrium limacinum for simultaneous high biomass, lipids and docosahexaenoic acid production

Docosahexaenoic acid (DHA) rich oil or biomass is currently being produced by fermentation of thraustochytrids by repeated fed-batch. Continuous cultivation has not been successful for DHA production because of excess carbon and limited nitrogen conditions requirement. The present study describes an alternative integrative fermentation strategy to simultaneously produce high cell density, lipids and DHA in continuous mode for Aurantiochytrium limacinum. The high cell density system (≥120 g/L DCW basis) on carbon feeding led to DHA productivity of 0.508 g/L.h on poultry waste based medium with a process time of 48-54 h. The strategy integrates the advantages of repeated fed-batch for high cell densities and DHA content in continuous cultivation.

Combined Metabolome and Lipidome Analyses for In-Depth Characterization of Lipid Accumulation in the DHA Producing Aurantiochytrium sp. T66

Thraustochytrids are marine heterotrophic microorganisms known for their potential to accumulate docosahexaenoic acid (DHA)-enriched lipids. There have been many attempts to improve thraustochytrid DHA bioprocesses, especially through traditional optimization of cultivation and media conditions. Nevertheless, thraustochytrid-based bioprocesses are still not commercially competitive for high volume-low cost production of DHA. Thus, it is realized that genetic and metabolic engineering strategies are needed for the development of commercially competitive thraustochytrid DHA cell factories. Here, we present an analytical workflow for high resolution phenotyping at metabolite and lipid levels to generate deeper insight into the thraustochytrid physiology, with particular focus on central carbon and redox metabolism. We use time-series sampling during unlimited growth and nitrogen depleted triggering of DHA synthesis and lipid accumulation (LA) to show-case our methodology. The mass spectrometric absolute quantitative metabolite profiling covered glycolytic, pentose phosphate pathway (PPP) and tricarboxylic acid cycle (TCA) metabolites, amino acids, complete (deoxy)nucleoside phosphate pools, CoA and NAD metabolites, while semiquantitative high-resolution supercritical fluid chromatography MS/MS was applied for the lipid profiling. Interestingly, trace amounts of a triacylglycerols (TG) with DHA incorporated in all three acyl positions was detected, while TGs 16:0_16:0_22:6 and 16:0_22:6_22:6 were among the dominant lipid species. The metabolite profiling data indicated that lipid accumulation is not limited by availability of the acyl chain carbon precursor acetyl-CoA nor reducing power (NADPH) but rather points to the TG head group precursor glycerol-3-phosphate as the potential cause at the metabolite level for the gradual decline in lipid production throughout the cultivation. This high-resolution phenotyping provides new knowledge of changes in the central metabolism during growth and LA in thraustochytrids and will guide target selection for metabolic engineering needed for further improvements of this DHA cell factory.

Thraustochytrid Cell Factories for Producing Lipid Compounds

Thraustochytrids can accumulate over 150 g/l biomass, containing up to 55% lipids, without any genetic modification. Their broad substrate utilization capacity, several effective key metabolic pathways, and a well-developed suite of bioprocess engineering strategies all point toward great promise for the future development of these marine protists.

Impact of low-intensity pulsed ultrasound on the growth of Schizochytrium sp. for omega-3 production

Schizochytrium sp. is a microalga that is known for its high content of oils or lipids. It has a high percentage of polyunsaturated fatty acids in the accumulated oil, especially docosahexaenoic acid (DHA). DHA is an important additive for the human diet. Large-scale production of Schizochytrium sp. can serve as an alternative source of DHA for humans as well as for fish feed, decreasing the burden on aqua systems. Therefore, research on improving the productivity of Schizochytrium attracts a lot of attention. We studied the potential of using low-intensity pulsed ultrasound (LIPUS) in the growth cycle of Schizochytrium sp. in shake flasks. Different intensities and treatment durations were tested. A positive effect of LIPUS on biomass accumulation was observed in the Schizochytrium sp. culture. Specifically, LIPUS stimulation at the ultrasound intensity of 400 mW/cm² with 20 min per treatment 10 times a day with equal intervals of 2.4 h between the treatments was found to enhance the growth of Schizochytrium biomass most effectively (by up to 20%). Due to the nature of cell division in Schizochytrium sp. which occurs via zoospore formation, LIPUS stimulation was inefficient if applied continuously during all 5 days of the growth cycle. Using microscopy, we studied the interval between zoospore formation in the culture and selected the optimal LIPUS application days (Days 0-1 and Days 4-5 of the 5-day growth cycle). Microscopic images have also shown that LIPUS stimulation enhances zoospore formation in Schizochytrium sp., leading to more active cell division in the culture. This study shows that LIPUS can serve as an additional tool for cost-efficiency improvement in the large-scale production of Schizochytrium as a sustainable and environmentally friendly source of omega-3 (DHA).

Lab-Scale Optimization of Aurantiochytrium sp. Culture Medium for Improved Growth and DHA Production

Thraustochytrids have gained increasing relevance over the last decades, due to their fast growth and outstanding capacity to accumulate polyunsaturated fatty acids (PUFAs), particularly docosahexaenoic acid (DHA). In this context, the present work aimed to optimize the growth performance and DHA yields by improving the culture medium of Aurantiochytrium sp. AF0043. Accordingly, two distinct culture media were optimized: (i) an inorganic optimized medium (IOM), containing only monosodium glutamate and glucose as nitrogen and carbon sources, respectively; and (ii) an organic and sustainable waste-based optimized medium (WOM), containing corn steep powder and glycerol, added in fed-batch mode, as nitrogen and carbon sources, respectively. Overall, the lab-scale optimization allowed to increase the biomass yield 1.5-fold and enhance DHA content 1.7-fold using IOM. Moreover, WOM enabled a 2-fold increase in biomass yield and a significant improvement in lipid contents, from 22.78% to 31.14%. However, DHA content was enhanced almost 3-fold, from an initial content of 10.12% to 29.66% of total fatty acids contained in the biomass. Therefore, these results strongly suggest, not only that the production pipeline was significantly improved but also confirmed the potential use of Aurantiochytrium sp. AF0043 as a source of DHA.

Oil crop wastes as substrate candidates for enhancing erythritol production by modified Yarrowia lipolytica via one-step solid state fermentation

Oil crop wastes are attractive feedstocks in microbial processes due to their low cost. However, the product yields can be limited by their undesirable nitrogen surplus. Present study proposed a one-step solid state fermentation (SSF) method for producing erythritol from unrefined oil crop wastes using a modified strain Y. lipolytica M53-S. Enhanced erythritol production (185.4 mg/gds) was obtained from peanut press cake mixed with 40% sesame meal and 10% waste cooking oil. The process was performed at pH 4.0 in 5 L flasks, with initial moisture content, NaCl addition, and inoculum size of 70%, 0.02 g/gds, and 7.5 × 10⁴ cells/gds, respectively. This procedure showed advantages in terms of lower material cost than that of submerged fermentation and shorter culture cycle (96 h) than other SSF processes. In repeated-batch fermentation, erythritol was continuously produced for seven cycles. This study presents a feasible approach in developing an efficient erythritol cultivation from nitrogen-rich wastes.

Metabolic engineering to enhance biosynthesis of both docosahexaenoic acid and odd-chain fatty acids in Schizochytrium sp. S31

BACKGROUND

Docosahexaenoic acid (DHA, C22:6) and odd-chain fatty acids (OCFAs, C15:0 and C17:0) have attracted great interest, since they have been widely used in food and therapeutic industries, as well as chemical industry, such as biodiesel production and improvement. The oil-producing heterotrophic microalgae Schizochytrium sp. 31 is one of main DHA-producing strains. Recently, it was found that Schizochytrium can also synthesize OCFAs; however, contents and titers of DHA and OCFAs in Schizochytrium are still low, which limit its practical application.

RESULTS

In this study, we found that acetyl-CoA carboxylase suffered from a feedback inhibition by C16-CoA in Schizochytrium, and relief of the inhibition resulted in improved both lipid content and the ratio of OCFAs in total fatty acids. Based on this finding, a novel strategy for elevating both DHA and OCFAs contents was established. First, the total lipid accumulation was increased by overexpressing a malic enzyme from Crypthecodinium cohnii to elevate NADPH supply. Second, the inhibition effect on acetyl-CoA carboxylase was relieved by overexpressing a codon-optimized ELO3 gene from Mortierella alpina, which encodes an elongase enzyme responsible for converting C16 into C18 fatty acids. After the above two-step engineering, contents of DHA and OCFAs were increased by 1.39- and 3.30-fold, reaching a level of 26.70 and 25.08% of dry cell weight, respectively, which are the highest contents reported so far for Schizochytrium. The titers of DHA and OCFAs were elevated by 1.08- and 2.57-fold, reaching a level of 3.54 and 3.32 g/L, respectively. Notably, the OCFAs titer achieved was 2.66-fold higher than the highest reported in Escherichia coli (1.25 g/L), implying potential value for industry application. To reveal the potential metabolic mechanism for the enhanced biosynthesis of both DHA and OCFAs, LC-MS metabolomic analysis was employed and the results showed that the pentose phosphate pathway and the glycolysis pathway were strengthened and intracellular propionyl-CoA concentration were also significantly increased in the engineered Schizochytrium, suggesting an increased supply of NADPH, acetyl-CoA, and propionyl-CoA for DHA and OCFAs accumulation.

CONCLUSIONS

The discovery provides a new source of OCFAs production, and proposes a new strategy to improve contents and titers of both DHA and OCFAs in Schizochytrium. These will be valuable for improving commercial potential of Schizochytrium and guiding the engineering strategy in other fatty acids producing heterotrophic microalga.

Development of a multi-stage continuous fermentation strategy for docosahexaenoic acid production by Schizochytrium sp

Docosahexaenoic acid (DHA) has wide-ranging benefits for normal development of the visual and nervous systems in infants. A sustainable source of DHA production through fermentation using Schizochytrium sp. has been developed. In this paper, we present the discovery of growth-uncoupled DHA production by Schizochytrium sp. and the development of corresponding kinetic models of fed-batch fermentations, which can be used to describe and predict the cell growth and substrate utilization as well as lipid and DHA production. Based on this kinetic model, a predictive model of multi-stage continuous fermentation process was established and used to analyze, optimize and design the process parameters. Optimal predicted processes of two-stage and three-stage continuous fermentation were developed and verified in lab-scale bioreactor based on the predicted process parameters. A successful three-stage continuous fermentation was achieved, which increased the lipid, DHA content and DHA productivity by 47.6, 64.3 and 97.1%, respectively, compared with two-stage continuous fermentation.

Nitrogen Feeding Strategies and Metabolomic Analysis To Alleviate High-Nitrogen Inhibition on Docosahexaenoic Acid Production in Crypthecodinium cohnii

It is well-known that high-nitrogen content inhibits cell growth and docosahexaenoic acid (DHA) biosynthesis in heterotrophic microalgae Crypthecodinium cohnii. In this study, two nitrogen feeding strategies, pulse-feeding and continuous-feeding, were evaluated to alleviate high-nitrogen inhibition effects on C. cohnii. The results showed that continuous-feeding with a medium solution containing 50% ( w/v) yeast extract at 2.1 mL/h during 12-96 h was the optimal nitrogen feeding strategy for the fermentation process, when glucose concentration was maintained at 15-27 g/L during the same period. With the optimized strategy, 71.2 g/L of dry cell weight and DHA productivity of 57.1 mg/L/h were achieved. In addition, metabolomic analysis was applied to determine the metabolic changes during different nitrogen feeding conditions, and the changes in amino acids, polysaccharides, purines, and pentose phosphate pathway were observed, providing valuable metabolite-level information for exploring the mechanism of the high-nitrogen inhibition effect and further improving DHA productivity in C. cohnii.

Development of a method for the valorization of fermentation wastewater and algal-residue extract in docosahexaenoic acid production by Schizochytrium sp

Fermentation wastewater (FW) and algal residue are major by-products of docosahexaenoic acid (DHA) fermentations utilizing Schizochytrium sp. In order to reduce production costs and environmental pollution, we explored the application of FW and algal-residue extract (AE) for DHA production. Components analysis showed that FW and AE contained some mineral elements and protein residues, respectively. When they were used for DHA fermentation, results showed that 20% replacement of fresh water by FW and 80% replacement of yeast extract nitrogen by AE reached DHA content of 22.23 g/L and 27.10 g/L, respectively. Furthermore, a novel medium that utilizes a mixture of FW and AE was applied for DHA fermentation, whereby the final DHA yield reached 28.45 g/L, 24.56% higher than conventional medium. The strategy of valorizing fermentation waste provides a new method for reducing the costs and reducing environmental pollution of microbial fermentations.

Overexpression of Malonyl-CoA: ACP Transacylase in Schizochytrium sp. to Improve Polyunsaturated Fatty Acid Production

Polyunsaturated fatty acids (PUFAs) have been widely applied in the food and medical industry. In this study, malonyl-CoA: ACP transacylase (MAT) was overexpressed through homologous recombination to improve PUFA production in Schizochytrium. The results showed that the lipid and PUFA concentration were increased by 10.1 and 24.5% with MAT overexpression, respectively. Metabolomics analysis revealed that the intracellular tricarboxylic acid cycle was weakened and glucose absorption was accelerated in the engineered strain. In the mevalonate pathway, intracellular carotene content was decreased, and the carbon flux was then redirected toward PUFA synthesis. Furthermore, a glucose fed-batch fermentation was finally performed with the engineered Schizochytrium. The total lipid yield was further increased to 110.5 g/L, 39.6% higher than the wild strain. Docosahexaenoic acid and eicosapentaenoic acid yield were enhanced to 47.39 g/L and 1.65 g/L with an increase of 81.5 and 172.5%, respectively. This study provided an effective metabolic engineering strategy for industrial PUFA production.