The lipid metabolism in thraustochytrids

Structural and Molecular Characterization of Squalene Synthase Belonging to the Marine Thraustochytrid Species Aurantiochytrium limacinum Using Bioinformatics Approach

The marine microorganisms thraustochytrids have been explored for their potential in the production of various bioactive compounds, such as DHA, carotenoids, and squalene. Squalene is a secondary metabolite of the triterpenoid class and is known for its importance in various industrial applications. The bioinformatic analysis for squalene synthase (SQS) gene (the first key enzyme in the tri-terpenoid synthesis pathway), that is prevailing among thraustochytrids, is poorly investigated. In-silico studies combining sequence alignments and bioinformatic tools helped in the preliminary characterization of squalene synthases found in Aurantiochytrium limacinum. The sequence contained highly conserved regions for SQS found among different species indicated the enzyme had all the regions for its functionality. The signal peptide sequence and transmembrane regions were absent, indicating an important aspect of the subcellular localization. Secondary and 3-D models generated using appropriate templates demonstrated the similarities with SQS of the other species. The 3-D model also provided important insights into possible active, binding, phosphorylation, and glycosylation sites.

Co-cultivation of Phaeodactylum tricornutum and Aurantiochytrium limacinum for polyunsaturated omega-3 fatty acids production

Marine protist Aurantiochytrium limacinum produces docosahexaenoic acid (DHA) as main polyunsaturated fatty acid (PUFA) and lacks any monounsaturated fatty acids (MUFA), while eicosapentaenoic acid (EPA) and MUFA's are produced by Phaeodactylum tricornutum. The marine diatom P. tricornutum was co-cultured with A.limacinum to match the EPA:DHA ratio of fish oil. Modulation in initial cell density ratio overcame the dominance of A.limacinum during co-cultivation and led to regulated proliferation of both species. Media engineering with nitrate and glycerol concentration yielded 2:1 (56.44: 30.11) mg g^-1 and 1:1 (47.43: 49.61) mg g^-1 EPA: DHA ratio. The oil and biomass obtained from co-cultivation comprised of MUFA's such as palmitoleic acid (2.65 mg g^-1) and oleic acid (1.25 mg g^-1) along with pigments like fucoxanthin (367.18 µg g^-1), β-carotene (8.98 µg g^-1) and astaxanthin (0.77 µg g^-1). Thus, co-cultivation of P. tricornutum with A. limacinum represented a unique strategy towards achieving desired fatty acid composition.

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

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

An emerging simple and effective approach to increase the productivity of thraustochytrids microbial lipids by regulating glycolysis process and triacylglycerols' decomposition

BACKGROUND

The oleaginous microorganism Schizochytrium sp. is widely used in scientific research and commercial lipid production processes. However, low glucose-to-lipid conversion rate (GLCR) and low lipid productivity of Schizochytrium sp. restrict the feasibility of its use.

RESULTS

Orlistat is a lipase inhibitor, which avoids triacylglycerols (TAGs) from hydrolysis by lipase. TAGs are the main storage forms of fatty acids in Schizochytrium sp. In this study, the usage of orlistat increased the GLCR by 21.88% in the middle stage of fermentation. Whereas the productivity of lipid increased 1.34 times reaching 0.73 g/L/h, the saturated fatty acid and polyunsaturated fatty acid yield increased from 21.2 and 39.1 to 34.9 and 48.5 g/L, respectively, indicating the advantages of using a lipase inhibitor in microbial lipids fermentation. Similarly, the system was also successful in Thraustochytrid Aurantiochytrium. The metabolic regulatory mechanisms stimulated by orlistat in Schizochytrium sp. were further investigated using transcriptomics and metabolomics. The results showed that orlistat redistributed carbon allocation and enhanced the energy supply when inhibiting the TAGs' degradation pathway. Therefore, lipase in Schizochytrium sp. prefers to hydrolyze saturated fatty acid TAGs into the β-oxidation pathway.

CONCLUSIONS

This study provides a simple and effective approach to improve lipid production, and makes us understand the mechanism of lipid accumulation and decomposition in Schizochytrium sp., offering new guidance for the exploitation of oleaginous microorganisms.

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.

Novel potential functions of amoeboid cells in thraustochytrids revealed by Aurantiochytrium limacinum BL10

The current study investigated the potential functions of amoeboid cell formation and migration in a thraustochytrid strain, Aurantiochytrium limacinum BL10. Our results showed that: (1) When the surface of an agar plate was inoculated with BL10, amoeboid cells mainly emerged on the periphery of isolated colonies. The amoeboid cells then migrated outwards to form small vegetative cell clusters, which favored rapid colony expansion. In addition, amoeboid cells were capable of self-recognition (i.e. they were able to distinguish BL10 from other thraustochytrid species), and could choose whether to evade (self colonies) or approach (non-self colonies). These observations indicated that amoeboid cells were employed by BL10 to help colonize empty territories and to outcompete other thraustochytrid species in previously colonized territories. (2) When the agar medium was soft, amoeboid cells were able to penetrate the surface and migrate throughout, thereby allowing BL10 to colonize the interior of the solid matrix. This finding suggested that amoeboid cell formation and migration may help Aurantiochytrium colonize the interior of solid matrices to obtain additional nutrients and spatial resources. The mechanisms underlying the regulation of amoeboid cell formation and migration as well as the extraordinary microbial social behaviors of BL10 are also discussed in this article.

PUFA synthase-independent DHA synthesis pathway in Parietichytrium sp. and its modification to produce EPA and n-3DPA

The demand for n-3 long-chain polyunsaturated fatty acids (n-3LC-PUFAs), such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), will exceed their supply in the near future, and a sustainable source of n-3LC-PUFAs is needed. Thraustochytrids are marine protists characterized by anaerobic biosynthesis of DHA via polyunsaturated fatty acid synthase (PUFA-S). Analysis of a homemade draft genome database suggested that Parietichytrium sp. lacks PUFA-S but possesses all fatty acid elongase (ELO) and desaturase (DES) genes required for DHA synthesis. The reverse genetic approach and a tracing experiment using stable isotope-labeled fatty acids revealed that the ELO/DES pathway is the only DHA synthesis pathway in Parietichytrium sp. Disruption of the C20 fatty acid ELO (C20ELO) and ∆4 fatty acid DES (∆4DES) genes with expression of ω3 fatty acid DES in this thraustochytrid allowed the production of EPA and n-3docosapentaenoic acid (n-3DPA), respectively, at the highest level among known microbial sources using fed-batch culture.

Key Targets for Improving Algal Biofuel Production

A number of technological challenges need to be overcome if algae are to be utilized for commercial fuel production. Current economic assessment is largely based on laboratory scale up or commercial systems geared to the production of high value products, since no industrial scale plant exits that are dedicated to algal biofuel. For macroalgae (‘seaweeds’), the most promising processes are anaerobic digestion for biomethane production and fermentation for bioethanol, the latter with levels exceeding those from sugar cane. Currently, both processes could be enhanced by increasing the rate of degradation of the complex polysaccharide cell walls to generate fermentable sugars using specifically tailored hydrolytic enzymes. For microalgal biofuel production, open raceway ponds are more cost-effective than photobioreactors, with CO2 and harvesting/dewatering costs estimated to be ~50% and up to 15% of total costs, respectively. These costs need to be reduced by an order of magnitude if algal biodiesel is to compete with petroleum. Improved economics could be achieved by using a low-cost water supply supplemented with high glucose and nutrients from food grade industrial wastewater and using more efficient flocculation methods and CO2 from power plants. Solar radiation of not <3000 h·yr−1 favours production sites 30° north or south of the equator and should use marginal land with flat topography near oceans. Possible geographical sites are discussed. In terms of biomass conversion, advances in wet technologies such as hydrothermal liquefaction, anaerobic digestion, and transesterification for algal biodiesel are presented and how these can be integrated into a biorefinery are discussed.

Multiproduct biorefinery from marine thraustochytrids towards a circular bioeconomy

Microalgal biotechnology research continues to expand due to largely unexplored marine environments and growing consumer interest in healthy products. Thraustochytrids, which are marine oleaginous protists, are known for their production of bioactives with significant applications in nutraceuticals, pharmaceuticals, and aquaculture. A wide range of high-value biochemicals, such as nutritional supplements (omega-3 fatty acids), squalene, exopolysaccharides (EPSs), enzymes, aquaculture feed, and biodiesel and pigment compounds, have been investigated. We discuss thraustochytrids as potential feedstocks to produce various bioactive compounds and advocate developing a biorefinery to offset production costs. We anticipate that future advances in cell manufacturing, lipidomic analysis, and nanotechnology-guided lipid extraction would facilitate large-scale cost-competitive production through these microbes.

An Oil Hyper-Accumulator Mutant Highlights Peroxisomal ATP Import as a Regulatory Step for Fatty Acid Metabolism in Aurantiochytrium limacinum

Thraustochytrids are marine protists that naturally accumulate triacylglycerol with long chains of polyunsaturated fatty acids, such as ω3-docosahexaenoic acid (DHA). They represent a sustainable response to the increasing demand for these "essential" fatty acids (FAs). Following an attempt to transform a strain of Aurantiochytrium limacinum, we serendipitously isolated a clone that did not incorporate any recombinant DNA but contained two to three times more DHA than the original strain. Metabolic analyses indicated a deficit in FA catabolism. However, whole transcriptome analysis did not show down-regulation of genes involved in FA catabolism. Genome sequencing revealed extensive DNA deletion in one allele encoding a putative peroxisomal adenylate transporter. Phylogenetic analyses and yeast complementation experiments confirmed the gene as a peroxisomal adenylate nucleotide transporter (AlANT1), homologous to yeast ScANT1 and plant peroxisomal adenylate nucleotide carrier AtPNC genes. In yeast and plants, a deletion of the peroxisomal adenylate transporter inhibits FA breakdown and induces FA accumulation, a phenotype similar to that described here. In response to this metabolic event, several compensatory mechanisms were observed. In particular, genes involved in FA biosynthesis were upregulated, also contributing to the high FA accumulation. These results support AlANT1 as a promising target for enhancing DHA production in Thraustochytrids.

Method Development Progress in Genetic Engineering of Thraustochytrids

Thraustochytrids are unicellular, heterotrophic marine eukaryotes. Some species are known to store surplus carbon as intracellular lipids, and these also contain the long-chain polyunsaturated fatty acid docosahexaenoic acid (DHA). Most vertebrates are unable to synthesize sufficient amounts of DHA, and this fatty acid is essential for, e.g., marine fish, domesticated animals, and humans. Thraustochytrids may also produce other commercially valuable fatty acids and isoprenoids. Due to the great potential of thraustochytrids as producers of DHA and other lipid-related molecules, a need for more knowledge on this group of organisms is needed. This necessitates the ability to do genetic manipulation of the different strains. Thus far, this has been obtained for a few strains, while it has failed for other strains. Here, we systematically review the genetic transformation methods used for different thraustochytrid strains, with the aim of aiding studies on strains not yet successfully transformed. The designs of transformation cassettes are also described and compared. Moreover, the potential problems when trying to establish transformation protocols in new thraustochytrid species/strains are discussed, along with suggestions utilized in other organisms to overcome similar challenges. The approaches discussed in this review could be a starting point when designing protocols for other non-model organisms.

High-value utilization of the waste hydrolysate of Dioscorea zingiberensis for docosahexaenoic acid production in Schizochytrium sp

The starch saccharification liquid of Dioscorea zingiberensis tubers (SSLD) is a glucose-rich agro-industrial waste. Herein, SSLD was used as a novel potential carbon source for the biosynthesis of docosahexaenoic acid (DHA) in Schizochytrium sp. to achieve waste recycling and high-value utilization. Component analysis showed that SSLD contains abundant nutrients, such as glucose, amino acids, phenolics and flavonoids. When the total sugar concentration in SSLD was optimized to 90 g/L, the biomass and DHA yield reached 44.85 and 6.60 g/L, respectively, which were 32.1% and 36.92% higher than that at pure glucose culture condition. Fermentation characteristics and gene expression analysis showed that SSLD could remarkably improve cell antioxidant capacity, which is beneficial to scavenge intracellular reactive oxygen species and increase the gene expression of antioxidant enzymes in Schizochytrium sp. Hence, SSLD is an effective and economic carbon source for DHA production in Schizochytrium sp.

Integrating metagenetics and high-throughput screening for bioprospecting marine thraustochytrids producers of long-chain polyunsaturated fatty acids

Omega-3 produced by marine thraustochytrids has appeared as an alternative to fish oil and an eco-friendly solution to overfishing. Herein, an integrative analysis of metagenetics and high-throughput screening was used for bioprospecting marine thraustochytrids from southern Brazil mangrove and coastal seawater. All sampled environments showed biodiversity and abundance of SAR clade. Environmental samples detected with potential lipid-accumulating labyrinthulomycetes were further processed for direct plating and pollen baiting isolation. Microtiter plate system and fluorescence spectroscopy were combined for high-throughput screening of 319 isolates to accumulate lipids. Twenty isolates were selected for submerged cultivation and lipid characterization. Among them, B36 isolate, identified as Aurantiochytrium sp. by 18s rRNA sequencing, achieved the highest biomass (25.60 g/l CDW) and lipids (17.12 g/l CDW). This lipid content had a high biological value with 44.37% LC-PUFAs and 34.6% DHA, which can be used as a sustainable source in vegan, seafood-free and animal feed diets.

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.

Lipid metabolism research in oleaginous fungus Mortierella alpina: Current progress and future prospects

The oleaginous fungus Mortierella alpina has distinct advantages in long-chain PUFAs production, and it is the only source for dietary arachidonic acid (ARA) certificated by FDA and European Commission. This review provides an overall introduction to M. alpina, including its major research methods, key factors governing lipid biosynthesis, metabolic engineering and omics studies. Currently, the research interests in M. alpina focus on improving lipid yield and fatty acid desaturation degree by enhancing fatty acid precursors and the reducing power NADPH, and genetic manipulation on PUFAs synthetic pathways is carried to optimise fatty acid composition. Besides, multi-omics studies have been applied to elucidate the global regulatory mechanism of lipogenesis in M. alpina. However, research challenges towards achieving a lipid cell factory lie in strain breeding and cost control due to the coenocytic mycelium, long fermentation period and insufficient conversion rate from carbon to lipid. We also proposed future research goals based on a multilevel regulating strategy: obtaining ideal chassis by directional evolution and high-throughput screening; rewiring central carbon metabolism and inhibiting competitive pathways by multi-gene manipulation system to enhance carbon to lipid conversion rate; optimisation of protein function based on post-translational modification; application of dynamic fermentation strategies suitable for different fermentation phases. By reviewing the comprehensive research progress of this oleaginous fungus, we aim to further comprehend the fungal lipid metabolism and provide reference information and guidelines for the exploration of microbial oils from the perspectives of fundamental research to industrial application.

ATP Drives Efficient Terpene Biosynthesis in Marine Thraustochytrids

Understanding carbon flux controlling mechanisms in a tangled metabolic network is an essential question of cell metabolism. Secondary metabolism, such as terpene biosynthesis, has evolved with low carbon flux due to inherent pathway constraints. Thraustochytrids are a group of heterotrophic marine unicellular protists and can accumulate terpenoids under the high-salt conditions in their natural environment. However, the mechanism behind terpene accumulation is not well understood. Here, we show that terpene biosynthesis in Thraustochytrium sp. ATCC 26185 is constrained by local thermodynamics in the mevalonate pathway. Thermodynamic analysis reveals metabolite limitation in the nondecarboxylative Claisen condensation of acetyl-coenzyme A (CoA) to the acetoacetyl-CoA step, catalyzed by the acetyl-CoA acetyltransferase (ACAT). Through a sodium-elicited mechanism, higher respiration leads to increased ATP investment into the mevalonate pathway, providing a strong thermodynamic driving force for enhanced terpene biosynthesis. Proteomic and metabolomic analyses further show that the increased ATP demands are fulfilled by shifting energy generation from carbohydrate to lipid oxidation. This study demonstrates a unique strategy in nature that uses ATP to drive a low-flux metabolic pathway, providing an alternative solution for efficient terpene metabolic engineering. IMPORTANCE Terpenoids are a large class of lipid molecules with important biological functions and diverse industrial and medicinal applications. Metabolic engineering for terpene production has been hindered by the low-flux distribution to its biosynthesis pathway. In practice, a high substrate load is generally required to reach high product titers. Here, we show that mevalonate-derived terpene biosynthesis is constrained by local pathway thermodynamics, which can only be partially relieved by increasing substrate levels. Through comparative omics and biochemical analyses, we discovered a unique mechanism for high terpene accumulation in marine protist thraustochytrids. Through a sodium-induced mechanism, thraustochytrids shift their energy metabolism from carbohydrate to lipid oxidation for enhanced ATP production, providing a strong thermodynamic driving force for efficient terpene biosynthesis. This study reveals an important mechanism in eukaryotes to overcome the thermodynamic constraint in low-flux pathways by increased ATP consumption. Engineering energy metabolism thus provides an important alternative to relieve flux constraints in low-flux and energy-consuming pathways.

Cultivation and diversity analysis of novel marine thraustochytrids

Thraustochytrids are a group of unicellular marine heterotrophic protists, and have long been known for their biotechnological potentials in producing squalene, polyunsaturated fatty acids (PUFAs) and other bioactive products. There are less than a hundred known strains from diverse marine habitats. Therefore, the discovery of new strains from natural environments is still one of the major limitations for fully exploring this interesting group of marine protists. At present, numerous attempts have been made to study thraustochytrids, mainly focusing on isolating new strains, analyzing the diversity in specific marine habitats, and increasing the yield of bioactive substances. There is a lack of a systematic study of the culturable diversity, and cultivation strategies. This paper reviews the distribution and diversity of culturable thraustochytrids from a range of marine environments, and describes in detail the most commonly used isolation methods and the control of culture parameters. Furthermore, the perspective approaches of isolation and cultivation for the discovery of new strains are discussed. Finally, the future directions of novel marine thraustochytrid research are proposed. The ultimate goal is to promote the awareness of biotechnological potentials of culturable thraustochytrid strains in industrial and biomedical applications.

Schizochytrium sp. (T18) Oil as a Fish Oil Replacement in Diets for Juvenile Rainbow Trout (Oncorhynchus mykiss): Effects on Growth Performance, Tissue Fatty Acid Content, and Lipid-Related Transcript Expression

In this study, we evaluated whether oil extracted from the marine microbe, Schizochytrium sp. (strain T18), with high levels of docosahexaenoic acid (DHA), could replace fish oil (FO) in diets for rainbow trout (Oncorhynchus mykiss). Three experimental diets were tested: (1) a control diet with fish oil (FO diet), (2) a microbial oil (MO) diet with a blend of camelina oil (CO) referred to as MO/CO diet, and (3) a MO diet (at a higher inclusion level). Rainbow trout (18.8 ± 2.9 g fish-1 initial weight ± SD) were fed for 8 weeks and evaluated for growth performance, fatty acid content and transcript expression of lipid-related genes in liver and muscle. There were no differences in growth performance measurements among treatments. In liver and muscle, eicosapentaenoic acid (EPA) was highest in trout fed the FO diet compared to the MO/CO and MO diets. Liver DHA was highest in trout fed the MO/CO diet compared to the FO and MO diets. Muscle DHA was highest in trout fed the MO and MO/CO diets compared to the FO diet. In trout fed the MO/CO diet, compared to the MO diet, fadsd6b was higher in both liver and muscle. In trout fed the FO or MO/CO diets, compared to the MO diet, cox1a was higher in both liver and muscle, cpt1b1a was higher in liver and cpt1a1a, cpt1a1b and cpt1a2a were higher in muscle. Schizochytrium sp. (T18) oil was an effective source of DHA for rainbow trout.

Optimizing Docosahexaenoic Acid (DHA) Production by Schizochytrium sp. Grown on Waste Glycerol

The aim of this study was to optimize biomass and docosahexaenoic acid (DHA) production by Schizochytrium sp. grown on waste glycerol as an organic carbon source. Parameters having a significant effect on biomass and DHA yields were screened using the fractional Plackett–Burman design and the response surface methodology (RSM). Schizochytrium sp. growth was most significantly influenced by crude glycerin concentration in the growth medium (150 g/dm3), process temperature (27 °C), oxygen in the bioreactor (49.99% v/v), and the concentration of peptone as a source of nitrogen (9.99 g/dm3). The process parameter values identified as optimal for producing high DHA concentrations in the biomass were as follows: glycerin concentration 149.99 g/dm3, temperature 26 °C, oxygen concentration 30% (v/v), and peptone concentration 2.21 g/dm3. The dry cell weight (DCW) obtained under actual laboratory conditions was 66.69 ± 0.66 g/dm3, i.e., 1.27% lower than the predicted value. The DHA concentration obtained in the actual culture was at 17.25 ± 0.33 g/dm3, which was 3.03% lower than the predicted value. The results obtained suggest that a two-step culture system should be employed, with the first phase focused on high production of Schizochytrium sp. biomass, and the second focused on increasing DHA concentration in the cells.

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.

Volatile Fatty Acids (VFAs) Generated by Anaerobic Digestion Serve as Feedstock for Freshwater and Marine Oleaginous Microorganisms to Produce Biodiesel and Added-Value Compounds

Given an increasing focus on environmental sustainability, microbial oils have been suggested as an alternative to petroleum-based products. However, microbial oil production relies on the use of costly sugar-based feedstocks. Substrate limitation, elevated costs, and risk of contamination have sparked the search for alternatives to sugar-based platforms. Volatile fatty acids are generated during anaerobic digestion of organic waste and are considered a promising substrate for microbial oil production. In the present study, two freshwater and one marine microalga along with two thraustochytrids were evaluated for their potential to produce lipids when cultivated on volatile fatty acids generated from food waste via anaerobic digestion using a membrane bioreactor. Freshwater microalgae Auxenochlorella protothecoides and Chlorella sorokiniana synthesized lipids rich in palmitic acid (C16:0), stearic acid (C18:0), oleic acid (C18:1), and linoleic acid (C18:2). This composition corresponds to that of soybean and jatropha oils, which are used as biodiesel feedstock. Production of added-value polyunsaturated fatty acids (PUFA) mainly omega-3 fatty acids was examined in three different marine strains: Aurantiochytrium sp. T66, Schizochytrium limacinum SR21, and Crypthecodinium cohnii. Only Aurantiochytrium sp. T66 seemed promising, generating 43.19% docosahexaenoic acid (DHA) and 13.56% docosapentaenoic acid (DPA) in total lipids. In summary, we show that A. protothecoides, C. sorokiniana, and Aurantiochytrium sp. T66 can be used for microbial oil production from food waste material.

Two-level factorial analysis of the effect of fructose on DHA biosynthetic capacity of Aurantiochytrium sp. SW1

Thraustochytrids are getting increasingly popular due to their high potential role as alternative producers of the high-valued ω-3 polyunsaturated fatty acids (PUFA), docosahexaenoic acid (DHA). While most thraustochytrids prefer glucose as the major carbon source, few strains have been reported to prefer fructose. One such strain is Aurantiochytrium sp. SW1. In this study, the effect of fructose on DHA accumulation by SW1 was investigated using a two-level full factorial design. Besides, biomass, lipid and DHA accumulation profiles of SW1 cultivated in fructose and glucose media were compared. Results revealed that fructose has a very significant positive effect on the volumetric DHA content. Meanwhile, its involvement in affecting DHA biosynthetic capacity, though significant, is not very profound. It was also found that when cultivated in fructose medium, SW1 had a less steep log phase compared to that of glucose medium. However, after 48h of cultivation, biomass and lipid accumulation in fructose medium outweighed the other. Volumetric DHA content in fructose medium at 96h was 11% higher than that of glucose medium. Overall, fructose was found to be a more suitable substrate for biomass, lipid and DHA accumulation in SW1 compared to the conventional source, glucose.

Microbial production of polyunsaturated fatty acids - high-value ingredients for aquafeed, superfoods, and pharmaceuticals

Polyunsaturated fatty acids (PUFAs), primarily docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), have received worldwide attention in recent years due to an increasing awareness of their uniqueness in improving diet and human health and their apparently inevitable shortage in global availability. Microbial cell factories are a major solution to supplying these precious molecules in sufficient amounts and providing PUFA-rich aquafeed, superfoods, and medical formulations. This review assesses the PUFA world markets and highlights recent advances in upgrading and streamlining microalgae, yeasts, fungi, and bacteria for high-level PUFA production and broadening of the PUFA spectrum.

Effect of Nitrogen Sources on Omega-3 Polyunsaturated Fatty Acid Biosynthesis and Gene Expression in Thraustochytriidae sp

The molecular mechanism that contributes to nitrogen source dependent omega-3 polyunsaturated fatty acid (n-3 PUFA) synthesis in marine oleaginous protists Thraustochytriidae sp., was explored in this study. The fatty acid (FA) synthesis was significantly influenced by the supplement of various levels of sodium nitrate (SN) (1–50 mM) or urea (1–50 mM). Compared with SN (50 mM) cultivation, cells from urea (50 mM) cultivation accumulated 1.16-fold more n-3 PUFAs (49.49% docosahexaenoic acid (DHA) (w/w, of total FAs) and 5.28% docosapentaenoic acid (DPA) (w/w, of total FAs)). Strikingly higher quantities of short chain FAs (<18 carbons) (52.22-fold of that in urea cultivation) were produced from SN cultivation. Ten candidate reference genes (RGs) were screened by using four statistical methods (geNorm, NormFinder, Bestkeeper and RefFinder). MFT (Mitochondrial folate transporter) and NUC (Nucleolin) were determined as the stable RGs to normalize the RT-qPCR (real-time quantitative polymerase chain reaction) data of essential genes related to n-3 PUFAs-synthesis. Our results elucidated that the gene transcripts of delta(3,5)-delta(2,4)-dienoyl-CoA isomerase, enoyl-CoA hydratase, fatty acid elongase 3, long-chain fatty acid acyl-CoA ligase, and acetyl-CoA carboxylase were up-regulated under urea cultivation, contributing to the extension and unsaturated bond formation. These findings indicated that regulation of the specific genes through nitrogen source could greatly stimulate n-3 PUFA production in Thraustochytriidae sp.

Different carbon and nitrogen sources regulated docosahexaenoic acid (DHA) production of Thraustochytriidae sp. PKU#SW8 through a fully functional polyunsaturated fatty acid (PUFA) synthase gene (pfaB)

Docosahexaenoic acid (DHA, C22:6) production in thraustochytrids is known to be mediated independently through polyunsaturated fatty acid (PUFA) synthase and fatty acid synthase systems. This study elucidates the unresolved effects of different carbon and nitrogen sources on the functionality of PUFA synthase subunit B (pfaB) and corresponding DHA production in Thraustochytriidae sp. PKU#SW8. Carbon and nitrogen sources showed significant effect on the pfaB gene expression and DHA production patterns, but these patterns did not correspond with each other, suggesting the strong role of substrates in differential induction of the two synthase systems. Nitrogen starvation increased DHA yield in parallel with upregulated gene expression, showing strong indication of PUFA synthase activity in N-deficient culture. The fully functional catalytic activity of PfaB subunit from strain PKU#SW8 in a heterologous host was also demonstrated. This study provides the direct evidence of pfaB gene actively for DHA biosynthesis in Thraustochytriidae sp. PKU#SW8.

Diverse Enzymes With Industrial Applications in Four Thraustochytrid Genera

Thraustochytrids are heterotrophic fungus-like protists that can dissolve organic matters with enzymes. Four strains, AP45, ASP1, ASP2, and ASP4, were isolated from the coastal water of Taiwan, and respectively identified as Aurantiochytrium sp., Schizochytrium sp., Parietichytrium sp., and Botryochytrium sp. based on 18S rRNA sequences. Transcriptome datasets of these four strains at days 3-5 were generated using Next Generation Sequencing technology, and screened for enzymes with potential industrial applications. Functional annotations based on KEGG database suggest that many unigenes of all four strains were related to the pathways of industrial enzymes. Most of all four strains contained homologous genes for 15 out of the 17 targeted enzymes, and had extra- and/or intra-cellular enzymatic activities, including urease, asparaginase, lipase, glucosidase, alkaline phosphatase and protease. Complete amino sequences of the first-time identified L-asparaginase and phytase in thraustochytrids were retrieved, and respectively categorized to the Type I and BPPhy families based on phylogenetic relationships, protein structural modeling and active sites. Milligram quantities of highly purified, soluble protein of urease and L-asparaginase were successfully harvested and analyzed for recombinant enzymatic activities. These analytical results highlight the diverse enzymes for wide-range applications in thraustochytrids.

PUFA-synthase-specific PPTase enhanced the polyunsaturated fatty acid biosynthesis via the polyketide synthase pathway in Aurantiochytrium

BACKGROUND

Phosphopantetheinyl transferase (PPTase) can change the acyl-carrier protein (ACP) from an inactive apo-ACP to an active holo-ACP that plays a key role in fatty acids biosynthesis. Currently, the PPTase has been proved to be involved in the biosynthesis of polyunsaturated fatty acids (PUFAs) via a polyketide synthase (PKS) pathway in Thraustochytrids, while its characteristics are not clarified.

RESULTS

Here, the heterologous PPTase gene (pfaE) from bacteria was first co-expressed with the PKS system (orfA-orfC) from Thraustochytrid Aurantiochytrium. Then, a new endogenous PPTase (ppt_a) in Aurantiochytrium was identified by homologous alignment and its function was verified in E. coli. Moreover, the endogenous ppt_a was then overexpressed in Aurantiochytrium, and results showed that the production and proportion of PUFAs, especially docosahexaenoic acid (DHA), in the transformant SD116::PPT_A were increased by 35.5% and 17.6%, respectively. Finally, higher DHA and PUFA proportion (53.9% and 64.5% of TFA, respectively) were obtained in SD116::PPT_A using a cerulenin feeding strategy.

CONCLUSIONS

This study has illustrated a PUFAs-synthase-specific PPTase in PKS system and provided a new strategy to improve the PUFA production in Thraustochytrids.

Illumina and PacBio DNA sequencing data, de novo assembly and annotation of the genome of Aurantiochytrium limacinum strain CCAP_4062/1

The complete genome of the thraustochytrid Aurantiochytrium limacinum strain CCAP_4062/1 was sequenced using both Illumina Novaseq 6000 and third generation sequencing technology PacBio RSII in order to obtain trustworthy assembly and annotation. The reads from both platforms were combined at multiple levels in order to obtain a reliable assembly, then compared to the A. limacinum ATCCⓇ MYA1381™ reference genome. The final assembly was annotated with the help of strain CCAP_4062/1 RNAseq data. A. limacinum strain CCAP_4062/1 is an industrial strain used for the production of very long chain polyunsaturated fatty acids, like the docosahexaenoic acid that is an essential fatty acid synthesised only at very low pace in humans and vertebrates . Thraustochytrids in general and Aurantiochytrium more specifically, are used for carotenoid and squalene production as well. Beside their biotechnological interest, thraustochytrids play a crucial role in both inshore and oceanic basins ecosystems. Genome sequences will foster biotechnological as well as ecological studies.

Use of Biofuel Industry Wastes as Alternative Nutrient Sources for DHA-Yielding Schizochytrium limacinum Production

The simultaneous use of crude glycerol and effluent from anaerobic digestate, both wastes derived from the biofuel industry, were tested in the frame of circular economy concept, as potential low-cost nutrient sources for the cultivation of rich in docosahexaenoic acid (DHA) oil microalgae strain Schizochytrium limacinum SR21. Initially, the optimal carbon and nitrogen concentration levels for high S. limacinum biomass and lipids production were determined, in a culture media containing conventional, high cost, organic nitrogen sources (yeast extract and peptone), micronutrients and crude glycerol at varying concentrations. Then, the effect of a culture media composed of crude glycerol (as carbon source) and effluent digestate at varying proportions on biomass productivity, lipid accumulation, proximate composition, carbon assimilation and fatty acid content were determined. It was shown that the biomass and total lipid content increased considerably with varying effluent concentrations reaching 49.2 g L−1 at 48% (v/v) of effluent concentration, while the lipid yield at the same effluent concentration reached 10.15 g L−1, compared to 17.0 g L−1 dry biomass and 10.2 g L−1 lipid yield when yeast extract and peptone medium with micronutrients was used. Compared to the control treatment, the above production was obtained with 48% less inorganic salts, which are needed for the preparation of the artificial sea water. It was shown that Schizochytrium limacinum SR21 was able to remediate 40% of the total organic carbon content of the biofuel wastes, while DHA productivity remained at low levels with saturated fatty acids comprising the main fraction of total fatty acid content. The results of the present study suggest that the simultaneous use of two waste streams from the biofuel industry can serve as potential nutrient sources for the growth of Schizochytrium limacinum SR21, replacing the high cost organic nutrients and up to one half the required artificial sea water salts, but upregulation of DHA productivity through optimization of the abiotic environment is necessary for industrial application, including aqua feed production.

Marine Protists and Rhodotorula Yeast as Bio-Convertors of Marine Waste into Nutrient-Rich Deposits for Mangrove Ecosystems

This paper represents a comprehensive study of two new thraustochytrids and a marine Rhodotorula red yeast isolated from Australian coastal waters for their abilities to be a potential renewable feedstock for the nutraceutical, food, fishery and bioenergy industries. Mixotrophic growth of these species was assessed in the presence of different carbon sources: glycerol, glucose, fructose, galactose, xylose, and sucrose, starch, cellulose, malt extract, and potato peels. Up to 14g DW/L (4.6gDW/L-day and 2.8gDW/L-day) of biomass were produced by Aurantiochytrium and Thraustochytrium species, respectively. Thraustochytrids biomass contained up to 33% DW of lipids, rich in omega-3 polyunsaturated docosahexaenoic acid (C22:6, 124mg/g DW); up to 10.2mg/gDW of squalene and up to 61μg/gDW of total carotenoids, composed of astaxanthin, canthaxanthin, echinenone, and β-carotene. Along with the accumulation of these added-value chemicals in biomass, thraustochytrid representatives showed the ability to secrete extracellular polysaccharide matrixes containing lipids and proteins. Rhodotorula sp lipids (26% DW) were enriched in palmitic acid (C16:0, 18mg/gDW) and oleic acid (C18:1, 41mg/gDW). Carotenoids (87μg/gDW) were mainly represented by β-carotene (up to 54μg/gDW). Efficient growth on organic and inorganic sources of carbon and nitrogen from natural and anthropogenic wastewater pollutants along with intracellular and extracellular production of valuable nutrients makes the production of valuable chemicals from isolated species economical and sustainable.

Human health benefits of very-long-chain polyunsaturated fatty acids from microalgae

Microalgae are single-cell, photosynthetic organisms whose biodiversity places them at the forefront of biological producers of high-value molecules including lipids and pigments. Some of these organisms particular are capable of synthesizing n-3 very long chain polyunsaturated fatty acids (VLC-PUFAs), known to have beneficial effects on human health. Indeed, VLC-PUFAs are the precursors of many signaling molecules in humans involved in the complexities of inflammatory processes. This mini-review provides an inventory of knowledge on the synthesis of VLC-PUFAs in microalgae and on the diversity of signaling molecules (prostanoids, leukotrienes, SPMs, EFOX, isoprostanoids) that arise in humans from VLC-PUFAs.

Assessment of Fatty Acids Profile and Omega-3 Polyunsaturated Fatty Acid Production by the Oleaginous Marine Thraustochytrid Aurantiochytrium sp. T66 Cultivated on Volatile Fatty Acids

Thraustochytrids are considered natural producers of omega-3 fatty acids as they can synthesize up to 70% docosahexaenoic acids (DHA) of total lipids. However, commercial and sustainable production of microbial DHA is limited by elevated cost of carbon substrates for thraustochytrids cultivation. This problem can be addressed by utilizing low-cost renewable substrates. In the present study, growth, lipid accumulation and fatty acid profiles of the marine thraustochytrid Aurantiochytrium sp. T66 (ATCC-PRA-276) cultivated on volatile fatty acids (C1, formic acid; C2, acetic acid; C3, propionic acid; C4, butyric acid; C5, valeric acid and C6, caproic acid) and glucose as control were evaluated for the first time. This strain showed an inability to utilize C3, C5 and C6 as a substrate when provided at >2 g/L, while efficiently utilizing C2 and C4 up to 40 g/L. The highest cell dry weight (12.35 g/L) and total lipid concentration (6.59 g/L) were attained when this strain was cultivated on 40 g/L of butyric acid, followed by cultivation on glucose (11.87 g/L and 5.34 g/L, respectively) and acetic acid (8.70 g/L and 3.43 g/L, respectively). With 40 g/L butyric acid, the maximum docosahexaenoic acid content was 2.81 g/L, corresponding to 42.63% w/w of total lipids and a yield of 0.23 g/g_{cell dry weight (CDW)}. This marine oleaginous microorganism showed an elevated potential for polyunsaturated fatty acids production at higher acetic and butyric acid concentrations than previously reported. Moreover, fluorescence microscopy revealed that growth on butyric acid caused cell size to increase to 45 µm, one of the largest values reported for oleaginous microorganisms, as well as the presence of numerous tiny lipid droplets.

The Nutritional and Pharmacological Potential of New Australian Thraustochytrids Isolated from Mangrove Sediments

Mangrove sediments represent unique microbial ecosystems that act as a buffer zone, biogeochemically recycling marine waste into nutrient-rich depositions for marine and terrestrial species. Marine unicellular protists, thraustochytrids, colonizing mangrove sediments have received attention due to their ability to produce large amounts of long-chain ω3-polyunsaturated fatty acids. This paper represents a comprehensive study of two new thraustochytrids for their production of valuable biomolecules in biomass, de-oiled cakes, supernatants, extracellular polysaccharide matrixes, and recovered oil bodies. Extracted lipids (up to 40% of DW) rich in polyunsaturated fatty acids (up to 80% of total fatty acids) were mainly represented by docosahexaenoic acid (75% of polyunsaturated fatty acids). Cells also showed accumulation of squalene (up to 13 mg/g DW) and carotenoids (up to 72 µg/g DW represented by astaxanthin, canthaxanthin, echinenone, and β-carotene). Both strains showed a high concentration of protein in biomass (29% DW) and supernatants (2.7 g/L) as part of extracellular polysaccharide matrixes. Alkalinization of collected biomass represents a new and easy way to recover lipid-rich oil bodies in the form of an aqueous emulsion. The ability to produce added-value molecules makes thraustochytrids an important alternative to microalgae and plants dominating in the food, pharmacological, nutraceutical, and cosmetics industries.

The Puzzling Conservation and Diversification of Lipid Droplets from Bacteria to Eukaryotes

Membrane compartments are amongst the most fascinating markers of cell evolution from prokaryotes to eukaryotes, some being conserved and the others having emerged via a series of primary and secondary endosymbiosis events. Membrane compartments comprise the system limiting cells (one or two membranes in bacteria, a unique plasma membrane in eukaryotes) and a variety of internal vesicular, subspherical, tubular, or reticulated organelles. In eukaryotes, the internal membranes comprise on the one hand the general endomembrane system, a dynamic network including organelles like the endoplasmic reticulum, the Golgi apparatus, the nuclear envelope, etc. and also the plasma membrane, which are linked via direct lateral connectivity (e.g. between the endoplasmic reticulum and the nuclear outer envelope membrane) or indirectly via vesicular trafficking. On the other hand, semi-autonomous organelles, i.e. mitochondria and chloroplasts, are disconnected from the endomembrane system and request vertical transmission following cell division. Membranes are organized as lipid bilayers in which proteins are embedded. The budding of some of these membranes, leading to the formation of the so-called lipid droplets (LDs) loaded with hydrophobic molecules, most notably triacylglycerol, is conserved in all clades. The evolution of eukaryotes is marked by the acquisition of mitochondria and simple plastids from Gram-positive bacteria by primary endosymbiosis events and the emergence of extremely complex plastids, collectively called secondary plastids, bounded by three to four membranes, following multiple and independent secondary endosymbiosis events. There is currently no consensus view of the evolution of LDs in the Tree of Life. Some features are conserved; others show a striking level of diversification. Here, we summarize the current knowledge on the architecture, dynamics, and multitude of functions of the lipid droplets in prokaryotes and in eukaryotes deriving from primary and secondary endosymbiosis events.

Digestion, Absorption, and Metabolism Characteristics of EPA-Enriched Phosphoethanolamine Plasmalogens Based on Gastrointestinal Functions in Healthy Mice

EPA-enriched phosphoethanolamine plasmalogens (EPA-pPE), widely present in marine creatures, is a unique glycerophospholipid with EPA at the sn-2 position of the glycerol backbone. EPA-pPE has been reported to exhibit numerous distinctive bioactivities. However, the digestion, absorption, and metabolism characteristics of EPA-pPE in vivo are not clear, which restrict the molecular mechanism analysis related to its distinctive activities. The aim of the present study was to illustrate the digestion, absorption, and metabolism characteristics of EPA-pPE by lipid analysis in serum, intestinal wall, and content after oral administration of EPA-pPE emulsion. Results showed the EPA percentage of total fatty acids in serum was increasing over time, with two peaks at 5 and 10 h by 1.89 ± 0.2 and 2.58 ± 0.27, respectively, and then fell from 1.89 ± 0.17 at 10 h to 1.35 ± 0.16 at 16 h. In small intestinal content, EPA-pPE was hydrolyzed to lyso-phospholipids and EPA by phospholipases A2 and the vinyl ether bond was retained at the sn-1 position. The released EPA could be quickly taken up into the enterocytes and enter circulation. The comparison of simulated digestion in vitro showed that the distinct digestion and absorption process of EPA-pPE was a unique phenomenon. EPA could be retained in serum at a high level for a substantial period of time, which suggested that EPA-pPE was not just a short-lived circulating molecule.