Genetic Engineering of Crypthecodinium cohnii to Increase Growth and Lipid Accumulation

Oleaginous Heterotrophic Dinoflagellates—Crypthecodiniaceae

The heterotrophic Crypthecodinium cohnii is a major model for dinoflagellate cell biology, and a major industrial producer of docosahexaenoic acid, a key nutraceutical and added pharmaceutical compound. Despite these factors, the family Crypthecodiniaceae is not fully described, which is partly attributable to their degenerative thecal plates, as well as the lack of ribotype-referred morphological description in many taxons. We report here significant genetic distances and phylogenetic cladding that support inter-specific variations within the Crypthecodiniaceae. We describe Crypthecodinium croucheri sp. nov. Kwok, Law and Wong, that have different genome sizes, ribotypes, and amplification fragment length polymorphism profiles when compared to the C. cohnii. The interspecific ribotypes were supported by distinctive truncation-insertion at the ITS regions that were conserved at intraspecific level. The long genetic distances between Crypthecodiniaceae and other dinoflagellate orders support the separation of the group, which includes related taxons with high oil content and degenerative thecal plates, to be ratified to the order level. The current study provides the basis for future specific demarcation-differentiation, which is an important facet in food safety, biosecurity, sustainable agriculture feeds, and biotechnology licensing of new oleaginous models.

Fermentation Wastes from Chrypthecodinium cohnii Lipid Production for Energy Recovery by Anaerobic Digestion

Wastes generated during the cultivation of marine microalga Crypthecodinium cohnii and after the lipid extraction process, were energetically valorized into biogas production through anaerobic digestion (AD). The tested wastes were extracted microalgae (Ae) with hexane (AeH) using supercritical extraction methods (AeS) and the supernatant obtained after culture medium centrifugation (M). The digestion of the algae biomass in the admixture with the supernatant medium (AeH+M+I and AeS+M+I) provided a higher methane content and a higher methane yield (582 and 440 L CH4/kg VS) than the substrates Ae and M, individually digested (155 and 96 L CH4/kg VS, respectively). Flow cytometry monitoring processes during AD indicated that the yield of the accumulated biogas was influenced by the operating conditions. The mixture of AeH+M+I was the only assay with a proportion of cells with less damaged membranes after AD, providing the highest methane yield and productivity (582 L CH4/kg VS and 31 L CH4/kg VS.d, respectively) and the highest energetic potential of 5.8 KWh/kg VS of all the substrates. From the results, AD integration to lipid production by C. cohnii to recover energy from the generated wastes enhanced the sustainability of the entire process and promoted the practice of zero waste.

The Biorefinery of the Marine Microalga Crypthecodinium cohnii as a Strategy to Valorize Microalgal Oil Fractions

Chrypthecodinium cohnii lipids have been almost exclusively used as a source of Docosahexaenoic acid (DHA). Such an approach wastes the remaining microalgal lipid fraction. The present work presents a novel process to produce C. cohnii biomass, using low-cost industrial by-products (raw glycerol and corn steep liquor), in a 7L-bioreactor, under fed-batch regime. At the end of the fermentation, the biomass concentration reached 9.2 g/L and the lipid content and lipid average productivity attained 28.0% (w/w dry cell weight) and 13.6 mg/L h, respectively. Afterwards the microalgal biomass underwent a saponification reaction to produce fatty acid (FA) soaps, which were further converted into FA ethyl ester (FA EE). C. cohnii FA EE mixture was then fractionated, using the urea complexation method at different temperatures, in order to obtain a polyunsaturated fatty acid ethyl ester (PUFA EE) rich fraction, that could be used for food/pharmaceutical/cosmetic purposes, and a saturated fatty acid ethyl ester (SAT EE) rich fraction, which could be used as biodiesel. The temperature that promoted the best separation between PUFA and SAT EE, was −18 °C, resulting in a liquid fraction with 91.6% (w/w) DHA, and a solid phase with 88.2% of SAT and monounsaturated fatty acid ethyl ester (MONOUNSAT), which could be used for biodiesel purposes after a hydrogenation step.

A Comparison of Dinoflagellate Thiolation Domain Binding Proteins Using In Vitro and Molecular Methods

Dinoflagellates play important roles in ecosystems as primary producers and consumers making natural products that can benefit or harm environmental and human health but are also potential therapeutics with unique chemistries. Annotations of dinoflagellate genes have been hampered by large genomes with many gene copies that reduce the reliability of transcriptomics, quantitative PCR, and targeted knockouts. This study aimed to functionally characterize dinoflagellate proteins by testing their interactions through in vitro assays. Specifically, nine Amphidinium carterae thiolation domains that scaffold natural product synthesis were substituted into an indigoidine synthesizing gene from the bacterium Streptomyces lavendulae and exposed to three A. carterae phosphopantetheinyl transferases that activate synthesis. Unsurprisingly, several of the dinoflagellate versions inhibited the ability to synthesize indigoidine despite being successfully phosphopantetheinated. However, all the transferases were able to phosphopantetheinate all the thiolation domains nearly equally, defying the canon that transferases participate in segregated processes via binding specificity. Moreover, two of the transferases were expressed during growth in alternating patterns while the final transferase was only observed as a breakdown product common to all three. The broad substrate recognition and compensatory expression shown here help explain why phosphopantetheinyl transferases are lost throughout dinoflagellate evolution without a loss in a biochemical process.

Cascading Crypthecodinium cohnii Biorefinery: Global Warming Potential and Techno-Economic Assessment

Prior to the commissioning of a new industrial biorefinery it is deemed necessary to evaluate if the new project will be beneficial or detrimental to climate change, one of the main drivers for the sustainable development goals (SDG) of the United Nations. In particular, how SDG 7, Clean and Efficient Energy, SDG 3, Good Health and Well Being, SDG 9, Industry Innovation and Infrastructure, and SDG 12, Responsible Production and Consumption, would engage in a new biorefinery design, beneficial to climate change, i.e., fostering SDG 13, Climate Action. This study uses life cycle assessment methodology (LCA) to delve in detail into the Global Warming Impact category, project scenario GHG savings, using a conventional and a dynamic emission flux approach until 2060 (30-year lifetime). Water, heat and electricity circularity are in place by using a water recirculation process and a combined heat and power unit (CHP). A new historical approach to derive low and higher-end commodity prices (chemicals, electricity, heat, jet/maritime fuel, DHA, N-fertilizer) is used for the calculation of the economic indicators: Return of investment (ROI) and inflation-adjusted return (IAR), based upon the consumer price index (CPI). Main conclusions are: supercritical fluid extraction is the hotspot of energy consumption; C. cohnii bio-oil without DHA has higher sulfur concentration than crude oil based jet fuel requiring desulfurization, however the sulfur levels are compatible with maritime fuels; starting its operation in 2030, by 2100 an overall GHG savings of 73% (conventional LCA approach) or 85% (dynamic LCA approach) is projected; economic feasibility for oil productivity and content of 0.14 g/L/h and 27% (w/w) oil content, respectively (of which 31% is DHA), occurs for DHA-cost 100 times higher than reference fish oil based DHA; however future genetic engineering achieving 0.4 g/L/h and 70% (w/w) oil content (of which 31% is DHA), reduces the threshold to 20 times higher cost than reference fish oil based DHA; N-fertilizer, district heating and jet fuel may have similar values then their fossil counterparts.

Dinoflagellate Phosphopantetheinyl Transferase (PPTase) and Thiolation Domain Interactions Characterized Using a Modified Indigoidine Synthesizing Reporter

Photosynthetic dinoflagellates synthesize many toxic but also potential therapeutic compounds therapeutics via polyketide/non-ribosomal peptide synthesis, a common means of producing natural products in bacteria and fungi. Although canonical genes are identifiable in dinoflagellate transcriptomes, the biosynthetic pathways are obfuscated by high copy numbers and fractured synteny. This study focuses on the carrier domains that scaffold natural product synthesis (thiolation domains) and the phosphopantetheinyl transferases (PPTases) that thiolate these carriers. We replaced the thiolation domain of the indigoidine producing BpsA gene from Streptomyces lavendulae with those of three multidomain dinoflagellate transcripts and coexpressed these constructs with each of three dinoflagellate PPTases looking for specific pairings that would identify distinct pathways. Surprisingly, all three PPTases were able to activate all the thiolation domains from one transcript, although with differing levels of indigoidine produced, demonstrating an unusual lack of specificity. Unfortunately, constructs with the remaining thiolation domains produced almost no indigoidine and the thiolation domain for lipid synthesis could not be expressed in E. coli. These results combined with inconsistent protein expression for different PPTase/thiolation domain pairings present technical hurdles for future work. Despite these challenges, expression of catalytically active dinoflagellate proteins in E. coli is a novel and useful tool going forward.

Crypthecodinium cohnii Growth and Omega Fatty Acid Production in Mediums Supplemented with Extract from Recycled Biomass

Crypthecodinium cohnii is a marine heterotrophic dinoflagellate that can accumulate high amounts of omega-3 polyunsaturated fatty acids (PUFAs), and thus has the potential to replace conventional PUFAs production with eco-friendlier technology. So far, C. cohnii cultivation has been mainly carried out with the use of yeast extract (YE) as a nitrogen source. In the present study, alternative carbon and nitrogen sources were studied: the extraction ethanol (EE), remaining after lipid extraction, as a carbon source, and dinoflagellate extract (DE) from recycled algae biomass C. cohnii as a source of carbon, nitrogen, and vitamins. In mediums with glucose and DE, the highest specific biomass growth rate reached a maximum of 1.012 h-1, while the biomass yield from substrate reached 0.601 g·g-1. EE as the carbon source, in comparison to pure ethanol, showed good results in terms of stimulating the biomass growth rate (an 18.5% increase in specific biomass growth rate was observed). DE supplement to the EE-based mediums promoted both the biomass growth (the specific growth rate reached 0.701 h-1) and yield from the substrate (0.234 g·g-1). The FTIR spectroscopy data showed that mediums supplemented with EE or DE promoted the accumulation of PUFAs/docosahexaenoic acid (DHA), when compared to mediums containing glucose and commercial YE.

Essential components of the xanthophyll cycle differ in high and low toxin Karenia brevis

The dinoflagellate Karenia brevis, blooms annually in the Gulf of Mexico, producing a suite of neurotoxins known as the brevetoxins. The cellular toxin content of K. brevis, however, is highly variable between or even within strains. Herein, we investigate physiological differences between high (KbHT) and low (KbLT) toxin producing cultures both derived from the Wilson strain, related to energy-dependent quenching (qE) by photosystem II, and reduced thiol content of the proteome. We demonstrate that gene and protein expression of the xanthophyll cycle enzyme diadinoxanthin de-epoxidase (Dde) and monogalactosyldiacylglycerol (MGDG) synthase are not significantly different in the two cultures. Using redox proteomics, we report a significantly higher reduced cysteine content in the low toxin proteome, including plastid localized thioredoxin reductase (Trx) which can result in inactivation of Dde and activation of MGDG synthase. We also report significant differences in the lipidomes of KbHT and KbLT with respect to MGDG, which facilitates the xanthophyll cycle.

Enhanced Production of Astaxanthin without Decrease of DHA Content in Aurantiochytrium limacinum by Overexpressing Multifunctional Carotenoid Synthase Gene

Aurantiochytrium limacinum produces both docosahexaenoic acid (DHA) and astaxanthin, respectively. Organisms that produce these industrially important materials more efficiently than microalgae are currently needed. In this study, we overexpressed a putative homolog of CarS, which is involved in synthesizing the astaxanthin precursor, β-carotene, in A. limacinum to increase carotenoid synthesis with the goal of obtaining strains that produce large amounts of both DHA and carotenoids. AlCarS transformants #1 and #18 produced significantly increased amounts of astaxanthin as assessed according to culture (up to 5.8-fold) and optical density (up to 9.3-fold). The improved astaxanthin production of these strains did not affect their DHA productivity. Additionally, their CarS expression levels were higher than those of the wild-type strain, suggesting that CarS overexpression enhanced β-carotene production, which in turn improved astaxanthin productivity. Although cell yields were slightly decreased, these features will be valuable in health food, medical care, and animal feed fields.

Repeated fed-batch strategy and metabolomic analysis to achieve high docosahexaenoic acid productivity in Crypthecodinium cohnii

Background

Docosahexaenoic acid (DHA) is essential for human diet. However, high production cost of DHA using C. cohnii makes it currently less competitive commercially, which is mainly caused by low DHA productivity. In recent years, repeated fed-batch strategies have been evaluated for increasing the production of many fermentation products. The reduction in terms of stability of culture system was one of the major challenges for repeated fed-batch fermentation. However, the possible mechanisms responsible for the decreased stability of the culture system in the repeated fed-batch fermentation are so far less investigated, restricting the efforts to further improve the productivity. In this study, a repeated fed-batch strategy for DHA production using C. cohnii M-1-2 was evaluated to improve DHA productivity and reduce production cost, and then the underlying mechanisms related to the gradually decreased stability of the culture system in repeated fed-batch culture were explored through LC– and GC–MS metabolomic analyses.

Results

It was discovered that glucose concentration at 15–27 g/L and 80% medium replacement ratio were suitable for the growth of C. cohnii M-1-2 during the repeated fed-batch culture. A four-cycle repeated fed-batch culture was successfully developed and assessed at the optimum cultivation parameters, resulting in increasing the total DHA productivity by 26.28% compared with the highest DHA productivity of 57.08 mg/L/h reported using C. cohnii, including the time required for preparing seed culture and fermentor. In addition, LC– and GC–MS metabolomics analyses showed that the gradually decreased nitrogen utilization capacity, and down-regulated glycolysis and TCA cycle were correlated with the decreased stability of the culture system during the long-time repeated fed-batch culture. At last, some biomarkers, such as Pyr, Cit, OXA, FUM, l-tryptophan, l-threonine, l-leucine, serotonin, and 4-guanidinobutyric acid, correlated with the stability of culture system of C. cohnii M-1-2 were identified.

Conclusions

The study proved that repeated fed-batch cultivation was an efficient and energy-saving strategy for industrial production of DHA using C. cohnii, which could also be useful for cultivation of other microbes to improve productivity and reduce production cost. In addition, the mechanisms study at metabolite level can also be useful to further optimize production processes for C. cohnii and other microbes.

Nuclear Gene Transformation in the Dinoflagellate Oxyrrhis marina

The lack of a robust gene transformation tool that allows proper expression of foreign genes and functional testing for the vast number of nuclear genes in dinoflagellates has greatly hampered our understanding of the fundamental biology in this ecologically important and evolutionarily unique lineage of microeukaryotes. Here, we report the development of a dinoflagellate expression vector containing various DNA elements from phylogenetically separate dinoflagellate lineages, an electroporation protocol, and successful expression of introduced genes in an early branching dinoflagellate, Oxyrrhis marina. This protocol, involving the use of Lonza's Nucleofector and a codon-optimized antibiotic resistance gene, has been successfully used to produce consistent results in several independent experiments for O. marina. It is anticipated that this protocol will be adaptable for other dinoflagellates and will allow characterization of many novel dinoflagellate genes.

Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

Omics Analysis for Dinoflagellates Biology Research

Dinoflagellates are important primary producers for marine ecosystems and are also responsible for certain essential components in human foods. However, they are also notorious for their ability to form harmful algal blooms, and cause shellfish poisoning. Although much work has been devoted to dinoflagellates in recent decades, our understanding of them at a molecular level is still limited owing to some of their challenging biological properties, such as large genome size, permanently condensed liquid-crystalline chromosomes, and the 10-fold lower ratio of protein to DNA than other eukaryotic species. In recent years, omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, have been applied to the study of marine dinoflagellates and have uncovered many new physiological and metabolic characteristics of dinoflagellates. In this article, we review recent application of omics technologies in revealing some of the unusual features of dinoflagellate genomes and molecular mechanisms relevant to their biology, including the mechanism of harmful algal bloom formations, toxin biosynthesis, symbiosis, lipid biosynthesis, as well as species identification and evolution. We also discuss the challenges and provide prospective further study directions and applications of dinoflagellates.

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.