Mechanistic understanding towards the effective lipid production of a microalgal mutant strain Scenedesmus sp. Z-4 by the whole genome bioinformation

Towards Lipid from Microalgae: Products, Biosynthesis, and Genetic Engineering

Microalgae can convert carbon dioxide into organic matter through photosynthesis. Thus, they are considered as an environment-friendly and efficient cell chassis for biologically active metabolites. Microalgal lipids are a class of organic compounds that can be used as raw materials for food, feed, cosmetics, healthcare products, bioenergy, etc., with tremendous potential for commercialization. In this review, we summarized the commercial lipid products from eukaryotic microalgae, and updated the mechanisms of lipid synthesis in microalgae. Moreover, we reviewed the enhancement of lipids, triglycerides, polyunsaturated fatty acids, pigments, and terpenes in microalgae via environmental induction and/or metabolic engineering in the past five years. Collectively, we provided a comprehensive overview of the products, biosynthesis, induced strategies and genetic engineering in microalgal lipids. Meanwhile, the outlook has been presented for the development of microalgal lipids industries, emphasizing the significance of the accurate analysis of lipid bioactivity, as well as the high-throughput screening of microalgae with specific lipids.

Microalgae biofuels: illuminating the path to a sustainable future amidst challenges and opportunities

The development of microalgal biofuels is of significant importance in advancing the energy transition, alleviating food pressure, preserving the natural environment, and addressing climate change. Numerous countries and regions across the globe have conducted extensive research and strategic planning on microalgal bioenergy, investing significant funds and manpower into this field. However, the microalgae biofuel industry has faced a downturn due to the constraints of high costs. In the past decade, with the development of new strains, technologies, and equipment, the feasibility of large-scale production of microalgae biofuel should be re-evaluated. Here, we have gathered research results from the past decade regarding microalgae biofuel production, providing insights into the opportunities and challenges faced by this industry from the perspectives of microalgae selection, modification, and cultivation. In this review, we suggest that highly adaptable microalgae are the preferred choice for large-scale biofuel production, especially strains that can utilize high concentrations of inorganic carbon sources and possess stress resistance. The use of omics technologies and genetic editing has greatly enhanced lipid accumulation in microalgae. However, the associated risks have constrained the feasibility of large-scale outdoor cultivation. Therefore, the relatively controllable cultivation method of photobioreactors (PBRs) has made it the mainstream approach for microalgae biofuel production. Moreover, adjusting the performance and parameters of PBRs can also enhance lipid accumulation in microalgae. In the future, given the relentless escalation in demand for sustainable energy sources, microalgae biofuels should be deemed a pivotal constituent of national energy planning, particularly in the case of China. The advancement of synthetic biology helps reduce the risks associated with genetically modified (GM) microalgae and enhances the economic viability of their biofuel production.

Effects of polyethylene terephthalate microplastics on cell growth, intracellular products and oxidative stress of Scenedesmus sp

Polyethylene terephthalate (PET) has been widely utilized in the synthesis of textile materials and packaging of foods and beverages. In recent years, it has been commonly detected in the form of microplastics (MPs) in wastewater. However, the effects of PET MPs on microalgal intracellular products and their interrelationships have been poorly investigated. In this study, the microalgae Scenedesmus sp. Strain H-1 was exposed to PET MPs to explore their effects on the growth, intracellular products (such as lipids, carbohydrates, and proteins), and antioxidative defense systems of Scenedesmus sp. The results demonstrated that PET MPs significantly reduced Scenedesmus sp. cell growth, with a maximum inhibition rate of 38.25% in the 500 mg L-1 treatment group. PET MPs had negative effects on glucose and nitrate utilization rates and reduced intracellular carbohydrates, intracellular proteins, and photosynthetic pigments. Surprisingly, PET MPs reduced acetyl-CoA carboxylase activity but induced lipid accumulation in microalgae. In addition, PET MPs significantly decreased the essential linoleic acid concentration and increased the palmitic acid content, resulting in reduced biodiesel quality. PET MPs induced the production of reactive oxygen species and malondialdehyde as well as the activities of superoxide dismutase and catalase. The results of the PCA indicated that the response mechanism of Scenedesmus sp. to PET MPs exposure was synergistic. This study provides fundamental data on the impact of MPs on the intracellular products of microalgae.

Advances in Algomics technology: Application in wastewater treatment and biofuel production

Advanced sustainable bioremediation is gaining importance with rising global pollution. This review examines microalgae's potential for sustainable bioremediation and process enhancement using multi-omics approaches. Recently, microalgae-bacterial consortia have emerged for synergistic nutrient removal, allowing complex metabolite exchanges. Advanced bioremediation requires effective consortium design or pure culture based on the treatment stage and specific roles. The strain potential must be screened using modern omics approaches aligning wastewater composition. The review highlights crucial research gaps in microalgal bioremediation. It discusses multi-omics advantages for understanding microalgal fitness concerning wastewater composition and facilitating the design of microalgal consortia based on bioremediation skills. Metagenomics enables strain identification, thereby monitoring microbial dynamics during the treatment process. Transcriptomics and metabolomics encourage the algal cell response toward nutrients and pollutants in wastewater. Multi-omics role is also summarized for product enhancement to make algal treatment sustainable and fit for sustainable development goals and growing circular bioeconomy scenario.

Exploring the Potential Role of Ribosomal Proteins to Enhance Potato Resilience in the Face of Changing Climatic Conditions

Potatoes have emerged as a key non-grain crop for food security worldwide. However, the looming threat of climate change poses significant risks to this vital food source, particularly through the projected reduction in crop yields under warmer temperatures. To mitigate potential crises, the development of potato varieties through genome editing holds great promise. In this study, we performed a comprehensive transcriptomic analysis to investigate microtuber development and identified several differentially expressed genes, with a particular focus on ribosomal proteins-RPL11, RPL29, RPL40 and RPL17. Our results reveal, by protein-protein interaction (PPI) network analyses, performed with the highest confidence in the STRING database platform (v11.5), the critical involvement of these ribosomal proteins in microtuber development, and highlighted their interaction with PEBP family members as potential microtuber activators. The elucidation of the molecular biological mechanisms governing ribosomal proteins will help improve the resilience of potato crops in the face of today's changing climatic conditions.

Clustered regularly interspaced short palindromic repeats (CRISPR) technology and genetic engineering strategies for microalgae towards carbon neutrality: A critical review

Carbon dioxide is the major greenhouse gas and regards as the critical issue of global warming and climate changes. The inconspicuous microalgae are responsible for 40% of carbon fixation among all photosynthetic plants along with a higher photosynthetic efficiency and convert the carbon into lipids, protein, pigments, and bioactive compounds. Genetic approach and metabolic engineering are applied to accelerate the growth rate and biomass of microalgae, hence achieve the mission of carbon neutrality. Meanwhile, CRISPR/Cas9 is efficiently to enhance the productivity of high-value compounds in microalgae for it is easier operation, more affordable and is able to regulate multiple genes simultaneously. The genetic engineering strategies provide the multidisciplinary concept to evolute and increase the CO₂ fixation rate through Calvin-Benson-Bassham cycle. Therefore, the technologies, bioinformatics tools, systematic engineering approaches for carbon neutrality and circular economy are summarized and leading one step closer to the decarbonization society in this review.

Focus on the role of synthetic phytohormone for mixotrophic growth and lipid accumulation by Chlorella pyrenoidosa

Synthetic phytohormone (SP) is regarded as an attractive candidate for microalgae cultivation due to its potential for high-value microalgae biomass production. Herein, α-naphthylacetic acid (NAA), indomethacin (IN) and 2,4-dichlorophenoxyacetic acid (2,4-D) were used for the mixotrophic cultivation of Chlorella pyrenoidosa with mariculture wastewater (MW) acidogenic fermentation effluent. The growth and lipid accumulation of Chlorella pyrenoidosa added with SP were enhanced, given their high bioavailability of the nutrients. Among these three SPs, IN was optimal for Chlorella pyrenoidosa growth, with the maximum optical density of 1.81. NAA exhibited the best performance for lipid production and the proportion of lipid reached 50.24%. Furthermore, the energy of Chlorella pyrenoidosa cultured with SP preferentially allocated to lipogenesis. To understand the mechanism of lipid accumulation in Chlorella pyrenoidosa in response to SP, the enzyme activities involved in carbon metabolism were determined. The malic enzyme (ME) and acetyl-CoA carboxylase (ACCase) were positively correlated with lipid accumulation. Phosphoenolpyruvate carboxylase (PEPC) was the negative feedback enzyme for lipid synthesis. The findings could provide valuable information for regulation mechanism of lipid accumulation and value-added products recovery by microalgae.

Genetic and non-genetic tailoring of microalgae for the enhanced production of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) - A review

The myriad health benefits associated with eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) laid the path for their application in the functional foods and nutraceutical industries. Fish being primarily exploited for extraction of EPA and DHA are unsustainable sources; thus, oleaginous microalgae turn out to be an alternative sustainable source. This review paper aims to provide the recent developments in the context of enhancing EPA and DHA production by utilising non-genetic tailoring and genetic tailoring methods. We have also summarized the legislation, public perception, and possible risks associated with the usage of genetically modified microalgae focusing on EPA and DHA production.

ARTP Mutagenesis of Schizochytrium sp. PKU#Mn4 and Clethodim-Based Mutant Screening for Enhanced Docosahexaenoic Acid Accumulation

Schizochytrium species are one of the best oleaginous thraustochytrids for high-yield production of docosahexaenoic acid (DHA, 22:6). However, the DHA yields from most wild-type (WT) strains of Schizochytrium are unsatisfactory for large-scale production. In this study, we applied the atmospheric and room-temperature plasma (ARTP) tool to obtain the mutant library of a previously isolated strain of Schizochytrium (i.e., PKU#Mn4). Two rounds of ARTP mutagenesis coupled with the acetyl-CoA carboxylase (ACCase) inhibitor (clethodim)-based screening yielded the mutant A78 that not only displayed better growth, glucose uptake and ACCase activity, but also increased (54.1%) DHA content than that of the WT strain. Subsequent optimization of medium components and supplementation improved the DHA content by 75.5 and 37.2%, respectively, compared with that of mutant A78 cultivated in the unoptimized medium. Interestingly, the ACCase activity of mutant A78 in a medium supplemented with biotin, citric acid or sodium citrate was significantly greater than that in a medium without supplementation. This study provides an effective bioengineering approach for improving the DHA accumulation in oleaginous microbes.

Enhancement of Lipid Productivity and Self-flocculation by Cocultivating Monoraphidium sp. FXY-10 and Heveochlorella sp. Yu Under Mixotrophic Mode

To maintain high microalgae lipid productivity and flocculation efficiency simultaneously and reduce the production cost of microalgae lipids, Monoraphidium sp. FXY-10 with high lipid-producing capacity and Heveochlorella sp. Yu with strong self-flocculation ability were cocultivated and studied. Cocultivated microalgae lipid productivity and flocculation efficiency were increased to 203.8 mg L-1 day-1 and 70.55%, respectively, which is potentially related to the excessive competitive depletion of nitrogen sources and the upregulation of correlative key genes in lipid anabolic metabolism. Under cocultivation conditions, microalgae cells could enter the stationary phase 2 days earlier than that under monocultivation conditions, thus reducing the culture time. Relative expression of the accD, ME, and rbcL genes was upregulated to varying degrees, and the enzyme activities of ACCase, ME, and RuBisCO were also significantly increased compared with those in monocultivation. Moreover, fatty acid composition showed that microalgae lipids in cocultivation exhibited potential as a feedstock for biodiesel.

Metabolic pathway analysis of walnut endophytic bacterium Bacillus subtilis HB1310 related to lipid production from fermentation of cotton stalk hydrolysate based on genome sequencing

OBJECTIVES

In this study, genome sequencing and metabolic analysis were used to identify and verify the key metabolic pathways for glucose and xylose utilization and fatty acid synthesis in the walnut endophytic bacterium (WEB) Bacillus subtilis HB1310.

RESULTS

The genome sequence of WEB HB1310 was generated with a size of 4.1 Mb and GC content of 43.5%. Genome annotation indicated that the Embden-Meyerhof-Parnas, pentose phosphate, and fatty acid synthesis pathways were mainly involved in mixed sugar utilization and lipid production. In particular, diverse and abundant fatty acid synthesis genes were observed in a higher number than in other Bacillus strains. The tricarboxylic acid cycle competitively shared the carbon flux flowing before 48 h, and the acetic acid fermentation competed after 72 h. Moreover, fatty acid synthase activity was highly correlated with lipid titer with a correlation coefficient of 0.9626, and NADPH might be more utilized for the lipid synthesis within 48 h.

CONCLUSIONS

This study is the first attempt to explain the metabolic mechanism of mixed sugar utilization and lipid production based on genomic information, which provides a theoretical basis for the metabolic regulation of bacterial lipid production from lignocellulosic hydrolysates.

Overexpression of the Transcription Factor AtLEC1 Significantly Improved the Lipid Content of Chlorella ellipsoidea

Microalgae are considered to be a highly promising source for the production of biodiesel. However, the regulatory mechanism governing lipid biosynthesis has not been fully elucidated to date, and the improvement of lipid accumulation in microalgae is essential for the effective production of biodiesel. In this study, LEAFY COTYLEDON1 (LEC1) from Arabidopsis thaliana, a transcription factor (TF) that affects lipid content, was transferred into Chlorella ellipsoidea. Compared with wild-type (WT) strains, the total fatty acid content and total lipid content of AtLEC1 transgenic strains were significantly increased by 24.20–32.65 and 22.14–29.91%, respectively, under mixotrophic culture conditions and increased by 24.4–28.87 and 21.69–30.45%, respectively, under autotrophic conditions, while the protein content of the transgenic strains was significantly decreased by 18.23–21.44 and 12.28–18.66%, respectively, under mixotrophic and autotrophic conditions. Fortunately, the lipid and protein content variation did not affect the growth rate and biomass of transgenic strains under the two culture conditions. According to the transcriptomic data, the expression of 924 genes was significantly changed in the transgenic strain (LEC1-1). Of the 924 genes, 360 were upregulated, and 564 were downregulated. Based on qRT-PCR results, the expression profiles of key genes in the lipid synthesis pathway, such as ACCase, GPDH, PDAT1, and DGAT1, were significantly changed. By comparing the differentially expressed genes (DEGs) regulated by AtLEC1 in C. ellipsoidea and Arabidopsis, we observed that approximately 59% (95/160) of the genes related to lipid metabolism were upregulated in AtLEC1 transgenic Chlorella. Our research provides a means of increasing lipid content by introducing exogenous TF and presents a possible mechanism of AtLEC1 regulation of lipid accumulation in C. ellipsoidea.

Microbial biodiesel production from industrial organic wastes by oleaginous microorganisms: Current status and prospects

This review aims to encourage the technical development of microbial biodiesel production from industrial-organic-wastes-derived volatile fatty acids (VFAs). To this end, this article summarizes the current status of several key technical steps during microbial biodiesel production, including (1) acidogenic fermentation of bio-wastes for VFA collection, (2) lipid accumulation in oleaginous microorganisms, (3) microbial lipid extraction, (4) transesterification of microbial lipids into crude biodiesel, and (5) crude biodiesel purification. The emerging membrane-based bioprocesses such as electrodialysis, forward osmosis and membrane distillation, are promising approaches as they could help tackle technical challenges related to the separation and recovery of VFAs from the fermentation broth. The genetic engineering and metabolic engineering approaches could be applied to design microbial species with higher lipid productivity and rapid growth rate for enhanced fatty acids synthesis. The enhanced in situ transesterification technologies aided by microwave, ultrasound and supercritical solvents are also recommended for future research. Technical limitations and cost-effectiveness of microbial biodiesel production from bio-wastes are also discussed, in regard to its potential industrial development. Based on the overview on microbial biodiesel technologies, an integrated biodiesel production line incorporating all the critical technical steps is proposed for unified management and continuous optimization for highly efficient biodiesel production.

Sustainable lipid and lutein production from Chlorella mixotrophic fermentation by food waste hydrolysate

Bioconversion of food waste into value-added products is a promising way to tackle the global food waste management problem. In this study, a novel valorisation strategy for bioenergy and lutein production via microalgal fermentation was investigated. Significant amount of glucose was recovered from enzymatic hydrolysis of food waste. The resultant hydrolysate was then utilised as culture medium in mixotrophic cultivation of Chlorella sp. to obtain high levels of lipid and lutein, whose accumulation patterns were consistent with molecular analyses. The resultant algal lipid derived from microalgal biomass using food hydrolysate was at high quality in terms of biodiesel properties. Further, in semi-continuous fermentation, the average algal biomass was 6.1 g L^-1 with 2.5 g L^-1 lipid and 38.5 mg L^-1 lutein using hydrolysate with an initial glucose concentration of 10 g L^-1. Meanwhile, the resultant algal biomass was 6.9 g L^-1 with 1.8 g L^-1 lipid and 63.0 mg L^-1 lutein using hydrolysate with an initial glucose concentration of 20 g L^-1, which suggests food waste hydrolysate could trigger algal products preferences. The experimental results of this study suggested the potential of microalgae as a platform for bioconversion of food waste into high-value products, especially sustainable bioenergy.

Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

BACKGROUND

Scenedesmus obliquus belongs to green microalgae and is widely used in aquaculture as feed, which is also explored for lipid production and bioremediation. However, genomic studies of this microalga have been very limited. Cell self-flocculation of microalgal cells can be used as a simple and economic method for harvesting biomass, and it is of great importance to perform genome-scale studies for the self-flocculating S. obliquus strains to promote their biotechnological applications.

RESULTS

We employed the Pacific Biosciences sequencing platform for sequencing the genome of the self-flocculating microalga S. obliquus AS-6-11, and used the MECAT software for de novo genome assembly. The estimated genome size of S. obliquus AS-6-11 is 172.3 Mbp with an N50 of 94,410 bp, and 31,964 protein-coding genes were identified. Gene Ontology (GO) and KEGG pathway analyses revealed 65 GO terms and 428 biosynthetic pathways. Comparing to the genome sequences of the well-studied green microalgae Chlamydomonas reinhardtii, Chlorella variabilis, Volvox carteri and Micractinium conductrix, the genome of S. obliquus AS-6-11 encodes more unique proteins, including one gene that encodes D-mannose binding lectin. Genes encoding the glycosylphosphatidylinositol (GPI)-anchored cell wall proteins, and proteins with fasciclin domains that are commonly found in cell wall proteins might be responsible for the self-flocculating phenotype, and were analyzed in detail. Four genes encoding both GPI-anchored cell wall proteins and fasciclin domain proteins are the most interesting targets for further studies.

CONCLUSIONS

The genome sequence of the self-flocculating microalgal S. obliquus AS-6-11 was annotated and analyzed. To our best knowledge, this is the first report on the in-depth annotation of the S. obliquus genome, and the results will facilitate functional genomic studies and metabolic engineering of this important microalga. The comparative genomic analysis here also provides new insights into the evolution of green microalgae. Furthermore, identification of the potential genes encoding self-flocculating proteins will benefit studies on the molecular mechanism underlying this phenotype for its better control and biotechnological applications as well.

Enhanced microalgal growth and lipid accumulation by addition of different nanoparticles under xenon lamp illumination

In this study, the growth and lipid accumulation of Scenedesmus sp. using different nanoparticles and light sources were investigated. Xenon lamp can produce a broad illumination spectrum, and exhibited better performance than light-emitting diode. SiC and g-C₃N₄ nanoparticles improved the biomass and lipid accumulation, whereas TiO₂ and TiC nanoparticles had inhibitory influence on microalgae. Lipid production can be improved by oxidative stress produced by combination of nanoparticles and xenon lamp irradiation. At the optimal SiC nanoparticles concentration of 150 mg L^-1 and photoperiod of 6:18 h, the maximum biomass concentration and total lipid content reached 3.18 g L^-1 and 40.26%, respectively. The addition of SiC nanoparticles could promote the substrate utilization rate and induce stress condition, thereby enhancing the activity of acetyl-CoA carboxylase and lipid biosynthesis. This research shows that SiC nanoparticles addition combined with xenon lamp illumination is a promising strategy to promote microalgal growth and lipid accumulation.

Improving lipid production by strain development in microalgae: Strategies, challenges and perspectives

Over the past decade, the number of original articles and reviews presenting microalgae as a promising feedstock for biodiesel has increased tremendously. Many improvements of microalgae have been achieved through selection and strain development for industrial applications. However, the large-scale production of lipids for commercialization is not yet realistic because the production is still much more expensive than that of agricultural products. This review summarizes recent research on the induction of lipid biosynthesis in microalgae and the various strategies of genetic and metabolic engineering for enhancing lipid production. Strain engineering targets are proposed based on these strategies. To address current limitations of strain engineering for lipid production, this review provides insights on recent engineering strategies based on molecular tools and methods, and also discusses further perspectives.