Genetic engineering of the Calvin cycle toward enhanced photosynthetic CO2 fixation in microalgae

Method for isolation of high molecular weight genomic DNA from Botryococcus biomass

The development of high molecular weight (HMW) genomic DNA (gDNA) extraction protocols for non-model species is essential to fully exploit long-read sequencing technologies in order to generate genome assemblies that can help answer complex questions about these organisms. Obtaining enough high-quality HMW gDNA can be challenging for these species, especially for tissues rich in polysaccharides such as biomass from species within the Botryococcus genus. The existing protocols based on column-based DNA extraction and biochemical lysis kits can be inefficient and may not be useful due to variations in biomass polysaccharide content. We developed an optimized protocol for the efficient extraction of HMW gDNA from Botryococcus biomass for use in long-read sequencing technologies. The protocol utilized an initial wash step with sorbitol to remove polysaccharides and yielded HMW gDNA concentrations up to 220 ng/μL with high purity. We then demonstrated the suitability of the HMW gDNA isolated from this protocol for long-read sequencing on the Oxford Nanopore PromethION platform for three Botryococcus species. Our protocol can be used as a standard for efficient HMW gDNA extraction in microalgae rich in polysaccharides and may be adapted for other challenging species.

Transcriptome analysis reveals the molecular mechanism of differences in growth between photoautotrophy and heterotrophy in Chlamydomonas reinhardtii

Background

The green alga Chlamydomonas reinhardtii can grow photoautotrophically utilizing light and CO2, and heterotrophically utilizing acetate. The physiological and biochemical responses of autotrophy and heterotrophy are different in C. reinhardtii. However, there is no complete understanding of the molecular physiology between autotrophy and heterotrophy. Therefore, we performed biochemical, molecular and transcriptome analysis of C. reinhardtii between autotrophy and heterotrophy.

Results

The cell growth characterization demonstrated that heterotrophic cell had enhanced growth rates, and autotrophic cell accumulated more chlorophyll. The transcriptome data showed that a total of 2,970 differentially expressed genes (DEGs) were identified from photoautotrophy 12h (P12h) to heterotrophy 12h (H12h). The DEGs were involved in photosynthesis, the tricarboxylic acid cycle (TCA), pyruvate and oxidative phosphorylation metabolisms. Moreover, the results of qRT-PCR revealed that the relative expression levels of malate dehydrogenase (MDH), succinate dehydrogenase (SDH), ATP synthase (ATPase), and starch synthase (SSS) were increased significantly from P12h and H12h. The protein activity of NAD-malate dehydrogenase (NAD-MDH) and succinate dehydrogenase (SDH) were significantly higher in the H12h group.

Conclusion

The above results indicated that the high growth rate observed in heterotrophic cell may be the effects of environmental or genetic regulation of photosynthesis. Therefore, the identification of novel candidate genes in heterotrophy will contribute to the development of microalga strains with higher growth capacity and better performance for biomass production.

Advances in microalgae-based carbon sequestration: Current status and future perspectives

The advancement in carbon dioxide (CO2) sequestration technology has received significant attention due to the adverse effects of CO2 on climate. The mitigation of the adverse effects of CO2 can be accomplished through its conversion into useful products or renewable fuels. In this regard, microalgae is a promising candidate due to its high photosynthesis efficiency, sustainability, and eco-friendly nature. Microalgae utilizes CO2 in the process of photosynthesis and generates biomass that can be utilized to produce various valuable products such as supplements, chemicals, cosmetics, biofuels, and other value-added products. However, at present microalgae cultivation is still restricted to producing value-added products due to high cultivation costs and lower CO2 sequestration efficiency of algal strains. Therefore, it is very crucial to develop novel techniques that can be cost-effective and enhance microalgal carbon sequestration efficiency. The main aim of the present manuscript is to explain how to optimize microalgal CO2 sequestration, integrate valuable product generation, and explore novel techniques like genetic manipulations, phytohormones, quantum dots, and AI tools to enhance the efficiency of CO2 sequestration. Additionally, this review provides an overview of the mass flow of different microalgae and their biorefinery, life cycle assessment (LCA) for achieving net-zero CO2 emissions, and the advantages, challenges, and future perspectives of current technologies. All of the reviewed approaches efficiently enhance microalgal CO2 sequestration and integrate value-added compound production, creating a green and economically profitable process.

New insights into Chlorella vulgaris applications

Environmental pollution is a big challenge that has been faced by humans in contemporary life. In this context, fossil fuel, cement production, and plastic waste pose a direct threat to the environment and biodiversity. One of the prominent solutions is the use of renewable sources, and different organisms to valorize wastes into green energy and bioplastics such as polylactic acid. Chlorella vulgaris, a microalgae, is a promising candidate to resolve these issues due to its ease of cultivation, fast growth, carbon dioxide uptake, and oxygen production during its growth on wastewater along with biofuels, and other productions. Thus, in this article, we focused on the potential of Chlorella vulgaris to be used in wastewater treatment, biohydrogen, biocement, biopolymer, food additives, and preservation, biodiesel which is seen to be the most promising for industrial scale, and related biorefineries with the most recent applications with a brief review of Chlorella and polylactic acid market size to realize the technical/nontechnical reasons behind the cost and obstacles that hinder the industrial production for the mentioned applications. We believe that our findings are important for those who are interested in scientific/financial research about microalgae.

A synthetic biology approach for the treatment of pollutants with microalgae

The increase in global population and industrial development has led to a significant release of organic and inorganic pollutants into water streams, threatening human health and ecosystems. Microalgae, encompassing eukaryotic protists and prokaryotic cyanobacteria, have emerged as a sustainable and cost-effective solution for removing these pollutants and mitigating carbon emissions. Various microalgae species, such as C. vulgaris, P. tricornutum, N. oceanica, A. platensis, and C. reinhardtii, have demonstrated their ability to eliminate heavy metals, salinity, plastics, and pesticides. Synthetic biology holds the potential to enhance microalgae-based technologies by broadening the scope of treatment targets and improving pollutant removal rates. This review provides an overview of the recent advances in the synthetic biology of microalgae, focusing on genetic engineering tools to facilitate the removal of inorganic (heavy metals and salinity) and organic (pesticides and plastics) compounds. The development of these tools is crucial for enhancing pollutant removal mechanisms through gene expression manipulation, DNA introduction into cells, and the generation of mutants with altered phenotypes. Additionally, the review discusses the principles of synthetic biology tools, emphasizing the significance of genetic engineering in targeting specific metabolic pathways and creating phenotypic changes. It also explores the use of precise engineering tools, such as CRISPR/Cas9 and TALENs, to adapt genetic engineering to various microalgae species. The review concludes that there is much potential for synthetic biology based approaches for pollutant removal using microalgae, but there is a need for expansion of the tools involved, including the development of universal cloning toolkits for the efficient and rapid assembly of mutants and transgenic expression strains, and the need for adaptation of genetic engineering tools to a wider range of microalgae species.

Knocking Out Chloroplastic Aldolases/Rubisco Lysine Methyltransferase Enhances Biomass Accumulation in Nannochloropsis oceanica under High-Light Stress

Rubisco large-subunit methyltransferase (LSMT), a SET-domain protein lysine methyltransferase, catalyzes the formation of trimethyl-lysine in the large subunit of Rubisco or in fructose-1,6-bisphosphate aldolases (FBAs). Rubisco and FBAs are both vital proteins involved in CO2 fixation in chloroplasts; however, the physiological effect of their trimethylation remains unknown. In Nannochloropsis oceanica, a homolog of LSMT (NoLSMT) is found. Phylogenetic analysis indicates that NoLSMT and other algae LSMTs are clustered in a basal position, suggesting that algal species are the origin of LSMT. As NoLSMT lacks the His-Ala/ProTrp triad, it is predicted to have FBAs as its substrate instead of Rubisco. The 18-20% reduced abundance of FBA methylation in NoLSMT-defective mutants further confirms this observation. Moreover, this gene (nolsmt) can be induced by low-CO2 conditions. Intriguingly, NoLSMT-knockout N. oceanica mutants exhibit a 9.7-13.8% increase in dry weight and enhanced growth, which is attributed to the alleviation of photoinhibition under high-light stress. This suggests that the elimination of FBA trimethylation facilitates carbon fixation under high-light stress conditions. These findings have implications in engineering carbon fixation to improve microalgae biomass production.

Cultivation of microalgae-bacteria consortium by waste gas-waste water to achieve CO2 fixation, wastewater purification and bioproducts production

The cultivation of microalgae and microalgae-bacteria consortia provide a potential efficient strategy to fix CO2 from waste gas, treat wastewater and produce value-added products subsequently. This paper reviews recent developments in CO2 fixation and wastewater treatment by single microalgae, mixed microalgae and microalgae-bacteria consortia, as well as compares and summarizes the differences in utilizing different microorganisms from different aspects. Compared to monoculture of microalgae, a mixed microalgae and microalgae-bacteria consortium may mitigate environmental risk, obtain high biomass, and improve the efficiency of nutrient removal. The applied microalgae include Chlorella sp., Scenedesmus sp., Pediastrum sp., and Phormidium sp. among others, and most strains belong to Chlorophyta and Cyanophyta. The bacteria in microalgae-bacteria consortia are mainly from activated sludge and specific sewage sources. Bioengineer in CBB cycle in microalgae cells provide effective strategy to achieve improvement of CO2 fixation or a high yield of high-value products. The mechanisms of CO2 fixation and nutrient removal by different microbial systems are also explored and concluded, the importance of microalgae in the technology is proven. After cultivation, microalgae biomass can be harvested through physical, chemical, biological and magnetic separation methods and used to produce high-value by-products, such as biofuel, feed, food, biochar, fertilizer, and pharmaceutical bio-compounds. Although this technology has brought many benefits, some challenging obstacles and limitation remain for industrialization and commercializing.

Strigolactone and nitric oxide collaborate synergistically to boost tomato seedling resilience to arsenic toxicity via modulating physiology and antioxidant system

Arsenic (As) poses a significant environmental threat as a metalloid toxin, adversely affecting the health of both plants and animals. Strigolactones (SL) and nitric oxide (NO) are known to play crucial roles in plant physiology. Therefore, the present experiment was designed to investigate the potential cumulative role of SL (GR24-0.20 μM) and NO (100 μM) in mitigating the adverse effect of AsV (53 μM) by modulating physiological mechanisms in two genotypes of tomato (Riogrand and Super Strain 8). A sample randomized design with four replicates was used to arrange the experimental pots in the growth chamber. 45-d old both tomato cultivars under AsV toxicity exhibited reduced morphological attributes (root and shoot length, root and shoot fresh weight, and root and shoot dry weight) and physiological and biochemical characteristics [chlorophyll (Chl) a and b content, activity of δ-aminolevulinic acid dehydratase activity (an enzyme responsible for Chl biosynthesis), and carbonic anhydrase activity (an enzyme responsible for photosynthesis), and enhanced Chl degradation, overproduction of reactive oxygen species (ROS) and lipid peroxidation due to enhanced malondialdehyde (MDA) content. However, the combined application of SL and NO was more effective in enhancing the tolerance of both varieties to AsV toxicity compared to individual application. The combined application of SL and NO improved growth parameters, biosynthesis of Chls, NO and proline. However, the combined application significantly suppressed cellular damage by inhibiting MDA and overproduction of ROS in leaves and roots, as confirmed by the fluorescent microscopy study and markedly upregulated the antioxidant enzymes (catalase, peroxidase, superoxide dismutase, ascorbate dismutase and glutathione reductase) activity. This study provides clear evidence that the combined application of SL and NO supplementation significantly improves the resilience of tomato seedlings against AsV toxicity. The synergistic effect of SL and NO was confirmed by the application of cPTIO (an NO scavenger) with SL and NO. However, further molecular studies could be imperative to conclusively validate the simultaneous role of SL and NO in enhancing plant tolerance to abiotic stress.

Towards circular economy: Potential of microalgae - bacterial-based biofertilizer on plants

Biofertilizers encompass microorganisms that can be applied to plants, subsequently establishing themselves within the plant's rhizosphere or internal structures. This colonization stimulates plant development by enhancing nutrient absorption from the host. While there is growing literature documenting the applications of microalgae-based and bacterial-based biofertilizers, the research focusing on the effectiveness of consortia formed by these microorganisms as short-term plant biofertilizers is notably insufficient. This study seeks to assess the effectiveness of microalgae-bacterial biofertilizers in promoting plant growth and their potential contribution to the circular economy. The review sheds light on the impact of microalgae-bacterial biofertilizers on plant growth parameters, delving into factors influencing their efficiency, microalgae-bacteria interactions, and effects on soil health. The insights from this review are poised to offer valuable guidance to stakeholders in agriculture, including farmers, environmental technologists, and businesses. These insights will aid in the development and investment in more efficient and sustainable methods for enhancing crop yields, aligning with the Sustainable Development Goals and principles of the circular economy.

Evaluating nutrient limitation in co-culture of Chlorella pyrenoidosa and Rhodobacter sphaeroides

The influence of nitrogen deficiency on microalgae-bacteria co-culture has been studied mostly with nitrogen-fixing bacteria. Photosynthetic bacteria (PSB), which are non-nitrogen-fixing bacteria, the impact of N deficiency on its co-culture with microalgae is unknown. In this study, Chlorella pyrenoidosa and Rhodobacter sphaeroides co-culture was cultivated photoheterotrophically with acetate. The impact of N starvation and different P supply levels on oil production were examined. When phosphorus was sufficient, N starvation increased the fatty acid methyl ester (FAME) content from 21.7 % to 28.2 %, and also increased the FAME yield (g CODFAME/g CODAcetate) from 0.17 to 0.22. However, the biomass and FAME productivities decreased. Sufficient phosphorus was also essential for a high growth rate and FAME productivity. Deficiencies in either N or P led to a decrease in the proportion of unsaturated FAMEs. iTRAQ analysis indicated N starvation promoted oil accumulation by driving the carbon flow to fatty acid synthesis in microalgae from co-culture. This study improves the understanding of biomass and lipid production via microalgae-PSB co-culture in photoheterotrophic cultivation. The mechanism of interaction between microalgae and bacteria needs further study.

Realization process of microalgal biorefinery: The optional approach toward carbon net-zero emission

Increasing carbon dioxide (CO2) emission has already become a dire threat to the human race and Earth's ecology. Microalgae are recommended to be engineered as CO2 fixers in biorefinery, which play crucial roles in responding climate change and accelerating the transition to a sustainable future. This review sorted through each segment of microalgal biorefinery to explore the potential for its practical implementation and commercialization, offering valuable insights into research trends and identifies challenges that needed to be addressed in the development process. Firstly, the known mechanisms of microalgal photosynthetic CO2 fixation and the approaches for strain improvement were summarized. The significance of process regulation for strengthening fixation efficiency and augmenting competitiveness was emphasized, with a specific focus on CO2 and light optimization strategies. Thereafter, the massive potential of microalgal refineries for various bioresource production was discussed in detail, and the integration with contaminant reclamation was mentioned for economic and ecological benefits. Subsequently, economic and environmental impacts of microalgal biorefinery were evaluated via life cycle assessment (LCA) and techno-economic analysis (TEA) to lit up commercial feasibility. Finally, the current obstacles and future perspectives were discussed objectively to offer an impartial reference for future researchers and investors.

Evaluating application of photosynthetic microbial fuel cell to exhibit efficient carbon sequestration with concomitant value-added product recovery from wastewater: A review

The emission of CO2 from industrial (24%) and different anthropogenic activities, like transportation (27%), electricity production (25%), and agriculture (11%), can lead to global warming, which in the long term can trigger substantial climate changes. In this regard, CO2 sequestration and wastewater treatment in tandem with bioenergy production through photosynthetic microbial fuel cell (PMFC) is an economical and sustainable intervention to address the problem of global warming and elevating energy demands. Therefore, this review focuses on the application of different PMFC as a bio-refinery approach to produce biofuels and power generation accompanied with the holistic treatment of wastewater. Moreover, CO2 bio-fixation and electron transfer mechanism of different photosynthetic microbiota, and factors affecting the performance of PMFC with technical feasibility and drawbacks are also elucidated in this review. Also, low-cost approaches such as utilization of bio-membrane like coconut shell, microbial growth enhancement by extracellular cell signalling mechanisms, and exploitation of genetically engineered strain towards the commercialization of PMFC are highlighted. Thus, the present review intends to guide the budding researchers in developing more cost-effective and sustainable PMFCs, which could lead towards the commercialization of this inventive technology.

Genetic engineering for biohydrogen production from microalgae

The development of biohydrogen as an alternative energy source has had great economic and environmental benefits. Hydrogen production from microalgae is considered a clean and sustainable energy production method that can both alleviate fuel shortages and recycle waste. Although algal hydrogen production has low energy consumption and requires only simple pretreatment, it has not been commercialized because of low product yields. To increase microalgal biohydrogen production several technologies have been developed, although they struggle with the oxygen sensitivity of the hydrogenases responsible for hydrogen production and the complexity of the metabolic network. In this review, several genetic and metabolic engineering studies on enhancing microalgal biohydrogen production are discussed, and the economic feasibility and future direction of microalgal biohydrogen commercialization are also proposed.

Environmental pollution mitigation through utilization of carbon dioxide by microalgae

Anthropogenic emissions of CO₂ have reached a critical level and the global surface temperature is expected to rise by 1.5 °C between 2030 and 2050. To ameliorate the current global warming scenario, the research community has been struggling to find more economical and innovative solutions for carbon sequestration. Among such techniques, the use of microalgal species such as Chlorella sp., Dunaliella tertiolecta, Spirulina platensis, Desmodesmus sp., and Nannochloropsis sp., among others have shown high carbon tolerance capacity (10-100%) for establishing carbon capture, utilization and storage systems. To make microalgal-based carbon capture more economical, the microalgal biomass (∼2 g/L) can be converted biofuels, pharmaceuticals and nutraceuticals through biorefinery approach with product yield in the range of 60-99.5%. Further, CRISPR-Cas9 has enabled the knockout of specific genes in microalgal species that can be used to generate low pH tolerant strains with high lipid production. Inspite of the emerging developments in pollution control by microalgae, only limited investigations are available on its economic aspects which indicate a production cost of ∼$ 0.5-15/kg microalgal biomass. This review intends to summarize the advancements in different carbon sequestration techniques while highlighting their mechanisms and major research areas that need attention for economical microalgae-based carbon sequestration.

Microalgae systems - environmental agents for wastewater treatment and further potential biomass valorisation

Water is the most valuable resource on the planet. However, massive anthropogenic activities generate threatening levels of biological, organic, and inorganic pollutants that are not efficiently removed in conventional wastewater treatment systems. High levels of conventional pollutants (carbon, nitrogen, and phosphorus), emerging chemical contaminants such as antibiotics, and pathogens (namely antibiotic-resistant ones and related genes) jeopardize ecosystems and human health. Conventional wastewater treatment systems entail several environmental issues: (i) high energy consumption; (ii) high CO₂ emissions; and (iii) the use of chemicals or the generation of harmful by-products. Hence, the use of microalgal systems (entailing one or several microalgae species, and in consortium with bacteria) as environmental agents towards wastewater treatment has been seen as an environmentally friendly solution to remove conventional pollutants, antibiotics, coliforms and antibiotic resistance genes. In recent years, several authors have evaluated the use of microalgal systems for the treatment of different types of wastewater, such as agricultural, municipal, and industrial. Generally, microalgal systems can provide high removal efficiencies of: (i) conventional pollutants, up to 99%, 99%, and 90% of total nitrogen, total phosphorus, and/or organic carbon, respectively, through uptake mechanisms, and (ii) antibiotics frequently found in wastewaters, such as sulfamethoxazole, ciprofloxacin, trimethoprim and azithromycin at 86%, 65%, 42% and 93%, respectively, through the most desirable microalgal mechanism, biodegradation. Although pathogens removal by microalgal species is complex and very strain-specific, it is also possible to attain total coliform and Escherichia coli removal of 99.4% and 98.6%, respectively. However, microalgal systems' effectiveness strongly relies on biotic and abiotic conditions, thus the selection of operational conditions is critical. While the combination of selected species (microalgae and bacteria), ratios and inoculum concentration allow the efficient removal of conventional pollutants and generation of high amounts of biomass (that can be further converted into valuable products such as biofuels and biofertilisers), abiotic factors such as pH, hydraulic retention time, light intensity and CO₂/O₂ supply also have a crucial role in conventional pollutants and antibiotics removal, and wastewater disinfection. However, some rationale must be considered according to the purpose. While alkaline pH induces the hydrolysis of some antibiotics and the removal of faecal coliforms, it also decreases phosphates solubility and induces the formation of ammonium from ammonia. Also, while CO₂ supply increases the removal of E. coli and Pseudomonas aeruginosa, as well as the microalgal growth (and thus the conventional pollutants uptake), it decreases Enterococcus faecalis removal. Therefore, this review aims to provide a critical review of recent studies towards the application of microalgal systems for the efficient removal of conventional pollutants, antibiotics, and pathogens; discussing the feasibility, highlighting the advantages and challenges of the implementation of such process, and presenting current case-studies of different applications of microalgal systems.

Mapping the field of microalgae CO2 sequestration: a bibliometric analysis

Microalgae CO₂ sequestration has gained considerable attention in the last three decades as a promising technology to slow global warming caused by CO₂ emissions. To provide a comprehensive and objective analysis of the research status, hot spots, and frontiers of CO₂ fixation by microalgae, a bibliometric approach was recently chosen for review. In this study, 1561 articles (1991-2022) from the Web of Science (WOS) on microalgae CO₂ sequestration were screened. A knowledge map of the domain was presented using VOSviewer and CiteSpace. It visually demonstrates the most productive journals (Bioresource Technology), countries (China and USA), funding sources, and top contributors (Cheng J, Chang JS, and their team) in the field of CO₂ sequestration by microalgae. The analysis also revealed that research hotspots changed over time and that recent research has focused heavily on improving carbon sequestration efficiency. Finally, commercialization of carbon fixation by microalgae is a key hurdle, and supports from other disciplines could improve carbon sequestration efficiency.

Lutein production from microalgae: A review

Lutein production from microalgae is a sustainable and economical strategy to offer the increasing global demands, but is still challenged with low lutein content at the high-cell density for commercial production. This review summarizes the suitable conditions for cell growth and lutein accumulation, and presents recent cultivation strategies to further improve lutein productivity. Light and nitrogen play critical roles in lutein biosynthesis that lead to the efficient multi-stage cultivation by increasing lutein content at the later stage. In addition, metabolic and genetic designs for carbon regulation and lutein biosynthesis are discussed at the molecule level. The in-situ lutein accumulation in fermenters by regulating carbon metabolism is considered as a cost-effective direction. Then, downstream processes are summarized for the efficient lutein recovery. Finally, challenges of current lutein production from microalgae are discussed. Meanwhile, potential solutions are proposed to improve lutein content and drive down costs of microalgal biomass.

Recent advances in CO2 fixation by microalgae and its potential contribution to carbon neutrality

Many countries and regions have set their schedules to achieve the carbon neutrality between 2030 and 2070. Microalgae are capable of efficiently fixing CO₂ and simultaneously producing biomass for multiple applications, which is considered one of the most promising pathways for carbon capture and utilization. This work reviews the current research on microalgae CO₂ fixation technologies and the challenges faced by the related industries and government agencies. The technoeconomic analysis indicates that cultivation is the major cost factor. Use of waste resources such as wastewater and flue gas can significantly reduce the costs and carbon footprints. The life cycle assessment has identified fossil-based electricity use as the major contributor to the global warming potential of microalgae-based CO₂ fixation approach. Substantial efforts and investments are needed to identify and bridge the gaps among the microalgae strain development, cultivation conditions and systems, and use of renewable resources and energy.

Transcriptome-based analysis of key pathways relating to yield formation stage of foxtail millet under different drought stress conditions

Although foxtail millet, as small Panicoid crop, is of drought resilient, drought stress has a significant effect on panicle of foxtail millet at the yield formation stage. In this study, the changes of panicle morphology, photosynthesis, antioxidant protective enzyme system, reactive oxygen species (ROS) system, and osmotic regulatory substance and RNA-seq of functional leaves under light drought stress (LD), heavy drought stress (HD), light drought control (LDCK) and heavy drought control (HDCK) were studied to get a snap-shot of specific panicle morphological changes, physiological responses and related molecular mechanisms. The results showed that the length and weight of panicle had decreased, but with increased empty abortive rate, and then yield dropped off 14.9% and 36.9%, respectively. The photosynthesis of millet was significantly decreased, like net photosynthesis rate, stomatal conductance and transpiration rate, especially under HD treatment with reluctant recovery from rehydration. Under LD and HD treatment, the peroxidase (POD) was increased by 34% and 14% and the same as H₂O₂ by 34.7% and 17.2% compared with LDCK and HDCK. The ability to produce and inhibit O^2- free radicals under LD treatment was higher than HD. The content of soluble sugar was higher under LD treatment but the proline was higher under HD treatment. Through RNA-seq analysis, there were 2,393 and 3,078 different genes expressed under LD and HD treatment. According to the correlation analysis between weighted gene coexpression network analysis (WGCNA) and physiological traits, the co-expression network of several modules with high correlation was constructed, and some hub genes of millet in response to drought stress were found. The expression changes relating to carbon fixation, sucrose and starch synthesis, lignin synthesis, gibberellin synthesis, and proline synthesis of millet were specifically analyzed. These findings provide a full perspective on how drought affects the yield formation of foxtail millet by constructing one work model thereby providing theoretical foundation for hub genes exploration and drought resistance breeding of foxtail millet.

Advances in Genetic Engineering in Improving Photosynthesis and Microalgal Productivity

Even though sunlight energy far outweighs the energy required by human activities, its utilization is a key goal in the field of renewable energies. Microalgae have emerged as a promising new and sustainable feedstock for meeting rising food and feed demand. Because traditional methods of microalgal improvement are likely to have reached their limits, genetic engineering is expected to allow for further increases in the photosynthesis and productivity of microalgae. Understanding the mechanisms that control photosynthesis will enable researchers to identify targets for genetic engineering and, in the end, increase biomass yield, offsetting the costs of cultivation systems and downstream biomass processing. This review describes the molecular events that happen during photosynthesis and microalgal productivity through genetic engineering and discusses future strategies and the limitations of genetic engineering in microalgal productivity. We highlight the major achievements in manipulating the fundamental mechanisms of microalgal photosynthesis and biomass production, as well as promising approaches for making significant contributions to upcoming microalgal-based biotechnology.

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.

Mitochondria and chloroplasts function in microalgae energy production

Microalgae are organisms that have the ability to perform photosynthesis, capturing CO₂ from the atmosphere to produce different metabolites such as vitamins, sugars, lipids, among others, many of them with different biotechnological applications. Recently, these microorganisms have been widely studied due to their possible use to obtain clean energy. It has been postulated that the growth of microalgae and the production of high-energy metabolites depend on the correct function of cellular organelles such as mitochondria and chloroplasts. Thus, the development of different genetic tools to improve the function of these organelles is of high scientific and technological interest. In this paper we review the recent advances in microalgae engineering and the role of cellular organelles in order to increase cell productivity and biomass.

Resource recovery from hydroponic wastewaters using microalgae-based biorefineries: A circular bioeconomy perspective

As the world's population grows, it is necessary to rethink how countries throughout the world produce food in order to replace the conventional and unsustainable agricultural techniques. Microalgae cultivation using a nutrient-rich solution from hydroponic systems not only presents a novel approach to solving problems pertaining to the impact of the discharges on the natural environment but also provides a plethora of other biotechnological applications particularly in the productions of high value-added products and plants growth stimulants, which can be potentially assimilated into the circular bioeconomy (CBE) in the hydroponic sector. In this review, the potential and practicability of microalgae to be merged into hydroponics CBE are reviewed. Overall, the integration of microalgal biorefineries in hydroponics systems can be realized after considering their Technology Readiness Level and System Readiness Level beforehand. Several suggestions on strains and hydroponics system improvement using existing biotechnological tools, Artificial Intelligence (AI) and nanobiotechnology in support of the CBE will be covered.

Microalgae-based biotechnological sequestration of carbon dioxide for net zero emissions

Excessive carbon dioxide (CO₂) emissions into the atmosphere have become a dire threat to the human race and environmental sustainability. The ultimate goal of net zero emissions requires combined efforts on CO₂ sequestration (natural sinks, biomass fixation, engineered approaches) and reduction in CO₂ emissions while delivering economic growth (CO₂ valorization for a circular carbon bioeconomy, CCE). We discuss microalgae-based CO₂ biosequestration, including flue gas cultivation, biotechnological approaches for enhanced CO₂ biosequestration, technological innovations for microalgal cultivation, and CO₂ valorization/biofuel productions. We highlight challenges to current practices and future perspectives with the goal of contributing to environmental sustainability, net zero emissions, and the CCE.

Life-cycle assessment of flue gas CO2 fixation from coal-fired power plant and coal chemical plant by microalgae

The technology of flue gas CO₂ fixation by microalgae is highly attractive in the era of CO₂ neutrality. However, CO₂ emission along the whole process has yet to be sufficiently evaluated. Here, a life-cycle assessment was performed to evaluate the energy conversion characteristics and environmental impacts of flue gas CO₂ fixation from coal-fired power plant (Case 1) and coal chemical plant (Case 2) by microalgae. The results show that total energy consumption and CO₂ gas emissions for Case 1 are 27.5-38.0 MJ/kg microalgae power (MP) and 5.7-7.7 kg CO₂ equiv/kg MP, respectively, which are lower than that for Case 2 (122.5-181.3 MJ/kg MP and 32.7-48.6 kg CO₂ equiv/kg MP). The CO₂ gas aeration rate and microalgae growth rate are the two most sensitive parameters for the energy conversion and net CO₂ emission. Therefore, increasing the CO₂ aeration efficiency and microalgae growth rate are key to advance the technology of flue gas CO₂ fixation by microalgae which will contribute to carbon naturality.

CO2 bio-mitigation using genetically modified algae and biofuel production towards a carbon net-zero society

CO₂ sequestration carried by biological methodologies shows enhanced potential and has the advantage that biomass produced from the captured CO₂ can be used for different applications. Bio-mitigation of carbons through a micro-algal system addresses a promising and feasible option. This review mostly focused on the role of algae, particular mechanisms, bioreactors in algae cultivation, and genetically modified algae in CO₂ fixation and energy generation systems. A combination of CO₂ bio-mitigation and biofuel production might deliver an extremely promising alternative to current CO₂ mitigation systems. Bio mitigation in which the excess carbon is captured and bio fixation which the carbon is captured by algae or autotrophs and used for producing biofuel. This review revealed that steps for biofuel production from algae include factors affecting, harvesting techniques, oil extraction and transesterification. This review helps environmentalists and researchers to assess the effect of algae-based biorefinery on the green environment.

Climate change-associated multifactorial stress combination: A present challenge for our ecosystems

Humans negatively influence Earth ecosystems and biodiversity causing global warming, climate change as well as man-made pollution. Recently, the number of different stress factors have increased, and when impacting simultaneously, the multiple stress conditions cause dramatic declines in plant and ecosystem health. Although much is known about how plants and ecosystems are affected by each individual stress, recent research efforts have diverted into how these biological systems respond to several of these stress conditions applied together. Studies of such "multifactorial stress combination" concept have reported a severe decrease in plant survival and microbiome biodiversity along the increasing number of factors in a consistent directional trend. In addition, these results are in concert with studies about how ecosystems and microbiota are affected by natural conditions imposed by climate change. Therefore, all this evidence should serve as an important warning in order to decrease pollutants, create strategies to deal with global warming, and increase the tolerance of plants to multiple stressful factors in combination. Here we review recent studies focused on the impact of abiotic stresses on plants, agrosystems and different ecosystems including forests and microecosystems. In addition, different strategies to mitigate the impact of climate change in ecosystems are discussed.

Recent Progress on Systems and Synthetic Biology of Diatoms for Improving Algal Productivity

Microalgae have drawn much attention for their potential applications as a sustainable source for developing bioactive compounds, functional foods, feeds, and biofuels. Diatoms, as one major group of microalgae with high yields and strong adaptability to the environment, have shown advantages in developing photosynthetic cell factories to produce value-added compounds, including heterologous bioactive products. However, the commercialization of diatoms has encountered several obstacles that limit the potential mass production, such as the limitation of algal productivity and low photosynthetic efficiency. In recent years, systems and synthetic biology have dramatically improved the efficiency of diatom cell factories. In this review, we discussed first the genome sequencing and genome-scale metabolic models (GEMs) of diatoms. Then, approaches to optimizing photosynthetic efficiency are introduced with a focus on the enhancement of biomass productivity in diatoms. We also reviewed genome engineering technologies, including CRISPR (clustered regularly interspaced short palindromic repeats) gene-editing to produce bioactive compounds in diatoms. Finally, we summarized the recent progress on the diatom cell factory for producing heterologous compounds through genome engineering to introduce foreign genes into host diatoms. This review also pinpointed the bottlenecks in algal engineering development and provided critical insights into the future direction of algal production.

Review of the structures and functions of algal photoreceptors to optimize bioproduct production with novel bioreactor designs for strain improvement

Microalgae are important renewable feedstock to produce biodiesel and high-value chemicals. Different wavelengths of light influence the growth and metabolic activities of algae. Recent research has identified the light-sensing proteins called photoreceptors that respond to blue or red light. Structural elucidations of algal photoreceptors have gained momentum over recent years. These include channelrhodopsins, PHOT proteins, animal-like cryptochromes, blue-light sensors utilizing flavin-adenine dinucleotide (BLUF) proteins. Pulsing light has also been investigated as a means to optimize energy inputs into bioreactors. This review summarizes the current structural and functional basis of photoreceptor modulation to optimize the growth, production of carotenoids and other high-value metabolites from microalgae. The review also encompasses novel photobioreactor designs that implement different light regimes including light wavelengths and time to optimize algal growth and desired metabolite profiles for high-value products. This article is protected by copyright. All rights reserved.

Fucoxanthin from marine microalgae: A promising bioactive compound for industrial production and food application

Fucoxanthin attracts increasing attentions due to its potential health benefits, which has been exploited in several food commodities. However, fucoxanthin available for industrial application is mainly derived from macroalgae, and is not yet sufficiently cost-effective compared with microalgae. This review focuses on the strategies to improve fucoxanthin productivity and approaches to reduce downstream costs in microalgal production. Here we comprehensively and critically discuss ways and methods to increase the cell growth rate and fucoxanthin content of marine microalgae, including strain screening, condition optimization, design of culture mode, metabolic and genetic engineering, and scale-up production of fucoxanthin. The approaches in downstream processes provide promising alternatives for fucoxanthin production from marine microalgae. Besides, this review summarizes fucoxanthin improvements in solubility and bioavailability by delivery system of emulsion, nanoparticle, and hydrogel, and discusses fucoxanthin metabolism with gut microbes. Fucoxanthin production from marine microalgae possesses numerous advantages in environmental sustainability and final profits to meet incremental global market demands of fucoxanthin. Strategies of adaptive evolution, multi-stage cultivation, and bioreactor improvements have tremendous potentials to improve economic viability of the production. Moreover, fucoxanthin is promising as the microbiota-targeted ingredient, and nanoparticles can protect fucoxanthin from external environmental factors for improving the solubility and bioavailability.

Biochemical and Morphological Changes Triggered by Nitrogen Stress in the Oleaginous Microalga Chlorella vulgaris

Oleaginous microalgae have been considered promising sources of biodiesel due to their high lipid content. Nitrogen limitation/starvation is one of the most prominent strategies to induce lipid accumulation in microalgae. Nonetheless, despite numerous studies, the mechanism underlying this approach is not well understood. The aim of this study was to investigate the effect of nitrogen limitation and starvation on biochemical and morphological changes in the microalga Chlorella vulgaris FACHB-1068, thereby obtaining the optimal nitrogen stress strategy for maximizing the lipid productivity of microalgal biomass. The results showed that nitrogen limitation (nitrate concentration < 21.66 mg/L) and starvation enhanced the lipid content but generally decreased the biomass productivity, pigment concentration, and protein content in algal cells. Comparatively, 3-day nitrogen starvation was found to be a more suitable strategy to produce lipid-rich biomass. It resulted in an increased biomass production and satisfactory lipid content of 266 mg/L and 31.33%, respectively. Besides, nitrogen starvation caused significant changes in cell morphology, with an increase in numbers and total size of lipid droplets and starch granules. Under nitrogen starvation, saturated fatty acids (C-16:0, C-20:0, and C-18:0) accounted for the majority of the total fatty acids (~80%), making C. vulgaris FACHB-1068 a potential feedstock for biodiesel production. Our work may contribute to a better understanding of the biochemical and morphological changes in microalgae under nitrogen stress. Besides, our work may provide valuable information on increasing the lipid productivity of oleaginous microalgae by regulating nitrogen supply.

Integrated metabolic tools reveal carbon alternative in Isochrysis zhangjiangensis for fucoxanthin improvement

This study explored the regulation of photosystem and central carbon metabolism in cell growth and fucoxanthin accumulation of Isochrysis zhangjiangensis via transcriptome analysis, targeted metabolite measurements, and flux balance analysis. High light promoted biomass accumulation but dramatically decreased fucoxanthin productivity. It suppressed the active photosystem and reduced chlorophyll content, but improved metabolic flux of Calvin-Benson-Bassham and tricarboxylic acid cycle for massive biomass accumulation. The CO₂ fixation was largely dependent on mitochondrial energy illustrated by the integrated metabolic tools. At a molecular level, glyceraldehyde-3-phosphate, acetyl-CoA, and pyruvate contents increased at exponential phase under high light, which tended to participate into fatty acid biosynthesis by the up-regulated ACCase. However, high light inhibited most genes involved in fucoxanthin biosynthesis and induced diadinoxanthin cycle to diatoxanthin form. Therefore, constant light at 100 μmol m^-2 s^-1 balancing biomass concentration and fucoxanthin content provided the highest fucoxanthin productivity at 3.06 mg L^-1 d^-1.

Improving microalgae for biotechnology - From genetics to synthetic biology - Moving forward but not there yet

Microalgae are a diverse group of photosynthetic organisms that can be exploited for the production of different compounds, ranging from crude biomass and biofuels to high value-added biochemicals and synthetic proteins. Traditionally, algal biotechnology relies on bioprospecting to identify new highly productive strains and more recently, on forward genetics to further enhance productivity. However, it has become clear that further improvements in algal productivity for biotechnology is impossible without combining traditional tools with the arising molecular genetics toolkit. We review recent advantages in developing high throughput screening methods, preparing genome-wide mutant libraries, and establishing genome editing techniques. We discuss how algae can be improved in terms of photosynthetic efficiency, biofuel and high value-added compound production. Finally, we critically evaluate developments over recent years and explore future potential in the field.

Chlorella vulgaris phycoremediation at low Cu+2 contents: Proteomic profiling of microalgal metabolism related to fatty acids and CO2 fixation

The aim of this work was to correlate metabolic changes with copper ions (Cu⁺²) bioremediation by microalgae C. vulgaris 097 CCMA-UFSCar at low Cu⁺² content. The metabolic effects include proteome changes related to fatty acid biosynthesis (value-added product) and carbon fixation (climate change mitigation). Cu⁺², even at low concentration, showed a significant negative impact on C. vulgaris growth. The microalgal bioremediation reached 100, 74, 38 and 26% for Cu⁺² content at 0.1; 0.3; 0.6 and 0.9 mg L^-1, respectively. Regarding proteomics, the numbers of proteins reduced (≈37%) from 581 proteins (control) to 369 proteins (0.9 mg of Cu⁺² L^-1) compared to control. The microalgal CO₂ fixation is strictly related to the Calvin cycle, particularly phase 1, in which ribulose bisphosphate carboxylase large chain (RuBisCO) produces two phosphoglycerate molecules from CO₂ and ribulose 1,5-bisphosphate. Then, phosphoglycerate can be metabolically reduced into glucose. When compared to control, the RuBisCO was underexpressed (≈50%). Similar changes in proteomic profiling of metabolism-related to fatty acid biosynthesis was observed. Nevertheless, no protein was found for the cultivation at 0.9 mg of Cu⁺² L^-1. Thus, the analysis of C. vulgaris proteomic data indicated that even at low concentration, Cu⁺² lead to drastic metabolic changes.

Adaptive laboratory evolution and reverse engineering enhances autotrophic growth in Pichia pastoris

Synthetic biology offers several routes for CO₂ conversion into biomass or bio-chemicals, helping to avoid unsustainable use of organic feedstocks, which negatively contribute to climate change. The use of well-known industrial organisms, such as the methylotrophic yeast Pichia pastoris (Komagataella phaffii), for the establishment of novel C1-based bioproduction platforms could wean biotechnology from feedstocks with alternative use in food production. Recently, the central carbon metabolism of P. pastoris was re-wired following a rational engineering approach, allowing the resulting strains to grow autotrophically with a μ_max of 0.008 h^-1, which was further improved to 0.018 h^-1 by adaptive laboratory evolution. Using reverse genetic engineering of single-nucleotide (SNPs) polymorphisms occurring in the genes encoding for phosphoribulokinase and nicotinic acid mononucleotide adenylyltransferase after evolution, we verified their influence on the improved autotrophic phenotypes. The reverse engineered SNPs lead to lower enzyme activities in putative branching point reactions and in reactions involved in energy balancing. Beyond this, we show how further evolution facilitates peroxisomal import and increases growth under autotrophic conditions. The engineered P. pastoris strains are a basis for the development of a platform technology, which uses CO₂ for production of value-added products, such as cellular biomass, technical enzymes and chemicals and which further avoids consumption of organic feedstocks with alternative use in food production. Further, the identification and verification of three pivotal steps may facilitate the integration of heterologous CBB cycles or similar pathways into heterotrophic organisms.

Transcriptome-Wide Gene Expression Plasticity in Stipa grandis in Response to Grazing Intensity Differences

Organisms have evolved effective and distinct adaptive strategies to survive. Stipa grandis is a representative species for studying the grazing effect on typical steppe plants in the Inner Mongolia Plateau. Although phenotypic (morphological and physiological) variations in S. grandis in response to long-term grazing have been identified, the molecular mechanisms underlying adaptations and plastic responses remain largely unknown. Here, we performed a transcriptomic analysis to investigate changes in gene expression of S. grandis under four different grazing intensities. As a result, a total of 2357 differentially expressed genes (DEGs) were identified among the tested grazing intensities, suggesting long-term grazing resulted in gene expression plasticity that affected diverse biological processes and metabolic pathways in S. grandis. DEGs were identified in RNA-Seq and qRT-PCR analyses that indicated the modulation of the Calvin–Benson cycle and photorespiration metabolic pathways. The key gene expression profiles encoding various proteins (e.g., ribulose-1,5-bisphosphate carboxylase/oxygenase, fructose-1,6-bisphosphate aldolase, glycolate oxidase, etc.) involved in these pathways suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of S. grandis. Our findings provide scientific clues for improving grassland use and protection and identifying important questions to address in future transcriptome studies.

Bio-conversion of CO2 into biofuels and other value-added chemicals via metabolic engineering

Carbon dioxide (CO₂) occurs naturally in the atmosphere as a trace gas, which is produced naturally as well as by anthropogenic activities. CO₂ is a readily available source of carbon that in principle can be used as a raw material for the synthesis of valuable products. The autotrophic organisms are naturally equipped to convert CO₂ into biomass by obtaining energy from sunlight or inorganic electron donors. This autotrophic CO₂ fixation has been exploited in biotechnology, and microbial cell factories have been metabolically engineered to convert CO₂ into biofuels and other value-added bio-based chemicals. A variety of metabolic engineering efforts for CO₂ fixation ranging from basic copy, paste, and fine-tuning approaches to engineering and testing of novel synthetic CO₂ fixing pathways have been demonstrated. In this paper, we review the current advances and innovations in metabolic engineering for bio-conversion of CO₂ into bio biofuels and other value-added bio-based chemicals.

Recent Advances in Carbon Dioxide Conversion: A Circular Bioeconomy Perspective

Managing the concentration of atmospheric CO2 requires a multifaceted engineering strategy, which remains a highly challenging task. Reducing atmospheric CO2 (CO2R) by converting it to value-added chemicals in a carbon neutral footprint manner must be the ultimate goal. The latest progress in CO2R through either abiotic (artificial catalysts) or biotic (natural enzymes) processes is reviewed herein. Abiotic CO2R can be conducted in the aqueous phase that usually leads to the formation of a mixture of CO, formic acid, and hydrogen. By contrast, a wide spectrum of hydrocarbon species is often observed by abiotic CO2R in the gaseous phase. On the other hand, biotic CO2R is often conducted in the aqueous phase and a wide spectrum of value-added chemicals are obtained. Key to the success of the abiotic process is understanding the surface chemistry of catalysts, which significantly governs the reactivity and selectivity of CO2R. However, in biotic CO2R, operation conditions and reactor design are crucial to reaching a neutral carbon footprint. Future research needs to look toward neutral or even negative carbon footprint CO2R processes. Having a deep insight into the scientific and technological aspect of both abiotic and biotic CO2R would advance in designing efficient catalysts and microalgae farming systems. Integrating the abiotic and biotic CO2R such as microbial fuel cells further diversifies the spectrum of CO2R.

High-throughput insertional mutagenesis reveals novel targets for enhancing lipid accumulation in Nannochloropsis oceanica

The microalga Nannochloropsis oceanica is considered a promising platform for the sustainable production of high-value lipids and biofuel feedstocks. However, current lipid yields of N. oceanica are too low for economic feasibility. Gaining fundamental insights into the lipid metabolism of N. oceanica could open up various possibilities for the optimization of this species through genetic engineering. Therefore, the aim of this study was to discover novel genes associated with an elevated neutral lipid content. We constructed an insertional mutagenesis library of N. oceanica, selected high lipid mutants by five rounds of fluorescence-activated cell sorting, and identified disrupted genes using a novel implementation of a rapid genotyping procedure. One particularly promising mutant (HLM23) was disrupted in a putative APETALA2-like transcription factor gene. HLM23 showed a 40%-increased neutral lipid content, increased photosynthetic performance, and no growth impairment. Furthermore, transcriptome analysis revealed an upregulation of genes related to plastidial fatty acid biosynthesis, glycolysis and the Calvin-Benson-Bassham cycle in HLM23. Insights gained in this work can be used in future genetic engineering strategies for increased lipid productivity of Nannochloropsis.

Microalgal-Bacterial Consortia as Future Prospect in Wastewater Bioremediation, Environmental Management and Bioenergy Production

In the recent years, microalgae have captured researchers' attention as the alternative feedstock for various bioenergy production such as biodiesel, biohydrogen, and bioethanol. Cultivating microalgae in wastewaters to simultaneously bioremediate the nutrient-rich wastewater and maintain a high biomass yield is a more economical and environmentally friendly approach. The incorporation of algal-bacterial interaction reveals the mutual relationship of microorganisms where algae are primary producers of organic compounds from CO₂, and heterotrophic bacteria are secondary consumers decomposing the organic compounds produced from algae. This review would provide an insight on the challenges and future development of algal-bacterial consortium and its contribution in promoting a sustainable route to greener industry. It is believed that microalgal-bacterial consortia will be implemented in the near-future for sub-sequential treatment of wastewater bioremediation, bioenergy production and CO₂ fixation, promoting sustainability and making extraordinary advancement in life sciences sectors.