Recent Developments on Genetic Engineering of Microalgae for Biofuels and Bio‐Based Chemicals

Antibiotic occurrence, environmental risks, and their removal from aquatic environments using microalgae: Advances and future perspectives

Antibiotic pollution has caused a continuous increase in the development of antibiotic-resistant bacteria and antibiotic-resistant genes (ARGs) in aquatic environments worldwide. Algae-based bioremediation technology is a promising eco-friendly means to remove antibiotics and highly resistant ARGs, and the generated biomass can be utilized to produce value-added products of industrial significance. This review discussed the prevalence of antibiotics and ARGs in aquatic environments and their environmental risks to non-target organisms. The potential of various microalgal species for antibiotic and ARG removal, their mechanisms, strategies for enhanced removal, and future directions were reviewed. Antibiotics can be degraded into non-toxic compounds in microalgal cells through the action of extracellular polymeric substances, glutathione-S-transferase, and cytochrome P450; however, antibiotic stress can alter microalgal gene expression and growth. This review also deciphered the effect of antibiotic stress on microalgal physiology, biomass production, and biochemical composition that can impact their commercial applications.

Harnessing genetic engineering to drive economic bioproduct production in algae

Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.

Cascading effects of trace metals enrichment on phytoplankton communities of the River Ganga in South Asia

Globally freshwater ecosystems and associated biota including phytoplankton communities are at extreme risk from trace metal pollution originating from geogenic as well as from anthropogenic sources such as release of untreated industrial effluents. In the present study influence of iron- and arsenic-enrichments on structure and metabolism of phytoplankton communities of River Ganga, one of the largest rivers of South Asia, was assessed under laboratory-based microcosm experiments. Surface water samples were collected and subsequently enriched with higher than recommended concentrations of iron (10 mg/L) and arsenic (10 μg/L). The set-up comprised of nine containers of 25 L volume with three containers each for iron- and arsenic-enrichment and was maintained for 30 days. Trace metal enrichment rapidly changed the phytoplankton community structure and chemistry of nutrients uptake. Iron-enrichment prompted diatom blooms comprising of Thalassiosira, succeeded by green algae Coelastrum. Arsenic-enrichment maintained cyanobacteria for longer time-spans compared to the control and iron-enriched containers but significantly lesser abundance of diatoms. Variations in community composition was also reflected in nutrient uptake rates with silicate release in the arsenic-enriched containers at the end of the experiment. Changes in macronutrient dynamics also altered genus growth rates wherein both iron- and arsenic appeared to lower the death rate of Thalassosira but stimulated growth of other genera including Skeletonema and Pandorina. Iron appeared to influence lesser number of genera compared to arsenic which altered growth rates of both diatoms and green algae. This consequently influenced the gross primary productivity values which lowered both in the iron- and arsenic-enriched containers compared to the control owing to decrease in phytoplankton diversity. Iron appeared to drive phytoplankton communities toward a less general and more specialized composition with high abundance of selective species comprising of small diatoms such as Thalassiosira, whereas arsenic appears to select for green algal enrichment in freshwater ecosystems.

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.

Reconstruction of a Genome-Scale Metabolic Model of Scenedesmus obliquus and Its Application for Lipid Production under Three Trophic Modes

Green microalgae have emerged as beneficial feedstocks for biofuel production. A systems-level understanding of the biochemical network is needed to harness the microalgal metabolic capacity for bioproduction. Genome-scale metabolic modeling (GEM) showed immense potential in rational metabolic engineering, utilizing biochemical flux distribution analysis. Here, we report the first GEM for the green microalga, Scenedesmus obliquus (iAR632), a promising biodiesel feedstock with high lipid-storing capability. iAR632 comprises 1467 reactions, 734 metabolites, and 632 genes distributed among 7 compartments. The model was optimized under three different trophic modes of microalgal cultivation, i.e., autotrophy, mixotrophy, and heterotrophy. The robustness of the reconstructed network was confirmed by analyzing its sensitivity to the biomass components. Pathway-level flux profiles were analyzed, and significant flux space expansion was noticed majorly in reactions associated with lipid biosynthesis. In agreement with the experimental observation, iAR632 predicted about 3.8-fold increased biomass and almost 4-fold higher lipid under mixotrophy than the other trophic modes. Thus, the assessment of the condition-specific metabolic flux distribution of iAR632 suggested that mixotrophy is the preferred cultivation condition for improved microalgal growth and lipid production. Overall, the reconstructed GEM and subsequent analyses will provide a systematic framework for developing model-driven strategies to improve microalgal bioproduction.

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.

Harnessing the advances of genetic engineering in microalgae for the production of cannabinoids

Cannabis is widely recognized as a medicinal plant owing to bioactive cannabinoids. However, it is still considered a narcotic plant, making it hard to be accessed. Since the biosynthetic pathway of cannabinoids is disclosed, biotechnological methods can be employed to produce cannabinoids in heterologous systems. This would pave the way toward biosynthesizing any cannabinoid compound of interest, especially minor substances that are less produced by a plant but have a high medicinal value. In this context, microalgae have attracted increasing scientific interest given their unique potential for biopharmaceutical production. In the present review, the current knowledge on cannabinoid production in different hosts is summarized and the biotechnological potential of microalgae as an emerging platform for synthetic production is put in perspective. A critical survey of genetic requirements and various transformation approaches are also discussed.

Antimicrobial activity of the Flo peptide produced in Scenedesmus acutus and Nannochloropsis oculata

The continuous increase of bacterial pathogen resistance to conventional antibiotics has challenged the research community to develop new antimicrobial strategies. Antimicrobial peptides (AMP) are a promising alternative to combat multidrug-resistant strains compared to conventional antibiotics because of their biocompatibility. In the present study, the Flo peptide, an AMP from the Moringa oleifera tree, was expressed in the chloroplast of the microalgae Nannochloropsis oculata and Scenedesmus acutus. The transgene insertion was verified by PCR amplification, and the homoplasmy was corroborated in spectinomycin-resistant lines. The identification and quantification of the peptide were performed using ELISA. The antimicrobial activity was studied against the Gram-negative Escherichia coli (ATCC 25,922) and Klebsiella pneumoniae (ATCC 700,603). The inflammatory response of the total soluble proteins of transplastomic N. oculata was assessed by measuring secretion of the cytokines IL-6, IL-10, and alpha-tumor necrosis (TNF-α), and cytotoxicity was assessed. These results provide a potential strategy to produce the Flo peptide in microalgae with antibacterial activities.

Screening of antibiotics to obtain axenic cell cultures of a marine microalga Chrysotila roscoffensis

Due to high growth rate, outstanding abiotic stress tolerance, and rich value-added substances, Chrysotila roscoffensis, belonging to the phylum of Haptophyta, can be considered as a versatile resource for industrial exploitation of bioactive compounds. However, the application potential of C. roscoffensis has drawn attention until just recently, and the understanding related to the biological properties of this species is still scarce. For example, the sensitivities of C. roscoffensis to antibiotics, which is essential for the verification of heterotrophic capacity and the establishment of efficient genetic manipulation system is still unavailable. Aiming to provide fundamental information for future exploitation, the sensitivities of C. roscoffensis to nine types of antibiotics were tested in this study. The results demonstrated that C. roscoffensis exhibited relatively high resistances to ampicillin, kanamycin, streptomycin, gentamicin, and geneticin, while was sensitive to bleomycin, hygromycin B, paromomycin, and chloramphenicol. Using the former five types of antibiotics, a bacteria removal strategy was established tentatively. Finally, the axenicity of treated C. roscoffensis was confirmed based on a multi-strategy method including solid plate, 16S rDNA amplification, and nuclear acid staining. This report can provide valuable information for the development of optimal selection markers, which are meaningful for more extensive transgenic studies in C. roscoffensis. Moreover, our study also paves the way for the establishment of heterotrophic/mixotrophic cultivation modes of C. roscoffensis.

Role of secondary metabolites in distressed microalgae

Proficient photosynthetic microalgae/cyanobacteria produce a remarkable amount of various biomolecules. Secondary metabolites (SM) represent high value products for global biotrend application. Production improvement can be achieved by nutritional, environmental, and physiological stress as a first line tools for their stimulation. In recent decade, an increasing interest in algal stress biology and omics techniques have deepened knowledge in this area. However, deep understanding and connection of specific stress elucidator are missing. Hence, the present review summarizes recent evidence with an emphasis on the carotenoids, phenolic, and less-discussed compounds (glycerol, proline, mycosporins-like amino acids). Even when they are synthesized at very low concentrations, it highlights the need to expand knowledge in this area using genome-editing tools and omics approaches.

Exploitation of renewable energy sources for water desalination using biological tools

The emerging impacts of climate change and the growing world population are driving the demand for more food resources and creating an urgent need for new water resources. About 93% of Earth's surface is made up of water bodies, mainly oceans. Seawater attracted a lot of attention in order to be used as a sustainable source of usable water. However, an essential step in harnessing this source of water is desalination. Utilizing renewable sources of energy, biology offers several tools for removal of salts. This article for the first time reviews all currently available biological water desalination tools and compares their efficiency with industrial systems. Bacteria are employed as electrical power generators to provide the energy needed for desalination in microbial desalination cells. Its salt removal efficiency varied from 0.8 to 30 g/L/d. Many strains of algal cells can grow in high concentrations of salts, adsorb and accumulate it inside the cell, and therefore could be used without prior treatment for seawater desalination. This biological tool can yield salt removal efficiency of 0.4-5 g/L/d. Biopolymers are also used for treatment of seawater through enhancing water evaporation as a component of solar steam generators. Despite significant advances in biological water desalination, further modifications and improvements are still needed to make its use sustainable and cost-effective.

Novel insights into indoor air purification capability of microalgae: characterization using multiple air quality parameters and comparison with common methods

Indoor air purification received more attention recently. In this study, the effects of six common indoor ornamental plants (Epripremnum aureum, Chlorphytum comosum, Aloe vera, Sedum sediforme, Cereus cv. Fairy Castle, and Sedum adolphii) and three kinds of microalgae (Chlorella sp. HQ, Scenedesmus sp. LX1, and C. vulgaris) on the removal of four types of air pollutants (particulate matters less than 2.5 (PM_2.5) and 10 μm (PM₁₀) in size, formaldehyde (HCHO) and total volatile organic compounds (VOC_S)) in test chamber compared with common physical purification methods (high efficiency particulate air filter and nano activated carbon absorption) were investigated. Their effects on oxygen, carbon dioxide, and relative humidity were also evaluated. The results showed that microalgae, especially C. vulgaris, was more suitable for removing PM_2.5 and PM₁₀, and the removal rates were 55.42 ± 25.77% and 45.76 ± 5.32%, respectively. The removal rates of HCHO and VOCs by all three kings of microalgae could reach 100%. Part of ornamental plants took a longer time to achieve 100% removal of HCHO and VOCs. Physical methods were weaker than ornamental plants and microalgae in terms of increased relative humidity and O₂ content. In general, microalgae, especially C. vulgaris could purify indoor air pollutants more efficiently. The above studies provided data and theoretical support for the purification of indoor air pollutants by microalgae.

Genetic engineering to enhance microalgal-based produced water treatment with emphasis on CRISPR/Cas9: A review

In recent years, the increased demand for and regional variability of available water resources, along with sustainable water supply planning, have driven interest in the reuse of produced water. Reusing produced water can provide important economic, social, and environmental benefits, particularly in water-scarce regions. Therefore, efficient wastewater treatment is a crucial step prior to reuse to meet the requirements for use within the oil and gas industry or by external users. Bioremediation using microalgae has received increased interest as a method for produced water treatment for removing not only major contaminants such as nitrogen and phosphorus, but also heavy metals and hydrocarbons. Some research publications reported nearly 100% removal of total hydrocarbons, total nitrogen, ammonium nitrogen, and iron when using microalgae to treat produced water. Enhancing microalgal removal efficiency as well as growth rate, in the presence of such relevant contaminants is of great interest to many industries to further optimize the process. One novel approach to further enhancing algal capabilities and phytoremediation of wastewater is genetic modification. A comprehensive description of using genetically engineered microalgae for wastewater bioremediation is discussed in this review. This article also reviews random and targeted mutations as a method to alter microalgal traits to produce strains capable of tolerating various stressors related to wastewater. Other methods of genetic engineering are discussed, with sympathy for CRISPR/Cas9 technology. This is accompanied by the opportunities, as well as the challenges of using genetically engineered microalgae for this purpose.

Perspective: Multiomics and Machine Learning Help Unleash the Alternative Food Potential of Microalgae

Food security has become a pressing issue in the modern world. The ever-increasing world population, ongoing COVID-19 pandemic, and political conflicts together with climate change issues make the problem very challenging. Therefore, fundamental changes to the current food system and new sources of alternative food are required. Recently, the exploration of alternative food sources has been supported by numerous governmental and research organizations, as well as by small and large commercial ventures. Microalgae are gaining momentum as an effective source of alternative laboratory-based nutritional proteins as they are easy to grow under variable environmental conditions, with the added advantage of absorbing carbon dioxide. Despite their attractiveness, the utilization of microalgae faces several practical limitations. Here, we discuss both the potential and challenges of microalgae in food sustainability and their possible long-term contribution to the circular economy of converting food waste into feed via modern methods. We also argue that systems biology and artificial intelligence can play a role in overcoming some of the challenges and limitations; through data-guided metabolic flux optimization, and by systematically increasing the growth of the microalgae strains without negative outcomes, such as toxicity. This requires microalgae databases rich in omics data and further developments on its mining and analytics methods.

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.

Fourth generation biofuel from genetically modified algal biomass for bioeconomic development

Biofuels from microalgae have promising potential for a sustainable bioeconomy. Algal strains' oil content and biomass yield are the most influential cost drivers in the fourth generation biofuel (FGB) production. Genetic modification is the key to improving oil accumulation and biomass yield, consequently developing the bioeconomy. This paper discusses current practices, new insights, and emerging trends in genetic modification and their bioeconomic impact on FGB production. It was demonstrated that enhancing the oil and biomass yield could significantly improve the probability of economic success and the net present value of the FGB production process. The techno-economic and socioeconomic burden of using genetically modified (GM) strains and the preventive control strategies on the bioeconomy of FGB production is reviewed. It is shown that the fully lined open raceway pond could cost up to 25% more than unlined ponds. The cost of a plastic hoop air-supported greenhouse covering cultivation ponds is estimated to be US 60,000$ /ha. The competitiveness and profitability of large-scale cultivation of GM biomass are significantly locked to techno-economic and socioeconomic drivers. Nonetheless, it necessitates further research and careful long-term follow-up studies to understand the mechanism that affects these parameters the most.

Microalgal Carotenoids: Therapeutic Application and Latest Approaches to Enhance the Production

Microalgae are microscopic photosynthetic organisms frequently found in fresh and marine water ecosystems. Various microalgal species have been considered a reservoir of diverse health-value products, including vitamins, proteins, lipids, and polysaccharides, and are broadly utilized as food and for the treatment of human ailments such as cancer, cardiovascular diseases, allergies, and immunodeficiency. Microalgae-derived carotenoids are the type of accessory pigment that possess light-absorbing potential and play a significant role in metabolic functions. To date, nearly a thousand carotenoids have been reported, but a very less number of microalgae have been used for the commercial production of carotenoids. This review article briefly discussed the carotenoids of microalgal origin and their therapeutic application. In addition, we have briefly compiled the optimization of culture parameters used to enhance microalgal carotenoid production. In addition, the latest biotechnological approaches used to improve the yields of carotenoid has also been discussed.

Recent advancements in astaxanthin production from microalgae: A review

Microalgae have emerged as the best source of high-value astaxanthin producers. Algal astaxanthin possesses numerous bioactivities hence the rising demand for several health applications and is broadly used in pharmaceuticals, aquaculture, health foods, cosmetics, etc. Among several low-priced synthetic astaxanthin, natural astaxanthin is still irreplaceable for human consumption and food-additive uses. This review highlights the recent development in production enhancement and cost-effective extraction techniques that may apply to large-scale astaxanthin biorefinery. Primarily, the biosynthetic pathway of astaxanthin is elaborated with the key enzymes involved in the metabolic process. Moreover, discussed the latest astaxanthin enhancement strategies mainly including chemicals as product inducers and byproducts inhibitors. Later, various physical, chemical, and biological cell disruption methods are compared for cell disruption efficiency, and astaxanthin extractability. The aim of this review is to provide a comprehensive review of advancements in astaxanthin research covering scalable upstream and downstream astaxanthin bioproduction aspects.

Recent Progress on Carotenoids Production from Microalgae: A review

The color of fruits and green vegetables is attributed to a pigment known as carotenoids. On the basis of presence and absence of oxygen, carotenoids are divided into two categories; carotenes which do not contain oxygen and xanthophylls which are oxygen carrier. Carotenoids are not only good anti-oxidant agents; they also exhibit anti-tumor properties. The structure of carotenoids consists of eight isoprene units, which forms a chain consisting of conjugated double bonds. The presence of conjugated double bond in carotenoids neutralize free radicals by accepting electrons from them. Till now, most of the carotenoids commercially available are produced chemically however, microalgae are a good source of carotenoids. Microalgae can produce the carotenoids in abundance using two-stage cultivation strategies. In first phase, microalgae are given with optimal growth conditions for maximum production of biomass, on the other hand, keeping the second phase for the storage of lipids or carotenoids in unfavorable conditions. The production of carotenoids in two-stage approach is increased by many times than the conventional single phase cultivation method. Carotenoids have many industrial applications.

Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections

Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.

A review on unit operations, challenges, opportunities, and strategies to improve algal based biodiesel and biorefinery

Globally, the demand for energy is increasing with an emphasis on green fuels for a sustainable future. As the urge for alternative fuels is accelerating, microalgae have emerged as a promising source that can not only produce high lipid but many other platform chemicals. Moreover, it is a better alternative in comparison to conventional feedstock due to yearlong easy and mass cultivation, carbon fixation, and value-added products extraction. To date, numerous studies have been done to elucidate these organisms for large-scale fuel production. However, enhancing the lipid synthesis rate and reducing the production cost still remain a major bottleneck for its economic viability. Therefore, this study compiles information on algae-based biodiesel production with an emphasis on its unit operations from strain selection to biofuel production. Additionally, strategies to enhance lipid accumulation by incorporating genetic, and metabolic engineering and the use of leftover biomass for harnessing bio-products have been discussed. Besides, implementing a biorefinery for extracting oil followed by utilizing leftover biomass to generate value-added products such as nanoparticles, biofertilizers, biochar, and biopharmaceuticals has also been discussed.

Two Foreign Antimicrobial Peptides Expressed in the Chloroplast of Porphyridium purpureum Possessed Antibacterial Properties

To solve the problem of antibiotic abuse in aquaculture and to utilize the application potential of antimicrobial peptides (AMPs), a chloroplast transformation system of Porphyridium purpureum was successfully constructed for effectively expressing two exogenous AMPs. The endogenous fragments of 16S rDNA/trnA-23S rDNA were used as flanking fragments for the homologous recombination in the chloroplast genome. Two AMPs encoded by the transformation vector were controlled by the native promoter psbB in a polycistron. The plasmids were transferred into P. purpureum via particle bombardment and the transformation vectors were screened using phosphinothricin (bar), a dominant selection marker under the control of the psbA promoter. Subsequently, in the positive transformed colonies, the exogenous fragments were found to be inserted in the flanking fragments directionally as expected and two foreign AMPs were successfully obtained. Finally, two exogenous peptides with antibacterial properties were obtained from the transformed strain. The two AMPs expressed by the transformed strain were shown to have similar inhibitory effects to antibiotics by inhibition tests. This suggested that AMPs can be introduced into aquaculture using baited microalgae, providing new ideas and ways to solve a series of aquaculture diseases caused by bacteria.

Random Mutagenesis as a Promising Tool for Microalgal Strain Improvement towards Industrial Production

Microalgae have become a promising novel and sustainable feedstock for meeting the rising demand for food and feed. However, microalgae-based products are currently hindered by high production costs. One major reason for this is that commonly cultivated wildtype strains do not possess the robustness and productivity required for successful industrial production. Several strain improvement technologies have been developed towards creating more stress tolerant and productive strains. While classical methods of forward genetics have been extensively used to determine gene function of randomly generated mutants, reverse genetics has been explored to generate specific mutations and target phenotypes. Site-directed mutagenesis can be accomplished by employing different gene editing tools, which enable the generation of tailor-made genotypes. Nevertheless, strategies promoting the selection of randomly generated mutants avoid the introduction of foreign genetic material. In this paper, we review different microalgal strain improvement approaches and their applications, with a primary focus on random mutagenesis. Current challenges hampering strain improvement, selection, and commercialization will be discussed. The combination of these approaches with high-throughput technologies, such as fluorescence-activated cell sorting, as tools to select the most promising mutants, will also be discussed.

Biodiversity risk assessment of genetically modified Chaetoceros gracilis for outdoor cultivation

A genetically modified (GM) strain of the diatom Chaetoceros gracilis expressing the phosphite dehydrogenase gene (ptxD), which is a useful gene both for the biological containment and the avoidance of microbial contamination, was characterized to estimate the risk against the biodiversity by laboratory experiments. GM strain could grow in the medium containing phosphite as a sole source of phosphorus, while its general characteristics such as growth, salt tolerance, heat and dehydration resistance in the normal phosphate-containing medium were equivalent to those of wild type (WT) strain. The increase in potential toxicity of GM strain against plant, crustacean, fish and mammal was also disproved. The dispersal ability of WT strain cultured in an outdoor raceway pond was investigated for 28 days by detecting the psb31 gene in vessels, settled at variable distances (between 5 and 60 m) from the pond. The diatom was detected only in one vessel placed 5 m apart. To estimate the influence on the environment, WT and GM strains were inoculated into freshwater, seawater and soil. The influence on the microbiome in those samples was assessed by 16S rRNA gene amplicon sequencing, in addition to the analysis of the survivability of those strains in the freshwater and the seawater. The results indicated that the effect to the microbiome and the survivability were comparable between WT and GM strains. All results showed that the introduction of the ptxD gene into the diatom had a low risk on biodiversity.

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.

Multi-omics approaches and genetic engineering of metabolism for improved biorefinery and wastewater treatment in microalgae

Microalgae, a group of photosynthetic microorganisms rich in diverse and novel bioactive metabolites, have been explored for the production of biofuels, high value-added compounds as food and feeds, and pharmaceutical chemicals as agents with therapeutic benefits. This article reviews the development of omics resources and genetic engineering techniques including gene transformation methodologies, mutagenesis, and genome-editing tools in microalgae biorefinery and wastewater treatment. The introduction of these enlisted techniques has simplified the understanding of complex metabolic pathways undergoing microalgal cells. The multiomics approach of the integrated omics datasets, big data analysis, and machine learning for the discovery of objective traits and genes responsible for metabolic pathways was reviewed. Recent advances and limitations of multiomics analysis and genetic bioengineering technology to facilitate the improvement of microalgae as the dual role of wastewater treatment and biorefinery feedstock production are discussed. This article is protected by copyright. All rights reserved.

Bioprospecting microbial hosts to valorize lignocellulose biomass - Environmental perspectives and value-added bioproducts

Current biorefinery approaches comprehend diverse biomass feedstocks and various conversion techniques to produce a variety of high-value biochemicals and biofuels. Lignocellulose is among the most abundant, bio-renewable, and sustainable bioresources on earth. It is regarded as a prodigious alternative raw feedstock to produce a large number of chemicals and biofuels. Producing biofuels and platform chemicals from lignocellulosic biomasses represent advantages in terms of energy and environmental perspectives. Lignocellulose is a main structural constituent of non-woody and woody plants consisting of lignin, cellulose, and hemicellulose. Efficient exploitation of all these components is likely to play a considerable contribution to the economic viability of the processes since lignocellulosic biomass often necessitate pretreatment for liberating fermentable sugars and added value products that might serve as feedstocks for microbial strains to produce biofuels and biochemicals. Developing robust microbial culture and advancements in metabolic engineering approaches might lead to the rapid construction of cell factories for the effective biotechnological transformation of biomass feedstocks to produce biorefinery products. In this comprehensive review, we discuss the recent progress in the valorization of agro-industrial wastes as prospective microbial feedstocks to produce a spectrum of high-value products, such as microbial pigments, biopolymers, industrial biocatalysts, biofuels, biologically active compounds, bioplastics, biosurfactants, and biocontrol agents with therapeutic and industrial potentialities. Lignocellulosic biomass architecture, compositional aspects, revalorization, and pretreatment strategies are outlined for efficient conversion of lignocellulosic biomass. Moreover, metabolic engineering approaches are briefly highlighted to develop cell factories to make the lignocellulose biorefinery platforms appealing.

Development of the "Applied Proteomics" Concept for Biotechnology Applications in Microalgae: Example of the Proteome Data in Nannochloropsis gaditana

Most of the marine ecosystems on our planet are still unknown. Among these ecosystems, microalgae act as a baseline due to their role as primary producers. The estimated millions of species of these microorganisms represent an almost infinite source of potentially active biocomponents offering unlimited biotechnology applications. This review considers current research in microalgae using the "omics" approach, which today is probably the most important biotechnology tool. These techniques enable us to obtain a large volume of data from a single experiment. The specific focus of this review is proteomics as a technique capable of generating a large volume of interesting information in a single proteomics assay, and particularly the concept of applied proteomics. As an example, this concept has been applied to the study of Nannochloropsis gaditana, in which proteomics data generated are transformed into information of high commercial value by identifying proteins with direct applications in the biomedical and agri-food fields, such as the protein designated UCA01 which presents antitumor activity, obtained from N. gaditana.

Advances in production of bioplastics by microalgae using food waste hydrolysate and wastewater: A review

Microalgae have emerged as an effective dual strategy for bio-valorisation of food processing wastewater and food waste hydrolysate which favours microalgae cultivation into producing value-added by products mainly lipids, carbohydrates, and proteins to the advantages of bioplastic production. Moreover, various microalgae have successfully removed high amount of organic pollutants from food processing wastewater prior discharging into the environment. Innovation of microalgae cultivating in food processing wastewater greatly reduced the cost of wastewater treatment compared to conventional approach in terms of lower carbon emissions, energy consumption, and chemical usage while producing microalgae biomass which can benefit low-cost fertilizer and bioplastic applications. The study on several microalgae species has all successfully grown on food waste hydrolysates showing high exponential growth rate and biomass production rich in proteins, lipids, carbohydrates, and fatty acids. Multiple techniques have been implemented for the extraction of food wastes to be incorporate into the bioplastic production.

CRISPRa/i with Adaptive Single Guide Assisted Regulation DNA (ASGARD) mediated control of Chlorella sorokiniana to enhance lipid and protein production

Chlorella species are indispensable microalgae for biorefinery but are hardly in DNA manipulation due to the high guanine-cytosine (GC) contents of DNA. In this study, we established a new approach via 20 guanines for sgRNA design, which is annotated as "Adaptive Single Guide Assisted Regulation DNA (ASGARD)" and coupling with CRISPR interference associated dCas9 system to overcome the difficulties. At first, C. sorokiniana was predominate as its faster growth rate when compared to C. vulgaris and C. variabilis in the culture using Tris-acetate-phosphate (TAP) medium. Among all the genetic transformants, gene regulation via CRISPRa-VP64 (CRISPRa) enhanced the protein contents up to 60% (w/w) of dry cell weight, where the highest concentration was 570 mg L^-1 . Meanwhile, CRISPRi-KRAB (CRISPRi) with ASGARD increased protein content to 65% and lipid formed in the range of 150-250 mg L^-1 . From the transcriptome analysis, we deciphered 468 genes down-regulated and 313 genes up-regulated via CRISPRi, while less difference existed in CRISPRa. This novel design and technology reveal a high potential of gene-regulating approach to other species for the biorefinery and bio-industry.

Reduced cytotoxicity of polyethyleneimine by covalent modification of antioxidant and its application to microalgal transformation

The conversion of carbon dioxide into valuable chemicals is an effective strategy for combating augmented concentrations of carbon dioxide in the environment. Microalgae photosynthetically produce valuable chemicals that are used as biofuels, sources for industrial materials, medicinal leads, and food additives. Thus, improvements in microalgal technology via genetic engineering may prove to be promising for the tailored production of novel metabolites. For the transformation of microalgae, nucleic acids such as plasmid DNA (pDNA) are delivered into the cells using physical and mechanical techniques, such as electroporation, bombardment with DNA-coated microprojectiles, and vortexing with glass beads. However, owing to the electrostatic repulsion between negatively charged cell walls and nucleic acids, the delivery of nucleic acids into the microalgal cells is challenging. To solve this issue, in this study, we investigated microalgal transformation via electroporation using polyplexes with linear polyethyleneimine (LPEI) and pDNA. However, the high toxicity of LPEI decreased the transformation efficiency in Chlamydomonas reinhardtii cells. We revealed that the toxicity of LPEI was due to oxidative stress resulting from the cellular uptake of LPEI. To suppress the toxicity of LPEI, an antioxidant, 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO), was covalently conjugated with LPEI; the conjugate was named as TEMPO-LPEI. Interestingly, with a cellular uptake tendency similar to that of LPEI, TEMPO-LPEI dramatically decreased oxidative stress and cytotoxicity. Electroporation using polyplexes of TEMPO-LPEI and pDNA enhanced the transformation efficiency, compared to those treated with bare pDNA and polyplexes of LPEI/pDNA. This result indicates that polycations conjugated with antioxidants could be useful in facilitating microalgal transformation.

Microalgae for high-value products: A way towards green nutraceutical and pharmaceutical compounds

Microalgae is a renewable bioresource with the potential to replace the conventional fossil-based industrial production of organic chemicals and pharmaceuticals. Moreover, the microalgal biomass contains carotenoids, vitamins, and other biomolecules that are widely used as food supplements. However, the microalgal biomass production, their composition variations, energy-intensive harvesting methods, optimized bio-refinery routes, and lack of techno-economic analysis are the major bottleneck for the life-sized commercialization of this nascent bio-industry. This review discusses the microalgae-derived key bioactive compounds and their applications in different sectors for human health. Furthermore, this review proposes advanced strategies to enhance the productivity of bioactive compounds and highlight the key challenges associated with a safety issue for use of microalgae biomass. It also provides a detailed global scenario and market demand of microalgal bioproducts. In conclusion, this review will provide the concept of microalgal biorefinery to produce bioactive compounds at industrial scale platform for their application in the nutraceutical and pharmaceutical sector considering their current and future market trends.

Advances in microalgal cell wall polysaccharides: a review focused on structure, production, and biological application

Microalgae have been shown to be useful in several biotechnological fields due to their feasible cultivation and high-value biomolecules production. Several substances of interest produced by microalgae, such as: proteins, lipids, and natural colorants, have already been explored. Based on the continuing demand for new natural molecules, microalgae could also be a valuable source of polysaccharides. Polysaccharides are extremely important in aquaculture, cosmetics, pharmaceutical, and food industries, and have great economic impact worldwide. Despite this, reviews on microalgal polysaccharide production, biological activity, and chemical structure are not abundant. Moreover, techniques of microalgal cultivation, coupled with carbohydrate production, need to be clarified in order to develop forward-looking technologies. The present review provides an overview of the main advances in microalgal cell wall polysaccharide production, as well as their associated potential biological applications and chemical structure. Several studies on future prospects, related to microalgae are presented, highlighting the key challenges in microalgal polysaccharide production.

Strategies for enhancing terpenoids accumulation in microalgae

Terpenoids represent one of the largest class of chemicals in nature, which play important roles in food and pharmaceutical fields due to diverse biological and pharmacological activities. Microorganisms are recognized as a promising source of terpenoids due to its short growth cycle and sustainability. Importantly, microalgae can fix inorganic carbon through photosynthesis for the growth of themselves and the biosynthesis of various terpenoids. Moreover, microalgae possess effective biosynthesis pathways of terpenoids, both the eukaryotic mevalonic acid (MVA) pathway and the prokaryotic methyl-D-erythritol 4-phosphate (MEP) pathway. In recent years, various genetic engineering strategies have been applied to increase target terpenoid yields, including overexpression of the rate-limited enzymes and inhibition of the competing pathways. However, since gene-editing tools are only built in some model microalgae, fermentation strategies that are easier to be operated have been widely successful in promoting the production of terpenoids, such as changing culture conditions and addition of chemical additives. In addition, an economical and effective downstream process is also an important consideration for the industrial production of terpenoids, and the solvent extraction and the supercritical fluid extraction method are the most commonly used strategies, especially in the industrial production of β-carotene and astaxanthin from microalgae. In this review, recent advancements and novel strategies used for terpenoid production are concluded and discussed, and new insights to move the field forward are proposed. KEY POINTS: • The MEP pathway is more stoichiometrically efficient than the MVA pathway. • Advanced genetic engineering and fermentation strategies can increase terpene yield. • SFE has a higher recovery of carotenoids than solvent extraction.

Agrobacterium tumefaciens-Mediated Nuclear Transformation of a Biotechnologically Important Microalga-Euglena gracilis

Euglena gracilis (E. gracilis) is an attractive organism due to its evolutionary history and substantial potential to produce biochemicals of commercial importance. This study describes the establishment of an optimized protocol for the genetic transformation of E. gracilis mediated by Agrobacterium (A. tumefaciens). E. gracilis was found to be highly sensitive to hygromycin and zeocin, thus offering a set of resistance marker genes for the selection of transformants. A. tumefaciens-mediated transformation (ATMT) yielded hygromycin-resistant cells. However, hygromycin-resistant cells hosting the gus gene (encoding β-glucuronidase (GUS)) were found to be GUS-negative, indicating that the gus gene had explicitly been silenced. To circumvent transgene silencing, GUS was expressed from the nuclear genome as transcriptional fusions with the hygromycin resistance gene (hptII) (encoding hygromycin phosphotransferase II) with the foot and mouth disease virus (FMDV)-derived 2A self-cleaving sequence placed between the coding sequences. ATMT of Euglena with the hptII-2A–gus gene yielded hygromycin-resistant, GUS-positive cells. The transformation was verified by PCR amplification of the T-DNA region genes, determination of GUS activity, and indirect immunofluorescence assays. Cocultivation factors optimization revealed that a higher number of transformants was obtained when A. tumefaciens LBA4404 (A₆₀₀ = 1.0) and E. gracilis (A₇₅₀ = 2.0) cultures were cocultured for 48 h at 19 °C in an organic medium (pH 6.5) containing 50 µM acetosyringone. Transformation efficiency of 8.26 ± 4.9% was achieved under the optimized cocultivation parameters. The molecular toolkits and method presented here can be used to bioengineer E. gracilis for producing high-value products and fundamental studies.

A novel, robust and mating-competent Chlamydomonas reinhardtii strain with an enhanced transgene expression capacity for algal biotechnology

In the future, algae biotechnology could play an important role in sustainable development, especially with regard to the production of valuable chemicals. Among the established laboratory strains with efficient transgene expression, there are none that have demonstrated the required robustness for industrial applications, which generally require growth at larger scale. Here, we created a robust and mating-competent cell line of the green microalga Chlamydomonas reinhardtii, which also possesses a high transgene expression capacity. This strain shows a comparably high resistance to shear stress by accumulating increased amounts of biomass under these conditions. As a proof-of-concept, a high phototrophic productivity of cadaverine from CO₂ and nitrate was demonstrated by efficiently expressing a bacterial l-lysine decarboxylase. In contrast to other established strains, this novel chassis strain for phototrophic production schemes is equipped with the traits required for industrial applications, by combining mating-competence, cell wall-mediated robustness and high level transgene expression.

Unlocking the Health Potential of Microalgae as Sustainable Sources of Bioactive Compounds

Microalgae are known to produce a plethora of compounds derived from the primary and secondary metabolism. Different studies have shown that these compounds may have allelopathic, antimicrobial, and antipredator activities. In addition, in vitro and in vivo screenings have shown that several compounds have interesting bioactivities (such as antioxidant, anti-inflammatory, anticancer, and antimicrobial) for the possible prevention and treatment of human pathologies. Additionally, the enzymatic pathways responsible for the synthesis of these compounds, and the targets and mechanisms of their action have also been investigated for a few species. However, further research is necessary for their full exploitation and possible pharmaceutical and other industrial applications. Here, we review the current knowledge on the chemical characteristics, biological activities, mechanism of action, and the enzymes involved in the synthesis of microalgal metabolites with potential benefits for human health.

Efficient Agrobacterium tumefaciens-mediated stable genetic transformation of green microalgae, Chlorella sorokiniana

The green oleaginous microalgae, Chlorella sorokiniana, is a highly productive Chlorella species and a potential host for the production of biofuel, nutraceuticals, and recombinant therapeutic proteins. The lack of a stable and efficient genetic transformation system is the major bottleneck in improving this species. We report an efficient and stable Agrobacterium tumefaciens-mediated transformation system for the first time in C. sorokiniana. Cocultivation of C. sorokiniana cells (optical density at λ ₆₈₀ = 1.0) with Agrobacterium at a cell density of OD₆₀₀ = 0.6, on BG11 agar medium (pH 5.6) supplemented with 100 μM of acetosyringone, for three days at 25 ± 2 °C in the dark, resulted in significantly higher transformation efficiency (220 ± 5 hygromycin-resistant colonies per 10⁶ cells). Transformed cells primarily selected on BG11 liquid medium with 30 mg/L hygromycin followed by selecting homogenous transformants on BG11 agar medium with 75 mg/L hygromycin. PCR analysis confirmed the presence of hptII, and the absence of virG amplification ruled out the Agrobacterium contamination in transformed microalgal cells. Southern hybridization confirmed the integration of the hptII gene into the genome of C. sorokiniana. The qRT-PCR and Western blot analyses confirmed hptII and GUS gene expression in the transgenic cell lines. The specific growth rate, biomass doubling time, PSII activity, and fatty-acid profile of transformed cells were found similar to wild-type untransformed cells, clearly indicating the growth and basic metabolic processes not compromised by transgene expression. This protocol can facilitate opportunities for future production of biofuel, carotenoids, nutraceuticals, and therapeutic proteins.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02750-7.

Incorporating a molecular antenna in diatom microalgae cells enhances photosynthesis

Diatom microalgae have great industrial potential as next-generation sources of biomaterials and biofuels. Effective scale-up of their production can be pursued by enhancing the efficiency of their photosynthetic process in a way that increases the solar-to-biomass conversion yield. A proof-of-concept demonstration is given of the possibility of enhancing the light absorption of algae and of increasing their efficiency in photosynthesis by in vivo incorporation of an organic dye which acts as an antenna and enhances cells’ growth and biomass production without resorting to genetic modification. A molecular dye (Cy5) is incorporated in Thalassiosira weissflogii diatom cells by simply adding it to the culture medium and thus filling the orange gap that limits their absorption of sunlight. Cy5 enhances diatoms’ photosynthetic oxygen production and cell density by 49% and 40%, respectively. Cy5 incorporation also increases by 12% the algal lipid free fatty acid (FFA) production versus the pristine cell culture, thus representing a suitable way to enhance biofuel generation from algal species. Time-resolved spectroscopy reveals Förster Resonance Energy Transfer (FRET) from Cy5 to algal chlorophyll. The present approach lays the basis for non-genetic tailoring of diatoms’ spectral response to light harvesting, opening up new ways for their industrial valorization.

Recombinant overexpression of the Escherichia coli acetyl-CoA carboxylase gene in Synechocystis sp. boosts lipid production

Microalgae have received continued attention as a potential source for biofuel production. However, the lack of suitable strains that provide a lipid-rich biomass and tolerate harsh condition inhibits their industrial application. This report describes an effort to transform Synechocystis sp. with genes encoding acetyl-CoA carboxylase (ACC), a key regulatory enzyme in the lipogenesis pathway, from the white mustard plant (Sinapis alba) and the bacterium Escherichia coli DH5α using chitosan nanoparticles. Although a recombinant plasmid encoding S. alba ACC failed to express, successful transformation was achieved with a recombinant plasmid encoding E. coli DH5α ACC. The successful transformant, Synechocystis sp. PAK13, exhibited increased ACC expression compared with its wild-type parent (11.8 vs. 7.2 ng), which significantly increased its lipid content (by 3.6-fold). Synechocystis sp. PAK13 also exhibited a significant (20%) reduction in photosynthetic pigments, a 1.52-fold higher glucose content and a 3.5-fold lower sucrose content than the wild-type. In conclusion, this report introduces a useful strategy to overexpress the ACC gene in microalgae, creating strains with improved lipid production that are suited to industrial applications.

Biocatalytic C-C Bond Formation for One Carbon Resource Utilization

The carbon-carbon bond formation has always been one of the most important reactions in C1 resource utilization. Compared to traditional organic synthesis methods, biocatalytic C-C bond formation offers a green and potent alternative for C1 transformation. In recent years, with the development of synthetic biology, more and more carboxylases and C-C ligases have been mined and designed for the C1 transformation in vitro and C1 assimilation in vivo. This article presents an overview of C-C bond formation in biocatalytic C1 resource utilization is first provided. Sets of newly mined and designed carboxylases and ligases capable of catalyzing C-C bond formation for the transformation of CO₂, formaldehyde, CO, and formate are then reviewed, and their catalytic mechanisms are discussed. Finally, the current advances and the future perspectives for the development of catalysts for C1 resource utilization are provided.