Genetic Engineering of Microalgae for Secondary Metabolite Production: Recent Developments, Challenges, and Future Prospects

Peroxisomal biogenesis factor 11 as a novel target to trigger lipid biosynthesis and salt stress resistance in oleaginous Tetradesmus obliquus

To overcome economic challenges in microalgal biofuel production, this study investigates the overexpression of peroxisome-localized peroxisomal biogenesis factor 11 (PEX11) to enhance lipid biosynthesis and improve salt stress resistance in Tetradesmus obliquus, aiming to advance microalgal biofuel production. Transgenic strains PEX11-2-1 and PEX11-2-2 exhibited a 2.13- and 2.51-fold increase in neutral lipid content and more cellular lipid droplets compared to WT, along with lipid yield and biomass escalating to 255.45 and 815.15 mg/L, respectively. This enhancement resulted from the redistribution of carbon precursors, increased intracellular reactive oxygen species, enhanced NADPH synthesis, and upregulation of lipid synthesis genes. Additionally, PEX11 improved salt stress tolerance by upregulating the expression of stress-responsive genes, including SnRK2 and PYRC. Fatty acid profile alterations, with increases in saturated fatty acids C16:0 and monounsaturated fatty acids C18:1, and decreases in polyunsaturated fatty acids, facilitated high-quality biofuel production. These findings highlight novel insights for advancing microalgae-based biorefinery.

Polyhydroxyalkanoates production from microalgae for sustainable bioplastics: A review

Microalgae have emerged as a promising and sustainable source for polyhydroxyalkanoates (PHA), which are increasingly recognized for their potential in bioplastics production. However, the widespread application of microalgae-derived PHA faces challenges related to economic feasibility and scalability. This review provides a comprehensive analysis of recent advancements in the cultivation and optimization of microalgae for PHA production, highlighting the critical role of nutrient limitation, particularly nitrogen and phosphorus, in enhancing PHA accumulation. This review also explores the effectiveness of various cultivation systems, including autotrophic, heterotrophic, and mixotrophic approaches, in maximizing PHA yields. Environmental factors such as light intensity, salinity, and pH are examined for their influence on PHA synthesis pathways. Additionally, it identifies key technical and economic challenges that must be addressed to commercialize microalgae-based bioplastics to fully harness the potential of microalgae in sustainable bioplastic production.

Unlocking the Therapeutic Potential of Algae-Derived Compounds in Hematological Malignancies

Algae are a rich source of bioactive compounds that have a wide range of beneficial effects on human health and can show significant potential in the treatment of hematological malignancies such as leukemia, lymphoma, and multiple myeloma. These diseases often pose a therapeutic challenge despite recent advances in treatment (e.g., the use of immunomodulatory drugs, proteasome inhibitors, CD38 monoclonal antibodies, stem cell transplant, and targeted therapy). A considerable number of patients experience relapses or resistance to the applied therapies. Algal compounds, alone or in combination with chemotherapy or other more advanced therapies, have exhibited antitumor and immunomodulatory effects in preclinical studies that may improve disease outcomes. These include the ability to induce apoptosis, inhibit tumor growth, and improve immune responses. However, most of these studies are conducted in vitro, often without in vivo validation or clinical trials. This paper summarizes the current evidence on the in vitro effects of algae extracts and isolated compounds on leukemia, lymphoma, and myeloma cell lines. In addition, we address the current advances in the application of algae-derived compounds as targeted drug carriers and their synergistic potential against hematologic malignancies.

Harnessing algal biomass for sustainable energy: cultivation, strain improvement, and biofuel production

The world faces pressing environmental challenges, including greenhouse gas emissions, global warming, climate change, and rising sea levels. Alongside, these issues, the depletion of fossil fuels has intensified the search for alternative energy sources. Algal biomass presents a promising long-term solution to these global problems. The quest for sustainable energy has driven significant research into algal biofuels as a viable alternative to fossil fuels. Algae offers several advantages as a feedstock for biofuel production, including high biomass yield, rapid growth rates, cost-effective cultivation, carbon dioxide fixation capabilities, and the potential to grow on non-arable land using non-potable water. This manuscript provides an overview of algal biomass cultivation using renewable feedstocks, identifies potential algal strains for biofuel production, and explores bioengineering advancements in algae. Additionally, strain improvement strategies to enhance biofuel yields are discussed. The review also addresses large-scale algal biomass cultivation for biofuel production, assesses its commercial viability, examines challenges faced by the biofuel industry, and outlines prospects for biofuel production using highly potent algal strains. By overcoming and addressing these challenges, algal biofuels have the potential to become a cornerstone of sustainable energy solutions.

Investigating the role of extracellular polymeric substances produced by Parachlorella kessleri in Zn(II) bioremediation using atomic force microscopy

Microalgae, such as Parachlorella kessleri, have significant potential for environmental remediation, especially in removing heavy metals like zinc from water. This study investigates how P. kessleri, isolated from a polluted river in Argentina, can remediate zinc. Using atomic force microscopy (AFM), the research examined the interactions between Zn particles and cells grown with different nitrogen sources-nitrate or ammonium. The results showed that cells grown with nitrate produced extracellular polymeric substances (EPS), while those grown with ammonium did not. Raman spectroscopy revealed distinct metabolic responses based on the nitrogen source, with nitrate-grown cells showing altered profiles after zinc exposure. Zinc exposure also changed the surface roughness and nanomechanical properties of the cells, particularly in those producing EPS. AFM force spectroscopy experiments then confirmed strong Zn binding to EPS in nitrate-grown cells, while interactions were weaker in ammonium-grown cells that lacked EPS. Overall, our results elucidate the critical role of EPS in Zn removal by P. kessleri cells and show that Zn remediation is mediated by EPS adsorption. This study underscores the significance of regulating nitrogen sources to stimulate EPS production, offering insights that are essential for subsequent bioremediation applications.

Harnessing the potential of microalgae for the production of monoclonal antibodies and other recombinant proteins

Monoclonal antibodies (mAbs) have become indispensable tools in various fields, from research to therapeutics, diagnostics, and industries. However, their production, primarily in mammalian cell culture systems, is cost-intensive and resource-demanding. Microalgae, diverse photosynthetic microorganisms, are gaining attention as a favorable option for manufacturing mAbs and various other recombinant proteins. This review explores the potential of microalgae as a robust expression system for biomanufacturing high-value proteins. It also highlights the diversity of microalgae species suitable for recombinant protein. Nuclear and chloroplast genomes of some microalgae have been engineered to express mAbs and other valuable proteins. Codon optimization, vector construction, and other genetic engineering techniques have significantly improved recombinant protein expression in microalgae. These accomplishments demonstrate the potential of microalgae for biopharmaceutical manufacturing. Microalgal biotechnology holds promise for revolutionizing the production of mAbs and other therapeutic proteins, offering a sustainable and cost-effective solution to address critical healthcare needs.

CRISPR/Cas9-Mediated Knockout of the Lycopene ε-Cyclase for Efficient Astaxanthin Production in the Green Microalga Chlamydomonas reinhardtii

Carotenoids are valuable pigments naturally occurring in all photosynthetic plants and microalgae as well as in selected fungi, bacteria, and archaea. Green microalgae developed a complex carotenoid profile suitable for efficient light harvesting and light protection and harbor great capacity for carotenoid production through the substantial power of the endogenous 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Previous works established successful genome editing and induced significant changes in the cellular carotenoid content in Chlamydomonas reinhardtii. This study employs a tailored carotenoid pathway for engineered bioproduction of the valuable ketocarotenoid astaxanthin. Functional knockout of lycopene ε-cyclase (LCYE) and non-homologous end joining (NHEJ)-based integration of donor DNA at the target site inhibit the accumulation of α-carotene and consequently lutein and loroxanthin, abundant carotenoids in C. reinhardtii without changes in cellular fitness. PCR-based screening indicated that 4 of 96 regenerated candidate lines carried (partial) integrations of donor DNA and increased ß-carotene as well as derived carotenoid contents. Iterative overexpression of CrBKT, PacrtB, and CrCHYB resulted in a 2.3-fold increase in astaxanthin accumulation in mutant ΔLCYE#3 (1.8 mg/L) compared to the parental strain UVM4, which demonstrates the potential of genome editing for the design of a green cell factory for astaxanthin bioproduction.

Microalgae-made human vaccines and therapeutics: A decade of advances

Microalgal emergence is a promising platform with two-decade historical background for producing vaccines and biopharmaceuticals. During that period, microalgal-based vaccines have reported successful production for various diseases. Thus, species selection is important for genetic transformation and delivery methods that have been developed. Although many vaccine prototypes have been produced for infectious and non-infectious diseases, fewer studies have reached immunological and immunoprotective evaluations. Microalgae-made vaccines for Staphylococcus aureus, malaria, influenza, human papilloma, and Zika viruses have been explored in their capacity to induce humoral or cellular immune responses and protective efficacies against experimental challenges. Therefore, specific pathogen antigens and immune system role are important and addressed in controlling these infections. Regarding non-communicable diseases, these vaccines have been investigated for breast cancer; microalgal-produced therapeutic molecules and microalgal-made interferon-α have been explored for hypertension and potential applications in treating viral infections and cancer, respectively. Thus, conducting immunological trials is emphasized, discussing the promising results observed in terms of immunogenicity, desired immune response for controlling affections, and challenges for achieving the desired protection levels. The potential advantages and hurdles associated with this innovative approach are highlighted, underlining the relevance of assessing immune responses in preclinical and clinical trials to validate the efficacy of these biopharmaceuticals. The promising future of this healthcare technology is also envisaged.

Perspectives on cultivation and harvesting technologies of microalgae, towards environmental sustainability and life cycle analysis

The development of algae is seen as a potential and ecologically sound approach to address the increasing demands in multiple sectors. However, successful implementation of processes is highly dependent on effective growing and harvesting methods. The present study provides a complete examination of contemporary techniques employed in the production and harvesting of algae, with a particular emphasis on their sustainability. The review begins by examining several culture strategies, encompassing open ponds, closed photobioreactors, and raceway ponds. The analysis of each method is conducted in a systematic manner, with a particular focus on highlighting their advantages, limitations, and potential for expansion. This approach ensures that the conversation is in line with the objectives of sustainability. Moreover, this study explores essential elements of algae harvesting, including the processes of cell separation, dewatering, and biomass extraction. Traditional methods such as centrifugation, filtration, and sedimentation are examined in conjunction with novel, environmentally concerned strategies including flocculation, electro-coagulation, and membrane filtration. It evaluates the impacts on the environment that are caused by the cultivation process, including the usage of water and land, the use of energy, the production of carbon dioxide, and the runoff of nutrients. Furthermore, this study presents a thorough examination of the current body of research pertaining to Life Cycle Analysis (LCA) studies, presenting a perspective that emphasizes sustainability in the context of algae harvesting systems. In conclusion, the analysis ends up with an examination ahead at potential areas for future study in the cultivation and harvesting of algae. This review is an essential guide for scientists, policymakers, and industry experts associated with the advancement and implementation of algae-based technologies.

An optimized approach towards bio-capture and carbon dioxide sequestration with microalgae Phormidium valderianum using response surface methodology

As carbon dioxide emissions rise, there's need for alternative strategies, including microorganisms, to capture and mitigate them. The present study investigated on the capability and tolerance of microalgal strain, Phormidium valderianum to capture gaseous CO2 at varying levels (5-30 %). A biomass productivity of 0.0216 ± 0.027 gL-1day-1 and rate of CO2 fixation of 0.035 gL-1day-1 was obtained for 25 % CO2 concentration. From this study, it is evident that higher CO2 levels led to elevated carbohydrate concentration. In addition, protein concentration doubled with the introduction of 25 % CO2. In optimization studies, pH 10, 25 % CO2, and 200 mg/L of Ca(OH)2 concentration was found to be optimal for biomass growth. A higher rate of CO2 fixation of 0.315 gL-1day-1 was achieved at these optimum conditions using response surface methodology. Furthermore, the study demonstrated that microalgae, Phormidium valderianum has the potential to serve as a promising alternative for capturing CO2 emissions.

Biosensors in microalgae: A roadmap for new opportunities in synthetic biology and biotechnology

Biosensors are powerful tools to investigate, phenotype, improve and prototype microbial strains, both in fundamental research and in industrial contexts. Genetic and biotechnological developments now allow the implementation of synthetic biology approaches to novel different classes of microbial hosts, for example photosynthetic microalgae, which offer unique opportunities. To date, biosensors have not yet been implemented in phototrophic eukaryotic microorganisms, leaving great potential for novel biological and technological advancements untapped. Here, starting from selected biosensor technologies that have successfully been implemented in heterotrophic organisms, we project and define a roadmap on how these could be applied to microalgae research. We highlight novel opportunities for the development of new biosensors, identify critical challenges, and finally provide a perspective on the impact of their eventual implementation to tackle research questions and bioengineering strategies. From studying metabolism at the single-cell level to genome-wide screen approaches, and assisted laboratory evolution experiments, biosensors will greatly impact the pace of progress in understanding and engineering microalgal metabolism. We envision how this could further advance the possibilities for unraveling their ecological role, evolutionary history and accelerate their domestication, to further drive them as resource-efficient production hosts.

CRISPR-based bioengineering in microalgae for production of industrially important biomolecules

Microalgae, as photosynthetic organisms, have the potential to produce biomolecules for use in food, feed, cosmetics, nutraceuticals, fuel, and other applications. Faster growth rates and higher protein and lipid content make microalgae a popular chassis for many industrial applications. However, challenges such as low productivity and high production costs have limited their commercialization. To overcome these challenges, bioengineering approaches such as genetic engineering, metabolic engineering, and synthetic biology have been employed to improve the productivity and quality of microalgae-based products. Genetic engineering employing genome editing tools like CRISPR/Cas allows precise and targeted genetic modifications. CRISPR/Cas systems are presently used to modify the genetic makeup of microalgae for enhanced production of specific biomolecules. However, these tools are yet to be explored explicitly in microalgae owing to some limitations. Despite the progress made in CRISPR-based bioengineering approaches, there is still a need for further research to optimize the production of microalgae-based products. This includes improving the efficiency of genome editing tools, understanding the regulatory mechanisms of microalgal metabolism, and optimizing growth conditions and cultivation strategies. Additionally, addressing the ethical, social, and environmental concerns associated with genetic modification of microalgae is crucial for the responsible development and commercialization of microalgae-based products. This review summarizes the advancements of CRISPR-based bioengineering for production of industrially important biomolecules and provides key considerations to use CRISPR/Cas systems in microalgae. The review will help researchers to understand the progress and to initiate genome editing experiments in microalgae.

A potential paradigm in CRISPR/Cas systems delivery: at the crossroad of microalgal gene editing and algal-mediated nanoparticles

Microalgae as the photosynthetic organisms offer enormous promise in a variety of industries, such as the generation of high-value byproducts, biofuels, pharmaceuticals, environmental remediation, and others. With the rapid advancement of gene editing technology, CRISPR/Cas system has evolved into an effective tool that revolutionised the genetic engineering of microalgae due to its robustness, high target specificity, and programmability. However, due to the lack of robust delivery system, the efficacy of gene editing is significantly impaired, limiting its application in microalgae. Nanomaterials have become a potential delivery platform for CRISPR/Cas systems due to their advantages of precise targeting, high stability, safety, and improved immune system. Notably, algal-mediated nanoparticles (AMNPs), especially the microalgae-derived nanoparticles, are appealing as a sustainable delivery platform because of their biocompatibility and low toxicity in a homologous relationship. In addition, living microalgae demonstrated effective and regulated distribution into specified areas as the biohybrid microrobots. This review extensively summarised the uses of CRISPR/Cas systems in microalgae and the recent developments of nanoparticle-based CRISPR/Cas delivery systems. A systematic description of the properties and uses of AMNPs, microalgae-derived nanoparticles, and microalgae microrobots has also been discussed. Finally, this review highlights the challenges and future research directions for the development of gene-edited microalgae.

Microbial Secondary Metabolites via Fermentation Approaches for Dietary Supplementation Formulations

Food supplementation formulations refer to products that are designed to provide additional nutrients to the diet. Vitamins, dietary fibers, minerals and other functional compounds (such as antioxidants) are concentrated in dietary supplements. Specific amounts of dietary compounds are given to the body through food supplements, and these include as well so-called non-essential compounds such as secondary plant bioactive components or microbial natural products in addition to nutrients in the narrower sense. A significant social challenge represents how to moderately use the natural resources in light of the growing world population. In terms of economic production of (especially natural) bioactive molecules, ways of white biotechnology production with various microorganisms have recently been intensively explored. In the current review other relevant dietary supplements and natural substances (e.g., vitamins, amino acids, antioxidants) used in production of dietary supplements formulations and their microbial natural production via fermentative biotechnological approaches are briefly reviewed. Biotechnology plays a crucial role in optimizing fermentation conditions to maximize the yield and quality of the target compounds. Advantages of microbial production include the ability to use renewable feedstocks, high production yields, and the potential for cost-effective large-scale production. Additionally, it can be more environmentally friendly compared to chemical synthesis, as it reduces the reliance on petrochemicals and minimizes waste generation. Educating consumers about the benefits, safety, and production methods of microbial products in general is crucial. Providing clear and accurate information about the science behind microbial production can help address any concerns or misconceptions consumers may have.

A review on microalgal-bacterial co-culture: The multifaceted role of beneficial bacteria towards enhancement of microalgal metabolite production

Mass microalgal-bacterial co-cultures have come to the fore of applied physiological research, in particularly for the optimization of high-value metabolite from microalgae. These co-cultures rely on the existence of a phycosphere which harbors unique cross-kingdom associations that are a prerequisite for the cooperative interactions. However, detailed mechanisms underpinning the beneficial bacterial effects onto microalgal growth and metabolic production are rather limited at the moment. Hence, the main purpose of this review is to shed light on how bacteria fuels microalgal metabolism or vice versa during mutualistic interactions, building upon the phycosphere which is a hotspot for chemical exchange. Nutrients exchange and signal transduction between two not only increase the algal productivity, but also facilitate in the degradation of bio-products and elevate the host defense ability. Main chemical mediators such as photosynthetic oxygen, N-acyl-homoserine lactone, siderophore and vitamin B12 were identified to elucidate beneficial cascading effects from the bacteria towards microalgal metabolites. In terms of applications, the enhancement of soluble microalgal metabolites is often associated with bacteria-mediated cell autolysis while bacterial bio-flocculants can aid in microalgal biomass harvesting. In addition, this review goes in depth into the discussion on enzyme-based communication via metabolic engineering such as gene modification, cellular metabolic pathway fine-tuning, over expression of target enzymes, and diversion of flux toward key metabolites. Furthermore, possible challenges and recommendations aimed at stimulating microalgal metabolite production are outlined. As more evidence emerges regarding the multifaceted role of beneficial bacteria, it will be crucial to incorporate these findings into the development of algal biotechnology.

The Effect of Oil-Rich Food Waste Substrates, Used as an Alternative Carbon Source, on the Cultivation of Microalgae-A Pilot Study

Microalgae are mostly phototrophic microorganisms present worldwide, showcasing great adaptability to their environment. They are known for producing essential metabolites such as carotenoids, chlorophylls, sterols, lipids, and many more. This study discusses the possibility of the mixotrophic abilities of microalgae in the presence of food waste oils. The utilization of food waste materials is becoming more popular as a research subject as its production grows every year, increasing the environmental burden. In this work, waste frying oil and coffee oil were tested for the first time as a nutrition source for microalgae cultivation. Waste frying oil is produced in large amounts all over the world and its simple purification is one of its greatest advantages as it only needs to be filtered from leftover food pieces. Coffee oil is extracted from waste spent coffee grounds as a by-product. The waste frying oil and coffee oil were added to the basic algal media as an alternative source of carbon. As a pilot study for further experimentation, the effect of oil in the medium, algal adaptability, and capability to survive were tested within these experiments. The growth and production characteristics of four algae and cyanobacteria strains were tested, of which the strain Desmodesmus armatus achieved exceptional results of chlorophyll (8.171 ± 0.475 mg/g) and ubiquinone (5.708 ± 0.138 mg/g) production. The strain Chlamydomonas reindhartii showed exceptional lipid accumulation in the range of 30-46% in most of the samples.

Site-specific gene knock-in and bacterial phytase gene expression in Chlamydomonas reinhardtii via Cas9 RNP-mediated HDR

In the present study, we applied the HDR (homology-directed DNA repair) CRISPR-Cas9-mediated knock-in system to accurately insert an optimized foreign bacterial phytase gene at a specific site of the nitrate reductase (NR) gene (exon 2) to achieve homologous recombination with the stability of the transgene and reduce insertion site effects or gene silencing. To this end, we successfully knocked-in the targeted NR gene of Chlamydomonas reinhardtii using the bacterial phytase gene cassette through direct delivery of the CRISPR/Cas9 system as the ribonucleoprotein (RNP) complex consisting of Cas9 protein and the specific single guide RNAs (sgRNAs). The NR insertion site editing was confirmed by PCR and sequencing of the transgene positive clones. Moreover, 24 clones with correct editing were obtained, where the phytase gene cassette was located in exon 2 of the NR gene, and the editing efficiency was determined to be 14.81%. Additionally, site-specific gene expression was analyzed and confirmed using RT-qPCR. Cultivation of the positive knocked-in colonies on the selective media during 10 generations indicated the stability of the correct editing without gene silencing or negative insertion site effects. Our results demonstrated that CRISPR-Cas9-mediated knock-in could be applied for nuclear expression of the heterologous gene of interest, and also confirmed its efficacy as an effective tool for site-specific gene knock-in, avoiding nuclear positional effects and gene silencing in C. reinhardtii. These findings could also provide a new perspective on the advantageous application of RNP-CRISPR/Cas9 gene-editing to accelerate the commercial production of complex recombinant proteins in the food-grade organism "C. reinhardtii".

Deciphering and engineering the polyunsaturated fatty acid synthase pathway from eukaryotic microorganisms

Polyunsaturated fatty acids (PUFAs) are important nutrients that play important roles in human health. In eukaryotes, PUFAs can be de novo synthesized through two independent biosynthetic pathways: the desaturase/elongase pathway and the PUFA synthase pathway. Among them, PUFAs synthesized through the PUFA synthase pathway typically have few byproducts and require fewer reduction equivalents. In the past 2 decades, numerous studies have been carried out to identify, analyze and engineer PUFA synthases from eukaryotes. These studies showed both similarities and differences between the eukaryotic PUFA synthase pathways and those well studied in prokaryotes. For example, eukaryotic PUFA synthases contain the same domain types as those in prokaryotic PUFA synthases, but the number and arrangement of several domains are different; the basic functions of same-type domains are similar, but the properties and catalytic activities of these domains are somewhat different. To further utilize the PUFA synthase pathway in microbial cell factories and improve the productivity of PUFAs, many challenges still need to be addressed, such as incompletely elucidated PUFA synthesis mechanisms and the difficult genetic manipulation of eukaryotic hosts. In this review, we provide an updated introduction to the eukaryotic PUFA synthase pathway, summarize the functions of domains and propose the possible mechanisms of the PUFA synthesis process, and then provide future research directions to further elucidate and engineer the eukaryotic PUFA synthase pathway for the maximal benefits of humans.

Plant-based expression platforms to produce high-value metabolites and proteins

Plant-based heterologous expression systems can be leveraged to produce high-value therapeutics, industrially important proteins, metabolites, and bioproducts. The production can be scaled up, free from pathogen contamination, and offer post-translational modifications to synthesize complex proteins. With advancements in molecular techniques, transgenics, CRISPR/Cas9 system, plant cell, tissue, and organ culture, significant progress has been made to increase the expression of recombinant proteins and important metabolites in plants. Methods are also available to stabilize RNA transcripts, optimize protein translation, engineer proteins for their stability, and target proteins to subcellular locations best suited for their accumulation. This mini-review focuses on recent advancements to enhance the production of high-value metabolites and proteins necessary for therapeutic applications using plants as bio-factories.

Current Status and Perspective on the Use of Viral-Based Vectors in Eukaryotic Microalgae

During the last two decades, microalgae have attracted increasing interest, both commercially and scientifically. Commercial potential involves utilizing valuable natural compounds, including carotenoids, polysaccharides, and polyunsaturated fatty acids, which are widely applicable in food, biofuel, and pharmaceutical industries. Conversely, scientific potential focuses on bioreactors for producing recombinant proteins and developing viable technologies to significantly increase the yield and harvest periods. Here, viral-based vectors and transient expression strategies have significantly contributed to improving plant biotechnology. We present an updated outlook covering microalgal biotechnology for pharmaceutical application, transformation techniques for generating recombinant proteins, and genetic engineering tactics for viral-based vector construction. Challenges in industrial application are also discussed.

Microalgae-Based PUFAs for Food and Feed: Current Applications, Future Possibilities, and Constraints

Microalgae are currently considered an attractive source of highly valuable compounds for human and animal consumption, including polyunsaturated fatty acids (PUFAs). Several microalgae-derived compounds, such as ω-3 fatty acids, pigments, and whole dried biomasses are available on the market and are mainly produced by culturing microalgae in open ponds, which can be achieved with low setup and maintenance costs with respect to enclosed systems. However, open tanks are more susceptible to bacterial and other environmental contamination, do not guarantee a high reproducibility of algal biochemical profiles and productivities, and constrain massive cultivation to a limited number of species. Genetic engineering techniques have substantially improved over the last decade, and several model microalgae have been successfully modified to promote the accumulation of specific value-added compounds. However, transgenic strains should be cultured in closed photobioreactors (PBRs) to minimize risks of contamination of aquatic environments with allochthonous species; in addition, faster growth rates and higher yields of compounds of interest can be achieved in PBRs compared to open ponds. In this review, we present information collected about the major microalgae-derived commodities (with a special focus on PUFAs) produced at industrial scale, as well genetically-engineered microalgae to increase PUFA production. We also critically analyzed the main bottlenecks that make large-scale production of algal commodities difficult, as well as possible solutions to overcome the main problems and render the processes economically and environmentally safe.