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

Advancements and hurdles in symbiotic microalgal co-cultivation strategies for wastewater treatment

Microalgae offer significant potential in various industrial applications, such as biofuel production and wastewater treatment, but the economic barriers to their cultivation and harvesting have been a major obstacle. However, a promising strategy involving co-cultivating microalgae in wastewater treatment could overcome the limitations of monocultivation and open the possibility for increased integration of microalgae into various industrial processes. This symbiotic relationship between microalgae and other microbes can enhance nutrient removal efficiency, increase value-added bioproduct production, promote carbon capture, and decrease energy consumption. However, unresolved challenges, such as the competition between microalgae and other microbes within the wastewater treatment system, may result in imbalances and reduced efficiency. The complexity of managing multiple microbes in a co-cultivation system poses difficulties in achieving stability and consistency in bioproduct production. In response to these challenges, strategies such as optimizing nutrient ratios, manipulating environmental conditions, understanding the dynamics of microbial relationships, and employing genetic modification to enhance the metabolic capabilities of microalgae and improve their competitiveness are critical in transitioning to a more sustainable path. Hence, this review will provide an in-depth analysis of recent advancements in symbiotic microalgal co-cultivation for applications in wastewater treatment and CO2 utilization, as well as discuss approaches for improving microalgal strains through genetic modification. Furthermore, the review will explore the use of efficient bioreactors, advanced control systems, and advancements in biorefinery processes.

Bioenergetic trade-offs can reveal the path to superior microbial CO2 fixation pathways

A comprehensive optimization of known prokaryotic autotrophic carbon dioxide (CO2) fixation pathways is presented that evaluates all their possible variants under different environmental conditions. This was achieved through a computational methodology recently developed that considers the trade-offs between energy efficiency (yield) and growth rate, allowing us to evaluate candidate metabolic modifications in silico for microbial conversions. The results revealed the superior configurations in terms of both yield (efficiency) and rate (driving force). The pathways from anaerobic organisms appear to fix carbon at lower net ATP cost than those found in aerobic organisms, and the reverse TCA cycle pathway shows the lowest overall energy cost and maximum adaptability across a broad range of CO2 and electron donor (H2) concentrations. The reverse tricarboxylic acid cycle and Wood-Ljungdahl pathways appear highly efficient under a broad range of conditions, while the 3-hydroxypropionate 4-hydroxybutyrate cycle and the 3-hydroxypropionate bicycle appear capable of generating large thermodynamic driving forces at only moderate ATP yield losses.IMPORTANCEBiotechnology can lead to cost-effective processes for capturing carbon dioxide using the natural or genetically engineered metabolic capabilities of microorganisms. However, introducing desirable genetic modifications into microbial strains without compromising their fitness (growth yield and rate) during industrial-scale cultivation remains a challenge. The approach and results presented can guide optimal pathway configurations for enhanced prokaryotic carbon fixation through metabolic engineering. By aligning strain modifications with these theoretically revealed near-optimal pathway configurations, we can optimally engineer strains of good fitness under open culture industrial-scale conditions.

Advancing sustainable agriculture through multi-omics profiling of biosolids for safe application: A review

Biosolids, derived from wastewater treatment processes, are valuable resources for soil amendment in agriculture due to their nutrient-rich composition. However, various contaminants of concern (CEC) such as pharmaceuticals, per-and poly-fluoroalkyl substances, endocrine disruptive chemicals, surfactants, pathogens, nanoplastics, and microplastics, are also reported in biosolids. The use of biosolids for agriculture may introduce these CEC into the soil, which raises concerns about their environmental and human health impacts. Moreover, the presence of pathogens (Escherichia coli, Salmonella sp., Shigella, Giardia, Rotavirus, etc.) even after treatment calls for microbial profiling of biosolids, especially in developing countries. Multi-omics approaches can be used as powerful tools for characterizing microbial communities and highlighting metabolic pathways. Moreover, these approaches also help in predicting the ecological and agronomic effects of biosolids application in agricultural soils. This review discusses the advantages and challenges of using biosolids in agriculture, considering the range of different CEC reported in biosolids. Moreover, the current legislation for the use of biosolids in agriculture is also presented, highlighting the limitations with respect to guidelines for emerging contaminants in biosolids. Furthermore, the role of the multi-omics approach in biosolids management, focusing on genomics, transcriptomics, proteomics, and metabolomics is also assessed. Multi-omics also allows for real-time monitoring, ensuring continuous optimization of biosolids towards changing environmental conditions. This dynamic approach not only enhances the safe use, but also enhances the sustainability of waste management practices, minimizing the negative effects. Finally, the future research directions for integrating the multi-omics approach into biosolid management practices are also suggested. The need for updating the legislative framework, continued innovation to promote sustainable and robust agricultural systems, bringing the process closer to the principles of a circular bioeconomy is also empahasized.

Biomedical application of microalgal-biomaterials hybrid system

Microalgae are a group of microorganisms containing chlorophyll A, which are highly photosynthetic and rich in nutrients. And they can produce multiple bioactive substances (peptides, proteins, polysaccharides, and fatty acids) for biomedical applications. Despite the unique advantages of microalgae-based biotherapy, the insufficient treatment efficiency limits its further application. With the development of nanotechnology, the combination of microalgae and biomaterials can improve therapeutic efficacies, which has attracted increasing attention. In this microalgal-biomaterials hybrid system, biomaterials with excellent optical and magnetic properties play an important role in biological therapy. Microalgae, as a natural vehicle, can increase oxygen content and alleviate hypoxia in diseased areas, further enhancing therapeutic effects. In this review, the synergistic therapeutic effects of microalgal-biomaterials hybrid system in different diseases (cancer, myocardial infarction, ischemia stroke, chronic infection, and intestinal diseases) are comprehensively summarized.

Recent advances in applying omic technologies for studying acetic acid bacteria in industrial vinegar production: A comprehensive review

Vinegar and related bioproducts containing acetic acid as the main component are among the most appreciated fermented foodstuffs in numerous European and Asian countries because of their exceptional organoleptic and bio-healthy properties. Regarding the acetification process and obtaining of final products, there is still a lack of knowledge on fundamental aspects, especially those related to the study of biodiversity and metabolism of the present microbiota. In this context, omic technologies currently allow for the massive analysis of macromolecules and metabolites for the identification and characterization of these microorganisms working in their natural media without the need for isolation. This review approaches comprehensive research on the application of omic tools for the identification of vinegar microbiota, mainly acetic acid bacteria, with subsequent emphasis on the study of the microbial diversity, behavior, and key molecular strategies used by the predominant groups throughout acetification. The current omics tools are enabling both the finding of new vinegar microbiota members and exploring underlying strategies during the elaboration process. The species Komagataeibacter europaeus may be a model organism for present and future research in this industry; moreover, the development of integrated meta-omic analysis may facilitate the achievement of numerous of the proposed milestones. This work might provide useful guidance for the vinegar industry establishing the first steps towards the improvement of the acetification conditions and the development of new products with sensory and bio-healthy profiles adapted to the agri-food market.

Metabolic engineering and synthetic biology strategies for producing high-value natural pigments in Microalgae

Microalgae are microorganisms capable of producing bioactive compounds using photosynthesis. Microalgae contain a variety of high value-added natural pigments such as carotenoids, phycobilins, and chlorophylls. These pigments play an important role in many areas such as food, pharmaceuticals, and cosmetics. Natural pigments have a health value that is unmatched by synthetic pigments. However, the current commercial production of natural pigments from microalgae is not able to meet the growing market demand. The use of metabolic engineering and synthetic biological strategies to improve the production performance of microalgal cell factories is essential to promote the large-scale production of high-value pigments from microalgae. This paper reviews the health and economic values, the applications, and the synthesis pathways of microalgal pigments. Overall, this review aims to highlight the latest research progress in metabolic engineering and synthetic biology in constructing engineered strains of microalgae with high-value pigments and the application of CRISPR technology and multi-omics in this context. Finally, we conclude with a discussion on the bottlenecks and challenges of microalgal pigment production and their future development prospects.

Microalgal co-cultivation -recent methods, trends in omic-studies, applications, and future challenges

The burgeoning human population has resulted in an augmented demand for raw materials and energy sources, which in turn has led to a deleterious environmental impact marked by elevated greenhouse gas (GHG) emissions, acidification of water bodies, and escalating global temperatures. Therefore, it is imperative that modern society develop sustainable technologies to avert future environmental degradation and generate alternative bioproduct-producing technologies. A promising approach to tackling this challenge involves utilizing natural microbial consortia or designing synthetic communities of microorganisms as a foundation to develop diverse and sustainable applications for bioproduct production, wastewater treatment, GHG emission reduction, energy crisis alleviation, and soil fertility enhancement. Microalgae, which are photosynthetic microorganisms that inhabit aquatic environments and exhibit a high capacity for CO2 fixation, are particularly appealing in this context. They can convert light energy and atmospheric CO2 or industrial flue gases into valuable biomass and organic chemicals, thereby contributing to GHG emission reduction. To date, most microalgae cultivation studies have focused on monoculture systems. However, maintaining a microalgae monoculture system can be challenging due to contamination by other microorganisms (e.g., yeasts, fungi, bacteria, and other microalgae species), which can lead to low productivity, culture collapse, and low-quality biomass. Co-culture systems, which produce robust microorganism consortia or communities, present a compelling strategy for addressing contamination problems. In recent years, research and development of innovative co-cultivation techniques have substantially increased. Nevertheless, many microalgae co-culturing technologies remain in the developmental phase and have yet to be scaled and commercialized. Accordingly, this review presents a thorough literature review of research conducted in the last few decades, exploring the advantages and disadvantages of microalgae co-cultivation systems that involve microalgae-bacteria, microalgae-fungi, and microalgae-microalgae/algae systems. The manuscript also addresses diverse uses of co-culture systems, and growing methods, and includes one of the most exciting research areas in co-culturing systems, which are omic studies that elucidate different interaction mechanisms among microbial communities. Finally, the manuscript discusses the economic viability, future challenges, and prospects of microalgal co-cultivation methods.

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

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

Enhanced sustainable integration of CO2 utilization and wastewater treatment using microalgae in circular economy concept

Microalgae have been shown to have a promising potential for CO₂ utilization and wastewater treatment which still faces the challenges of high resource and energy requirements. The implementation of the circular economy concept is able to address the issues that limit the application of microalgae-based technologies. In this review, a comprehensive discussion on microalgae-based CO₂ utilization and wastewater treatment was provided, and the integration of this technology with the circular economy concept, for long-term economic and environmental benefits, was described. Furthermore, technological challenges and feasible strategies towards the improvement of microalgae cultivation were discussed. Finally, necessary regulations and effective policies favoring the implementation of microalgae cultivation into the circular economy were proposed. These are discussed to support sustainable development of microalgae-based bioremediation and bioproduction. This work provides new insights into the implementation of the circular economy concept into microalgae-based CO₂ utilization and wastewater treatment to enhance sustainable production.