Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review

Decarboxylase mediated oxalic acid metabolism is important to antioxidation and detoxification rather than pathogenicity in Magnaporthe oryzae

Oxalic acid (OA), an essential pathogenic factor, has been identified in several plant pathogens, and researchers are currently pursuing studies on interference with OA metabolism as a treatment for related diseases. However, the metabolic route in Magnaporthe oryzae remains unknown. In this study, we describe D-erythroascorbic acid-mediated OA synthesis and its metabolic and clearance pathways in rice blast fungus. By knocking out the D-arabino-1,4-lactone oxidase gene (Moalo1), one-third of oxalic acid remained in M. oryzae, indicating a main pathway for oxalic acid production. M. oryzae OxdC (MoOxdC) is an oxalate decarboxylase that appears to play a role in relieving oxalic acid toxicity. Loss of Mooxdc does not affect mycelial growth, conidiophore development, or appressorium formation in M. oryzae; however, the antioxidant and pathogenic abilities of the mutant were enhanced. This is owing to Mooxdc deletion upregulated a series of OA metabolic genes, including the oxalate oxidase gene (Mooxo) and Moalo1, as well as both OA transporter genes. Simultaneously, as feedback to the tricarboxylic acid (TCA) cycle, the decrease of formic acid in ΔMooxdc leads to the reduction of acetyl-CoA content, and two genes involved in the β-oxidation of fatty acids were also upregulated, which enhanced the fatty acid metabolism of the ΔMooxdc. Overall, this work reveals the role of OA in M. oryzae. We found that OA metabolism was mainly involved in the growth and development of M. oryzae, OA as a byproduct of D-erythroascorbic acid after removing H2O2, the OA-associated pathway ensures the TCA process and ATP supply.

Astaxanthin biosynthesis for functional food development and space missions

Astaxanthin (AXT), a natural carotenoid, has strong antioxidant and anti-ageing effects and can reduce ultraviolet light-induced damage to cells and DNA, stimulate the immune system, and improve cardiovascular disease prognosis. Despite its wide applications in the: nutraceutical, cosmetic, aquaculture, and pharmaceutical industries, AXT industrial production and application are hindered by natural source scarcity, low production efficiency, and high requirements. This review compares the qualitative differences of AXT derived from different natural sources, evaluates the upstream procedures for AXT expression in different chassis organisms, and investigates synthetic biology- and cell factory-based strategies for the industrial production of natural AXT. Synthetic biology is a promising novel strategy for reprogramming plants or microorganisms to produce AXT. Additionally, genetic engineering using cell factories extends beyond terrestrial applications, as it may contribute to the long-term sustainability of human health during space exploration and migration endeavors. This review provides a theoretical basis for the efficient and accurate genetic engineering of AXT from the microalga Haematococcuspluvialis, providing a valuable reference for future research on the biomanufacturing of AXT and other biological metabolites.

Functional characterization of GAPDH2 through overexpression and dsRNA-mediated RNA interference in Synechocystis

Glyceraldehyde-3-phosphate dehydrogenase 2 (GAPDH2) plays a vital role in cell growth, stress responses, and various cellular processes in organisms. However, its functional characterization in cyanobacteria, particularly in Synechocystis sp. PCC 6803, remains largely unexplored, especially concerning its overexpression and RNA interference (RNAi) via double-stranded RNA (dsRNA). This study aimed to investigate the biological role of GAPDH2 in Synechocystis sp. PCC 6803 by cloning its complete coding sequence (SyGAPDH2). The SyGAPDH2 protein comprises 350 amino acids with a molecular weight of 86.480 kDa and an isoelectric point of 5.03. The sequence alignment analysis revealed two conserved domains: NADH (Nicotinamide Adenine Dinucleotide)-quinone oxidoreductase subunit NuoI and NADH-ubiquinone/plastoquinone oxidoreductase chain 6. Similarly, Phylogenetic analysis demonstrated high sequence similarity of 96 % and 94 % with Coliform (Gammaproteobacteria bacterium), respectively. We further explored the functional significance of SyGAPDH2 through overexpression using the PpsbAII+SyGAPDH2 vector and double stranded RNA (dsRNA)-mediated silencing with dsGAPDH2. Overexpression significantly enhanced cell growth, while dsRNA-mediated suppression resulted in reduced cell proliferation, with effects observed 12 h post-treatment and persisting up to 36 h. These findings emphasize the essential regulatory role of SyGAPDH2 in cellular development and stress response. This study contributes to our understanding of GAPDH2 functional importance in cyanobacteria, providing a foundation for future investigations into its subcellular localization, additional functional roles, and broader regulatory mechanisms within cyanobacterial cellular processes.

Metabolic engineering and cultivation strategies for efficient production of fucoxanthin and related carotenoids

Fucoxanthin, a bioactive carotenoid derived from algae, has attracted considerable attention for its applications in health, cosmetics, and nutrition. Advances in metabolic engineering, such as the overexpression of pathway-specific enzymes and enhancement of precursor availability, have shown promising results in improving production efficiency. However, despite its high value, the biosynthetic pathway of fucoxanthin remains only partially elucidated, posing significant challenges for metabolic engineering efforts. Recent studies have identified previously unknown enzymes and regulatory elements within the pathway, providing opportunities for further productivity enhancements through targeted metabolic modifications. Additionally, adaptive evolution, mutagenesis-driven strain development, and optimized cultivation conditions have demonstrated significant potential to boost fucoxanthin yields. This review consolidates the latest insights into the biosynthetic pathway of fucoxanthin and highlights metabolic engineering strategies aimed at enhancing the production of fucoxanthin and related carotenoids, offering approaches to design high-yielding strains. Furthermore, recent advancements in random mutagenesis and cultivation technology are discussed. By integrating these developments, more economically viable and environmentally sustainable fucoxanthin production systems can be achieved. KEY POINTS : • Insights into fucoxanthin biosynthesis enable targeted metabolic engineering. • ALE and cultivation strategies complement metabolic engineering efforts. • Balanced push-pull-block strategies improve fucoxanthin production efficiency.

Unveiling astaxanthin: biotechnological advances, delivery systems and versatile applications in nutraceuticals and cosmetics

Astaxanthin (ASX), "king of carotenoids", is a xanthophyll carotenoid that is characterized by a distinct reddish-orange hue, procured from diverse sources including plants, microalgae, fungi, yeast, and lichens. It exhibits potent antioxidant and anti-ageing properties and has been demonstrated to mitigate ultraviolet-induced cellular and DNA damage, enhance immune system function, and improve cardiovascular diseases. Despite its broad utilization across nutraceutical, cosmetic, aquaculture, and pharmaceutical sectors, the large-scale production and application of ASX are constrained by the limited availability of natural sources, low production yields and stringent production requirements. This review provides a comprehensive analysis of ASX applications, emphasizing its dual roles in cosmetic and nutraceutical fields. It integrates insights into the qualitative differences of ASX from various natural sources and assesses biosynthetic pathways across organisms. Advanced biotechnological strategies for industrial-scale production are explored alongside innovative delivery systems, such as emulsions, films, microcapsules, nanoliposomes, and nanoparticles, designed to enhance ASX's bioavailability and functional efficacy. By unifying perspectives on its nutraceutical and cosmetic applications, this review highlights the challenges and advancements in formulation and commercialization. Prospective research directions for optimizing ASX's production and applications are also discussed, providing a roadmap for its future development.

Seven critical challenges in synthetic one-carbon assimilation and their potential solutions

Synthetic C1 assimilation holds the promise of facilitating carbon capture while mitigating greenhouse gas emissions, yet practical implementation in microbial hosts remains relatively limited. Despite substantial progress in pathway design and prototyping, most efforts stay at the proof-of-concept stage, with frequent failures observed even under in vitro conditions. This review identifies seven major barriers constraining the deployment of synthetic C1 metabolism in microorganisms and proposes targeted strategies for overcoming these issues. A primary limitation is the low catalytic activity of carbon-fixing enzymes, particularly carboxylases, which restricts the overall pathway performance. In parallel, challenges in expressing multiple heterologous genes-especially those encoding metal-dependent or oxygen-sensitive enzymes-further hinder pathway functionality. At the systems level, synthetic C1 pathways often exhibit poor flux distribution, limited integration with the host metabolism, accumulation of toxic intermediates, and disruptions in redox and energy balance. These factors collectively reduce biomass formation and compromise product yields in biotechnological setups. Overcoming these interconnected challenges is essential for moving synthetic C1 assimilation beyond conceptual stages and enabling its application in scalable, efficient bioprocesses towards a circular bioeconomy.

Minimized Dark Consumption of Calvin Cycle Intermediates Facilitates the Initiation of Photosynthesis in Synechocystis sp. PCC 6803

Cyanobacteria intricately regulate their metabolic pathways during the diurnal cycle to ensure survival and growth. Under dark conditions, the breakdown of glycogen, an energy reserve, in these organisms replenishes Calvin cycle intermediates, especially downstream glycolytic metabolites, which are necessary for photosynthesis initiation upon light irradiation. However, it remains unclear how the accumulation of these intermediates is maintained in the dark despite limited glycogen availability. Therefore, in this study, we investigated the regulation of downstream glycolytic metabolites of the Calvin cycle under dark and light conditions using Synechocystis sp. PCC 6803. Our results showed that during the dark period, low pyruvate kinase (Pyk) activity ensured metabolite accumulation, while endogenous Pyk overexpression significantly lowered the accumulation of glycolytic intermediates. Remarkably, wild-type Synechocystis maintained oxygen evolution ability throughout dark treatment for over 2 d, while Pyk overexpression resulted in decreased oxygen evolution after 16 h of dark treatment. These results indicated that limiting Pyk activity via darkness treatment facilitates photosynthetic initiation by maintaining glycolytic intermediates. Similarly, phosphoenolpyruvate carboxylase (PepC) overexpression decreased oxygen evolution under dark treatment; however, its effect was lower than that of Pyk. Furthermore, we noted that as PepC overexpression decreased the levels of glycolytic intermediates in the dark, sugar phosphates in the Calvin-Benson-Bassham (CBB) cycle showed high accumulation, suggesting that sugar phosphates play important roles in supporting photosynthesis initiation. Therefore, our study highlights the importance of controlling the metabolic pathways through which glycolytic and CBB cycle intermediates are consumed (defined as cataplerosis of the CBB cycle) to ensure stable photosynthesis.

Intracellular metabolomic profiling of Picochlorum sp. under diurnal conditions mimicking outdoor light, temperature, and seasonal variations

INTRODUCTION

This study focuses on metabolic profiling of a robust marine green algal strain Picochlorum sp. MCC39 that exhibits resilient growth under diverse outdoor open pond conditions. Given its potential for producing high-value chemicals through metabolic engineering, understanding its metabolic dynamics is crucial for pathway modification.

OBJECTIVES

This study primarily aimed to investigate the metabolic response of Picochlorum sp. to environmental changes. Unlike heterotrophs, algae are subject to diurnal light and temperature, which affect their growth rates and metabolism. Using an environmental photobioreactor (ePBR), we explored how the algal strain adapts to fluctuations in light intensities and temperature within a simulated pond environment.

METHODS

We performed a reverse phase ion pairing-LC/MS-MS based metabolome profiling of the MCC39 strain cultivated in simulated pond conditions in ePBR. The experimental setup included diurnal and bi-seasonal variations in light intensities and temperature.

RESULTS

The metabolome profile revealed significant differences in 85 metabolites, including amino acids, carboxylic acids, sugar phosphates, purines, pyrimidines, and dipeptides, which exhibited up to 25-fold change in relative concentration with diurnal variations. Seasonal variations also influenced the production of storage molecules, revealing a discernible pattern. The accumulation pattern of metabolites involved in cellular wall formation and energy generation indicated a well-coordinated initiation of photosynthesis and the Calvin cycle with the onset of light.

CONCLUSION

The results contribute to a deeper understanding of the adaptability and metabolic response of Picochlorum sp., laying the groundwork for future advancements in algal strain modification.

Microalgae growth-promoting bacteria for cultivation strategies: Recent updates and progress

Microalgae growth-promoting bacteria (MGPB), both actinobacteria and non-actinobacteria, have received considerable attention recently because of their potential to develop microalgae-bacteria co-culture strategies for improved efficiency and sustainability of the water-energy-environment nexus. Owing to their diverse metabolic pathways and ability to adapt to diverse conditions, microalgal-MGPB co-cultures could be promising biological systems under uncertain environmental and nutrient conditions. This review proposes the recent updates and progress on MGPB for microalgae cultivation through co-culture strategies. Firstly, potential MGPB strains for microalgae cultivation are introduced. Following, microalgal-MGPB interaction mechanisms and applications of their co-cultures for biomass production and wastewater treatment are reviewed. Moreover, state-of-the-art studies on synthetic biology and metabolic network analysis, along with the challenges and prospects of opting these approaches for microalgal-MGPB co-cultures are presented. It is anticipated that these strategies may significantly improve the sustainability of microalgal-MGPB co-cultures for wastewater treatment, biomass valorization, and bioproducts synthesis in a circular bioeconomy paradigm.

Tailoring nitrogen and phosphorus levels for tunable glycogen and protein production in halophilic Cyanobacterium aponinum PCC10605

Cyanobacteria hold promise for simultaneous carbon capture and chemicals production, but the regulation and effect of nitrogen (N) and phosphorus (P) remains unclear. This study investigates major productions of glycogen, protein, and C-phycocyanin (C-PC) in Cyanobacterium aponinum PCC10605 under different N/P levels, alongside changes in light and CO2. Increasing nitrate (NO3-) from 2 to 6 mM resulted in a 9.7-fold increase in C-PC and reduced glycogen to 8.9 %. On the other hand, elevating phosphorus from 0.1 to 2 mM under limited nitrogen enhanced biomass and glycogen through the upregulation of carbonic anhydrase, ADP-glucose pyrophosphorylase, and glycogen phosphorylase. Changes in phosphorus levels and CO2 inlet concentrations affected metabolites accumulation and carbon capture efficiency, leading to the best condition of 76 % uptake capacity in direct air capture (DAC). All findings underscore the trade-off between glycogen and protein, representing the importance of N/P levels in nutrient modulation of PCC10605.

Electric Polarization-Dependent Absorption and Photocurrent Generation in Limnospira indica Immobilized on Boron-Doped Diamond

We present the change of light absorption of cyanobacteria in response to externally applied electrical polarization. Specifically, we studied the relation between electrical polarization and changes in light absorbance for a biophotoelectrode assembly comprising boron-doped diamond as semiconducting electrode and live Limnospira indicaPCC 8005 trichomes embedded in either polysaccharide (agar) or conductive conjugated polymer (PEDOT-PSS) matrices. Our study involves the monitoring of cyanobacterial absorbance and the measurement of photocurrents at varying wavelengths of illumination for switched electric fields, i.e., using the bioelectrode either as an anode or as cathode. We observed changes in the absorbance characteristics, indicating a direct causal relationship between electrical polarization and absorbing properties of L. indica. Our finding opens up a potential avenue for optimization of the performance of biophotovoltaic devices through controlled polarization. Furthermore, our results provide fundamental insights into the wavelength-dependent behavior of a bio photovoltaic system using live cyanobacteria.

Metabolomics-based development of bioproduction processes toward industrial-scale production

Microbial biomanufacturing offers a promising, environment-friendly platform for next-generation chemical production. However, its limited industrial implementation is attributed to the slow production rates of target compounds and the time-intensive engineering of high-yield strains. This review highlights how metabolomics expedites bioproduction development, as demonstrated through case studies of its integration into microbial strain engineering, culture optimization, and model construction. The Design-Build-Test-Learn (DBTL) cycle serves as a standard workflow for strain engineering. Process development, including the optimization of culture conditions and scale-up, is crucial for industrial production. In silico models facilitate the development of strains and processes. Metabolomics is a powerful driver of the DBTL framework, process development, and model construction.

Perspectives for Using CO2 as a Feedstock for Biomanufacturing of Fuels and Chemicals

Microbial cell factories offer an eco-friendly alternative for transforming raw materials into commercially valuable products because of their reduced carbon impact compared to conventional industrial procedures. These systems often depend on lignocellulosic feedstocks, mainly pentose and hexose sugars. One major hurdle when utilizing these sugars, especially glucose, is balancing carbon allocation to satisfy energy, cofactor, and other essential component needs for cellular proliferation while maintaining a robust yield. Nearly half or more of this carbon is inevitably lost as CO2 during the biosynthesis of regular metabolic necessities. This loss lowers the production yield and compromises the benefit of reducing greenhouse gas emissions-a fundamental advantage of biomanufacturing. This review paper posits the perspectives of using CO2 from the atmosphere, industrial wastes, or the exhausted gases generated in microbial fermentation as a feedstock for biomanufacturing. Achieving the carbon-neutral or -negative goals is addressed under two main strategies. The one-step strategy uses novel metabolic pathway design and engineering approaches to directly fix the CO2 toward the synthesis of the desired products. Due to the limitation of the yield and efficiency in one-step fixation, the two-step strategy aims to integrate firstly the electrochemical conversion of the exhausted CO2 into C1/C2 products such as formate, methanol, acetate, and ethanol, and a second fermentation process to utilize the CO2-derived C1/C2 chemicals or co-utilize C5/C6 sugars and C1/C2 chemicals for product formation. The potential and challenges of using CO2 as a feedstock for future biomanufacturing of fuels and chemicals are also discussed.

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.

Trace impurities in sodium phosphate influences the physiological activity of Escherichia coli in M9 minimal medium

In the field of applied microbiology, reproducibility and experimental variability are important factors that influence both basic research as well as process development for industrial applications. Experimental reproducibility and accuracy depend not only on culture conditions such as temperature and aeration but also on raw materials and procedures used for media preparation. The M9 minimal medium is one of the most common synthetic media for culturing Escherichia coli and other bacteria. This synthetic medium can be used to observe and evaluate the physiological activity of microbes under minimal nutritional requirements and determine the limiting factor for the desired phenotype. Although one of the advantages using the M9 medium is that its composition can be modulated, it is difficult to control presence of trace components and impurities from the reagents for preparing this medium. Herein, we showed that trace ingredients present in the reagents used for M9 media preparation affect the bacterial physiological activities (e.g., cell growth, substrate consumption, and byproduct formation). Additionally, we systematically identified the trace ingredient that influenced phenotypic differences. Our results showed that the selection of reagents and accuracy during reagent preparation is important for experimental reproducibility in the field of bio-engineering and systems biology focused on the systematic and continuous development of biomolecular systems (e.g., biorefinery, metabolic engineering, and synthetic biology).

Thermodynamic principle to enhance enzymatic activity using the substrate affinity

Understanding how to tune enzymatic activity is important not only for biotechnological applications, but also to elucidate the basic principles guiding the design and optimization of biological systems in nature. So far, the Michaelis-Menten equation has provided a fundamental framework of enzymatic activity. However, there is still no concrete guideline on how the parameters should be optimized towards higher activity. Here, we demonstrate that tuning the Michaelis-Menten constant ([Formula: see text]) to the substrate concentration ([Formula: see text]) enhances enzymatic activity. This guideline ([Formula: see text]) was obtained mathematically by assuming that thermodynamically favorable reactions have higher rate constants, and that the total driving force is fixed. Due to the generality of these thermodynamic considerations, we propose [Formula: see text] as a general concept to enhance enzymatic activity. Our bioinformatic analysis reveals that the [Formula: see text] and in vivo substrate concentrations are consistent across a dataset of approximately 1000 enzymes, suggesting that even natural selection follows the principle [Formula: see text].

Metabolic sink engineering in cyanobacteria: Perspectives and applications

Recent advances in metabolic engineering have made cyanobacteria emerge as promising and attractive microorganisms for sustainable production, by exploiting their natural capability for producing metabolites. The potential of metabolically engineered cyanobacterium would depend on its source-sink balance in the same way as other phototrophs. In cyanobacteria, the amount of light energy harvested (Source) is incompletely utilized by the cell to fix carbon (sink) resulting in wastage of the absorbed energy causing photoinhibition and cellular damage leading to lowered photosynthetic efficiency. Although regulatory pathways like photo-acclimation and photoprotective processes can be helpful unfortunately they limit the cell's metabolic capacity. This review describes approaches for source-sink balance and engineering heterologous metabolic sinks in cyanobacteria for enhanced photosynthetic efficiency. The advances for engineering additional metabolic pathways in cyanobacteria are also described which will provide a better understanding of the cyanobacterial source-sink balance and approaches for efficient cyanobacterial strains for valuable metabolites.

Assessing and reducing phenotypic instability in cyanobacteria

Cyanobacteria have promising potential as sustainable cell factories. However, one challenge that is still largely unreported in scaling-up cyanobacteria bioproduction is phenotypic instability, where the emergence and selection of nonproducing cells leading to loss in production has longer evolutionary timescales to take place in industrial-scale bioreactors. Quantifying phenotypic instability early on in strain development allows researchers to make informed decisions on whether to proceed with scalable designs, or if present, devise countermeasures to reduce instability. One particularly effective strategy to mitigate instability is the use of genome-scale metabolic models to design growth-coupled production strains. In silico studies have predicted that creating certain cofactor imbalances or removing recycling reactions in cyanobacteria can be exploited to stably produce a wide variety of metabolites.

Improved salt tolerance of Synechococcus elongatus PCC 7942 by heterologous synthesis of compatible solute ectoine

Salt stress is one of the essential abiotic stresses for the survival of cyanobacteria. However, the realization of large-scale cultivation of cyanobacteria is inseparable from the utilization of abundant seawater resources. Therefore, research on the regulatory mechanism, as well as the improvement of salt tolerance of cyanobacteria is fundamental. Ectoine, a compatible solute which was found in halophilic microorganisms, has potentiality to confer salt tolerance. Here in this article, the salt tolerance of Synechococcus elongatus PCC 7942 (Syn7942) was significantly improved via expressing the ectoine biosynthetic pathway, reaching an increased final OD₇₅₀ by 20% under 300 mM NaCl and 80% under 400 mM NaCl than that of wild-type (WT), respectively. Encouragingly, the engineered strain could even survive under 500 mM NaCl which was lethal to WT. In addition, by introducing the ectoine synthetic pathway into the sucrose-deficient strain, the salt tolerance of the obtained strain Syn7942/Δsps-ect was restored to the level of WT under 300 mM NaCl stress, demonstrating that ectoine could substitute for sucrose to combat against salt stress in Syn7942. In order to study the difference in the regulation of mechanism on the salt adaptation process after replacing sucrose with ectoine, transcriptomic analysis was performed for Syn7942/Δsps-ect and WT. The differentially expressed gene analysis successfully identified 19 up-regulated genes and 39 down-regulated genes in Syn7942/Δsps-ect compared with WT under salt stress condition. The results also showed that the global regulation of Syn7942/Δsps-ect and WT had certain differences in the process of salt adaptation, in which Syn7942/Δsps-ect reduced the demand for the intensity of sulfur metabolism in this process. This study provides a valuable reference for further salt tolerance engineering in cyanobacteria.

Fluorescent Probe Combined with Photoelectric Analysis Technology for Detection of Escherichia coli

Food safety is facing great challenges in preventing foodborne diseases caused by pathogenic pollution, especially in resource-limited areas. The rapid detection technique of microorganisms, such as immunological methods and molecular biological methods, plays a crucial key in timely bioanalysis and disease treatment strategies. However, it is difficult for these methods to simultaneously meet the criteria of simple operation, high specificity, and sensitivity, as well as low cost. Coconut water is known as the "water of life" in Hainan. It is a refreshing and nutritious beverage which is widely consumed due to its beneficial properties to health. Coconut water processing is an important pillar industry in Hainan. The detection of pathogenic microorganisms, such as Escherichia coli, in coconut water has become an important factor which has restricted the upgrading and development of this industry. Based on the needs of industrial development, we developed a microbial photoelectric detection system which was composed of a fluorescent probe detection reagent and a photoelectric sensor detection device. This system combined microbial enzyme targets, selective fluorescent substrate metabolism characteristics, and a photoelectric sensor signal transduction mechanism, which produce a strong signal with a high signal-to-noise ratio. The microbial detection system developed here has a simple structure, simple and convenient operation, short detecting time (≥2 h), and high sensitivity (1 CFU/mL). This system may also enable early warning and monitoring programs for other pathogenic microorganisms in order to promote the overall competitiveness of the Hainan coconut water industry.

Changes in intracellular energetic and metabolite states due to increased galactolipid levels in Synechococcus elongatus PCC 7942

The lipid composition of thylakoid membranes is conserved from cyanobacteria to green plants. However, the biosynthetic pathways of galactolipids, the major components of thylakoid membranes, are known to differ substantially between cyanobacteria and green plants. We previously reported on a transformant of the unicellular rod-shaped cyanobacterium Synechococcus elongatus PCC 7942, namely SeGPT, in which the synthesis pathways of the galactolipids monogalactosyldiacylglycerol and digalactosyldiacylglycerol are completely replaced by those of green plants. SeGPT exhibited increased galactolipid content and could grow photoautotrophically, but its growth rate was slower than that of wild-type S. elongatus PCC 7942. In the present study, we investigated pleiotropic effects that occur in SeGPT and determined how its increased lipid content affects cell proliferation. Microscopic observations revealed that cell division and thylakoid membrane development are impaired in SeGPT. Furthermore, physiological analyses indicated that the bioenergetic state of SeGPT is altered toward energy storage, as indicated by increased levels of intracellular ATP and glycogen. We hereby report that we have identified a new promising candidate as a platform for material production by modifying the lipid synthesis system in this way.

C1-based biomanufacturing: Advances, challenges and perspectives

One-carbon (C1) compounds have emerged as a key research focus due to the growth of metabolic engineering and synthetic biology as affordable and sustainable nonfood sugar feedstocks for energy-efficient and environmentally friendly biomanufacturing. This paper summarizes and discusses current developments in C1 compounds for biomanufacturing. First, two primary groups of microbes that use C1 compounds (native and synthetic) are introduced, and the traits, categorization, and functions of C1 microbes are summarized. Second, engineering strategies for C1 utilization are compiled and reviewed, including reconstruction of C1-utilization pathway, enzyme engineering, cofactor engineering, genome-scale modeling, and adaptive laboratory evolution. Third, a review of C1 compounds' uses in the synthesis of biofuels and high-value compounds is presented. Finally, potential obstacles to C1-based biomanufacturing are highlighted along with future research initiatives.

Metabolic and Microbial Community Engineering for Four-Carbon Dicarboxylic Acid Production from CO2-Derived Glycogen in the Cyanobacterium Synechocystis sp. PCC6803

The four-carbon (C4) dicarboxylic acids, fumarate, malate, and succinate, are the most valuable targets that must be exploited for CO₂-based chemical production in the move to a sustainable low-carbon future. Cyanobacteria excrete high amounts of C4 dicarboxylic acids through glycogen fermentation in a dark anoxic environment. The enhancement of metabolic flux in the reductive TCA branch in the Cyanobacterium Synechocystis sp. PCC6803 is a key issue in the C4 dicarboxylic acid production. To improve metabolic flux through the anaplerotic pathway, we have created the recombinant strain PCCK, which expresses foreign ATP-forming phosphoenolpyruvate carboxykinase (PEPck) concurrent with intrinsic phosphoenolpyruvate carboxylase (Ppc) overexpression. Expression of PEPck concurrent with Ppc led to an increase in C4 dicarboxylic acids by autofermentation. Metabolome analysis revealed that PEPck contributed to an increase in carbon flux from hexose and pentose phosphates into the TCA reductive branch. To enhance the metabolic flux in the reductive TCA branch, we examined the effect of corn-steep liquor (CSL) as a nutritional supplement on C4 dicarboxylic acid production. Surprisingly, the addition of sterilized CSL enhanced the malate production in the PCCK strain. Thereafter, the malate and fumarate excreted by the PCCK strain are converted into succinate by the CSL-settling microorganisms. Finally, high-density cultivation of cells lacking the acetate kinase gene showed the highest production of malate and fumarate (3.2 and 2.4 g/L with sterilized CSL) and succinate (5.7 g/L with non-sterile CSL) after 72 h cultivation. The present microbial community engineering is useful for succinate production by one-pot fermentation under dark anoxic conditions.

Role of regulatory pathways and multi-omics approaches for carbon capture and mitigation in cyanobacteria

Cyanobacteria are known for their metabolic potential and carbon capture and sequestration capabilities. These cyanobacteria are not only an effective source for carbon minimization and resource mobilization into value-added products for biotechnological gains. The present review focuses on the detailed description of carbon capture mechanisms exerted by the various cyanobacterial strains, the role of important regulatory pathways, and their subsequent genes responsible for such mechanisms. Moreover, this review will also describe effectual mechanisms of central carbon metabolism like isoprene synthesis, ethylene production, MEP pathway, and the role of Glyoxylate shunt in the carbon sequestration mechanisms. This review also describes some interesting facets of using carbon assimilation mechanisms for valuable bio-products. The role of regulatory pathways and multi-omics approaches in cyanobacteria will not only be crucial towards improving carbon utilization but also will give new insights into utilizing cyanobacterial bioresource for carbon neutrality.

CRISPRi-enhanced direct photosynthetic conversion of carbon dioxide to succinic acid by metabolically engineered cyanobacteria

Engineering photoautotrophic microorganisms to directly convert carbon dioxide into platform chemicals is an attractive approach for chemical sustainability and carbon mitigation. Here, an engineered cyanobacterium Synechococcus elongatus PCC 7942 was developed to produce succinic acid directly from ambient carbon dioxide. Inhibition of succinate dehydrogenase and glycogen synthase by CRIPSR interference increased carbon flux towards succinic acid. Dual inhibition of these two genes led to an 82 % increase in titer. The resulting strain produced 4.8 g/L of succinic acid in a 28-days cultivation. However, cells after the 28-days cultivation became non-viable and cannot continue production. This issue was addressed by re-inoculation with fresh cells into the production medium. This strategy enabled continuous succinic acid accumulation, reaching a final titer of 8.9 g/L. This study provides a sustainable route to succinic acid directly from carbon dioxide and a potential method to overcome the low titer limitation of cyanobacterial-based bioproduction for practical applications.

Enhancement of black and odorous water treatment coupled with accelerated lipid production by microalgae exposed to 12C6+ heavy-ion beam irradiation

In this study, Auxenochlorella protothecoides (AP-CK) was selected due to its reported high growth potential in sterilized black and odorous water (SBOW). In order to improve the resource utilization level of microalgae for wastewater treatment, AP-CK was mutated using ¹²C⁶⁺ heavy-ion beam irradiation, and a high lipid-containing mutant (AP-34#) was isolated and further evaluated to treat original black and odorous water (OBOW). Compared with the wild type, the maximum removal rates of COD, NH₄⁺-N and TP of the mutant increased by 8.12 ± 0.33%, 10.43 ± 0.54% and 11.97 ± 0.16%, respectively, while maximum dissolved oxygen content increased from 0 to 4.36 ± 0.25 mg/L. Besides, the mutant lipid yield increased by 115.87 ± 3.22% over the wild type in OBOW. The fatty acid profile of AP-34# grown in SBOW and OBOW showed higher proportion of saturated fatty acids (C16:0 and C18:0) and valuable polyunsaturated fatty acids (mainly C20:5n3 and C22:6n3) which are more suitable for biodiesel production and value-added products, respectively. This work provides a new perspective on improving the characteristics of microalgae and an innovative approach for resource-based microalgae wastewater treatment through bioremediation of black and odorous water.

Towards green biomanufacturing of high-value recombinant proteins using promising cell factory: Chlamydomonas reinhardtii chloroplast

Microalgae are cosmopolitan organisms in nature with short life cycles, playing a tremendous role in reducing the pressure of industrial carbon emissions. Besides, microalgae have the unique advantages of being photoautotrophic and harboring both prokaryotic and eukaryotic expression systems, becoming a popular host for recombinant proteins. Currently, numerous advanced molecular tools related to microalgal transgenesis have been explored and established, especially for the model species Chlamydomonas reinhardtii (C. reinhardtii hereafter). The development of genetic tools and the emergence of new strategies further increase the feasibility of developing C. reinhardtii chloroplasts as green factories, and the strong genetic operability of C. reinhardtii endows it with enormous potential as a synthetic biology platform. At present, C. reinhardtii chloroplasts could successfully produce plenty of recombinant proteins, including antigens, antibodies, antimicrobial peptides, protein hormones and enzymes. However, additional techniques and toolkits for chloroplasts need to be developed to achieve efficient and markerless editing of plastid genomes. Mining novel genetic elements and selectable markers will be more intensively studied in the future, and more factors affecting protein expression are urged to be explored. This review focuses on the latest technological progress of selectable markers for Chlamydomonas chloroplast genetic engineering and the factors that affect the efficiency of chloroplast protein expression. Furthermore, urgent challenges and prospects for future development are pointed out.

Metabolomics revealed the photosynthetic performance and metabolomic characteristics of Euglena gracilis under autotrophic and mixotrophic conditions

Photosynthetic and metabolomic performance of Euglena gracilis was examined and compared under autotrophic and mixotrophic conditions. Autotrophic protozoa (AP) obtained greater biomass (about 33% higher) than the mixotrophic protozoa (MP) after 12 days of growth. AP maintained steady photosynthesis, while MP showed a remarkable decrease in photosynthetic efficiency and dropped to an extremely low level at day 12. In MP, low light absorption and photosynthetic electron transport efficiency, and high energy dissipation were reflected by the chlorophyll (chl a) fluorescence (OJIP) of the protozoa. The values of Ψ_O, Φ_Eo, and ET_O/RC of MP decreased to extremely low levels, to 1/15, 1/46, and 1/9 those of AP, respectively, while DI_O/RC increased to approximately 16 times that of AP. A total of 137 metabolites were showed significant differences between AP and MP. AP accumulated more monosaccharide, lipids, and alkaloids, while MP produced more amino acids, peptides, and long-chain fatty acids including poly-unsaturated fatty acids. The top nine most important enriched pathways obtained from KEGG mapping were related to ABC transporters, biosynthesis of amino acids, purine metabolism, and carbohydrate metabolism. There were significant differences between AP and MP in photosynthetic activity, metabolites, and metabolic pathways. This work presented useful information for the production of high value bioproducts in E. gracilis cultured under different nutritional conditions.

Combinatorial CRISPR Interference Library for Enhancing 2,3-BDO Production and Elucidating Key Genes in Cyanobacteria

Cyanobacteria can convert CO₂ to chemicals such as 2,3-butanediol (2,3-BDO), rendering them promising for renewable production and carbon neutralization, but their applications are limited by low titers. To enhance cyanobacterial 2,3-BDO production, we developed a combinatorial CRISPR interference (CRISPRi) library strategy. We integrated the 2,3-BDO pathway genes and a CRISPRi library into the cyanobacterium PCC7942 using the orthogonal CRISPR system to overexpress pathway genes and attenuate genes that inhibit 2,3-BDO formation. The combinatorial CRISPRi library strategy allowed us to inhibit fbp, pdh, ppc, and sps (which catalyzes the synthesis of fructose-6-phosphate, acetyl-coenzyme A, oxaloacetate, and sucrose, respectively) at different levels, thereby allowing for rapid screening of a strain that enhances 2,3-BDO production by almost 2-fold to 1583.8 mg/L. Coupled with a statistical model, we elucidated that differentially inhibiting all the four genes enhances 2,3-BDO synthesis to varying degrees. fbp and pdh suppression exerted more profound effects on 2,3-BDO production than ppc and sps suppression, and these four genes can be repressed simultaneously without mutual interference. The CRISPRi library approach paves a new avenue to combinatorial metabolic engineering of cyanobacteria.

Exploitation of Hetero- and Phototrophic Metabolic Modules for Redox-Intensive Whole-Cell Biocatalysis

The successful realization of a sustainable manufacturing bioprocess and the maximization of its production potential and capacity are the main concerns of a bioprocess engineer. A main step towards this endeavor is the development of an efficient biocatalyst. Isolated enzyme(s), microbial cells, or (immobilized) formulations thereof can serve as biocatalysts. Living cells feature, beside active enzymes, metabolic modules that can be exploited to support energy-dependent and multi-step enzyme-catalyzed reactions. Metabolism can sustainably supply necessary cofactors or cosubstrates at the expense of readily available and cheap resources, rendering external addition of costly cosubstrates unnecessary. However, for the development of an efficient whole-cell biocatalyst, in depth comprehension of metabolic modules and their interconnection with cell growth, maintenance, and product formation is indispensable. In order to maximize the flux through biosynthetic reactions and pathways to an industrially relevant product and respective key performance indices (i.e., titer, yield, and productivity), existing metabolic modules can be redesigned and/or novel artificial ones established. This review focuses on whole-cell bioconversions that are coupled to heterotrophic or phototrophic metabolism and discusses metabolic engineering efforts aiming at 1) increasing regeneration and supply of redox equivalents, such as NAD(P/H), 2) blocking competing fluxes, and 3) increasing the availability of metabolites serving as (co)substrates of desired biosynthetic routes.

Progress and perspectives for microbial production of farnesene

Farnesene is increasingly used in industry, agriculture, and other fields due to its unique and excellent properties, necessitating its efficient synthesis. Microbial synthesis is an ideal farnesene production method. Recently, researchers have used several strategies to optimize the production performance of microorganisms. This review summarized these strategies, including regulation of farnesene synthesis pathways, and proposed some emerging tools and methods in stain engineering. Meanwhile, new farnesene biosynthetic pathways and effective farnesene production from cheap or waste substrates were emphatically introduced. Finally, future farnesene biosynthesis challenges were discussed.