Microbial succinic acid production: Natural versus metabolic engineered producers

Succinic acid - A run-through of the latest perspectives of production from renewable biomass

Succinic acid (SA) production is continuously rising, as its applications in diverse end-product generation are getting broader and more expansive. SA is an eco-friendly bulk product that acts as a valuable intermediate in different processes and might substitute other petrochemical-based products due to the inner capacity of microbes to biosynthesize it. Moreover, large amounts of SA can be obtained through biotechnological ways starting from renewable resources, imprinting at the same time the concept of a circular economy. In this context, the target of the present review paper is to bring an overview of SA market demands, production, biotechnological approaches, new strategies of production, and last but not least, the possible limitations and the latest perspectives in terms of natural biosynthesis of SA.

Untargeted metabolomic analysis reveals the mechanism of Enterococcus faecium agent induced CaCO3 scale inhibition

In this study, a lactic acid bacterium, Enterococcus faecium, was found to prevent CaCO₃ precipitation through its metabolism. On analysis of all stages of E. faecium growth, static jar tests demonstrated that stationary phase E. faecium broth possessed the highest inhibition efficiency of 97.3% at a 0.4% inoculation dosage, followed by the decline and log phases with efficiencies of 90.03% and 76.07%, respectively. Biomineralization experiments indicated that E. faecium fermented the substrate to produce organic acid, which resulted in modulation of the pH and alkalinity of the environment and thus inhibited CaCO₃ precipitation. Surface characterization techniques indicated that the CaCO₃ crystals precipitated by the E. faecium broth tended to be significantly distorted and formed other organogenic calcite crystals. The scale inhibition mechanisms were revealed by untargeted metabolomic analysis on log and stationary phase E. faecium broth. In total, 264 metabolites were detected, 28 of which were differential metabolites (VIP ≥ 1 and p < 0.05). Of these, 15 metabolites were upregulated in stationary phase broth, and 13 metabolites were downregulated in log phase broth. Metabolic pathway analysis suggested that improved glycolysis and the TCA cycle were the main reasons for enhancement of the antiscaling performance of E. faecium broth. These findings have significant implications for microbial metabolism-induced CaCO₃ scale inhibition.

Utilizing rice straw and sugarcane bagasse as low-cost feedstocks towards sustainable production of succinic acid

Succinic acid (SA) has been produced from rice straw (RS) and sugarcane bagasse (SB) as low-cost feedstocks in this study through sequential peracetic acid (PA) and alkaline peroxide (AP) pretreatment assisted by ultrasound and pre-hydrolysis followed by simultaneous saccharification and fermentation (PSSF). The effect of yeast extract (YE) concentration, inoculum concentration, and biomass type on SA production was investigated. The results showed that SA production from RS and SB was significantly affected by the YE concentration. Final concentration and yield of SA produced were significantly increased along with the increasing of YE concentration. Moreover, inoculum concentration significantly affected the SA production from SB. Higher inoculum concentration led to higher SA production. On the other hand, SA production from RS was not significantly affected by the inoculum concentration. Using RS as the feedstock, the highest SA production was achieved on the medium containing 15 g/L YE with 5 % v/v inoculum, obtaining SA concentration and yield of 3.64 ± 0.1 g/L and 0.18 ± 0.05 g/g biomass, respectively. Meanwhile, the highest SA production from SB was acquired on the medium containing 10 g/L YE with 7.5 % v/v inoculum, resulting SA concentration and yield of 5.1 ± 0.1 g/L and 0.25 ± 0.05 g/g biomass, respectively. This study suggested that RS and SB are potential to be used as low-cost feedstocks for sustainable and environmentally friendly SA production through ultrasonic-assisted PA and AP pretreatment and PSSF.

Antimicrobial Resistance and Recent Alternatives to Antibiotics for the Control of Bacterial Pathogens with an Emphasis on Foodborne Pathogens

Antimicrobial resistance (AMR) is one of the most important global public health problems. The imprudent use of antibiotics in humans and animals has resulted in the emergence of antibiotic-resistant bacteria. The dissemination of these strains and their resistant determinants could endanger antibiotic efficacy. Therefore, there is an urgent need to identify and develop novel strategies to combat antibiotic resistance. This review provides insights into the evolution and the mechanisms of AMR. Additionally, it discusses alternative approaches that might be used to control AMR, including probiotics, prebiotics, antimicrobial peptides, small molecules, organic acids, essential oils, bacteriophage, fecal transplants, and nanoparticles.

Metabolic engineering of Mannheimia succiniciproducens for malic acid production using dimethylsulfoxide as an electron acceptor

Microbial production of various TCA intermediates and related chemicals through the reductive TCA cycle has been of great interest. However, rumen bacteria that naturally possess strong reductive TCA cycle have been rarely studied to produce these chemicals, except for succinic acid, due to their dependence on fumarate reduction to transport electrons for ATP synthesis. In this study, malic acid (MA), a dicarboxylic acid of industrial importance, was selected as a target chemical for mass production using Mannheimia succiniciproducens, a rumen bacterium possessing a strong reductive branch of the TCA cycle. The metabolic pathway was reconstructed by eliminating fumarase to prevent MA conversion to fumarate. The respiration system of M. succiniciproducens was reconstructed by introducing the Actinobacillus succinogenes dimethylsulfoxide (DMSO) reductase to improve cell growth using DMSO as an electron acceptor. Also, the cell membrane was engineered by employing Pseudomonas aeruginosa cis-trans isomerase to enhance MA tolerance. High inoculum fed-batch fermentation of the final engineered strain produced 61 g/L of MA with an overall productivity of 2.27 g/L/h, which is the highest MA productivity reported to date. The systems metabolic engineering strategies reported in this study will be useful for developing anaerobic bioprocesses for the production of various industrially important chemicals.

Deciphering the Fingerprint of Dissolved Organic Matter in the Soil Amended with Biodegradable and Conventional Microplastics Based on Optical and Molecular Signatures

Biodegradable polymers are promoted as promising alternatives for conventional non-degradable plastics, but they may also negatively impact soil ecosystems. Here, we estimated the effects of biodegradable (polylactide (PLA) and polybutylene succinate (PBS)) and non-biodegradable (polyethylene (PE) and polystyrene (PS)) microplastics at a concentration of 1% (w/w) on dissolved organic matter (DOM) in two soil types, a black soil (BS) and a yellow soil (YS), by using fluorescence excitation-emission matrix spectroscopy and ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). PBS significantly increased the contents of soil dissolved organic carbon (DOC) and the relative intensities of protein-like components. The turnover rates of soil DOM were statistically higher in PBS treatments (0.106 and 0.196, p < 0.001) than those in other microplastic groups. The FT-ICR-MS results indicated that more labile-active DOM molecules were preferentially obtained in biodegradable microplastic treatments, which may be attributed to the polymer degradation. The conventional microplastics showed no significant effects on the optical characteristics but changed the molecular compositions of the soil DOM. More labile DOM molecules were observed in BS samples treated with PE compared to the control, while the conventional microplastics decreased the DOM lability in YS soil. The distinct priming effects of plastic-leached DOM may trigger the DOM changes in different soils. This study provided important information for further understanding the impact of microplastics on soil carbon processes.

Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools

Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.

Metabolomics for the design of new metabolic engineering strategies for improving aerobic succinic acid production in Escherichia coli

INTRODUCTION

Glycerol is a byproduct from the biodiesel industry that can be biotransformed by Escherichia coli to high added-value products such as succinate under aerobic conditions. The main genetic engineering strategies to achieve this aim involve the mutation of succinate dehydrogenase (sdhA) gene and also those responsible for acetate synthesis including acetate kinase, phosphate acetyl transferase and pyruvate oxidase encoded by ackA, pta and pox genes respectively in the ΔsdhAΔack-ptaΔpox (M4) mutant. Other genetic manipulations to rewire the metabolism toward succinate consist on the activation of the glyoxylate shunt or blockage the pentose phosphate pathway (PPP) by deletion of isocitrate lyase repressor (iclR) or gluconate dehydrogenase (gnd) genes on M4-ΔiclR and M4-Δgnd mutants respectively.

OBJECTIVE

To deeply understand the effect of the blocking of the pentose phosphate pathway (PPP) or the activation of the glyoxylate shunt, metabolite profiles were analyzed on M4-Δgnd, M4-ΔiclR and M4 mutants.

METHODS

Metabolomics was performed by FT-IR and GC-MS for metabolite fingerprinting and HPLC for quantification of succinate and glycerol.

RESULTS

Most of the 65 identified metabolites showed lower relative levels in the M4-ΔiclR and M4-Δgnd mutants than those of the M4. However, fructose 1,6-biphosphate, trehalose, isovaleric acid and mannitol relative concentrations were increased in M4-ΔiclR and M4-Δgnd mutants. To further improve succinate production, the synthesis of mannitol was suppressed by deletion of mannitol dehydrogenase (mtlD) on M4-ΔgndΔmtlD mutant that increase ~ 20% respect to M4-Δgnd.

CONCLUSION

Metabolomics can serve as a holistic tool to identify bottlenecks in metabolic pathways by a non-rational design. Genetic manipulation to release these restrictions could increase the production of succinate.

The Effect of Molecular Weight on the (Re)-Processability and Material Properties of Bio-Based, Thermoreversibly Cross-Linked Polyesters

A (partially) bio-based short-chain polyester is prepared through interfacial polycondensation of furan-functionalized diphenolic acid with terephthalic chloride. The furan groups along the backbone of the obtained polyester are able to form a covalent network (PE-fur/Bism) with various ratios of 1,1′-(methylenedi-4,1-phenylene)bismaleimide via the thermoreversible Diels–Alder (DA) reaction. Several techniques have been employed to characterize the polyester network, including 1H-NMR, gel permeation chromatography (GPC), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and dynamic mechanical thermal analysis (DMTA). The polyester base polymer displays a glass transition temperature of 115 °C, whereas the temperatures at which the retro-Diels–Alder (rDA) reaction takes place lie above 130 °C for the various polyester/bismaleimide networks. Excellent thermoreversibility and recyclability of the polyester resin have been shown through DSC and DMTA measurements.

Bio-Based Aromatic Polyesters Reversibly Crosslinked via the Diels–Alder Reaction

Diphenolic acid is functionalized with furfuryl amine and subsequently incorporated in a (partly) bio-based polyester through interfacial polycondensation with terepthalic chloride. The furan groups present in the resulting polyester are able to form a thermoreversible covalent network with different bismaleimide moieties via the Diels–Alder (DA) reaction. Our analysis of the polymer network by 1H-NMR clearly shows the formation of both possible stereoisomers (endo and exo) from the Diels–Alder coordination of furan and maleimide. Furthermore, it was found that these isomers can be reversibly interchanged at temperatures below the reported retro Diels–Alder reaction temperature, a phenomenon often claimed but, until present, never directly observed, for thermally reversible polymeric systems. Finally, a proof of principle for reversibility and recyclability is shown.

Combined Impact of Magnetic Force and Spaceflight Conditions on Escherichia Coli Physiology

Changes in bacterial physiology caused by the combined action of the magnetic force and microgravity were studied in Escherichia coli grown using a specially developed device aboard the International Space Station. The morphology and metabolism of E. coli grown under spaceflight (SF) or combined spaceflight and magnetic force (SF + MF) conditions were compared with ground cultivated bacteria grown under standard (control) or magnetic force (MF) conditions. SF, SF + MF, and MF conditions provided the up-regulation of Ag43 auto-transporter and cell auto-aggregation. The magnetic force caused visible clustering of non-sedimenting bacteria that formed matrix-containing aggregates under SF + MF and MF conditions. Cell auto-aggregation was accompanied by up-regulation of glyoxylate shunt enzymes and Vitamin B12 transporter BtuB. Under SF and SF + MF but not MF conditions nutrition and oxygen limitations were manifested by the down-regulation of glycolysis and TCA enzymes and the up-regulation of methylglyoxal bypass. Bacteria grown under combined SF + MF conditions demonstrated superior up-regulation of enzymes of the methylglyoxal bypass and down-regulation of glycolysis and TCA enzymes compared to SF conditions, suggesting that the magnetic force strengthened the effects of microgravity on the bacterial metabolism. This strengthening appeared to be due to magnetic force-dependent bacterial clustering within a small volume that reinforced the effects of the microgravity-driven absence of convectional flows.

Synthesis of Bio-based monomers and polymers using microbes for a sustainable bioeconomy

As a result of environmental concerns and the depletion of biomass assets, eco-friendly, renewable biomass-based chemical extraction has recently received significant attention. Bio-based chemicals can be prepared using different renewable feedstockbio-resources through microbial fermentation. Chemicals produced from renewable feedstockscan reduce ecological consequences from improper disposal and repurpose them into valuable products. Biodegradability, biocompatibility and non-toxicity, particularly in biomedical applications, have inspired researchers towards developing novel technologies that have social benefit. Among semi-synthetic and synthetic polymeric materials, utilization of natural bio-based monomeric materials can provide opportunities for sustainable development of novel non-toxic, biodegradable and biocompatible products. The purpose of this work is to give a summary of research into the generation of natural bio-based succinic acid (SA) monomer, the development of poly(butylene succinate) (PBS) as biodegradable polymer, PBS-based nanocomposites and their innovative uses.

Valorisation of xylose to renewable fuels and chemicals, an essential step in augmenting the commercial viability of lignocellulosic biorefineries

Biologists and engineers are making tremendous efforts in contributing to a sustainable and green society. To that end, there is growing interest in waste management and valorisation. Lignocellulosic biomass (LCB) is the most abundant material on the earth and an inevitable waste predominantly originating from agricultural residues, forest biomass and municipal solid waste streams. LCB serves as the renewable feedstock for clean and sustainable processes and products with low carbon emission. Cellulose and hemicellulose constitute the polymeric structure of LCB, which on depolymerisation liberates oligomeric or monomeric glucose and xylose, respectively. The preferential utilization of glucose and/or absence of the xylose metabolic pathway in microbial systems cause xylose valorization to be alienated and abandoned, a major bottleneck in the commercial viability of LCB-based biorefineries. Xylose is the second most abundant sugar in LCB, but a non-conventional industrial substrate unlike glucose. The current review seeks to summarize the recent developments in the biological conversion of xylose into a myriad of sustainable products and associated challenges. The review discusses the microbiology, genetics, and biochemistry of xylose metabolism with hurdles requiring debottlenecking for efficient xylose assimilation. It further describes the product formation by microbial cell factories which can assimilate xylose naturally and rewiring of metabolic networks to ameliorate xylose-based bioproduction in native as well as non-native strains. The review also includes a case study that provides an argument on a suitable pathway for optimal cell growth and succinic acid (SA) production from xylose through elementary flux mode analysis. Finally, a product portfolio from xylose bioconversion has been evaluated along with significant developments made through enzyme, metabolic and process engineering approaches, to maximize the product titers and yield, eventually empowering LCB-based biorefineries. Towards the end, the review is wrapped up with current challenges, concluding remarks, and prospects with an argument for intense future research into xylose-based biorefineries.

Current Progress in Production of Building-Block Organic Acids by Consolidated Bioprocessing of Lignocellulose

Several organic acids have been indicated among the top value chemicals from biomass. Lignocellulose is among the most attractive feedstocks for biorefining processes owing to its high abundance and low cost. However, its highly complex nature and recalcitrance to biodegradation hinder development of cost-competitive fermentation processes. Here, current progress in development of single-pot fermentation (i.e., consolidated bioprocessing, CBP) of lignocellulosic biomass to high value organic acids will be examined, based on the potential of this approach to dramatically reduce process costs. Different strategies for CBP development will be considered such as: (i) design of microbial consortia consisting of (hemi)cellulolytic and valuable-compound producing strains; (ii) engineering of microorganisms that combine biomass-degrading and high-value compound-producing properties in a single strain. The present review will mainly focus on production of organic acids with application as building block chemicals (e.g., adipic, cis,cis-muconic, fumaric, itaconic, lactic, malic, and succinic acid) since polymer synthesis constitutes the largest sector in the chemical industry. Current research advances will be illustrated together with challenges and perspectives for future investigations. In addition, attention will be dedicated to development of acid tolerant microorganisms, an essential feature for improving titer and productivity of fermentative production of acids.

Developments of biobased plasticizers for compostable polymers in the green packaging applications: A review

The demand for biobased materials for various end-uses in the bioplastic industry is substantially growing due to increasing awareness of health and environmental concerns, along with the toxicity of synthetic plasticizers such as phthalates. This fact has stimulated new regulations requiring the replacement of synthetic conventional plasticizers, particularly for packaging applications. Biobased plasticizers have recently been considered as essential additives, which may be used during the processing of compostable polymers to enormously boost biobased packaging applications. The development and utilization of biobased plasticizers derived from epoxidized soybean oil, castor oil, cardanol, citrate, and isosorbide have been broadly investigated. The synthesis of biobased plasticizers derived from renewable feedstocks and their impact on packaging material performance have been emphasized. Moreover, the effect of biobased plasticizer concentration, interaction, and compatibility on the polymer properties has been examined. Recent developments have resulted in the replacement of synthetic plasticizers by biobased counterparts. Particularly, this has been the case for some biodegradable thermoplastics-based packaging applications.

Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability

Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO₂ and CH₄) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.

Potential Valorization of Organic Waste Streams to Valuable Organic Acids through Microbial Conversion: A South African Case Study

The notion of a “biobased economy” in the context of a developing country such as South Africa (SA) necessitates the development of technologies that utilize sustainable feedstocks, have simple and robust operations, are feasible at small scale and produce a variety of valuable bioproducts, thus fitting the biorefinery concept. This case study focuses on the microbial production of higher-value products from selected organic waste streams abundant in the South African agricultural sector using microbes adapted to utilize different parts of biomass waste streams. A ruminant-based carboxylate platform based on mixed or undefined anaerobic co-cultures of rumen microorganisms can convert the carbohydrate polymers in the lignocellulosic part of organic waste streams to carboxylic acids that can be upgraded to biofuels or green chemicals. Furthermore, yeast and fungi can convert the simpler carbohydrates (such as the sugars and malic acid in grape and apple pomace) to ethanol and high-value carboxylic acids, such as lactic, fumaric, succinic and citric acid. This review will discuss the combinational use of the ruminal carboxylate platform and native or recombinant yeasts to valorize biomass waste streams through the production of higher-value organic acids with various applications.

Comparative untargeted metabolome analysis of ruminal fluid and feces of Nelore steers (Bos indicus)

We conducted a study to identify the fecal metabolite profile and its proximity to the ruminal metabolism of Nelore steers based on an untargeted metabolomic approach. Twenty-six Nelore were feedlot with same diet during 105 d. Feces and rumen fluid were collected before and at slaughter, respectively. The metabolomics analysis indicated 49 common polar metabolites in the rumen and feces. Acetate, propionate, and butyrate were the most abundant polar metabolites in both bio-samples. The rumen presented significantly higher concentrations of the polar compounds when compared to feces (P < 0.05); even though, fecal metabolites presented an accentuated representability of the ruminal fluid metabolites. All fatty acids present in the ruminal fluid were also observed in the feces, except for C20:2n6 and C20:4n6. The identified metabolites offer information on the main metabolic pathways (higher impact factor and P < 0.05), as synthesis and degradation of ketone bodies; the alanine, aspartate and glutamate metabolisms, the glycine, serine; and threonine metabolism and the pyruvate metabolism. The findings reported herein on the close relationship between the ruminal fluid and feces metabolic profiles may offer new metabolic information, in addition to facilitating the sampling for metabolism investigation in animal production and health routines.

Membrane Purification Techniques for Recovery of Succinic Acid Obtained from Fermentation Broth during Bioconversion of Lignocellulosic Biomass: Current Advances and Future Perspectives

Recently, the bioconversion of biomass into biofuels and biocommodities has received significant attention. Although green technologies for biofuel and biocommodity production are advancing, the productivity and yield from these techniques are low. Over the past years, various recovery and purification techniques have been developed and successfully employed to improve these technologies. However, these technologies still require improvement regarding the energy-consumption-related costs, low yield and product purity. In the context of sustainable green production, this review presents a broad review of membrane purification technologies/methods for succinic acid, a biocommodity obtained from lignocellulosic biomass. In addition, a short overview of the global market for sustainable green chemistry and circular economy systems or zero waste approach towards a sustainable waste management is presented. Succinic acid, the available feedstocks for its production and its industrial applications are also highlighted. Downstream separation processes of succinic acid and the current studies on different downstream processing techniques are critically reviewed. Furthermore, critical analysis of membrane-based downstream processes of succinic acid production from fermentation broth is highlighted. A short review of the integrated-membrane-based process is discussed, as well, because integrating “one-pot” lignocellulosic bioconversion to succinic acid with downstream separation processing is considered a critical issue to address. In conclusion, speculations on outlook are suggested.

Impact of nitrogen deficiency on succinic acid production by engineered strains of Yarrowia lipolytica

Yarrowia lipolytica strains PGC01003 and PGC202 engineered for succinic acid production were studied and compared to the wild type strain W29. For the first time, these two strains were characterized in a chemically defined medium. Strain growth and organic acid production were investigated in fed-batch mode with glycerol as carbon and energy source. This study evaluated the impact of nitrogen deficiency strategy to redirect carbon flux toward succinic acid synthesis. Strain PGC01003 produced 19 g L^-1 succinic acid with an overall yield of 0.23 g g^-1 and an overall productivity of 0.23 g L^-1 h^-1, while strain PGC202 produced 33 g L^-1 succinic acid with an overall yield of 0.12 g g^-1 and a productivity of 0.57 g L^-1 h^-1. Nitrogen limitation effectively stopped biomass growth and increased succinic acid yield of PGC01003 and PGC202 by 18 % and 62 %, respectively. However, the specific succinic acid production rate was reduced by 77 % and 66 %, respectively.

One step forward, two steps back: Transcriptional advancements and fermentation phenomena in Actinobacillus succinogenes 130Z

Within the field of bioproduction, non-model organisms offer promise as bio-platform candidates. Non-model organisms can possess natural abilities to consume complex feedstocks, produce industrially useful chemicals, and withstand extreme environments that can be ideal for product extraction. However, non-model organisms also come with unique challenges due to lack of characterization. As a consequence, developing synthetic biology tools, predicting growth behavior, and building computational models can be difficult. There have been many advancements that have improved work with non-model organisms to address broad limitations, however each organism can come with unique surprises. Here we share our work in the non-model bacterium Actinobacillus succinognes 130Z, which includes both advancements in synthetic biology toolkit development and pitfalls in unpredictable fermentation behaviors. To develop a synthetic biology “tool kit” for A. succinogenes, information gleaned from a growth study and antibiotic screening was used to characterize 22 promoters which demonstrated a 260-fold range of fluorescence protein expression. The strongest of the promoters was incorporated into an inducible system for tunable gene control in A. succinogenes using the promoter for the lac operon as a template. This system flaunted a 481-fold range of expression and no significant basal expression. These findings were accompanied by unexpected changes in fermentation products characterized by a loss of succinic acid and increase in lactic acid after approximately 10 months in the lab. During evaluation of the fermentation shifts, new tests of the synthetic biology tools in a succinic acid producing strain revealed a significant loss in their functionality. Contamination and mutation were ruled out as causes and further testing is needed to elucidate the driving factors. The significance of this work is to share a successful tool development strategy that could be employed in other non-model species, report on an unfortunate phenomenon that needs addressed for further development of A. succinogenes, and provide a cautionary tale for those undertaking non-model research. In sharing our findings, we seek to provide tools and necessary information for further development of A. succinogenes as a platform for bioproduction of succinic acid and to illustrate the importance of diligent and long-term observation when working with non-model bacteria.

Characterization of JEN family carboxylate transporters from the acid-tolerant yeast Pichia kudriavzevii and their applications in succinic acid production

The unconventional yeast Pichia kudriavzevii is renowned for its ability to survive at low pH and has been exploited for the industrial production of various organic acids, especially succinic acid (SA). However, P. kudriavzevii can also utilize the di- and tricarboxylate intermediates of the Krebs cycle as the sole carbon sources for cell growth, which may adversely affect the extracellular accumulation of SA. Because the carboxylic acid transport machinery of P. kudriavzevii remains poorly understood, here, we focused on studying its SA transportation process from the perspective of mining and characterization of dicarboxylate transporters in a newly isolated acid-tolerant P. kudriavzevii strain CY902. Through genome sequencing and transcriptome analysis, two JEN family carboxylate transporters (PkJEN2-1 and PkJEN2-2) were found to be involved in SA transport. Substrate specificity analysis revealed that both PkJEN proteins are active dicarboxylate transporters, that can effectively import succinate, fumarate and L-malate into the cell. In addition, PkJEN2-1 can transport α-ketoglutarate, while PkJEN2-2 cannot. Since PkJEN2-1 shows higher transcript abundance than PkJEN2-2, its role in dicarboxylate transport is more important than PkJEN2-2. In addition, PKJEN2-2 is also responsible for the uptake of citrate. To our best knowledge, this is the first study to show that a JEN2 subfamily transporter is involved in tricarboxylate transport in yeast. A combination of model-based structure analysis and rational mutagenesis further proved that amino acid residues 392-403 of the tenth transmembrane span (TMS-X) of PkJEN2-2 play an important role in determining the specificity of the tricarboxylate substrate. Moreover, these two PkJEN transporters only exhibited inward transport activity for SA, and simultaneous inactivation of both PkJEN transporters reduced the SA influx, resulting in enhanced extracellular accumulation of SA in the late stage of fermentation. This work provides useful information on the mechanism of di-/tricarboxylic acid utilization in P. kudriavzevii, which will help improve the organic acid production performance of this microbial chassis.

Socio-Economic and Environmental Impacts of Biomass Valorisation: A Strategic Drive for Sustainable Bioeconomy

In the late twentieth century, the only cost-effective opportunity for waste removal cost at least several thousand dollars, but nowadays, a lot of improvement has occurred. The biomass and waste generation problems attracted concerned authorities to identify and provide environmentally friendly sustainable solutions that possess environmental and economic benefits. The present study emphasises the valorisation of biomass and waste produced by domestic and industrial sectors. Therefore, substantial research is ongoing to replace the traditional treatment methods that potentially acquire less detrimental effects. Synthetic biology can be a unique platform that invites all the relevant characters for designing and assembling an efficient program that could be useful to handle the increasing threat for human beings. In the future, these engineered methods will not only revolutionise our lives but practically lead us to get cheaper biofuels, producing bioenergy, pharmaceutics, and various biochemicals. The bioaugmentation approach concomitant with microbial fuel cells (MFC) is an example that is used to produce electricity from municipal waste, which is directly associated with the loading of waste. Beyond the traditional opportunities, herein, we have spotlighted the new advances in pertinent technology closely related to production and reduction approaches. Various integrated modern techniques and aspects related to the industrial sector are also discussed with suitable examples, including green energy and other industrially relevant products. However, many problems persist in present-day technology that requires essential efforts to handle thoroughly because significant valorisation of biomass and waste involves integrated methods for timely detection, classification, and separation. We reviewed and proposed the anticipated dispensation methods to overcome the growing stream of biomass and waste at a distinct and organisational scale.

Uncoupling growth and succinic acid production in an industrial Saccharomyces cerevisiae strain

This study explores the relation between biomass‐specific succinic acid (SA) production rate and specific growth rate of an engineered industrial strain of Saccharomyces cerevisiae, with the aim to investigate the extent to which growth and product formation can be uncoupled. Ammonium‐limited aerobic chemostat and retentostat cultures were grown at different specific growth rates under industrially relevant conditions, that is, at a culture pH of 3 and with sparging of a 1:1 CO₂–air mixture. Biomass‐specific SA production rates decreased asymptotically with decreasing growth rate. At near‐zero growth rates, the engineered strain maintained a stable biomass‐specific SA production rate for over 500 h, with a SA yield on glucose of 0.61 mol mol⁻¹. These results demonstrate that uncoupling of growth and SA production could indeed be achieved. A linear relation between the biomass‐specific SA production rate and glucose consumption rate indicated the coupling of SA production rate and the flux through primary metabolism. The low culture pH resulted in an increased death rate, which was lowest at near‐zero growth rates. Nevertheless, a significant amount of non‐viable biomass accumulated in the retentostat cultures, thus underlining the importance of improving low‐pH tolerance in further strain development for industrial SA production with S. cerevisiae.

Co-production of acetoin and succinic acid by metabolically engineered Enterobacter cloacae

BACKGROUND

Renewable chemicals have attracted attention due to increasing interest in environmental concerns and resource utilization. Biobased production of industrial compounds from nonfood biomass has become increasingly important as a sustainable replacement for traditional petroleum-based production processes depending on fossil resources. Therefore, we engineered an Enterobacter cloacae budC and ldhA double-deletion strain (namely, EC∆budC∆ldhA) to redirect carbon fluxes and optimized the culture conditions to co-produce succinic acid and acetoin.

RESULTS

In this work, E. cloacae was metabolically engineered to enhance its combined succinic acid and acetoin production during fermentation. Strain EC∆budC∆ldhA was constructed by deleting 2,3-butanediol dehydrogenase (budC), which is involved in 2,3-butanediol production, and lactate dehydrogenase (ldhA), which is involved in lactic acid production, from the E. cloacae genome. After redirecting and fine-tuning the E. cloacae metabolic flux, succinic acid and acetoin production was enhanced, and the combined production titers of acetoin and succinic acid from glucose were 17.75 and 2.75 g L^-1, respectively. Moreover, to further improve acetoin and succinic acid production, glucose and NaHCO₃ modes and times of feeding were optimized during fermentation of the EC∆budC∆ldhA strain. The maximum titers of acetoin and succinic acid were 39.5 and 20.3 g L^-1 at 72 h, respectively.

CONCLUSIONS

The engineered strain EC∆budC∆ldhA is useful for the co-production of acetoin and succinic acid and for reducing microbial fermentation costs by combining processes into a single step.

Promising advancement in fermentative succinic acid production by yeast hosts

As a platform chemical with various applications, succinic acid (SA) is currently produced by petrochemical processing from oil-derived substrates such as maleic acid. In order to replace the environmental unsustainable hydrocarbon economy with a renewable environmentally sound carbohydrate economy, bio-based SA production process has been developed during the past two decades. In this review, recent advances in the valorization of solid organic wastes including mixed food waste, agricultural waste and textile waste for efficient, green and sustainable SA production have been reviewed. Firstly, the application, market and key global players of bio-SA are summarized. Then achievements in SA production by several promising yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica are detailed, followed by calculation and comparison of SA production costs between oil-based substrates and raw materials. Lastly, challenges in engineered microorganisms and fermentation processes are presented together with perspectives on the development of robust yeast SA producers via genome-scale metabolic optimization and application of low-cost raw materials as fermentation substrates. This review provides valuable insights for identifying useful directions for future bio-SA production improvement.

Metabolic engineering of Aspergillus niger via ribonucleoprotein-based CRISPR-Cas9 system for succinic acid production from renewable biomass

BACKGROUND

Succinic acid has great potential to be a new bio-based building block for deriving a number of value-added chemicals in industry. Bio-based succinic acid production from renewable biomass can provide a feasible approach to partially alleviate the dependence of global manufacturing on petroleum refinery. To improve the economics of biological processes, we attempted to explore possible solutions with a fungal cell platform. In this study, Aspergillus niger, a well-known industrial production organism for bio-based organic acids, was exploited for its potential for succinic acid production.

RESULTS

With a ribonucleoprotein (RNP)-based CRISPR-Cas9 system, consecutive genetic manipulations were realized in engineering of the citric acid-producing strain A. niger ATCC 1015. Two genes involved in production of two byproducts, gluconic acid and oxalic acid, were disrupted. In addition, an efficient C₄-dicarboxylate transporter and a soluble NADH-dependent fumarate reductase were overexpressed. The resulting strain SAP-3 produced 17 g/L succinic acid while there was no succinic acid detected at a measurable level in the wild-type strain using a synthetic substrate. Furthermore, two cultivation parameters, temperature and pH, were investigated for their effects on succinic acid production. The highest amount of succinic acid was obtained at 35 °C after 3 days, and low culture pH had inhibitory effects on succinic acid production. Two types of renewable biomass were explored as substrates for succinic acid production. After 6 days, the SAP-3 strain was capable of producing 23 g/L and 9 g/L succinic acid from sugar beet molasses and wheat straw hydrolysate, respectively.

CONCLUSIONS

In this study, we have successfully applied the RNP-based CRISPR-Cas9 system in genetic engineering of A. niger and significantly improved the succinic acid production in the engineered strain. The studies on cultivation parameters revealed the impacts of pH and temperature on succinic acid production and the future challenges in strain development. The feasibility of using renewable biomass for succinic acid production by A. niger has been demonstrated with molasses and wheat straw hydrolysate.

Recent advances in additive manufacturing of engineering thermoplastics: challenges and opportunities

There are many limitations within three-dimensional (3D) printing that hinder its adaptation into industries such as biomedical, cosmetic, processing, automotive, aerospace, and electronics. The disadvantages of 3D printing include the inability of parts to function in weight-bearing applications, reduced mechanical performance from anisotropic properties of printed products, and limited intrinsic material performances such as flame retardancy, thermal stability, and/or electrical conductivity. Many of these shortcomings have prevented the adaptation of 3D printing into product development, especially with few novel researched materials being sold commercially. In many cases, high-performance engineering thermoplastics (ET) provide a basis for increased thermal and mechanical performances to address the shortcomings or limitations of both selective laser sintering and extrusion 3D printing. The first strategy to combat these limitations is to fabricate blends or composites. Novel printing materials have been implemented to reduce anisotropic properties and losses in strength. Additives such as flame retardants generate robust materials with V0 flame retardancy ratings, and compatibilizers can improve thermal or dimensional stability. To serve the electronic industry better, the addition of carbon black at only 4 wt%, to an ET matrix has been found to improve the electrical conductivity by five times the magnitude. Surface modifications such as photopolymerization have improved the usability of ET in automotive applications, whereas the dynamic chemical processes increased the biocompatibility of ET for medical device materials. Thermal resistant foam from polyamide 12 and fly ash spheres were researched and fabricated as possible insulation materials for automotive industries. These works and others have not only generated great potential for additive manufacturing technologies, but also provided solutions to critical challenges of 3D printing.

Engineering Saccharomyces cerevisiae for Succinic Acid Production From Glycerol and Carbon Dioxide

Previously, our lab replaced the endogenous FAD-dependent pathway for glycerol catabolism in S. cerevisiae by the synthetic NAD-dependent dihydroxyacetone (DHA) pathway. The respective modifications allow the full exploitation of glycerol’s higher reducing power (compared to sugars) for the production of the platform chemical succinic acid (SA) via a reductive, carbon dioxide fixing and redox-neutral pathway in a production host robust for organic acid production. Expression cassettes for three enzymes converting oxaloacetate to SA in the cytosol (“SA module”) were integrated into the genome of UBR2_CBS-DHA, an optimized CEN.PK derivative. Together with the additional expression of the heterologous dicarboxylic acid transporter DCT-02 from Aspergillus niger, a maximum SA titer of 10.7 g/L and a yield of 0.22 ± 0.01 g/g glycerol was achieved in shake flask (batch) cultures. Characterization of the constructed strain under controlled conditions in a bioreactor supplying additional carbon dioxide revealed that the carbon balance was closed to 96%. Interestingly, the results of the current study indicate that the artificial “SA module” and endogenous pathways contribute to the SA production in a highly synergistic manner.

A novel biocatalyst, Enterobacter aerogenes LU2, for efficient production of succinic acid using whey permeate as a cost-effective carbon source

BACKGROUND

Succinic acid (SA), a valuable chemical compound with a broad range of industrial uses, has become a subject of global interest in recent years. The bio-based production of SA by highly efficient microbial producers from renewable feedstock is significantly important, regarding the current trend of sustainable development.

RESULTS

In this study, a novel bacterial strain, LU2, was isolated from cow rumen and recognized as an efficient producer of SA from lactose. Proteomic and genetic identifications as well as phylogenetic analysis were performed, and strain LU2 was classified as an Enterobacter aerogenes species. The optimal conditions for SA production were 100 g/L lactose, 10 g/L yeast extract, and 20% inoculum at pH 7.0 and 34 °C. Under these conditions, approximately 51.35 g/L SA with a yield of 53% was produced when batch fermentation was conducted in a 3-L stirred bioreactor. When lactose was replaced with whey permeate, the highest SA concentration of 57.7 g/L was achieved with a yield and total productivity of 62% and 0.34 g/(L*h), respectively. The highest productivity of 0.67 g/(L*h) was observed from 48 to 72 h of batch fermentation, when E. aerogenes LU2 produced 16.23 g/L SA.

CONCLUSIONS

This study shows that the newly isolated strain E. aerogenes LU2 has great potential as a new biocatalyst for producing SA from whey permeate.

Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer

Enterobacter aerogenes LU2 was isolated from cow rumen and recognized as a potential succinic acid producer in our previous study. Here, we present the first complete genome sequence of this new, wild strain and report its basic genetic features from a biotechnological perspective. The MinION single-molecule nanopore sequencer supported by the Illumina MiSeq platform yielded a circular 5,062,651 bp chromosome with a GC content of 55% that lacked plasmids. A total of 4,986 genes, including 4,741 protein-coding genes, 22 rRNA-, 86 tRNA-, and 10 ncRNA-encoding genes and 127 pseudogenes, were predicted. The genome features of the studied strain and other Enterobacteriaceae strains were compared. Functional studies on the genome content, metabolic pathways, growth, and carbon transport and utilization were performed. The genomic analysis indicates that succinic acid can be produced by the LU2 strain through the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. Antibiotic resistance genes were determined, and the potential for bacteriocin production was verified. Furthermore, one intact prophage region of length ~31,9 kb, 47 genomic islands (GIs) and many insertion sequences (ISs) as well as tandem repeats (TRs) were identified. No clustered regularly interspaced short palindromic repeats (CRISPRs) were found. Finally, comparative genome analysis with well-known succinic acid producers was conducted. The genome sequence illustrates that the LU2 strain has several desirable traits, which confirm its potential to be a highly efficient platform for the production of bulk chemicals.

Metabolic engineering of a fast-growing cyanobacterium Synechococcus elongatus PCC 11801 for photoautotrophic production of succinic acid

BACKGROUND

Cyanobacteria, a group of photosynthetic prokaryotes, are being increasingly explored for direct conversion of carbon dioxide to useful chemicals. However, efforts to engineer these photoautotrophs have resulted in low product titers. This may be ascribed to the bottlenecks in metabolic pathways, which need to be identified for rational engineering. We engineered the recently reported, fast-growing and robust cyanobacterium, Synechococcus elongatus PCC 11801 to produce succinate, an important platform chemical. Previously, engineering of the model cyanobacterium S. elongatus PCC 7942 has resulted in succinate titer of 0.43 g l^-1 in 8 days.

RESULTS

Building on the previous report, expression of α-ketoglutarate decarboxylase, succinate semialdehyde dehydrogenase and phosphoenolpyruvate carboxylase yielded a succinate titer of 0.6 g l^-1 in 5 days suggesting that PCC 11801 is better suited as host for production. Profiling of the engineered strains for 57 intermediate metabolites, a number of enzymes and qualitative analysis of key transcripts revealed potential flux control points. Based on this, we evaluated the effects of overexpression of sedoheptulose-1,7-bisphosphatase, citrate synthase and succinate transporters and knockout of succinate dehydrogenase and glycogen synthase A. The final construct with seven genes overexpressed and two genes knocked out resulted in photoautotrophic production of 0.93 g l^-1 succinate in 5 days.

CONCLUSION

While the fast-growing strain PCC 11801 yielded a much higher titer than the model strain, the efficient photoautotrophy of this novel isolate needs to be harnessed further for the production of desired chemicals. Engineered strains of S. elongatus PCC 11801 showed dramatic alterations in the levels of several metabolites suggesting far reaching effects of pathway engineering. Attempts to overexpress enzymes deemed to be flux controlling led to the emergence of other potential rate-limiting steps. Thus, this process of debottlenecking of the pathway needs to be repeated several times to obtain a significantly superior succinate titer.

Advances in microbial production of medium-chain dicarboxylic acids for nylon materials

Medium-chain dicarboxylic acids (MDCAs) are widely used in the production of nylon materials, and among which, succinic, glutaric, adipic, pimelic, suberic, azelaic and sebacic acids are particularly important for that purpose.

A New Strategy for Effective Succinic Acid Production by Enterobacter sp. LU1 Using a Medium Based on Crude Glycerol and Whey Permeate

The newly-isolated strain Enterobacter sp. LU1, which has previously been shown to be an effective producer of succinic acid on glycerol with the addition of lactose, was used for further intensive works aimed at improving the production parameters of the said process. The introduction of an initial stage of gentle culture aeration allowed almost 47 g/L of succinic acid to be obtained after 168 h of incubation, which is almost two times faster than the time previously taken to obtain this amount. Furthermore, the replacement of glycerol with crude glycerin and the replacement of lactose with whey permeate allowed the final concentration of succinic acid to be increased to 54 g/L. Considering the high content of yeast extract (YE) in the culture medium, tests were also performed with a reduced YE content via its partial substitution with urea. Although this substitution led to a deterioration of the kinetic parameters of the production process, using the fed-batch strategy, it allowed a succinic acid concentration of 69 g/L to be obtained in the culture medium, the highest concentration ever achieved using this process. Furthermore, the use of microaerophilic conditions meant that the addition of lactose to the medium was not required, with 37 g/L of succinic acid being produced on crude glycerol alone.

Fixation of CO2, electron donor and redox microenvironment regulate succinic acid production in Citrobacter amalonaticus

Biological sequestration of CO₂ for generating value added products is an emerging strategy. Succinic acid (SA) is an important C4 building block chemical, and its biological production via CO₂ sequestration, holds many practical applications. This study presents an in-depth insight on SA production using isolated strain belonging to genus Citrobacter, more closely related to Citrobacter amalonaticus by considering critical process parameters such as different carbon sources at various initial concentrations, buffering agent (NaHCO₃) concentrations and different pH conditions. The effect of H₂ gas as an electron donor and availability of CO₂ during SA production was also evaluated. The results from this work demonstrated that the isolated strain depicted the ability to utilize diverse carbon sources and highest SA production was achieved with sucrose as a substrate, indicating that reduced carbon substrates help in maximizing the redox potential. Incorporation of CO₂ and H₂ not only enhanced the production of SA but also affected the total acids profile favoring the production of SA over lactic, formic and acetic acids. Additional supply of CO₂ and H₂ led to maximum SA production of 12.07 gL^-1, productivity of 0.36 gL^-1 h^-1 and SA yield of 48.5%. In control operation when no gases were supplied and in other test conditions where either of the gases were supplied, lactic acid was the major end product followed by acetic acid. The positive effect of CO₂ for SA production provides scope for sustainable integration of SA and the CO₂-generating biofuel industries or industrial side streams.

Compatibility of utilising nitrogen-rich oil palm trunk sap for succinic acid fermentation by Actinobacillus succinogenes 130Z

In this study, the potential of oil palm trunk (OPT) sap as a sole substrate for succinic acid (SA) production was evaluated using Actinobacillus succinogenes 130Z. After OPT sap was characterised, the effects of adding carbonate, yeast extract (YE) and minerals to this medium were investigated in an attempt to develop a low-cost fermentation medium. The OPT sap alone, gave comparable SA yield and productivity (0.54 g/g and 0.35 g/L/h) to those supplemented with YE (0.50 g/g and 0.36 g/L/h) and minerals (0.55 g/g and 0.40 g/L/h). The findings showed that OPT sap has sufficient amount of nutrients for SA biosynthesis by A. succinogenes 130Z and could potentially reduce cost without requiring expensive nutrients supplementation.

Organic acids as antimicrobial food agents: applications and microbial productions

Food safety is a global health and socioeconomic concern since many people still suffer from various acute and life-long diseases, which are caused by consumption of unsafe food. Therefore, ensuring safety of the food is one of the most essential issues in the food industry, which needs to be considered during not only food composition formulation but also handling and storage. For safety purpose, various chemical preservatives have been used so far in the foods. Recently, there has been renewed interest in replacing chemically originated food safety compounds with natural ones in the industry, which can also serve as antimicrobial agents. Among these natural compounds, organic acids possess the major portion. Therefore, in this paper, it is aimed to review and compile the applications, effectiveness, and microbial productions of various widely used organic acids as antimicrobial agents in the food industry.

Effective production of succinic acid from coconut water (Cocos nucifera) by metabolically engineered Escherichia coli with overexpression of Bacillus subtilis pyruvate carboxylase

Succinic acid is an important acid which is used in medicine and pharmaceutical companies. Metabolically engineered Escherichia coli strain was used for the effective production of succinic acid using Cocos nucifera water, which contained 5.00 ± 0.02 g/L glucose, 6.10 ± 0.01 g /L fructose and 6.70 ± 0.02 g /L sucrose. Fermentation of C. nucifera water with E. coli M6PM produced a final concentration of 11.78 ± 0.02 g/L succinic acid and yield of 1.23 ± 0.01 mol/mol, 0.66 ± 0.01 g/g total sugars after 72 h dual-phase fermentation in M9 medium while modeled sugar was 0.38 ± 0.02 mol/mol total sugars. It resulted in 72% of the maximum theoretical yield of succinic acid. Here we show that novel substrate of C. nucifera water resulted in effective production of succinic acid. These investigations unveil the importance of C. nucifera water as a substrate for the production of biochemicals.