Microbial Production of Malic Acid from Biofuel-Related Coproducts and Biomass

Advances in Aureobasidium research: Paving the path to industrial utilization

We here explore the potential of the fungal genus Aureobasidium as a prototype for a microbial chassis for industrial biotechnology in the context of a developing circular bioeconomy. The study emphasizes the physiological advantages of Aureobasidium, including its polyextremotolerance, broad substrate spectrum, and diverse product range, making it a promising candidate for cost-effective and sustainable industrial processes. In the second part, recent advances in genetic tool development, as well as approaches for up-scaled fermentation, are described. This review adds to the growing body of scientific literature on this remarkable fungus and reveals its potential for future use in the biotechnological industry.

CO2-mediated bloater defect can be induced by the uncontrolled growth of Enterobacteriaceae in cucumber fermentation

Enterobacteriaceae are known to proliferate in cucumber juice, deriving energy from the fermentation of sugars to organic acids and ethanol, and theoretically generating carbon dioxide (CO2). We hypothesized that the CO2 produced by the indigenous Enterobacteriaceae in the early stage of cucumber fermentation accumulates in the fermenting fruits causing bloater defect. The ability of seven Enterobacteriaceae, indigenous to cucumber, to grow and produce CO2 in cucumber juice medium (CJM), a sterile model system for cucumber fermentation, was characterized. The induction of bloater defect in cucumber fermentation conducted with pasteurized and acidified fruits was also evaluated. The generation times of the seven Enterobacteriaceae in CJM ranged between 0.25 and 8.20 h and resulted in carbon dioxide (CO2) production to estimated amounts of 7.22-171.5 mM. Enterobacter cancerogenus and Enterobacter nimipressuralis were among the bacteria that produced the most and the least CO2 in CJM, respectively, at estimated mM concentrations of 171.58 ± 42.96 and 16.85 ± 6.53. Inoculation of E. cancerogenus and E. nimipressuralis in acidified and pasteurized cucumbers resulted in the production of 138 and 27 mM CO2, respectively. Such Enterobacteriaceae produced 2% hydrogen in the model cucumber fermentations. A bloater index of 25.4 and 17.4 was calculated from the cucumbers fermented by E. cancerogenus and E. nimipressuralis, respectively, whereas no defect was observed in the fruits collected from uninoculated control fermentation jars. It is concluded that the metabolic activity of the Enterobacteriaceae indigenous to cucumber can produce sufficient CO2 in cucumber fermentations to induce bloater defect.

An enzyme-centric approach for constructing an amperometric l-malate biosensor with a long and programmable linear range

l-Malate is a key flavor enhancer and acidulant in the food and beverage industry, particularly winemaking. Enzyme-based amperometric biosensors offer convenience for monitoring its concentration. However, only a small number of off-the-shelf malate-oxidizing enzymes have been used in previous devices. These typically have linear ranges poorly suited for the l-malate concentrations found in fruit processing and winemaking, making it necessary to use precisely diluted samples. Here, we describe a pipeline of database-mining, gene synthesis, recombinant expression, and spectrophotometric assays to characterize previously untested enzymes for their suitability in biosensors. The pipeline yielded a bespoke biocatalyst-the Ascaris suum malic enzyme carrying mutation R181Q [AsME(R181Q)]. Our first prototype with AsME(R181Q) had an ultra-wide linear range of 50-200 mM l-malate, corresponding to concentrations found in undiluted fruit juices (including grape). Changing the dication from Mg2+ to Mn2+ increased sensitivity five-fold and adding citrate (100 mM) increased it another six-fold, albeit decreasing the linear range to 1-10 mM. To our knowledge, this is the first time an l-malate biosensor with a tuneable combination of sensitivity and linear range has been described. The sensor response was also tested in the presence of various molecules abundant in juices and wines, with ascorbate shown to be a potent interferent. Interference was mitigated by the addition of ascorbate oxidase, allowing for differential measurements on an undiluted, untreated wine sample that corresponded well with commercial l-malate testing kits. Overall, this work demonstrates the power of an enzyme-centric approach for designing electrochemical biosensors with improved operational parameters and novel functionality.

Recent advances in the production of malic acid by native fungi and engineered microbes

Malic acid is mainly produced by chemical methods which lead to various environmental sustainability concerns associated with CO₂ emissions and resulting global warming. Since malic acid is naturally synthesized, microorganisms offer an eco-friendly and cost-effective alternative for its production. An additional advantage of microbial production is the synthesis of pure L-form of malic acid. Due to its numerous applications, biotechnologically- produced L-malic acid is a much sought-after platform chemical. Malic acid can be produced by microbial fermentation via oxidative/reductive TCA and glyoxylate pathways. This article elaborates the potential and limitations of high malic acid producing native fungi belonging to Aspergillus, Penicillium, Ustilago and Aureobasidium spp. The utilization of industrial side streams and low value renewable substrates such as crude glycerol and lignocellulosic biomass is also discussed with a view to develop a competitive bio-based production process. The major impediments present in the form of toxic compounds from lignocellulosic residues or synthesized during fermentation along with their remedial measures are also described. The article also focuses on production of polymalic acid from renewable substrates which opens up a cost-cutting dimension in production of this biodegradable polymer. Finally, the recent strategies being employed for its production in recombinant organisms have also been covered.

Malic acid: fermentative production and applications

Microbial metabolites have gained lot of industrial interest. These are currently employed in various industries including pharmaceuticals, chemical, textiles, food etc. Organic acids are among the important microbial products. Production of microbial organic acids present numerous advantages like agro-industrial waste may be utilized as substrate, low production cost, natural in origin and production is environment friendly. Malic acid is an organic acid (C4 dicarboxylic acid) that can be produced by microbes. It is also useful in industrial sectors as food, chemicals, and pharmaceuticals etc. Production/extraction of malic acid has been reported from fruits, egg shells, microbes, via chemical synthesis, bio-transformation and from renewable sources. Microbial production of malic acid seems very promising due to various advantages and the approach is environment-friendly. In recent years, researchers have focused on fermentative microbial production of malic acid and possibility of using agro-industrial waste as raw substrates. In current article, malic acid production along with applications has been discussed with recent advances in the area.

Integrated Physiological, Transcriptomic, and Metabolomic Analyses of the Response of Peach to Nitrogen Levels during Different Growth Stages

This study performed physiological, transcriptome, and metabolite analyses of peach fruit under different nitrogen (N) conditions at different growth stages. Nitrogen management directly affected the yield, fruit quality, and metabolites of peach in different growth stages. Different fertilizing time influenced yield and leaf N concentration. RNA-Seq was used to analyze the influence of N levels at the fruit pit hardening (PH) and fruit expansion (FE) stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed differentially expressed genes (DEGs) related to carbon and nitrogen metabolite processes. Metabolome analysis shows that applying different nitrogen fertilizers at different growth stages of peach mainly affected metabolites related to carbon and amino acids. This research provides insight into the metabolic processes underlying different N responses during different growth stages and provides a foundation to improve the efficiency of N use in peach.

Influence of Carbon Sources on the Phenolic Compound Production by Euglena gracilis Using an Untargeted Metabolomic Approach

Industrial development and urbanization has led to the diverse presence of metals in wastewater that are often improperly treated. The microalgae Euglena gracilis can tolerate high concentrations of metal via the excretion of organic metabolites, including phenolics. This study aims to evaluate how carbon amendment stimulates phenolic compound production by E. gracilis. The number, relative intensity and molecular composition of the phenolic compounds were significantly different between each of four carbon amended cultures (i.e., glutamic acid, malic acid, glucose, reduced glutathione) during the log phase. Phenolic compounds were mainly produced during the minimum growth rate, likely a response to stressful conditions. A better understanding of phenolic compounds production by E. gracilis and the impact of growth conditions will help identify conditions that favor certain phenolic compounds for dietary and metal chelation applications.

A Review on the Production of C4 Platform Chemicals from Biochemical Conversion of Sugar Crop Processing Products and By-Products

The development and commercialization of sustainable chemicals from agricultural products and by-products is necessary for a circular economy built on renewable natural resources. Among the largest contributors to the final cost of a biomass conversion product is the cost of the initial biomass feedstock, representing a significant challenge in effective biomass utilization. Another major challenge is in identifying the correct products for development, which must be able to satisfy the need for both low-cost, drop-in fossil fuel replacements and novel, high-value fine chemicals (and/or commodity chemicals). Both challenges can be met by utilizing wastes or by-products from biomass processing, which have very limited starting cost, to yield platform chemicals. Specifically, sugar crop processing (e.g., sugarcane, sugar beet) is a mature industry that produces high volumes of by-products with significant potential for valorization. This review focuses specifically on the production of acetoin (3-hydroxybutanone), 2,3-butanediol, and C4 dicarboxylic (succinic, malic, and fumaric) acids with emphasis on biochemical conversion and targeted upgrading of sugar crop products/by-products. These C4 compounds are easily derived from fermentations and can be converted into many different final products, including food, fragrance, and cosmetic additives, as well as sustainable biofuels and other chemicals. State-of-the-art literature pertaining to optimization strategies for microbial conversion of sugar crop byproducts to C4 chemicals (e.g., bagasse, molasses) is reviewed, along with potential routes for upgrading and valorization. Directions and opportunities for future research and industrial biotechnology development are discussed.

The signaling pathways involved in metabolic regulation and stress responses of the yeast-like fungi Aureobasidium spp

Aureobasidium spp. can use a wide range of substrates and are widely distributed in different environments, suggesting that they can sense and response to various extracellular signals and be adapted to different environments. It is true that their pullulan, lipid and liamocin biosynthesis and cell growth are regulated by the cAMP-PKA signaling pathway; Polymalate (PMA) and pullulan biosynthesis is controlled by the Ca²⁺ and TORC1 signaling pathways; the HOG1 signaling pathway determines high osmotic tolerance and high pullulan and liamocin biosynthesis; the Snf1/Mig1 pathway controls glucose repression on pullulan and liamocin biosynthesis; DHN-melanin biosynthesis and stress resistance are regulated by the CWI signaling pathway and TORC1 signaling pathway. In addition, the HSF1 pathway may control cell growth of some novel strains of A. melanogenum at 37 °C. However, the detailed molecular mechanisms of high temperature growth and thermotolerance of some novel strains of A. melanogenum and glucose derepression in A. melanogenum TN3-1 are still unclear.

Added-Value Chemicals from Lignin Oxidation

Lignin is the second most abundant component, next to cellulose, in lignocellulosic biomass. Large amounts of this polymer are produced annually in the pulp and paper industries as a coproduct from the cooking process-most of it burned as fuel for energy. Strategies regarding lignin valorization have attracted significant attention over the recent decades due to lignin's aromatic structure. Oxidative depolymerization allows converting lignin into added-value compounds, as phenolic monomers and/or dicarboxylic acids, which could be an excellent alternative to aromatic petrochemicals. However, the major challenge is to enhance the reactivity and selectivity of the lignin structure towards depolymerization and prevent condensation reactions. This review includes a comprehensive overview of the main contributions of lignin valorization through oxidative depolymerization to produce added-value compounds (vanillin and syringaldehyde) that have been developed over the recent decades in the LSRE group. An evaluation of the valuable products obtained from oxidation in an alkaline medium with oxygen of lignins and liquors from different sources and delignification processes is also provided. A review of C4 dicarboxylic acids obtained from lignin oxidation is also included, emphasizing catalytic conversion by O2 or H2O2 oxidation.

Engineering of a Biosensor in Response to Malate in Bacillus licheniformis

Malate is an essential intermediate in the tricarboxylic acid (TCA) cycle; it also has valuable uses in medicine and food. The production of malate with a microbial synthesis method is still in its early stages. One of the key problems in metabolic engineering is that the dynamic and subtle changes in malate are difficult to detect. It remains critical to develop techniques with direct and precise detection of malate in microbial metabolism, which facilitates high-throughput screening of the engineered strains. In this study, a genetically encoded biosensor in response to malate was constructed in B. licheniformis. Key regulator MalR and the action site of the biosensor were first identified. Then, the output of the reporter gene expression was amplified by introducing a strong constitutive promoter and iteratively tuning the action sites. The engineered biosensor can respond to malate from 5 to 15 g/L; within this range, it shows a linear correlation between eGFP fluorescence and malate concentration. This biosensor enrich our toolbox of synthetic biology in pathway engineering for malate production in microorganisms.

Organic Acid Profiles of Phosphate Solubilizing Bacterial Strains in the Presence of Different Insoluble Phosphatic Sources Under In vitro Buffered Conditions

The production of weak organic acids by microorganisms has been attributed as the prime reason for the solubilization of insoluble phosphates under both in vitro and soil conditions. Literature seems to be heavily biased towards gluconic acid production by microbes and its subsequent release into the environment as the key factor responsible for phosphate solubilization. This has found credibility since gluconic acid being a product of the Kreb’s cycle is often detected in large quantities in the culture media, when assayed under in vitro conditions. In the present work, the organic acid profiles of four elite phosphate solubilising isolates were determined in the presence of different insoluble sources of phosphates, under in vitro buffered culture conditions by HPLC (High-Performance Liquid Chromatography). While most previous studies did not use a buffered culture media for elucidating the organic acid profile of phosphate solubilizing bacterial isolates, we used a buffered media for estimation of the organic acid profiles. The results revealed that apart from gluconic acid, malic acid is produced in significant levels by phosphate solubilizing bacterial isolates, and there seems to be a differential pattern of production of these two organic acids by the isolates in the presence of different insoluble phosphate sources.

Bioconversion of syringyl lignin into malic acid by Burkholderia sp. ISTR5

Syringyl monomeric units are the most common intermediates encountered during hardwood lignin degradation. In the present study, efficient utilization of syringaldehyde (SAld), syringic acid (SAc) by Burkholderia sp. ISTR5 (R5) has been shown. The proteogenomic analysis of Burkholderia sp. ISTR5 was done to understand the enzymes involved in the degradation of syringaldehyde and syringic acid. Various proteins such as aldehyde dehydrogenase, laccase, and oxidoreductases were highly upregulated during growth on syringaldehyde and syringic acid. R5 completely transformed both the substrates SAld and SAc to other hydrocarbons in 48 h and 24 h, respectively. Moreover, bioconversion of syringyl lignins followed an unusual pathway and accumulated a considerable amount of industrially valuable chemical malic acid in the reaction titer. This study shows the robust chassis of R5 to cope with the aromatic aldehydic stress and simultaneous bioconversion into valuable products for an efficient biorefinery.

Expanding the anaerobic digestion map: A review of intermediates in the digestion of food waste

Anaerobic digestion is a promising technology as a renewable source of energy products, but these products have low economic value and process control is challenging. Identifying intermediates formed throughout the process could enhance understanding and offer opportunities for improved monitoring, control, and valorisation. In this review, intermediates present in the anaerobic digestion process are identified and discussed, including the following: volatile fatty acids, carboxylic acid, amino acids, furans, terpenes and phytochemicals. The key limitations associated with exploiting these intermediates are also addressed including challenging mixed cultures of microbiology, complex feedstocks, and difficult extraction and separation techniques.

Integration of metabolic pathway manipulation and promoter engineering for the fine-tuned biosynthesis of malic acid in Bacillus coagulans

Bacillus coagulans, a thermophilic facultative anaerobe, is a favorable chassis strain for the biosynthesis of desired products. In this study, B. coagulans was converted into an efficient malic acid producer by metabolic engineering and promoter engineering. Promoter mapping revealed that the endogenous promoter P_ldh was a tandem promoter. Accordingly, a promoter library was developed, covering a wide range of relative transcription efficiencies with small increments. A reductive tricarboxylic acid pathway was established in B. coagulans by introducing the genes encoding pyruvate carboxylase (pyc), malate dehydrogenase (mdh), and phosphoenolpyruvate carboxykinase (pckA). Five promoters of various strengths within the library were screened to fine-tune the expression of pyc to improve the biosynthesis of malic acid. In addition, genes involved in the competitive metabolic pathways were deleted to focus the substrate and energy flux toward malic acid. Dual-phase fed-batch fermentation was performed to increase the biomass of the strain, further improving the titer of malic acid to 25.5 g/L, with a conversion rate of 0.3 g/g glucose. Our study is a pioneer research using promoter engineering and genetically modified B. coagulans for the biosynthesis of malic acid, providing an effective approach for the industrialized production of desired products using B. coagulans.

Sustainable production and biomedical application of polymalic acid from renewable biomass and food processing wastes

Polymalic acid (PMA), a homopolymer of L-malic acid (MA) generated from a yeast-like fungus Aureobasidium pullulans, has unique properties and many applications in food, biomedical, and environmental fields. Acid hydrolysis of PMA, releasing the monomer MA, has become a novel process for the production of bio-based MA, which currently is produced by chemical synthesis using petroleum-derived feedstocks. Recently, current researches attempted to develop economically competitive process for PMA and MA production from renewable biomass feedstocks. Compared to lignocellulosic biomass, PMA and MA production from low-value food processing wastes or by-products, generated from corn, sugarcane, or soybean refinery industries, showed more economical and sustainable for developing a MA derivatives platform from biomass biorefinery to chemical conversion. In the review, we compared the process feasibility for PMA fermentation with lignocellulosic biomass and food process wastes. Some useful strategies for metabolic engineering are summarized. Its changeable applicability and future prospects in food and biomedical fields are also discussed.

Reaction of H2 with mitochondria-relevant metabolites using a multifunctional molecular catalyst

The Krebs cycle is the fuel/energy source for cellular activity and therefore of paramount importance for oxygen-based life. The cycle occurs in the mitochondrial matrix, where it produces and transfers electrons to generate energy-rich NADH and FADH₂, as well as C₄-, C₅-, and C₆-polycarboxylic acids as energy-poor metabolites. These metabolites are biorenewable resources that represent potential sustainable carbon feedstocks, provided that carbon-hydrogen bonds are restored to these molecules. In the present study, these polycarboxylic acids and other mitochondria-relevant metabolites underwent dehydration (alcohol-to-olefin and/or dehydrative cyclization) and reduction (hydrogenation and hydrogenolysis) to diols or triols upon reaction with H₂, catalyzed by sterically confined iridium-bipyridyl complexes. The investigation of these single-metal site catalysts provides valuable molecular insights into the development of molecular technologies for the reduction and dehydration of highly functionalized carbon resources.

Continuous Flow Upgrading of Selected C2-C6 Platform Chemicals Derived from Biomass

The ever increasing industrial production of commodity and specialty chemicals inexorably depletes the finite primary fossil resources available on Earth. The forecast of population growth over the next 3 decades is a very strong incentive for the identification of alternative primary resources other than petro-based ones. In contrast with fossil resources, renewable biomass is a virtually inexhaustible reservoir of chemical building blocks. Shifting the current industrial paradigm from almost exclusively petro-based resources to alternative bio-based raw materials requires more than vibrant political messages; it requires a profound revision of the concepts and technologies on which industrial chemical processes rely. Only a small fraction of molecules extracted from biomass bears significant chemical and commercial potentials to be considered as ubiquitous chemical platforms upon which a new, bio-based industry can thrive. Owing to its inherent assets in terms of unique process experience, scalability, and reduced environmental footprint, flow chemistry arguably has a major role to play in this context. This review covers a selection of C₂ to C₆ bio-based chemical platforms with existing commercial markets including polyols (ethylene glycol, 1,2-propanediol, 1,3-propanediol, glycerol, 1,4-butanediol, xylitol, and sorbitol), furanoids (furfural and 5-hydroxymethylfurfural) and carboxylic acids (lactic acid, succinic acid, fumaric acid, malic acid, itaconic acid, and levulinic acid). The aim of this review is to illustrate the various aspects of upgrading bio-based platform molecules toward commodity or specialty chemicals using new process concepts that fall under the umbrella of continuous flow technology and that could change the future perspectives of biorefineries.

Making natural products from renewable feedstocks: back to the roots?

This review highlights the utilization of biomass-derived building blocks in the total synthesis of natural products.

Membrane-assisted β-poly(L-malic acid) production from bagasse hydrolysates by Aureobasidium pullulans ipe-1

Membrane-assisted β-poly(L-malic acid) (PMLA) production from bagasse hydrolysates was developed. For the first time, it was found that mixing the acid and enzyme hydrolysates was unfavorable for PMLA production because too high hexose: pentose ratio and glucose concentration in the mixed sugar could inhibit the assimilation of pentose. 120 g/L sugar concentrations in the acid hydrolysate was suitable for PMLA production with 23.2 g/L PMLA and 34.7 g/L biomass. Moreover, an integrated membrane process consisting of ultrafiltration, nanofiltration and reverse osmosis membranes could concentrate sugars and adjust acetic acid concentration prior to fermentation of lignocellulosic sugars. Meanwhile, it was found that 1.46 g/L acetic acid was preferred for PMLA production from enzyme hydrolysate or sole glucose which respectively increased PMLA production and cell growth by 25.4% and 5.9% from sole glucose, while it showed no significant enhancement in PMLA production with a higher cell growth and productivity from acid hydrolysate.

Optimized pH and Its Control Strategy Lead to Enhanced Itaconic Acid Fermentation by Aspergillus terreus on Glucose Substrate

Biological itaconic acid production can by catalyzed by Aspergillus terreus (a filamentous fungi) where the fermentation medium pH is of prominent importance. Therefore, in this work, we investigated what benefits the different pH regulation options might offer in enhancing the process. The batch itaconic acid fermentation data underwent a kinetic analysis and the pH control alternatives were ranked subsequently. It would appear that the pH-shift strategy (initial adjustment of pH to 3 and its maintenance at 2.5 after 48 h) resulted in the most attractive fermentation pattern and could hence be recommended to achieve itaconic acid production with an improved performance using A. terreus from carbohydrate, such as glucose. Under this condition, the itaconic acid titer potential, the maximal itaconic acid (titer) production rate, the length of lag-phase and itaconic acid yield were 87.32 g/L, 0.22 g/L/h, 56.04 h and 0.35 g/g glucose, respectively.

Engineering of Escherichia coli for Krebs cycle-dependent production of malic acid

Background

Malate is a C4-dicarboxylic acid widely used as an acidulant in the food and beverage industry. Rational engineering has been performed in the past for the development of microbial strains capable of efficient production of this metabolite. However, as malate can be a precursor for specialty chemicals, such as 2,4-dihydroxybutyric acid, that require additional cofactors NADP(H) and ATP, we set out to reengineer Escherichia coli for Krebs cycle-dependent production of malic acid that can satisfy these requirements.

Results

We found that significant malate production required at least simultaneous deletion of all malic enzymes and dehydrogenases, and concomitant expression of a malate-insensitive PEP carboxylase. Metabolic flux analysis using ¹³C-labeled glucose indicated that malate-producing strains had a very high flux over the glyoxylate shunt with almost no flux passing through the isocitrate dehydrogenase reaction. The highest malate yield of 0.82 mol/mol was obtained with E. coli Δmdh Δmqo ΔmaeAB ΔiclR ΔarcA which expressed malate-insensitive PEP carboxylase Ppc^K620S and NADH-insensitive citrate synthase GltA^R164L. We also showed that inactivation of the dicarboxylic acid transporter DcuA strongly reduced malate production arguing for a pivotal role of this permease in malate export.

Conclusions

Since more NAD(P)H and ATP cofactors are generated in the Krebs cycle-dependent malate production when compared to pathways which depend on the function of anaplerotic PEP carboxylase or PEP carboxykinase enzymes, the engineered strain developed in this study can serve as a platform to increase biosynthesis of malate-derived metabolites such as 2,4-dihydroxybutyric acid.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0959-y) contains supplementary material, which is available to authorized users.

Methyl Perillate as a Highly Functionalized Natural Starting Material for Terephthalic Acid

Renewable commodity chemicals can be generated from plant materials. Often abundant materials such as sugars are used for this purpose. However, these lack appropriate functionalities and, therefore, they require extensive chemical modifications before they can be used as commodity chemicals. The plant kingdom is capable of producing an almost endless variety of compounds, including compounds with highly appropriate functionalities, but these are often not available in high quantities. It has been demonstrated that it is possible to produce functionalized plant compounds on a large scale by fermentation in microorganisms. This opens up the potential to exploit plant compounds that are less abundant, but functionally resemble commodity chemicals more closely. To elaborate this concept, we demonstrate the suitability of a highly functionalized plant compound, methyl perillate, as a precursor for the commodity chemical terephthalic acid.