Mathematical modelling of clostridial acetone-butanol-ethanol fermentation

Mathematical modeling of ABE fermentation on glucose substrate with Zn supplementation for enhanced butanol production

Supplementation or limitation of some micronutrients during acetone-butanol-ethanol (ABE) fermentation has led to improvement in butanol yield and productivity. A mechanistic model of ABE fermentation offers insights in understanding these complex interactions and improving productivity through optimal culture conditions. This study proposes a mechanistic kinetic model of ABE fermentation by two Clostridium Acetobutylicum strains, L7 and ATCC 824 using glucose as sole carbon source without zinc and with various zinc doses. The model incorporates enzyme regulation by zinc on several glycolytic, acidogenesis and solventogenesis enzymes. The model was fitted and validated to experimental data collected from the published literature. The simulated results were in compliance with the experimental data, most importantly indicating higher glucose consumption and butanol productivity when supplemented with zinc compared to the control culture. The average squared correlation factor (R2) between the experimental and the simulated results, without and with zinc, were 0.99 and 0.96 for glucose, and 0.89 and 0.95 for butanol, respectively. A sensitivity analysis performed on the fitted and validated model indicated that the glucose consumption and growth parameters most influenced the model outputs. The developed model can be used as a template for modeling ABE fermentation under different combinations of micronutrients that may offer improved butanol yield and productivity.

Formate as a supplementary substrate facilitates sugar metabolism and solvent production by Clostridium beijerinckii NCIMB 8052

Microbial utilization and conversion of organic one-carbon compounds, such as formate and methanol that can be easily produced from CO₂, has emerged as an attractive approach for biorefinery. In this study, we discovered Clostridium beijerinckii NCIMB 8052, a typical solventogenic Clostridium strain, to be a native formate-utilizing bacterium. ¹³C isotope analysis showed that formate could be metabolized via both assimilation and dissimilation pathways in C. beijerinckii NCIMB 8052. Notably, the use of formate as the supplementary substrate by this strain could significantly enhance its glucose consumption and ABE (acetone-butanol-ethanol) production, largely due to the up-regulation of genes responsible for glycolysis and glucose transport under formate stress. Based on these findings, we further improved formate tolerance of C. beijerinckii NCIMB 8052 by adaptive laboratory evolution, generating an evolved strain Cbei-FA01. The Cbei-FA01 strain could produce 23.0 g/L of ABE solvents using glucose and formate as dual substrates, ∼50% higher than that of the wild-type strain under the same condition. Moreover, such a promotion effect of formate on ABE production by Cbei-FA01 was also observed in fermenting a glucose-xylose mixture. This work reveals a previously unreported role of formate in biological ABE production, providing a new approach to utilize this one-carbon source.

Structural Evolution of MOF-Derived RuCo, A General Catalyst for the Guerbet Reaction

Guerbet alcohols, a class of β-branched terminal alcohols, find widespread application because of their low melting points and excellent fluidity. Because of the limitations in the activity and selectivity of existing Guerbet catalysts, Guerbet alcohols are not currently produced via the Guerbet reaction but via hydroformylation of oil-derived alkenes followed by aldol condensation. In pursuit of a one-step synthesis of Guerbet alcohols from simple linear alcohol precursors, we show that MOF-derived RuCo alloys achieve over a million turnovers in the Guerbet reaction of 1-propanol, 1-butanol, and 1-pentanol. The active catalyst is formed in situ from ruthenium-impregnated metal-organic framework MFU-1. XPS and XAS studies indicate that the precatalyst is composed of Ru precursor trapped inside the MOF pores with no change in the oxidation state or coordination environment of Ru upon MOF incorporation. The significantly higher reactivity of Ru-impregnated MOF versus a physical mixture of Ru precursor and MOF suggests that the MOF plays an important role in templating the formation of the active catalyst and/or its stabilization. XPS reveals partial reduction of both ruthenium and MOF-derived cobalt under the Guerbet reaction conditions, and TEM/EDX imaging shows that Ru is decorated on the edges of dense nanoparticles, as well as thin nanoplates of CoOx. The use of ethanol rather than higher alcohols as a substrate results in lower turnover frequencies, and RuCo recovered from ethanol upgrading lacks nanostructures with plate-like morphology and does not exhibit Ru-enrichment on the surface and edge sites. Notably, 1H and 31P NMR studies show that through use of K3PO4 as a base promoter in the RuCo-catalyzed alcohol upgrading, the formation of carboxylate salts, a common side product in the Guerbet reaction, was effectively eliminated.

Self-Synchronized Oscillatory Metabolism of Clostridium pasteurianum in Continuous Culture

By monitoring the real-time gas production (CO2 and H2) and redox potential at high sampling frequency in continuous culture of Clostridium pasteurianum on glycerol as sole carbohydrate, the self-synchronized oscillatory metabolism was revealed and studied. The oscillations in CO2 and H2 production were in sync with each other and with both redox potential and glycerol in the continuous stirred tank reactor (CSTR). There is strong evidence that the mechanism for this is in the regulation of the oxidative pathway of glycerol metabolism, including glycolysis, and points toward complex, concerted cycles of enzyme inhibition and activation by pathway intermediates and/or redox equivalents. The importance of understanding such an “oscillatory metabolism” is for developing a stable and highly productive industrial fermentation process for butanol production, as unstable oscillations are unproductive. It is shown that the oscillatory metabolism can be eradicated and reinstated and that the period of oscillations can be altered by modification of the operating parameters. Synchronized oscillatory metabolism impacted the product profile such that it lowered the selectivity for butanol and increased the selectivity for ethanol. This elucidates a possible cause for the variability in the product profile of C. pasteurianum that has been reported in many previous studies.

Clostridium sp. as Bio-Catalyst for Fuels and Chemicals Production in a Biorefinery Context

Clostridium sp. is a genus of anaerobic bacteria capable of metabolizing several substrates (monoglycerides, diglycerides, glycerol, carbon monoxide, cellulose, and more), into valuable products. Biofuels, such as ethanol and butanol, and several chemicals, such as acetone, 1,3-propanediol, and butyric acid, can be produced by these organisms through fermentation processes. Among the most well-known species, Clostridium carboxidivorans, C. ragsdalei, and C. ljungdahlii can be highlighted for their ability to use gaseous feedstocks (as syngas), obtained from the gasification or pyrolysis of waste material, to produce ethanol and butanol. C. beijerinckii is an important species for the production of isopropanol and butanol, with the advantage of using hydrolysate lignocellulosic material, which is produced in large amounts by first-generation ethanol industries. High yields of 1,3 propanediol by C. butyricum are reported with the use of another by-product from fuel industries, glycerol. In this context, several Clostridium wild species are good candidates to be used as biocatalysts in biochemical or hybrid processes. In this review, literature data showing the technical viability of these processes are presented, evidencing the opportunity to investigate them in a biorefinery context.

Clostridium butyricum population balance model: Predicting dynamic metabolic flux distributions using an objective function related to extracellular glycerol content

BACKGROUND

Extensive experimentation has been conducted to increment 1,3-propanediol (PDO) production using Clostridium butyricum cultures in glycerol, but computational predictions are limited. Previously, we reconstructed the genome-scale metabolic (GSM) model iCbu641, the first such model of a PDO-producing Clostridium strain, which was validated at steady state using flux balance analysis (FBA). However, the prediction ability of FBA is limited for batch and fed-batch cultures, which are the most often employed industrial processes.

RESULTS

We used the iCbu641 GSM model to develop a dynamic flux balance analysis (DFBA) approach to predict the PDO production of the Colombian strain Clostridium sp IBUN 158B. First, we compared the predictions of the dynamic optimization approach (DOA), static optimization approach (SOA), and direct approach (DA). We found no differences between approaches, but the DOA simulation duration was nearly 5000 times that of the SOA and DA simulations. Experimental results at glycerol limitation and glycerol excess allowed for validating dynamic predictions of growth, glycerol consumption, and PDO formation. These results indicated a 4.4% error in PDO prediction and therefore validated the previously proposed objective functions. We performed two global sensitivity analyses, finding that the kinetic input parameters of glycerol uptake flux had the most significant effect on PDO predictions. The other input parameters evaluated during global sensitivity analysis were biomass composition (precursors and macromolecules), death constants, and the kinetic parameters of acetic acid secretion flux. These last input parameters, all obtained from other Clostridium butyricum cultures, were used to develop a population balance model (PBM). Finally, we simulated fed-batch cultures, predicting a final PDO production near to 66 g/L, almost three times the PDO predicted in the best batch culture.

CONCLUSIONS

We developed and validated a dynamic approach to predict PDO production using the iCbu641 GSM model and the previously proposed objective functions. This validated approach was used to propose a population model and then an increment in predictions of PDO production through fed-batch cultures. Therefore, this dynamic model could predict different scenarios, including its integration into downstream processes to predict technical-economic feasibilities and reducing the time and costs associated with experimentation.

Metabolic dependent and independent pH-drop shuts down VirSR quorum sensing in Clostridium perfringens

Clostridium perfringens produces various exotoxins and enzymes that cause food poisoning and gas gangrene. The genes involved in virulence are regulated by the agr-like quorum sensing (QS) system, which consists of a QS signal synthesis system and a VirSR two-component regulatory system (VirSR TCS) which is a global regulatory system composed of signal sensor kinase (VirS) and response regulator (VirR). We found that the perfringolysin O gene (pfoA) was transiently expressed during mid-log phase of bacterial growth; its expression was rapidly shut down thereafter, suggesting the existence of a self-quorum quenching (sQQ) system. The sQQ system was induced by the addition of stationary phase culture supernatant (SPCS). Activity of the sQQ system was heat stable, and was present following filtration through the ultrafiltration membrane, suggesting that small molecules acted as sQQ agents. In addition, sQQ was also induced by pure acetic and butyric acids at concentrations equivalent to those in the stationary phase culture, suggesting that organic acids produced by C. perfringens were involved in sQQ. In pH-controlled batch culture, sQQ was greatly diminished; expression level of pfoA extended to late-log growth phase, and was eventually increased by one order of magnitude. Furthermore, hydrochloric acid induced sQQ at the same pH as was used in organic acids. SPCS also suppressed the expression of genes regulated by VirSR TCS. Overall, the expression of virulence factors of C. perfringens was downregulated by the sQQ system, which was mediated by primary acidic metabolites and acidic environments. This suggested the possibility of pH-controlled anti-virulence strategies.

A Bibliometric Analysis of Research on Supported Ionic Liquid Membranes during the 1995-2015 Period: Study of the Main Applications and Trending Topics

A bibliometric analysis based on Scopus database was performed to identify the global research trends related to Supported Ionic Liquid Membranes (SILMs) during the time period from 1995 to 2015. This work tries to improve the understanding of the most relevant research topics and applications. The results from the analysis reveal that only after 2005 the research efforts focused on SILMs became significant, since the references found before that year are scarce. The most important research works on the four main application groups for SILMs defined in this work (carbon dioxide separation, other gas phase separations, pervaporation and liquid phase separations) were summarized in this paper. Carbon dioxide separation appeared as the application that has received by far the most attention according to the research trends during the analysed period. Comments about other significant applications that are gaining attention, such as the employment of SILMs in analytical tasks or their consideration for the production of fuel cells, have been included.

Glucose bioconversion profile in the syngas-metabolizing species Clostridium carboxidivorans

Some clostridia produce alcohols (ethanol, butanol, hexanol) from gases (CO, CO₂, H₂) and others from carbohydrates (e.g., glucose). C. carboxidivorans can metabolize both gases as well as glucose. However, its bioconversion profile on glucose had not been reported. It was observed that C. carboxidivorans does not follow a typical solventogenic stage when grown on glucose. Indeed, at pH 6.2, it produced first a broad range of acids (acetic, butyric, hexanoic, formic, and lactic acids), several of which are generally not found, under similar conditions, during gas fermentation. Medium acidification did not allow the conversion of fatty acids into solvents. Production of some alcohols from glucose was observed in C. carboxidivorans but at high pH rather than under acidic conditions, and the total concentration of those solvents was low. At high pH, formic acid was produced first and later converted to acetic acid, but organic acids were not metabolized at low pH.