Glycerol fermentation by a new 1,3-propanediol-producing microorganism:Enterobacter agglomerans

 According to their ability to synthesize 1,3-propanediol from glycerol, two species were isolated from the anoxic mud of a distillery waste-water digestor: Clostridium butyricum and Enterobacter agglomerans. The latter, a facultatively anaerobic gram-negative bacterium, is described for the first time as a microorganism producing 1,3-propanediol from glycerol. The products of glycerol conversion by E. agglomerans were identified using nuclear magnetic resonance. A 20-g/l glycerol solution was fermented mainly to 1,3-propanediol (0.51 mol/mol) and acetate (0.18 mol/mol). Ethanol, formate, lactate and succinate were formed as by-products. Gas production was very low; 1,3-propanediol production perfectly balanced the oxido-reduction state of the microorganism. Acetate was the predominant metabolite generating energy for growth. High-glycerol-concentration fermentations (71 g/l and 100 g/l) resulted in an increase of the 1,3-propanediol yield (0.61 mol/mol) at the expense of lactate and ethanol production. Specific rates of glycerol consumption and 1, 3-propanediol and acetate production increased whereas the growth rate decreased. The decrease in ATP yield was linearly correlated with the specific rate of 1,3-propanediol production. Incomplete glycerol consumption (about 40 g/l) was systematically observed when high glycerol concentrations were used. The unbalanced oxido-reduction state, the low carbon recovery and the detection of an unknown compound by HPLC observed in these cases indicate the formation of another metabolite, which is possibly an inhibitory factor. Received: 17 November 1994 / Accepted: 15 December 1994     

Production of 1,3-Propanediol from Glucose by Recombinant <Emphasis Type="Italic">Escherichia coli</Emphasis> BL21(DE3)

A range of recombinant strains of Escherichia coli were developed to produce 1,3-propanediol (1,3-PDO), an important C3 diol, from glucose. Two modules, the glycerol-producing pathway converting dihydroxyacetone phosphate to glycerol and the 1,3-PDO-producing pathway converting glycerol to 1,3-PDO, were introduced into E. coli. In addition, to avoid oxidative assimilation of the produced glycerol, glycerol oxidative pathway was deleted. Furthermore, to enhance the carbon flow to the Embden- Meyerhof-Parnas pathway, the Entner-Doudoroff pathway was disrupted by deleting 6-phosphogluconate dehydratase and 2-keto-3-deoxy-6-phosphogluconate aldolase. Finally, the acetate production pathway was removed to minimize the production of acetate, a major and toxic by-product. Flask experiments were carried out to examine the performance of the developed recombinant E. coli. The best strain could produce 1,3-PDO with a yield of 0.47 mol/mol glucose. Along with 1,3-PDO, glycerol was produced with a yield of 0.33 mol/mol glucose.     

Effects of Acetate and Butyrate During Glycerol Fermentation by Clostridium butyricum

The effects of acetate and butyrate during glycerol fermentation to 1,3-propanediol at pH 7.0 by Clostridium butyricum CNCM 1211 were studied. At pH 7.0, the calculated quantities of undissociated acetic and butyric acids were insufficient to inhibit bacterial growth. The initial addition of acetate or butyrate at concentrations of 2.5 to 15 gL⁻¹ had distinct effects on the metabolism and growth of Clostridium butyricum. Acetate increased the biomass and butyrate production, reducing the lag time and 1,3-propanediol production. In contrast, the addition of butyrate induced an increase in 1,3-propanediol production (yield: 0.75 mol/mol glycerol, versus 0.68 mol/mol in the butyrate-free culture), and reduced the biomass and butyrate production. It was calculated that reduction of butyrate production could provide sufficient NADH to increase 1,3-propanediol production. The effects of acetate and butyrate highlight the metabolic flexibility of Cl. butyricum CNCM 1211 during glycerol fermentation. Received: 2 January 2001 / Accepted: 6 February 2001     

Improvement of butanol fermentation by supplementation of butyric acid produced from a brown alga

This study investigated butanol fermentation using glucose and culture broth containing butyrate from the butyrate fermentation of a brown alga, Laminaria japonica. Prior to the use of the biologically-produced butyrate, the initial glucose in tryptone-yeast extract acetate (TYA) medium was first optimized for butanol fermentation using Clostridium saccharoperbutylacetonicum N1-4 ATCC 27021^T. Then, a commercially-acquired (synthetic) butyrate was supplemented to the TYA medium containing the optimal glucose concentration (around 30 and 60 g/L). According to the experimental results, the highest butanol carbon yield (0.580 C-mol/C-mol) was obtained from the fermentation of 36.65 g/L glucose and 7.29 g/L synthetic butyrate. Fermentation of a similar amount of glucose (32.28 g/L) in the absence of butyrate gave a butanol carbon yield of 0.402 C-mol/C-mol. For the experiment with fermented butyrate, a 100 g/L biomass of brown alga was fermented by Clostridium tyrobutyricum ATCC 25755 and the culture broth containing butyrate was used to prepare TYA medium after removing the bacterial cells. Fermentation using the synthetic butyrate and the biologically-produced butyrate (4.95 g/L) gave a comparable butanol concentration (13.23 g/L) and butanol carbon yield (0.513 C-mol/C-mol). Overall, this study proved that the addition of fermented butyrate from brown alga fermentation could be an effective way to improve butanol production. Furthermore, the reuse of spent medium and the absence of rigorous purification of the broth containing butyrate would lower the production cost of the fermentation.     

Fermentation of crude glycerol from biodiesel production by <Emphasis Type="Italic">Clostridium pasteurianum</Emphasis>

Clostridium pasteurianum can utilize glycerol as the sole carbon source for the production of butanol and 1,3-propanediol. Crude glycerol derived from biodiesel production has been shown to be toxic to the organism even in low concentrations. By examination of different pretreatments we found that storage combined with activated stone carbon addition facilitated the utilization of crude glycerol. A pH-controlled reactor with in situ removal of butanol by gas stripping was used to evaluate the performance. The fermentation pattern on pretreated crude glycerol was quite similar to that on technical grade glycerol. C. pasteurianum was able to utilize 111 g/l crude glycerol. The average consumption rate was 2.49 g/l/h and maximum consumption rate was 4.08 g/l/h. At the maximal glycerol consumption rate butanol was produced at 1.3 g/l/h. These rates are higher than those previously reported for fermentations on technical grade glycerol by the same strain. A process including pretreatment and subsequent fermentation of the crude glycerol could be usable for industrial production of butanol by C. pasteurianum.     

The fermentation of glycerol byClostridium butyricum LMG 1212t2 and 1213t1 andC. pasteurianum LMG 3285

Summary In batch culture on reiinforced clostridial medium strain-dependent product profiles from glycerol revealed unusual fermentation products such as propionate and n-propanol with Clostridium butyricum LMG 1213t₁, and 1,3-propanediol with C. butyricum LMG 1212t₂ and C. pasteurianium LMG 3285. Only the latter two strains were able to grow on glycerol in a minimal medium. Nicotinamide adenine dinucleotide (NAD⁺)-dependent dehydrogenase activities were detected with 1,3-propanediol and n-butanol as substrate (the latter only after a lag period) in cell-free extracts of C. butyricum LMG 1212t₂ and with 1,3-propanediol, n-butanol and ethanol in cell-free extracts of C. pasteurianum LMG 3285. The data indicated the existance of a specific 1,3-propanediol dehydrogenase in both organisms. In a chemostat, C. butyricum LMG 1212t₂ converted 65% of the glycerol supplied as sole carbon and energy source to 1,3-propanediol without H₂ production. Increasing concentration of acetate in the inflow medium resulted in less 1,3-propanediol and more butyrate and H₂ production. C. pasteurianum LMG 3285 converted somewhat more than half of the glycerol supplied as sole energy and carbon source to n-butanol with significant concomitant H₂ production. This fermentation pattern was hardly affected by acetate as co-substrate. Offprint requests to: P. De Vos     

Influence of iron,phosphate and methyl viologen on glycerol fermentation of Clostridium butyricum

 The effect of methyl viologen addition, and iron and phosphate limitation on product distribution during glycerol fermentation of Clostridium butyricum DSM 5431 was investigated in continuous culture. Special attention was paid to the gaseous products H₂ and CO₂, which were measured on-line. In all three cases, an increased yield of 1,3-propanediol linked to a decreased hydrogen release was observed, indicating that a higher proportion of electrons was channelled from reduced ferredoxin towards NADH₂ production. The specific substrate consumption rates and the specific production rates revealed that this increase in propanediol yield was not obtained at the expense of glycolysis products but by an increased substrate conversion (overflow metabolism). The acetate/ butyrate ratio during glycerol fermentation was essentially influenced by the availability of iron. It was substantially increased when the culture turned from iron excess to iron-limited conditions. Therefore iron limitation proved to be a suitable means to achieve high 1,3-propanediol yields and to reduce butyrate formation. Received: 29 August 1995 / Accepted: 20 September 1995     

Improved n-butanol production by a non-acetone producing Clostridium pasteurianum DSMZ 525 in mixed substrate fermentation

The kinetics of growth, acid and solvent production in batch culture of Clostridium pasteurianum DSMZ 525 were examined in mixed or mono-substrate fermentations. In pH-uncontrolled batch cultures, the addition of butyric acid or glucose significantly enhanced n-butanol production and the ratio of butanol/1,3-propanediol. In pH-controlled batch culture at pH?=?6, butyric acid addition had a negative effect on growth and did not lead to a higher n-butanol productivity. On the other hand, mixed substrate fermentation using glucose and glycerol enhanced the growth and acid production significantly. Glucose limitation in the mixed substrate fermentation led to the reduction or inhibition of the glycerol consumption by the growing bacteria. Therefore, for the optimal growth and n-butanol production by C. pasteurianum, a limitation of either substrate should be avoided. Under optimized batch conditions, n-butanol concentration and maximum productivity achieved were 21 g/L, and 0.96 g/L?×?h, respectively. In comparison, mixed substrate fermentation using biomass hydrolysate and glycerol gave a n-butanol concentration of 17 g/L with a maximum productivity of 1.1 g/L?×?h. In terms of productivity and final n-butanol concentration, the results demonstrated that C. pasteurianum DSMZ 525 is well suitable for n-butanol production from mixed substrates of biomass hydrolysate and glycerol and represents an alternative promising production strain.     

Sugar-glycerol cofermentations in lactobacilli: the fate of lactate.

The simultaneous fermentation of glycerol and sugar by lactobacillus brevis B22 and Lactobacillus buchneri B190 increases both the growth rate and total growth. The reduction of glycerol to 1,3-propanediol by the lactobacilli was found to influence the metabolism of the sugar cofermented by channelling some of the intermediate metabolites (e.g., pyruvate) towards NADH-producing (rather than NADH-consuming) reactions. Ultimately, the absolute requirement for NADH to prevent the accumulation of 3-hydroxypropionaldehyde leads to a novel lactate-glycerol cofermentation. As a result, additional ATP can be made not only by (i) converting pyruvate to acetate via acetyl phosphate rather than to the ethanol usually found and (ii) oxidizing part of the intermediate pyruvate to acetate instead of the usual reduction to lactate but also by (iii) reoxidation of accumulated lactate to acetate via pyruvate. The conversion of lactate to pyruvate is probably catalyzed by NAD-independent lactate dehydrogenases that are found only in the cultures oxidizing lactate and producing 1,3-propanediol, suggesting a correlation between the expression of these enzymes and a raised intracellular NAD/NADH ratio. The enzymes metabolizing glycerol (glycerol dehydratase and 1,3-propanediol dehydrogenase) were expressed in concert without necessary induction by added glycerol, although their expression may also be influenced by the intracellular NAD/NADH ratio set by the different carbohydrates fermented.     

Carbon and electron flow in Clostridium butyricum grown in chemostat culture on glucose-glycerol mixtures

Summary The metabolism of C. butyricum was manipulated, at neutral pH and in carbon limited chemostat cultures by changing the overall degree of reduction of the substrate, using mixtures of glucose and glycerol. Cultures grown on glucose alone produced only acids (acetate, butyrate and lactate). When the glycerol (in C moles)/glucose+glycerol (in C moles) ratio was progressively changed from 0 to 1 a corresponding increase of 1,3-propanediol production occured and an immediate and drastic decrease of the specific rate of acetate production was observed while the specific rate of butyrate production only decreased slightly. For glycerol (in C moles)/glucose+glycerol (in C moles) ratios higher than 0.5, the q_{NAD(P)H from Fd} and the CO₂/H₂ molar ratio increased sharply, the first becoming positive and the second higher than 1. This indicates a complete reversion of the electron flow: part of reduced ferredoxin produced by the phosphoroclastic cleavage of pyruvate to acetyl-CoA was diverted from H₂ formation toward NAD(P) reduction by the ferredoxin-NAD(P) reductase(s) in order to produce NAD(P)H. This change in the electron flow was associated to an increase in the specific rate and the yield of 1,3-propanediol production related to glycerol.     

Towards improved butanol production through targeted genetic modification of Clostridium pasteurianum

Declining fossil fuel reserves, coupled with environmental concerns over their continued extraction and exploitation have led to strenuous efforts to identify renewable routes to energy and fuels. One attractive option is to convert glycerol, a by-product of the biodiesel industry, into n-butanol, an industrially important chemical and potential liquid transportation fuel, using Clostridium pasteurianum. Under certain growth conditions this Clostridium species has been shown to predominantly produce n-butanol, together with ethanol and 1,3-propanediol, when grown on glycerol. Further increases in the yields of n-butanol produced by C. pasteurianum could be accomplished through rational metabolic engineering of the strain. Accordingly, in the current report we have developed and exemplified a robust tool kit for the metabolic engineering of C. pasteurianum and used the system to make the first reported in-frame deletion mutants of pivotal genes involved in solvent production, namely hydA (hydrogenase), rex (Redox response regulator) and dhaBCE (glycerol dehydratase). We were, for the first time in C. pasteurianum, able to eliminate 1,3-propanediol synthesis and demonstrate its production was essential for growth on glycerol as a carbon source. Inactivation of both rex and hydA resulted in increased n-butanol titres, representing the first steps towards improving the utilisation of C. pasteurianum as a chassis for the industrial production of this important chemical.     

Fermentation characteristics of Clostridium pasteurianum LMG 3285 grown on glucose and mannitol

Clostridium pasteurianum fermented glucose to acetate, butyrate, CO₂ and H₂. In batch cultures the fermentation pattern was only slightly affected by culture pH over the range 8·0 to 5·5. The acetate/butyrate ratio was always higher than or equal to one. Between 2·14 and 2·33 mol H₂ was produced per mol glucose fermented. At unregulated pH, more butanol and less butyrate was formed. In a carbon-limited chemostat, the steady-state acetate/butyrate ratio was always lower than one. H₂ production was approximately 1·70 mol per mol glucose consumed. Substantial amounts of extracellular protein were formed. With decreasing pH, acetate and formate production decreased, while H₂ production was highest at pH 6.0. With increasing dilution rate ( D ), the product spectrum hardly changed, but more biomass was formed. Y _glucose^max and Y _ATP^max were 55·97 and 31·48 g dry weight per mol glucose or ATP respectively. With increasing glucose input the formation of fatty acids and H₂ slightly decreased.
Continuous cultures fermented mannitol to acetate, butyrate, butanol, CO₂ and H₂. With acetate as co-substrate, butanol production and molar growth yields, Y _mannitol and Y _ATP, markedly decreased, while the butyrate and H₂ production increased. The latter reached a value of 2·21 mol H₂ per mol mannitol consumed.     

Fermentation of glycerol to 1,3-propanediol: use of cosubstrates

Three fermentable substances, glucose, 1,2-ethanediol and 1,2-propanediol were checked as cosubstrates for the fermentation of glycerol by Clostridium butyricum and Citrobacter freundii with the aim of achieving a complete conversion of glycerol to 1,3-propanediol. Glucose was fermented by C. butyricum mainly to acetate, CO₂ and reducing equivalents in the presence of glycerol and contributed markedly to the 1,3-propanediol yield. However, because of relatively slow growth on glucose, complete conversion was not achieved. If the two glycols were used as cosubstrates for glycerol fermentation, the 1,3-propanediol yield did not increase but dimished considerably, as they were converted to more reduced products, i.e. alcohols instead of acids. From 1,2-propanediol 2-propanol was formed in addition to 1-propanol. The ratio of the propanols was dependent on the culture conditions.     

Improved electrocompetence and metabolic engineering of Clostridium pasteurianum reveals a new regulation pattern of glycerol fermentation

Clostridium pasteurianum produces industrially valuable chemicals such as n‐butanol and 1,3‐propanediol from fermentations of glycerol and glucose. Metabolic engineering for increased yields of selective compounds is not well established in this microorganism. In order to study carbon fluxes and to selectively increase butanol yields, we integrated the latest advances in genome editing to obtain an electrocompetent Clostridium pasteurianum strain for further engineering. Deletion of the glycerol dehydratase large subunit (dhaB) using an adapted S. pyogenes Type II CRISPR/Cas9 nickase system resulted in a 1,3‐propanediol‐deficient mutant producing butanol as the main product. Surprisingly, the mutant was able to grow on glycerol as the sole carbon source. In spite of reduced growth, butanol yields were highly increased. Metabolic flux analysis revealed an important role of the newly identified electron bifurcation pathway for crotonyl‐CoA to butyryl‐CoA conversion in the regulation of redox balance. Compared to the parental strain, the electron bifurcation pathway flux of the dhaB mutant increased from 8 to 46% of the overall flux from crotonyl‐CoA to butyryl‐CoA and butanol, indicating a new, 1,3‐propanediol‐independent pattern of glycerol fermentation in Clostridium pasteurianum.     

Continuous production of acetone and butanol by Clostridium acetobutylicum in a two-stage phosphate limited chemostat

Summary When Clostridium acetobutylicum was grown in continuous culture under phosphate limitation (0.74 mM) at a pH of 4.3, glucose was fermented to butanol, acetone and ethanol as the major products. At a dilution rate of D=0.025 h^–1 and a glucose concentration of 300 mM, the maximal butanol and acetone concentrations were 130 mM and 74 mM, respectively. 20% of the glucose remained in the medium. On the basis of these results a two-stage continuous process was developed in which 87.5% of the glucose was converted into butanol, acetone and ethanol. The cells and minor amounts of acetate and butyrate accounted for the remaining 12.5% of the substrate. The first stage was run at D=0.125 h^–1 and 37° C and the second stage at D=0.04 h^–1 and 33° C. High yields of butanol and acetone were also obtained in batch culture under phosphate limitation.     

Glycerol and propanediols degradation by Desulfovibrio alcoholovorans in pure culture in the presence of sulfate, or in syntrophic association with Methanospirillum hungatei

Abstract In a mineral medium containing sulfate as terminal electron acceptor, the sulfate-reducing bacterium Desulfovibrio alcoholovorans oxidized stoichiometrically 1 mol glycerol to 1 mol acetate and 1 mol 1,3-propanediol to 1 mol acetate with the concomitant reduction of 0.75 and 1 mol sulfate, respectively; 1 mol 1,2-propanediol was degraded to 0.8 mol acetate and 0.1 mol proprionate, with the reduction of approximately 1 mol sulfate. The maximum specific growth rates (μ_max in h⁻¹) were 0.22, 0.086 and 0.09 with glycerol, 1,3-propanediol and 1,2-propanediol, respectively. The growth yields were 12.7 g, 11.1 g and 7.2 g dry weight/mol 1,3-propanediol, glycerol and 1,2-propanediol degraded, respectively. The growth yields and maximum specific growth rates of the H₂-transferring associations were also calculated. In the absense of sulfate, all these reduced substrates were degraded to acids and methane when D. alcoholovorans was cocultured with Methanospirillum hungatei . Changes in the metabolic pathway were observed in the degradation of 1,2- and 1,3-propanediol. The metabolic efficiency of D. alcoholovorans to degrade glycerol, 1.2- and 1,3-propanediol is discussed.     

Regulation of carbon and electron flow in Clostridium butyricum VPI 3266 grown on glucose-glycerol mixtures

The metabolism of Clostridium butyricum was manipulated at pH 6.5 and in phosphate-limited chemostat culture by changing the overall degree of reduction of the substrate using mixtures of glucose and glycerol. Cultures grown on glucose alone produced only acids (acetate, butyrate, and lactate) and a high level of hydrogen. In contrast, when glycerol was metabolized, 1,3-propanediol became the major product, the specific rate of acid formation decreased, and a low level of hydrogen was observed. Glycerol consumption was associated with the induction of (i) a glycerol dehydrogenase and a dihydroxyacetone kinase feeding glycerol into the central metabolism and (ii) an oxygen-sensitive glycerol dehydratase and an NAD-dependent 1,3-propanediol dehydrogenase involved in propanediol formation. The redirection of the electron flow from hydrogen to NADH formation was associated with a sharp decrease in the in vitro hydrogenase activity and the acetyl coenzyme A (CoA)/free CoA ratio that allows the NADH-ferredoxin oxidoreductase bidirectional enzyme to operate so as to reduce NAD in this culture. The decrease in acetate and butyrate formation was not explained by changes in the concentration of phosphotransacylases and acetate and butyrate kinases but by changes in in vivo substrate concentrations, as reflected by the sharp decrease in the acetyl-CoA/free CoA and butyryl-CoA/free CoA ratios and the sharp increase in the ATP/ADP ratio in the culture grown with glucose and glycerol compared with that in the culture grown with glucose alone. As previously reported for Clostridium acetobutylicum (L. Girbal, I. Vasconcelos, and P. Soucaille, J. Bacteriol. 176:6146-6147, 1994), the transmembrane pH of C. butyricum is inverted (more acidic inside) when the in vivo activity of hydrogenase is decreased (cultures grown on glucose-glycerol mixture). For both cultures, the stoichiometry of the H(+) ATPase was shown to remain constant and equal to 3 protons exported per molecule of ATP consumed.     

Coordination of metabolic pathways: Enhanced carbon conservation in 1,3-propanediol production by coupling with optically pure lactate biosynthesis

Metabolic engineering has emerged as a powerful tool for bioproduction of both fine and bulk chemicals. The natural coordination among different metabolic pathways contributes to the complexity of metabolic modification, which hampers the development of biorefineries. Herein, the coordination between the oxidative and reductive branches of glycerol metabolism was rearranged in Klebsiella oxytoca to improve the 1,3-propanediol production. After deliberating on the product value, carbon conservation, redox balance, biological compatibility and downstream processing, the lactate-producing pathway was chosen for coupling with the 1,3-propanediol-producing pathway. Then, the other pathways of 2,3-butanediol, ethanol, acetate, and succinate were blocked in sequence, leading to improved d-lactate biosynthesis, which as return drove the 1,3-propanediol production. Meanwhile, efficient co-production of 1,3-propanediol and l-lactate was also achieved by replacing ldhD with ldhL from Bacillus coagulans. The engineered strains PDL-5 and PLL co-produced over 70 g/L 1,3-propanediol and over 100 g/L optically pure d-lactate and l-lactate, respectively, with high conversion yields of over 0.95 mol/mol from glycerol.     

Fermentation of raw glycerol to 1,3-propanediol by new strains ofClostridium butyricum

Industrial glycerol obtained through the transesterification process using rapeseed oil did not support growth of several strains ofClostridium butyricum obtained from bacterial culture collections. Ten new strains ofC. butyricum were obtained from mud samples from a river, a stagnant pond, and a dry canal. These new isolates fermented the commercial glycerol and produced 1,3-propanediol as a major fermentation product with concomitant production of acetic and butyric acids. Four of the ten isolates were able to grow on industrial glycerol obtained from rapeseed oil. One strain,C. butyricum E5, was very resistant to high levels of glycerol and 1,3-propanediol. Using fed-batch fermentation, 109 g L^–1 of industrial glycerol were converted into 58 g of 1,3-propanediol, 2.2 g of acetate and 6.1 g of butyrate per liter.