The role of 1,3-propanediol production in fermentation of glycerol by Clostridium pasteurianum

From pre-culture to solvent: current trends in Clostridium acetobutylicum cultivation

The biological production of butanol via ABE (acetone-butanol-ethanol) fermentation using Clostridium acetobutylicum has a storied history of over 100 years, initially driven by the demand for synthetic rubber during World War I and later for industrial applications. Despite its decline due to the rise of petrochemical alternatives, renewed interest has emerged due to the global shift towards sustainable energy sources and rising oil prices. This review highlights the challenges in the cultivation process of C. acetobutylicum, such as strain degeneration, solvent toxicity, and substrate costs, and presents recent advancements aimed at overcoming these issues. Detailed documentation of the entire cultivation process including cell conservation, pre-culture, and main culture is seen as a fundamental step to facilitate further progress in research. Key strategies to improve production efficiency were identified as controlling pH to facilitate the metabolic shift from acidogenesis to solventogenesis, employing in situ product removal techniques, and advancing metabolic engineering for improved solvent tolerance of C. acetobutylicum. Furthermore, the use of renewable resources, particularly lignocellulosic biomass, positions ABE fermentation as a viable solution for sustainable solvent production. By focusing on innovative research avenues, including co-cultivation and bioelectrochemical systems, the potential for C. acetobutylicum to contribute significantly to a bio-based economy can be realized. KEY POINTS: • Historical significance and revival of ABE fermentation with Clostridium acetobutylicum • Current challenges and innovative solutions in cultivating C. acetobutylicum • New avenues for enhancing productivity and sustainability.

Hydrogen online monitoring based on thermal conductivity for anaerobic microorganisms

H₂ -producing microorganisms are a promising source of sustainable biohydrogen. However, most H₂ -producing microorganisms are anaerobes, which are difficult to cultivate and characterize. While several methods for measuring H₂ exist, common H₂ sensors often require oxygen, making them unsuitable for anaerobic processes. Other sensors can often not be operated at high gas humidity. Thus, we applied thermal conductivity (TC) sensors and developed a parallelized, online H₂ monitoring for time-efficient characterization of H₂ production by anaerobes. Since TC sensors are nonspecific for H₂ , the cross-sensitivity of the sensors was evaluated regarding temperature, gas humidity, and CO₂ concentrations. The systems' measurement range was validated with two anaerobes: a high H₂ -producer (Clostridium pasteurianum) and a low H₂ -producer (Phocaeicola vulgatus). Online monitoring of H₂ production in shake flask cultivations was demonstrated, and H₂ transfer rates were derived. Combined with online CO₂ and pressure measurements, molar gas balances of the cultivations were closed, and an anaerobic respiration quotient was calculated. Thus, insight into the effect of medium components and inhibitory cultivation conditions on H₂ production with the model anaerobes was gained. The presented online H₂ monitoring method can accelerate the characterization of anaerobes for biohydrogen production and reveal metabolic changes without expensive equipment and offline analysis.

Enhancing 1,3-Propanediol Productivity in the Non-Model Chassis Clostridium beijerinckii through Genetic Manipulation

Biotechnological processes at biorefineries are considered one of the most attractive alternatives for valorizing biomasses by converting them into bioproducts, biofuels, and bioenergy. For example, biodiesel can be obtained from oils and grease but generates glycerol as a byproduct. Glycerol recycling has been studied in several bioprocesses, with one of them being its conversion to 1,3-propanediol (1,3-PDO) by Clostridium. Clostridium beijerinckii is particularly interesting because it can produce a range of industrially relevant chemicals, including solvents and organic acids, and it is non-pathogenic. However, while Clostridium species have many potential advantages as chassis for synthetic biology applications, there are significant limitations when considering their use, such as their limited genetic tools, slow growth rate, and oxygen sensitivity. In this work, we carried out the overexpression of the genes involved in the synthesis of 1,3-PDO in C. beijerinckii Br21, which allowed us to increase the 1,3-PDO productivity in this strain. Thus, this study contributed to a better understanding of the metabolic pathways of glycerol conversion to 1,3-PDO by a C. beijerinckii isolate. Also, it made it possible to establish a transformation method of a modular vector in this strain, therefore expanding the limited genetic tools available for this bacterium, which is highly relevant in biotechnological applications.

Extractive adsorption of 1,3-propanediol on a novel polystyrene macroporous resin enclosing medium and long-chain alcohols as extractant

Extractive adsorption is an integrated separation method employing a novel resin with both particle and liquid characteristics in terms of adsorption and extraction. In this study, the novel extractive adsorption polystyrene-divinylbenzene (PS-DVB) macroporous resin was synthesized by suspension polymerization, in which n-octanol (OL-PS-DVB) or mixed alcohols of n-octanol, undecyl alcohol, and tetradecyl alcohol (MA-PS-DVB) were added as porogen and enclosed in the resin skeleton after the reaction. The characterization of the two novel resins of OL-PS-DVB and MA-PS-DVB showed that they have large specific surface areas of 48.7 and 17.4 m2/g, respectively. Additionally, the two synthesized resins have much higher static adsorption capacities of 1,3-propanediol (511 and 473 mg/g) and dynamic adsorption capacities (312 and 267 mg/g) than traditional resins, because extractants enclosed in the resin can increase the adsorption capacity. Through Langmuir equation, the theoretical static maximum adsorption capacity of the mixed alcohols resin is 515 mg/g at 298 K and Gibbs free energy change of adsorption was -3781 J/mol, indicating that the adsorption process was spontaneous. In addition, the sorbent concentration effect in the resin was generated at high 1,3-propanediol (1,3-PDO) concentrations. The fitting of the Flocculation model can reveal that there is a possible relation between adsorption and flocculation. Compared to OL-PS-DVB, MA-PS-DVB showed better performance in the recovery yield of 1,3-PDO and other byproducts, the removal rates of the inorganic salt and protein, and the efficiency of recycled resin. For MA-PS-DVB, the recovery of 1,3-PDO, butyrate acid, acetic acid, and residual glycerol was 97.1%, 94.7%, 93.3%, and 90.3%, respectively. Simultaneously, the resin of MA-PS-DVB could remove 93.8% of inorganic salts and 90.9% of proteins in the concentrated fermentation broth. The two synthesized resins of OL-PS-DVB and MA-PS-DVB still had 90% or 92% of capacity for extractive adsorption of 1,3-propanediol after 10 times of recycling, which exhibited potential application in the separation of 1,3-propanediol from fermentation broth.

Single and multiplexed gene repression in solventogenic Clostridium via Cas12a-based CRISPR interference

The Gram-positive, spore-forming, obligate anaerobic firmicute species that make up the Clostridium genus have broad feedstock consumption capabilities and produce value-added metabolic products, but genetic manipulation is difficult, limiting their broad appeal. CRISPR-Cas systems have recently been applied to Clostridium species, primarily using Cas9 as a counterselection marker in conjunction with plasmid-based homologous recombination. CRISPR interference is a method that reduces gene expression of specific genes via precision targeting of a nuclease deficient Cas effector protein. Here, we develop a dCas12a-based CRISPR interference system for transcriptional gene repression in multiple mesophilic Clostridium species. We show the Francisella novicida Cas12a-based system has a broader applicability due to the low GC content in Clostridium species compared to CRISPR Cas systems derived from other bacteria. We demonstrate >99% reduction in transcript levels of targeted genes in Clostridium acetobutylicum and >75% reduction in Clostridium pasteurianum. We also demonstrate multiplexed repression via use of a single synthetic CRISPR array, achieving 99% reduction in targeted gene expression and elucidating a unique metabolic profile for their reduced expression. Overall, this work builds a foundation for high throughput genetic screens without genetic editing, a key limitation in current screening methods used in the Clostridium community.

Metabolomic and kinetic investigations on the electricity-aided production of butanol by Clostridium pasteurianum strains

In this contribution, we studied the effect of electro-fermentation on the butanol production of Clostridium pasteurianum strains by a targeted metabolomics approach. Two strains were examined: an electrocompetent wild type strain (R525) and a mutant strain (dhaB mutant) lacking formation of 1,3-propanediol (PDO). The dhaB-negative strain was able to grow on glycerol without formation of PDO, but displayed a high initial intracellular NADH/NAD ratio which was lowered subsequently by upregulation of the butanol production pathway. Both strains showed a 3-5 fold increase of the intracellular NADH/NAD ratio when exposed to cathodic current in a bioelectrochemical system (BES). This drove an activation of the butanol pathway and resulted in a higher molar butanol to PDO ratio for the R525 strain. Nonetheless, macroscopic electron balances suggest that no significant amount of electrons derived from the BES was harvested by the cells. Overall, this work points out that electro-fermentation can be used to trigger metabolic pathways and improve product formation, even when the used microbe cannot be considered electroactive. Accordingly, further studies are required to unveil the underlying (regulatory) mechanisms.

Introduction of glycine synthase enables uptake of exogenous formate and strongly impacts the metabolism in Clostridium pasteurianum

Autotrophic or mixotrophic use of one-carbon (C1) compounds is gaining importance for sustainable bioproduction. In an effort to integrate the reductive glycine pathway (rGP) as a highly promising pathway for the assimilation of CO₂ and formate, genes coding for glycine synthase system from Gottschalkia acidurici were successfully introduced into Clostridium pasteurianum, a non-model host microorganism with industrial interests. The mutant harboring glycine synthase exhibited assimilation of exogenous formate and reduced CO₂ formation. Further metabolic data clearly showed large impacts of expression of glycine synthase on the product metabolism of C. pasteurianum. In particular, 2-oxobutyrate (2-OB) was observed for the first time as a metabolic intermediate of C. pasteurianum and its secretion was solely triggered by the expression of glycine synthase. The perturbation of C1 metabolism is discussed regarding its interactions with pathways of the central metabolism, acidogenesis, solventogenesis, and amino acid metabolism. The secretion of 2-OB is considered as a consequence of metabolic and redox instabilities due to the activity of glycine synthase and may represent a common metabolic response of Clostridia in enhanced use of C1 compounds.

Increased Selectivity for Butanol in Clostridium Pasteurianum Fermentations via Butyric Acid Addition or Dual Feedstock Strategy

Volatility of the petroleum market has renewed research into butanol as an alternate fuel. In order to increase the selectivity for butanol during glycerol fermentation with Clostridium pasteurianum, butyric acid can be added to the medium. In this manuscript, different methods of extracellular butyric acid addition are explored, as well as self-generation of butyric acid fermented from sugars in a co-substrate strategy. Molasses was used as an inexpensive sugar substrate, and the optimal molasses to glycerol ratio was found to allow the butyric acid to be taken back up into the cells and increase the productivity of butanol from all carbon sources. When butyric acid is added directly into the media, there was no significant difference between chemically pure butyric acid, or butyric acid rich supernatant from a separate fermentation. When low concentrations of butyric acid (1 or 2 g/L) are added to the initial media, an inhibitory effect is observed, with no influence on the butanol selectivity. However, when added later to the fermentation, over 1 g/L butyric acid is taken into the cells and increased the relative carbon yield from 0.449 to 0.519 mols carbon in product/mols carbon in substrate. An optimized dual substrate fermentation strategy in a pH-controlled reactor resulted in the relative carbon yield rising from 0.439 when grown on solely glycerol, to 0.480 mols C product/mols C substrate with the dual substrate strategy. An additional benefit is the utilization of a novel source of sugars to produce butanol from C. pasteurianum. The addition of butyric acid, regardless of how it is generated, under the proper conditions can allow for increased selectivity for butanol from all substrates.

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.

Increased Butanol Yields through Cosubstrate Fermentation of Jerusalem Artichoke Tubers and Crude Glycerol by Clostridium pasteurianum DSM 525

Clostridium pasteurianum DSM 525 can produce butanol, 1,3-propanediol, and ethanol from glycerol. The product distribution can be tilted toward butanol when adding butyric acid. The strain predominantly produces acetic and butyric acids when grown on saccharides. Hence, butyrate formed from saccharide conversion can be used to stimulate butanol production from glycerol under cosubstrate cultivation. The optimal cosubstrate ratio was determined, and under optimal conditions, a butanol yield and a productivity of 0.27 ± 0.01 g_butanol g^-1 _{(glycerol + sugar)} ^-1 and 0.74 ± 0.02 g L^-1 h^-1 were obtained. On the basis of these results, batch fermentation in a 5 L bioreactor was performed using Jerusalem artichoke hydrolysate (carbohydrate source) and crude glycerol (residue from biodiesel production) at the previously determined optimal condition. A butanol yield and a productivity of 0.28 ± 0.007 g_butanol g_{(glycerol+sugar)} ^-1 and 0.55 ± 0.008 g L^-1 h^-1 were achieved after 27 h fermentation, indicating the suitability of those low-cost carbon sources as cosubstrates for butanol production via C. pasteurianum.

Clostridial conversion of corn syrup to Acetone-Butanol-Ethanol (ABE) via batch and fed-batch fermentation

Corn syrup - a commercial product derived from saccharification of corn starch - was used to produce acetone-butanol-ethanol (ABE) by Clostridium spp. Screening of commercial Clostridium spp., substrate inhibition tests and fed-batch experiments were carried out to improve ABE production using corn syrup as only carbon source. The screening tests carried out in batch mode using a production media containing 50 g/L corn syrup revealed that C. saccharobutylicum was the best performer in terms of total solvent concentration (12.46 g/L), yield (0.30 g/g) and productivity (0.19 g/L/h) and it was selected for successive experiments. Concentration of corn syrup higher than 50 g/L resulted in no solvents production. Fed-batch fermentation improved ABE production with respect to batch fermentation: the butanol and solvent concentration increased up to 8.70 and 16.68 g/L, respectively. The study demonstrated the feasibility of producing solvents via ABE fermentation using corn syrup as a model substrate of concentrated sugar mixtures.

Production of 1,3-propanediol using a novel 1,3-propanediol dehydrogenase from isolated Clostridium butyricum and co-biotransformation of whole cells

In this study, a newly strain named Clostridium butyricum YJH-09 were isolated from the sample of pond soil and identified through physiological, biochemical and 16S rDNA analysis. Then, the dhaT gene encoding a novel 1,3-propanediol dehydrogenase (PDOR) was cloned from this strain and expressed in Escherichia coli BL21(DE3). Subsequently, the recombinant PDOR was purified and the optimal pH and temperature, specific activities and kinetic parameter were investigated. Furthermore, the whole cells of Clostridium butyricum YJH-09 mixed with BL21-dhaT were used to produce 1,3-PD through co-biotransformation. As results, 25.88g/L of 1,3-PD was generated with 0.54g/g yield from 50g/L glycerol in 30h, and the 1,3-PD production was increased more than 2-fold compared with wild type strain alone. This research would offer useful information for further development of the biosynthesis of 1,3-PD.

Environmentally-friendly strategy for separation of 1,3-propanediol using biocatalytic conversion

Glycerol waste from the biodiesel production can be used as a carbon source in the production of 1,3-propanediol (1,3-PD) through microbial fermentation. However, downstream processing is a major bottleneck that restricts its biological production. Here, we investigated an environmentally-friendly method to enzymatically separate 1,3-PD. The transformation of 1,3-PD to an ester was achieved by exploiting the esterification reaction with fatty acids under lipase catalysis. The reaction efficiency was optimized using different poly-alcohols that were existed in the fermentation broth reacted with a fatty acid. Whereas the 1,3-PD conversion reached 62%, only a 0.06% and 0.08% conversion was reached for 2,3-butanediol and glycerol, illustrating the former's more efficient separation. The recovery efficiency of 1,3-PD was 96%. Finally, 1,3-PD was obtained by lipase-directed ester hydrolysis. Taken together, the bio-catalyzed separation process presented here is a novel and promising method for recovering 1,3-PD.

Value-adding conversion and volume reduction of sewage sludge by anaerobic co-digestion with crude glycerol

In this study, conversion of sewage sludge to biogas by anaerobic co-digestion with crude glycerol was examined. When 0.126g/L crude glycerol was added to the reactor, only methane was produced. Upon addition of 5.04g/L crude glycerol, hydrogen production occurred, and a significant amount of 1,3-propanediol (1,3-PDO) was generated in the liquid phase. On day 6, the dry weight was largely composed of organic acids (48%) and 1,3-PDO (17%), which are water-soluble. Degradation of 1,3-PDO was very slow, which is advantageous for recovery. Crude glycerol, which contains alkaline substances, promoted organic matter degradation by microorganisms, which possibly affected biogas and 1,3-PDO production. Addition of 0.630-2.52g/L glycerol initially led to hydrogen production, followed by methane production a few days later, which stabilized within 1week. In conclusion, adjustment of the crude glycerol concentration allows controllable conversion to value-added products for co-digestion.

Glycerol Production and Transformation: A Critical Review with Particular Emphasis on Glycerol Reforming Reaction for Producing Hydrogen in Conventional and Membrane Reactors

Glycerol represents an emerging renewable bio-derived feedstock, which could be used as a source for producing hydrogen through steam reforming reaction. In this review, the state-of-the-art about glycerol production processes is reviewed, with particular focus on glycerol reforming reactions and on the main catalysts under development. Furthermore, the use of membrane catalytic reactors instead of conventional reactors for steam reforming is discussed. Finally, the review describes the utilization of the Pd-based membrane reactor technology, pointing out the ability of these alternative fuel processors to simultaneously extract high purity hydrogen and enhance the whole performances of the reaction system in terms of glycerol conversion and hydrogen yield.

Substrate dependent modulation of butanol to ethanol ratio in non-acetone forming Clostridium sporogenes NCIM 2918

Present study reports a non-acetone producing Clostridium sporogenes strain as a potential producer of liquid biofuels. Alcohol production was positively regulated by sorbitol and instant dry yeast as carbon and nitrogen sources respectively. Media optimization resulted in maximum butanol and ethanol titer (gL^-1) of 12.1 and 7.9 respectively. Depending on the combination of carbon sources, the organism was found to manipulate its metabolism towards synthesis of either ethanol or butanol, thereby affecting the total alcohol titer. Among various dual substrate combinations, glucose-glycerol mixture in the ratio of 60:40 resulted in maximum butanol and ethanol titer (gL^-1) of 11.9 and 12.1 respectively with total alcohol productivity of 0.59gL^-1h^-1. In the mixture, when pure glycerol was replaced with crude glycerol, butanol and ethanol titer (gL^-1) of 11.2 and 11.7 was achieved. Hence, the strain shows immense potential for biofuels production using crude glycerol as cheap substrate.

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.

Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum

Clostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism’s genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism’s defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated φ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy. Methylome analysis of sequencing reads provided a near-complete glimpse into the organism’s restriction-modification systems. We also unveiled the chief C. pasteurianum Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus, which was found to exemplify a Type I-B system. Finally, we show that C. pasteurianum possesses a highly complex fermentative metabolism whereby the metabolic pathways enlisted by the cell is governed by the degree of reductance of the substrate. Four distinct fermentation profiles, ranging from exclusively acidogenic to predominantly alcohologenic, were observed through redox consideration of the substrate. A detailed discussion of the organism’s central metabolism within the context of metabolic engineering is provided.