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

Microbial electrosynthesis: opportunities for microbial pure cultures

Microbial electrosynthesis (MES) is an emerging technology that couples renewable electricity to microbial production processes. Although advances in MES performance have been driven largely by microbial mixed cultures, we see a great limitation in the diversity, and hence value, of products that can be achieved in undefined mixed cultures. By contrast, metabolic control of pure cultures and genetic engineering could greatly expand the scope of MES, and even of broader electrobiotechnology, to include targeted high-value products. To leverage this potential, we advocate for more efforts and activities to develop engineered electroactive microbes for synthesis, and we highlight the need for a standardized electrobioreactor infrastructure that allows the establishment and engineering of electrobioprocesses with these novel biocatalysts.

Effect of pH on metabolic pathway shift in fermentation and electro-fermentation of xylose by Clostridium autoethanogenum

Clostridium autoethanogenum can to convert waste gases (CO2, CO, H2) and xylose from hydrolyzed biomass into acetate, lactate, formate, ethanol and 2,3-butanediol, being a candidate for the transformation of waste streams of lignocellulosic biorefineries. Electro-fermentation (EF) modify the pattern of traditional fermentations resulting in improved product yields as has been shown when using Clostridium strains. The aim of this work was to evaluate the influence of pH on microbial growth and product distribution during fermentation and EF of xylose by C. autoethanogenum DSM10061. Fermentation and EF were carried out in a H-type reactor at three controlled pH: 5.0, 5.5 and 5.8, and at a fixed potential of -600 mV (versus Ag/AgCl) in the EF. The experiments showed that maximum biomass concentration increased as the pH increased in fermentation and EF. In accordance with maximum biomass reached, the highest substrate conversion was observed at pH 5.8 for both systems, with 76.80 % in fermentation and 96.18 % in EF. Moreover, the highest concentrations of acetic acid (1.41 ± 0.07 g L-1) and ethanol (1.45 ± 0.15 g L-1) were obtained at the end of cultures in the EF at pH 5.8. The production of lactic and formic acid decreased by the application of the external potential regardless of the pH value, reaching the lowest productivity at pH 5.8. In contrast, the specific productivity of acetic acid and ethanol was lower in both fermentation and EF at the lowest pH. Furthermore, the presence of 0.06 g L-1 of 2,3-butanediol was only detected in EF at pH 5.8. The results revealed that EF modulated microbial metabolism, which can be explained by a possible increased generation of NADP+/NADPH cofactors, which would redirect the metabolic pathway to more reduced products.

Main genome characteristics of butanol-producing Clostridium sp. UCM В-7570 strain

The rapid development of new molecular methods and approaches, sequencing technologies, has provided new insights into genetic and structural features of bacterial genomes. Information about the genetic organization of metabolic pathways and their regulatory elements has greatly contributed to the increase in the number of studies related to the construction of new bacterial strains with improved characteristics. In this study, the entire genome of the producing strain Clostridium sp. UCM В-7570 from the "Collection of producing strains of microorganisms and plant lines for food and agricultural biotechnology" of Institute of Food Biotechnology and Genomics of the National Academy of Sciences of Ukraine was sequenced and characterized. The genome was assembled into the scaffold with a total size of 4,470,321 bp and a GC content of 29.7%. The total number of genes identified was 4262, of which 4057 encoded proteins, 10 were rRNA operons, and 80 were tRNA genes. The genes of the sequenced genome encoding enzymes involved in butanol fermentation were found and analyzed. They were organized into cluster structures, and their protein sequences were found to be similar to the corresponding strains of C. acetobutylicum, C. beijerinckii, and C. pasteurianum type strains with the highest similarity to the latter. Thus, Clostridium sp. UCM В-7570 producing strain was identified as C. pasteurianum and suggested for metabolic engineering purposes.

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.

Electrochemically mediated bioconversion and integrated purification greatly enhanced co-production of 1,3-propanediol and organic acids from glycerol in an industrial bioprocess

In this study, we show how electrochemically mediated bioconversion can greatly increase the co-production of 1,3-propanediol and organic acids from glycerol in an industrial bioprocess using a Clostridum pasteurianum mutant. Remarkably, an enhanced butyrate formation was observed due to a weakened butanol pathway of the mutant. This allowed the strain to have a higher ATP generation for an enhanced growth, higher glycerol consumption and PDO production. The PDO titer reached as high as 120.67 g/L at a cathodic current of -400 mA, which is 33% higher than that without electricity, with a concurrent increase of butyric acid by 80%. To fully recover the increased PDO and organic acids, a novel downstream process combining thin film evaporation of PDO and esterification of organic acids with ethanol was developed. This enables the efficient co-production of PDO, ethyl acetate and ethyl butyrate with a high overall carbon use of 87%.

Highly selective butanol production by manipulating electron flow via cathodic electro-fermentation

Butanol production by solventogenic Clostridia shows great potential to combat the energy crisis, but is still challenged by low butanol selectivity and high downstream cost. In this study, a novel cathodic electro-fermentation (CEF) system mediated by methyl viologen (MV) was proposed and sequentially optimized to obtain highly selective butanol production. Under the optimal conditions (-0.60 V cathode potential, 0.50 mM MV, 30 g/L glucose), 7.17 ± 0.55 g/L butanol production were achieved with the yield of 0.32 ± 0.02 g/g. With the supplement of 4 g/L butyric acid as co-substrate, butanol production further improved to 13.14 ± 1.14 g/L with butanol yield and selectivity as high as 0.43 ± 0.01 g/g and 90.44 ± 1.66%, respectively. The polarized electrode enabled the unbalanced fermentation towards butanol formation and MV further inhibited hydrogen production, both of which contributed to the high-level butanol production and selectivity. The MV-mediated CEF system is a promising approach for cost-effective bio-butanol production.

Control of redox potential in a novel continuous bioelectrochemical system led to remarkable metabolic and energetic responses of Clostridium pasteurianum grown on glycerol

Background

Electro-fermentation (EF) is an emerging tool for bioprocess intensification. Benefits are especially expected for bioprocesses in which the cells are enabled to exchange electrons with electrode surfaces directly. It has also been demonstrated that the use of electrical energy in BES can increase bioprocess performance by indirect secondary effects. In this case, the electricity is used to alter process parameters and indirectly activate desired pathways. In many bioprocesses, oxidation-reduction potential (ORP) is a crucial process parameter. While C. pasteurianum fermentation of glycerol has been shown to be significantly influenced electrochemically, the underlying mechanisms are not clear. To this end, we developed a system for the electrochemical control of ORP in continuous culture to quantitatively study the effects of ORP alteration on C. pasteurianum by metabolic flux analysis (MFA), targeted metabolomics, sensitivity and regulation analysis.

Results

In the ORP range of −462 mV to −250 mV, the developed algorithm enabled a stable anodic electrochemical control of ORP at desired set-points and a fixed dilution rate of 0.1 h⁻¹. An overall increase of 57% in the molar yield for 1,3-propanediol was observed by an ORP increase from −462 to −250 mV. MFA suggests that C. pasteurianum possesses and uses cellular energy generation mechanisms in addition to substrate-level phosphorylation. The sensitivity analysis showed that ORP exerted its strongest impact on the reaction of pyruvate-ferredoxin-oxidoreductase. The regulation analysis revealed that this influence is mainly of a direct nature. Hence, the observed metabolic shifts are primarily caused by direct inhibition of the enzyme upon electrochemical production of oxygen. A similar effect was observed for the enzyme pyruvate-formate-lyase at elevated ORP levels.

Conclusions

The results show that electrochemical ORP alteration is a suitable tool to steer the metabolism of C. pasteurianum and increase product yield for 1,3-propanediol in continuous culture. The approach might also be useful for application with further anaerobic or anoxic bioprocesses. However, to maximize the technique's efficiency, it is essential to understand the chemistry behind the ORP change and how the microbial system responds to it by transmitted or direct effects.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01902-5.

Electro-fermentation: Sustainable bioproductions steered by electricity

The market of biobased products obtainable via fermentation processes is steadily increasing over the past few years, driven by the need to create a decarbonized economy. To date, industrial fermentation (IF) employs either pure or mixed microbial cultures (MMC) whereby the type of the microbial catalysts and the used feedstock affect metabolic pathways and, in turn, the type of product(s) generated. In many cases, especially when dealing with MMC, the economic viability of IF is hindered by factors such as the low attained product titer and selectivity, which ultimately challenge the downstream recovery and purification steps. In this context, electro-fermentation (EF) represents an innovative approach, based on the use of a polarized electrode interface to trigger changes in the rate, yield, titer or product distribution deriving from traditional fermentation processes. In principle, the electrode in EF can act as an electron acceptor (i.e., anodic electro-fermentation, AEF) or donor (i.e., cathodic electro-fermentation, CEF), or simply as a mean to control the oxidation-reduction potential of the fermentation broth. However, the molecular and biochemical basis underlying the EF process are still largely unknown. This review paper provides a comprehensive overview of recent literature studies including both AEF and CEF examples with either pure or mixed microbial cultures. A critical analysis of biochemical, microbiological, and engineering aspects which presently hamper the transition of the EF technology from the laboratory to the market is also presented.

Phenotype analysis of cultivation processes via unsupervised machine learning: Demonstration for Clostridium pasteurianum

A novel approach of phenotype analysis of fermentation‐based bioprocesses based on unsupervised learning (clustering) is presented. As a prior identification of phenotypes and conditional interrelations is desired to control fermentation performance, an automated learning method to output reference phenotypes (defined as vector of biomass‐specific rates) was developed and the necessary computing process and parameters were assessed. For its demonstration, time series data of 90 Clostridium pasteurianum cultivations were used which feature a broad spectrum of solventogenic and acidogenic phenotypes, while 14 clusters of phenotypic manifestations were identified. The analysis of reference phenotypes showed distinct differences, where potential conditionalities were exemplary isolated. Further, cluster‐based balancing of carbon and ATP or the use of reference phenotypes as indicator for bioprocess monitoring were demonstrated to highlight the perks of this approach. Overall, such analysis depends strongly on the quality of the data and experimental validations will be required before conclusions. However, the automated, streamlined and abstracted approach diminishes the need of individual evaluation of all noisy dataset and showed promising results, which could be transferred to strains with comparably wide‐ranging phenotypic manifestations or as indicators for repeated bioprocesses with clearly defined target.