Acetone-butanol fermentation revisited

Omics-based analyses revealed metabolic responses of Clostridium acetobutylicum to lignocellulose-derived inhibitors furfural, formic acid and phenol stress for butanol fermentation

BACKGROUND

Clostridium acetobutylicum is a model fermentative anaerobe for consolidated bioprocessing of lignocellulose hydrolysates into acetone-butanol-ethanol (ABE). However, the main inhibitors (acids, furans and phenols) ubiquitous in lignocellulose hydrolysates strictly limit the conversion efficiency. Thus, it is essential to understand the underlying mechanisms of lignocellulose hydrolysate inhibitors to identify key industrial bottlenecks that undermine efficient biofuel production. The recently developed omics strategy for intracellular metabolites and protein quantification now allow for the in-depth mapping of strain metabolism and thereby enable the resolution of the underlying mechanisms.

RESULTS

The toxicity of the main inhibitors in lignocellulose hydrolysates against C. acetobutylicum and ABE production was systematically investigated, and the changes in intracellular metabolism were analyzed by metabolomics and proteomics. The toxicity of the main lignocellulose hydrolysate inhibitors at the same dose was ranked as follows: formic acid > phenol > furfural. Metabolomic analysis based on weighted gene coexpression network analysis (WGCNA) revealed that the three inhibitors triggered the stringent response of C. acetobutylicum. Proteomic analysis based on peptide mass spectrometry (MS) supported the above results and provided more comprehensive conclusions. Under the stress of three inhibitors, the metabolites and key enzymes/proteins involved in glycolysis, reductive tricarboxylic acid (TCA) cycle, acetone-butanol synthesis and redox metabolism were lower than those in the control group. Moreover, proteins involved in gluconeogenesis, the oxidative TCA cycle, thiol peroxidase (TPX) for oxidative stress were significantly upregulated, indicating that inhibitor stress induced the stress response and metabolic regulation. In addition, the three inhibitors also showed stress specificity related to fatty acid synthesis, ATP synthesis, nucleic acid metabolism, nicotinic acid metabolism, cell wall synthesis, spore synthesis and flagellum synthesis and so on.

CONCLUSIONS

Integrated omics platforms provide insight into the cellular responses of C. acetobutylicum to cytotoxic inhibitors released during the deconstruction of lignocellulose. This insight allows us to fully improve the strain to adapt to a challenging culture environment, which will prove critical to the industrial efficacy of C. acetobutylicum.

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.

Metabolic engineering of Escherichia coli for the production of butyric acid at high titer and productivity

BACKGROUND

Several anaerobic bacteria produce butyric acid, a commodity chemical with use in chemical, pharmaceutical, food and feed industries, using complex media with acetate as a co-product. Butyrate titer of various recombinant Escherichia coli did not exceed 10 g l^-1 in batch fermentations in any of the media tested.

RESULTS

A recombinant E. coli (strain LW393) that produced butyrate as the major fermentation product was constructed with genes from E. coli, Clostridium acetobutylicum and Treponema denticola. Strain LW393 produced 323 ± 6 mM (28.4 ± 0.4 g l^-1) butyric acid in batch fermentations in mineral salt medium with glucose as C source at a yield of 0.37 ± 0.01 g (g glucose consumed)^-1. Butyrate accounted for 90% of the total products produced by the culture. Supplementing this medium with yeast extract further increased butyric acid titer to 375 ± 4 mM. Average volumetric productivity of butyrate with xylose as C source was 0.89 ± 0.07 g l^-1 h^-1.

CONCLUSIONS

The butyrate titer reported in this study is about 2.5-3-times higher than the values reported for other recombinant E. coli and this is achieved in mineral salt medium with an expectation of lower purification and production cost of butyrate.

Continuous Butanol Fermentation of Dilute Acid-Pretreated De-oiled Rice Bran by Clostridium acetobutylicum YM1

Continuous fermentation of dilute acid-pretreated de-oiled rice bran (DRB) to butanol by the Clostridium acetobutylicum YM1 strain was investigated. Pretreatment of DRB with dilute sulfuric acid (1%) resulted in the production of 42.12 g/L total sugars, including 25.57 g/L glucose, 15.1 g/L xylose and 1.46 g/L cellobiose. Pretreated-DRB (SADRB) was used as a fermentation medium at various dilution rates, and a dilution rate of 0.02 h^-1 was optimal for solvent production, in which 11.18 g/L of total solvent was produced (acetone 4.37 g/L, butanol 5.89 g/L and ethanol 0.92 g/L). Detoxification of SADRB with activated charcoal resulted in the high removal of fermentation inhibitory compounds. Fermentation of detoxified-SADRB in continuous fermentation with a dilution rate of 0.02 h^-1 achieved higher concentrations of solvent (12.42 g/L) and butanol (6.87 g/L), respectively, with a solvent productivity of 0.248 g/L.h. This study showed that the solvent concentration and productivity in continuous fermentation from SADRB was higher than that obtained from batch culture fermentation. This study also provides an economic assessment for butanol production in continuous fermentation process from DRB to validate the commercial viability of this process.

Biotransformation of organic acids to their corresponding alcohols by Thermoanaerobacter pseudoethanolicus

Higher order alcohols, such as 1-butanol and 1-hexanol, have a large number of applications but are currently prepared from non-renewable feedstocks. Here, the ability of Thermoanaerobacter pseudoethanolicus to reduce short-chain fatty acids to their corresponding alcohols using reducing potential generated by glucose catabolism with yields between 21.0 and 61.0%. ¹³C-labelled acetate, 1-propionate and 1-butyrate demonstrates that exogenously added fatty acids are indeed reduced to their corresponding alcohols. This mode of producing primary alcohols from fatty acids using a thermophilic anaerobe opens the door for the production of such alcohols from low-value materials using an inexpensive source of reducing potential.

The metabolomic scent of cancer disease progression in soft tissue sarcoma: A case report

BACKGROUND

The purpose of this case report is to describe the potential that metabolomics breath analysis may have in cancer disease monitoring. The advances in mass spectrometry instrumentation allow the accurate real-time analysis of volatile metabolites exhaled in the breath. The application of such non-invasive devices may provide innovative and complementary monitoring of the physio-pathological conditions of cancer patients.

CASE PRESENTATION

A 59-year-old Caucasian woman with spindle cell malignant mesenchymal sarcoma of the presacral region started a first-line therapy with non-pegylated liposomal doxorubicin and ifosfamide associated with pelvic radiant treatment. After two cycles of chemotherapy plus radiotherapy, a significant pulmonary disease progression was reported. Thus, a second-line therapy with trabectedin was administered. However, after only two cycles of treatment a re-staging computed tomography scan reported further cancer disease progression of the target pulmonary lesions as well as occurrence of new satellite bilateral nodules. Real-time analysis of breath exhaled volatile organic compounds, performed by select ion flow tube mass spectrometry (SIFT-MS) during the follow-up of the patient, showed a specific metabolic pattern not observed in the breath of other soft tissue sarcoma patients who achieved clinical benefit from the treatments.

CONCLUSIONS

This case report revealed the importance of the non-invasive real-time volatile organic compounds breath analysis to distinguish individual specific chemo-resistance phenotypes among soft tissue sarcoma patients. Such observation seems to suggest that breath metabolomics may be particularly useful for monitoring cancer disease progression in soft tissue sarcoma patients where only cost-effective diagnostic tools, such as positron emission tomography and computed tomography, are available.

Seed Pretreatment for Increased Hydrogen Production Using Mixed-Culture Systems with Advantages over Pure-Culture Systems

Hydrogen is an important source of energy and is considered as the future energy carrier post-petroleum era. Nowadays hydrogen production through various methods is being explored and developed to minimize the production costs. Biological hydrogen production has remained an attractive option, highly economical despite low yields. The mixed-culture systems use undefined microbial consortia unlike pure-cultures that use defined microbial species for hydrogen production. This review summarizes mixed-culture system pretreatments such as heat, chemical (acid, alkali), microwave, ultrasound, aeration, and electric current, amongst others, and their combinations to improve the hydrogen yields. The literature representation of pretreatments in mixed-culture systems is as follows: 45–50% heat-treatment, 15–20% chemical, 5–10% microwave, 10–15% combined and 10–15% other treatment. In comparison to pure-culture mixed-culture offers several advantages, such as technical feasibility, minimum inoculum steps, minimum media supplements, ease of operation, and the fact it works on a wide spectrum of low-cost easily available organic wastes for valorization in hydrogen production. In comparison to pure-culture, mixed-culture can eliminate media sterilization (4 h), incubation step (18–36 h), media supplements cost ($4–6 for bioconversion of 1 kg crude glycerol (CG)) and around 10–15 Millijoule (MJ) of energy can be decreased for the single run.

Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level

Clostridium beijerinckii NRRL B-598 is a sporulating, butanol and hydrogen producing strain that utilizes carbohydrates by the acetone-butanol-ethanol (ABE) fermentative pathway. The pathway consists of two metabolic phases, acidogenesis and solventogenesis, from which the latter one can be coupled with sporulation. Thorough transcriptomic profiling during a complete life cycle and both metabolic phases completed with flow cytometry, microscopy and a metabolites analysis helped to find out key genes involved in particular cellular events. The description of genes/operons that are closely involved in metabolism or the cell cycle is a necessary condition for metabolic engineering of the strain and will be valuable for all C. beijerinckii strains and other Clostridial species. The study focused on glucose transport and catabolism, hydrogen formation, metabolic stress response, binary fission, motility/chemotaxis and sporulation, which resulted in the composition of the unique image reflecting clostridial population changes. Surprisingly, the main change in expression of individual genes was coupled with the sporulation start and not with the transition from acidogenic to solventogenic metabolism. As expected, solvents formation started at pH decrease and the accumulation of butyric and acetic acids in the cultivation medium.

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

Constraint-based modeling (CBM) is increasingly used to analyze the metabolism of complex microbial communities involved in ecology, biomedicine, and various biotechnological processes. While CBM is an established framework for studying the metabolism of single species with linear stoichiometric models, CBM of communities with balanced growth is more complicated, not only due to the larger size of the multi-species metabolic network but also because of the bilinear nature of the resulting community models. Moreover, the solution space of these community models often contains biologically unrealistic solutions, which, even with model linearization and under application of certain objective functions, cannot easily be excluded. Here we present RedCom, a new approach to build reduced community models in which the metabolisms of the participating organisms are represented by net conversions computed from the respective single-species networks. By discarding (single-species) net conversions that violate a minimality criterion in the exchange fluxes, it is ensured that unrealistic solutions in the community model are excluded where a species altruistically synthesizes large amounts of byproducts (instead of biomass) to fulfill the requirements of other species. We employed the RedCom approach for modeling communities of up to nine organisms involved in typical degradation steps of anaerobic digestion in biogas plants. Compared to full (bilinear and linearized) community models, we found that the reduced community models obtained with RedCom are not only much smaller but allow, also in the largest model with nine species, extensive calculations required to fully characterize the solution space and to reveal key properties of communities with maximum methane yield and production rates. Furthermore, the predictive power of the reduced community models is significantly larger because they predict much smaller ranges of feasible community compositions and exchange fluxes still being consistent with measurements obtained from enrichment cultures. For an enrichment culture for growth on ethanol, we also used metaproteomic data to further constrain the solution space of the community models. Both model and proteomic data indicated a dominance of acetoclastic methanogens (Methanosarcinales) and Desulfovibrionales being the least abundant group in this microbial community.

Microbial communities are involved in many fundamental processes in nature, health and biotechnology. The elucidation of interdependencies between the involved players of microbial communities and how the interactions shape the composition, behavior and characteristic features of the consortium has become an important branch of microbiology research. Many communities are based on the exchange of metabolites between the species and constraint-based metabolic modeling has become an important approach for a formal description and quantitative analysis of these metabolic dependencies. However, the complexity of the models rises quickly with a growing number of organisms and the space of predicted feasible behaviors often includes unrealistic solutions. Here we present RedCom, a new approach to build reduced stoichiometric models of balanced microbial communities based on net conversions of the single-species models. We demonstrate the applicability of our RedCom approach by modeling communities of up to nine organisms involved in degradation steps of anaerobic digestion in biogas plants. As one of the first studies in this field, we compare simulation results from the community models with experimental data of laboratory-scale biogas reactors for growth on ethanol and glucose-cellulose media. The results also demonstrate a higher predictive power of the RedCom vs. the full models.

Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant

We report on the nearly complete genome sequence of Clostridium beijerinckii strain Br21, formerly isolated from a sugarcarne vinasse wastewater treatment plant. The resulting genome is ca. 5.9 Mbp in length and resembles the size of previously published C. beijerinckii genomes. We annotated the genome sequence and predicted a total of 5323 genes. Strain Br21 has a genetic toolkit that allows it to exploit diverse sugars that are often found after lignocellulosic biomass pretreatment to yield products of commercial interest. Besides the whole set of genes encoding for enzymes underlying hydrogen production, the genome of the new strain includes genes that enable carbon sources conversion into butanol, ethanol, acetic acid, butyric acid, and the chemical block 1,3-propanediol, which is used to obtain polymers. Moreover, the genome of strain Br21 has a higher number of ORFs with predicted beta-glucosidase activity as compared to other C. beijerinckii strains described in the KEGG database. These characteristics make C. beijerinckii strain Br21 a remarkable candidate for direct use in biotechnological processes and attest that it is a potential biocatalyst supplier.

Butanol Synthesis Routes for Biofuel Production: Trends and Perspectives

Butanol has similar characteristics to gasoline, and could provide an alternative oxygenate to ethanol in blended fuels. Butanol can be produced either via the biotechnological route, using microorganisms such as clostridia, or by the chemical route, using petroleum. Recently, interest has grown in the possibility of catalytic coupling of bioethanol into butanol over various heterogenic systems. This reaction has great potential, and could be a step towards overcoming the disadvantages of bioethanol as a sustainable transportation fuel. This paper summarizes the latest research on butanol synthesis for the production of biofuels in different biotechnological and chemical ways; it also compares potentialities and limitations of these strategies.

Direct IBE fermentation from mandarin orange wastes by combination of Clostridium cellulovorans and Clostridium beijerinckii

For a resolution of reducing carbon dioxide emission and increasing food production to respond to the growth of global population, production of biofuels from non-edible biomass is urgently required. Abundant orange wastes, such as peel and strained lees, are produced as by-product of orange juice, which is available non-edible biomass. However, d-limonene included in citrus fruits often inhibits yeast growth and makes the ethanol fermentation difficult. This study demonstrated that isopropanol-butanol-ethanol fermentation ability of Clostridium beijerinckii and cellulosic biomass degrading ability of C. cellulovorans were cultivated under several concentrations of limonene. As a result, C. cellulovorans was able to grow even in the medium containing 0.05% limonene (v/v) and degraded 85% of total sugar from mandarin peel and strained lees without any pretreatments. More interestingly, C. beijerinckii produced 0.046 g butanol per 1 g of dried strained lees in the culture supernatant together with C. cellulovorans.

Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii

BACKGROUND

Clostridium spp. can synthesize valuable chemicals and fuels by utilizing diverse waste-stream substrates, including starchy biomass, lignocellulose, and industrial waste gases. However, metabolic engineering in Clostridium spp. is challenging due to the low efficiency of gene transfer and genomic integration of entire biosynthetic pathways.

RESULTS

We have developed a reliable gene transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii based on the conjugal transfer of donor plasmids containing large transgene cassettes (> 5 kb) followed by the inducible activation of Himar1 transposase to promote integration. We established a conjugation protocol for the efficient generation of transconjugants using the Gram-positive origins of replication repL and repH. We also investigated the impact of DNA methylation on conjugation efficiency by testing donor constructs with all possible combinations of Dam and Dcm methylation patterns, and used bisulfite conversion and PacBio sequencing to determine the DNA methylation profile of the C. ljungdahlii genome, resulting in the detection of four sequence motifs with N⁶-methyladenosine. As proof of concept, we demonstrated the transfer and genomic integration of a heterologous acetone biosynthesis pathway using a Himar1 transposase system regulated by a xylose-inducible promoter. The functionality of the integrated pathway was confirmed by detecting enzyme proteotypic peptides and the formation of acetone and isopropanol by C. ljungdahlii cultures utilizing syngas as a carbon and energy source.

CONCLUSIONS

The developed multi-gene delivery system offers a versatile tool to integrate and stably express large biosynthetic pathways in the industrial promising syngas-fermenting microorganism C. ljungdahlii. The simple transfer and stable integration of large gene clusters (like entire biosynthetic pathways) is expanding the range of possible fermentation products of heterologously expressing recombinant strains. We also believe that the developed gene delivery system can be adapted to other clostridial strains as well.

Nutrient modulation based process engineering strategy for improved butanol production from Clostridium acetobutylicum

The present study demonstrates a process engineering strategy to achieve high butanol titer and productivity from wild type Clostridium acetobutylicum MTCC 11274. In the first step, two different media were optimized with the objectives of maximizing the biomass and butanol productivity, respectively. In the next step, attributes of these two media compositions were integrated to design a two-stage fed-batch process which resulted in maximal butanol productivity of 0.55 g L^-1 h^-1 with titer of 13.1 g L^-1 . Further, two-stage fed-batch process along with combinatorial use of magnesium limitation and calcium supplementation resulted in the highest butanol titer and productivity of 16.5 g L^-1 and 0.59 g L^-1 h^-1 , respectively. Finally, integration of the process with gas stripping and modulation of feeding duration resulted in a cumulative butanol titer of 54.3 g L^-1 and productivity of 0.58 g L^-1 h^-1 . The strategy opens up possibility of developing a viable butanol bioprocess. © 2019 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2771, 2019.

Enhanced butanol production by optimization of medium parameters using Clostridium acetobutylicum YM1

A new isolate of the solvent-producing Clostridium acetobutylicum YM1 was used to produce butanol in batch culture fermentation. The effects of glucose concentration, butyric acid addition and C/N ratio were studied conventionally (one-factor-at-a-time). Moreover, the interactions between glucose concentration, butyric acid addition and C/N ratio were further investigated to optimize butanol production using response surface methodology (RSM). A central composite design was applied, and a polynomial regression model with a quadratic term was used to analyze the experimental data using analysis of variance (ANOVA). ANOVA revealed that the model was highly significant (p < 0.0001) and the effects of the glucose and butyric acid concentrations on butanol production were significant. The model validation experiment showed 13.82 g/L butanol was produced under optimum conditions. Scale up fermentation in optimized medium resulted in 17 g/L of butanol and 21.71 g/L of ABE. The experimental data of scale up in 5 L bioreactor and flask scale were fitted to kinetic mathematical models published in the literature to estimate the kinetic parameters of the fermentation. The models used gave the best fit for butanol production, biomass and glucose consumption for both flask scale and bioreactor scale up.

Biobutanol production from coffee silverskin

BACKGROUND

Coffee silverskin, a by-product from coffee roasting industries, was evaluated as a feedstock for biobutanol production by acetone-butanol-ethanol fermentation. This lignocellulosic biomass contained approximately 30% total carbohydrates and 30% lignin. Coffee silverskin was subjected to autohydrolysis at 170 °C during 20 min, with a biomass-to-solvent ratio of 20%, and a subsequent enzymatic hydrolysis with commercial enzymes in order to release simple sugars. The fermentability of the hydrolysate was assessed with four solventogenic strains from the genus Clostridium. In addition, fermentation conditions were optimised via response surface methodology to improve butanol concentration in the final broth.

RESULTS

The coffee silverskin hydrolysate contained 34.39 ± 2.61 g/L total sugars, which represents a sugar recovery of 34 ± 3%. It was verified that this hydrolysate was fermentable without the need of any detoxification method and that C. beijerinckii CECT 508 was the most efficient strain for butanol production, attaining final values of 4.14 ± 0.21 g/L acetone, 7.02 ± 0.27 g/L butanol and 0.25 ± 0.01 g/L ethanol, consuming 76.5 ± 0.8% sugars and reaching a butanol yield of 0.269 ± 0.008 gB/gS under optimal conditions.

CONCLUSIONS

Coffee silverskin could be an adequate feedstock for butanol production in biorefineries. When working with complex matrices like lignocellulosic biomass, it is essential to select an adequate bacterial strain and to optimize its fermentation conditions (such as pH, temperature or CaCO3 concentration).

Effect of Operating Conditions and Immobilization on Butanol Enhancement in an Extractive Fermentation Using Non-ionic Surfactant

The present study was undertaken in order to investigate effect of diverse parameters such as fermentation media, pH, initial concentration of biomass, different surfactant concentrations, and immobilization on increasing butanol and total solvent production. Cheng's fermentation media was successfully tested and perceived to increase final solvents concentration. Controlled pH at 12th and 24th hours had negative effect on butanol enhancement; however, it resulted in more butyric acid production which remained accumulated. Ten percent (v/v) biomass was evaluated to increase final solvents concentration and hence butanol yield compared to 20% and 30% (v/v) of initial biomass concentrations. Effect of surfactant concentration (3-20%) was studied on butanol production. Six percent (v/v) L62 resulted in 49% higher final butanol concentration compared to control. Simultaneous immobilization and fermentation showed higher butanol production (16.8 g/L with 6%) which was attributed to partial immobilization of biomass.

Reviving the Weizmann process for commercial n-butanol production

Developing a commercial process for the biological production of n-butanol is challenging as it needs to combine high titer, yield, and productivities. Here we engineer Clostridium acetobutylicum to stably and continuously produce n-butanol on a mineral media with glucose as sole carbon source. We further design a continuous process for fermentation of high concentration glucose syrup using in situ extraction of alcohols by distillation under low pressure and high cell density cultures to increase the titer, yield, and productivity of n-butanol production to the level of 550 g/L, 0.35 g/g, and 14 g/L/hr, respectively. This process provides a mean to produce n-butanol at performance levels comparable to that of corn wet milling ethanol plants using yeast as a biocatalyst. It may hold the potential to be scaled-up at pilot and industrial levels for the commercial production of n-butanol.

Organic solvent n-butanol is produced mainly by petrochemical method. Here, the authors revive the historical Weizmann process by engineering Clostridium acetobutylicum strain and developing low pressure distillation and high cell density cultures for n-butanol continuous production at high-yield titer and productivity.

Hydrogen-Cycling during Solventogenesis in Clostridium acetobutylicum American Type Culture Collection (ATCC) 824 Requires the [NiFe]-Hydrogenase for Energy Conservation

Clostridium acetobutylicum has traditionally been used for production of acetone, butanol, and ethanol (ABE). Butanol is a commodity chemical due in part to its suitability as a biofuel; however, the current yield of this product from biological systems is not economically feasible as an alternative fuel source. Understanding solvent phase physiology, solvent tolerance, and their genetic underpinning is key for future strain optimization of the bacterium. This study shows the importance of a [NiFe]-hydrogenase in solvent phase physiology. C. acetobutylicum genes ca_c0810 and ca_c0811, annotated as a HypF and HypD maturation factor, were found to be required for [NiFe]-hydrogenase activity. They were shown to be part of a polycistronic operon with other hyp genes. Hydrogenase activity assays of the ΔhypF/hypD mutant showed an almost complete inactivation of the [NiFe]-hydrogenase. Metabolic studies comparing ΔhypF/hypD and wild type (WT) strains in planktonic and sessile conditions indicated the hydrogenase was important for solvent phase metabolism. For the mutant, reabsorption of acetate and butyrate was inhibited during solventogenesis in planktonic cultures, and less ABE was produced. During sessile growth, the ΔhypF/hypD mutant had higher initial acetone: butanol ratios, which is consistent with the inability to obtain reduced cofactors via H2 uptake. In sessile conditions, the ΔhypF/hypD mutant was inhibited in early solventogenesis, but it appeared to remodel its metabolism and produced mainly butanol in late solventogenesis without the uptake of acids. Energy filtered transmission electron microscopy (EFTEM) mapped Pd(II) reduction via [NiFe]-hydrogenase induced H2 oxidation at the extracelluar side of the membrane on WT cells. A decrease of Pd(0) deposits on ΔhypF/hypD comparatively to WT indicates that the [NiFe]-hydrogenase contributed to the Pd(II) reduction. Calculations of reaction potentials during acidogenesis and solventogenesis predict the [NiFe]-hydrogenase can couple NAD+ reduction with membrane transport of electrons. Extracellular oxidation of H2 combined with the potential for electron transport across the membrane indicate that the [NiFe}-hydrogenase contributes to proton motive force maintenance via hydrogen cycling.

Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

BACKGROUND

Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer regarding its genotype and phenotype under various conditions. However, a link between these two levels, lying in the description of the gene regulation mechanisms, is missing for this strain, due to the lack of transcriptomic data.

RESULTS

In this paper, we present a transcription profile of the strain over the whole fermentation using an RNA-Seq dataset covering six time-points with the current highest dynamic range among solventogenic clostridia. We investigated the accuracy of the genome sequence and particular genome elements, including pseudogenes and prophages. While some pseudogenes were highly expressed, all three identified prophages remained silent. Furthermore, we identified major changes in the transcriptional activity of genes using differential expression analysis between adjacent time-points. We identified functional groups of these significantly regulated genes and together with fermentation and cultivation kinetics captured using liquid chromatography and flow cytometry, we identified basic changes in the metabolism of the strain during fermentation. Interestingly, C. beijerinckii NRRL B-598 demonstrated different behavior in comparison with the closely related strain C. beijerinckii NCIMB 8052 in the latter phases of cultivation.

CONCLUSIONS

We provided a complex analysis of the C. beijerinckii NRRL B-598 fermentation profile using several technologies, including RNA-Seq. We described the changes in the global metabolism of the strain and confirmed the uniqueness of its behavior. The whole experiment demonstrated a good reproducibility. Therefore, we will be able to repeat the experiment under selected conditions in order to investigate particular metabolic changes and signaling pathways suitable for following targeted engineering.

Alginate Adsorbent Immobilization Technique Promotes Biobutanol Production by Clostridium acetobutylicum Under Extreme Condition of High Concentration of Organic Solvent

In Acetone-Butanol-Ethanol fermentation, bacteria should tolerate high concentrations of solvent products, which inhibit bacteria growth and limit further increase of solvents to more than 20 g/L. Moreover, this limited solvent concentration significantly increases the cost of solvent separation through traditional approaches. In this study, alginate adsorbent immobilization technique was successfully developed to assist in situ extraction using octanol which is effective in extracting butanol but presents strong toxic effect to bacteria. The adsorbent improved solvent tolerance of Clostridium acetobutylicum under extreme condition of high concentration of organic solvent. Using the developed technique, more than 42% of added bacteria can be adsorbed to the adsorbent. Surface area of the adsorbent was more than 10 times greater than sodium alginate. Scanning electron microscope image shows that an abundant amount of pore structure was successfully developed on adsorbents, promoting bacteria adsorption. In adsorbent assisted ABE fermentation, there was 21.64 g/L butanol in extracting layer compared to negligible butanol produced with only the extractant but without the adsorbent, for the reason that adsorbent can reduce damaging exposure of C. acetobutylicum to octanol. The strategy can improve total butanol production with respect to traditional culture approach by more than 2.5 fold and save energy for subsequent butanol recovery, which effects can potentially make the biobutanol production more economically practical.

Diauxic growth of Clostridium acetobutylicum ATCC 824 when grown on mixtures of glucose and cellobiose

Clostridium acetobutylicum, a promising organism for biomass transformation, has the capacity to utilize a wide variety of carbon sources. During pre-treatments of (ligno) cellulose through thermic and/or enzymatic processes, complex mixtures of oligo saccharides with beta 1,4-glycosidic bonds can be produced. In this paper, the capability of C. acetobutylicum to ferment glucose and cellobiose, alone and in mixtures was studied. Kinetic studies indicated that a diauxic growth occurs when both glucose and cellobiose are present in the medium. In mixtures, D-glucose is the preferred substrate even if cells were pre grown with cellobiose as the substrate. After the complete consumption of glucose, the growth kinetics exhibits an adaptation time, of few hours, before to be able to use cellobiose. Because of this diauxic phenomenon, the nature of the carbon source deriving from a cellulose hydrolysis pre-treatment could strongly influence the kinetic performances of a fermentation process with C. acetobutylicum.

Butyrate-based n-butanol production from an engineered Shewanella oneidensis MR-1

n-Butanol is considered as the next-generation biofuel, because its physiochemical properties are very similar to fossil fuels and it could be produced by Clostridia under anaerobic culture. Due to the difficulties of strict anaerobic culture, a host which can be used with facultative environment was being searched for n-butanol production. As an alternative, Shewanella oneidensis MR-1, which is known as facultative bacteria, was selected as a host and studied. A plasmid containing adhE2 encoding alcohol dehydrogenase, various CoA transferases (ctfAB, atoAD, pct, and ACT), and acs encoding acetyl-CoA synthetase were introduced and examined to S. oneidensis MR-1 to produce n-butanol. As a result, ctfAB, acs, and adhE2 overexpression in S. oneidensis-pJM102 showed the highest n-butanol production in the presence of 2% of N-acetylglucosamine (NAG), 0.3% of butyrate, and 0.1 mM of IPTG for 96 h under microaerobic condition. When more NAG and butyrate were fed, n-butanol production was enhanced, producing up to 160 mg/L of n-butanol. When metal ions or extra electrons were added to S. oneidensis-pJM102 for n-butanol production, metal ion as electron acceptor or supply of extra electron showed no significant effect on n-butanol production. Overall, we made a newly engineered S. oneidensis that could utilize NAG and butyrate to produce n-butanol. It could be used in further microaerobic condition and electricity supply studies.

Flow cytometry analysis of Clostridium beijerinckii NRRL B-598 populations exhibiting different phenotypes induced by changes in cultivation conditions

BACKGROUND

Biobutanol production by clostridia via the acetone-butanol-ethanol (ABE) pathway is a promising future technology in bioenergetics , but identifying key regulatory mechanisms for this pathway is essential in order to construct industrially relevant strains with high tolerance and productivity. We have applied flow cytometric analysis to C. beijerinckii NRRL B-598 and carried out comparative screening of physiological changes in terms of viability under different cultivation conditions to determine its dependence on particular stages of the life cycle and the concentration of butanol.

RESULTS

Dual staining by propidium iodide (PI) and carboxyfluorescein diacetate (CFDA) provided separation of cells into four subpopulations with different abilities to take up PI and cleave CFDA, reflecting different physiological states. The development of a staining pattern during ABE fermentation showed an apparent decline in viability, starting at the pH shift and onset of solventogenesis, although an appreciable proportion of cells continued to proliferate. This was observed for sporulating as well as non-sporulating phenotypes at low solvent concentrations, suggesting that the increase in percentage of inactive cells was not a result of solvent toxicity or a transition from vegetative to sporulating stages. Additionally, the sporulating phenotype was challenged with butanol and cultivation with a lower starting pH was performed; in both these experiments similar trends were obtained-viability declined after the pH breakpoint, independent of the actual butanol concentration in the medium. Production characteristics of both sporulating and non-sporulating phenotypes were comparable, showing that in C. beijerinckii NRRL B-598, solventogenesis was not conditional on sporulation.

CONCLUSION

We have shown that the decline in C. beijerinckii NRRL B-598 culture viability during ABE fermentation was not only the result of accumulated toxic metabolites, but might also be associated with a special survival strategy triggered by pH change.

Recent advances and strategies in process and strain engineering for the production of butyric acid by microbial fermentation

Butyric acid is an important platform chemical, which is widely used in the fields of food, pharmaceutical, energy, etc. Microbial fermentation as an alternative approach for butyric acid production is attracting great attention as it is an environmentally friendly bioprocessing. However, traditional fermentative butyric acid production is still not economically competitive compared to chemical synthesis route, due to the low titer, low productivity, and high production cost. Therefore, reduction of butyric acid production cost by utilization of alternative inexpensive feedstock, and improvement of butyric acid production and productivity has become an important target. Recently, several advanced strategies have been developed for enhanced butyric acid production, including bioprocess techniques and metabolic engineering methods. This review provides an overview of advances and strategies in process and strain engineering for butyric acid production by microbial fermentation. Additionally, future perspectives on improvement of butyric acid production are also proposed.

Understanding regulation in substrate dependent modulation of growth and production of alcohols in Clostridium sporogenes NCIM 2918 through metabolic network reconstruction and flux balance analysis

Flux Balance Analysis was performed for Clostridium sporogenes NCIM 2918 grown on sole glucose and glycerol or glucose-glycerol combinations at varied concentrations. During acidogenesis, glucose and glucose-glycerol combinations favored improved growth and butyric acid production. Glycerol fermentation was however marked by reduced growth and predominant ethanol synthesis. Further, with increase of glycerol fraction in glucose-glycerol blend, flux towards ethanol synthesis linearly increased with simultaneous decrease in butanol flux. Elevated ATP demand due to improved growth was satisfied by upregulated carbon flux towards butyric acid synthesis during both glucose and dual substrate fermentations. Possible repression of pyruvate carboxylase by glycerol resulting in downturn of carbon uptake flux towards TCA cycle through anaplerotic reaction may be responsible for reduced growth in glycerol fermentation. Ammonium acetate mediated induction of acetic acid utilization, during acidogenesis, led to excess acetyl-CoA generation and its subsequent metabolism to lesser reduced products, butyric acid or ethanol.

Performance enhancement of a polydimethylsiloxane membrane for effective n-butanol pervaporation by bonding multi-silyl-functional MCM-41

In the current work, MCM-41/polydimethylsiloxane (PDMS) mixed matrix membrane (MMM) was prepared for effective n-butanol pervaporation from a model aqueous solution. In order to improve the compatibility between MCM-41 and PDMS, different types of silane coupling agents including n-propyltrimethoxysilane (PTMS), n-octyltrimethoxysilane (OTMS), n-dodecyltrimethoxysilane (DTMS) and n-hexadecyltrimethoxysilane (HDTMS) were used to modify the MCM-41. The results showed that the highest n-butanol separation performance was achieved by bonding 20 wt% of PTMS-modified MCM-41 with PDMS. Under these conditions, total flux of 1476 g m-2 h-1 was obtained when separating a 1.5 wt% n-butanol aqueous solution at 55 °C. The total flux increased by nearly 40% compared to the pure PDMS membrane with no obvious changes of the n-butanol separation factor at the same time. The curing process of the casting solution was also significantly improved after MCM-41 modification.

Enhanced isopropanol-butanol-ethanol mixture production through manipulation of intracellular NAD(P)H level in the recombinant Clostridium acetobutylicum XY16

BACKGROUND

The formation of by-products, mainly acetone in acetone-butanol-ethanol (ABE) fermentation, significantly affects the solvent yield and downstream separation process. In this study, we genetically engineered Clostridium acetobutylicum XY16 isolated by our lab to eliminate acetone production and altered ABE to isopropanol-butanol-ethanol (IBE). Meanwhile, process optimization under pH control strategies and supplementation of calcium carbonate were adopted to investigate the interaction between the reducing force of the metabolic networks and IBE production.

RESULTS

After successful introduction of secondary alcohol dehydrogenase into C. acetobutylicum XY16, the recombinant XY16 harboring pSADH could completely eliminate acetone production and convert it into isopropanol, indicating great potential for large-scale production of IBE mixtures. Especially, pH could significantly improve final solvent titer through regulation of NADH and NADPH levels in vivo. Under the optimal pH level of 4.8, the total IBE production was significantly increased from 3.88 to 16.09 g/L with final 9.97, 4.98 and 1.14 g/L of butanol, isopropanol, and ethanol. Meanwhile, NADH and NADPH levels were maintained at optimal levels for IBE formation compared to the control one without pH adjustment. Furthermore, calcium carbonate could play dual roles as both buffering agency and activator for NAD kinase (NADK), and supplementation of 10 g/L calcium carbonate could finally improve the IBE production to 17.77 g/L with 10.51, 6.02, and 1.24 g/L of butanol, isopropanol, and ethanol.

CONCLUSION

The complete conversion of acetone into isopropanol in the recombinant C. acetobutylicum XY16 harboring pSADH could alter ABE to IBE. pH control strategies and supplementation of calcium carbonate were effective in obtaining high IBE titer with high isopropanol production. The analysis of redox cofactor perturbation indicates that the availability of NAD(P)H is the main driving force for the improvement of IBE production.