Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423.

BACKGROUND: There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of acetone, butanol and ethanol (ABE) or Isopropanol, Butanol and Ethanol (IBE) by anaerobic fermentation has already a long industrial history. Isopropanol has recently received a specific interest and the best studied natural isopropanol producer is C. beijerinckii DSM 6423 (NRRL B-593). This strain metabolizes sugars into a mix of IBE with only low concentrations of ethanol produced (< 1 g/L). However, despite its relative ancient discovery, few genomic details have been described for this strain. Research efforts including omics and genetic engineering approaches are therefore needed to enable the use of C. beijerinckii as a microbial cell factory for production of isopropanol. RESULTS: The complete genome sequence and a first transcriptome analysis of C. beijerinckii DSM 6423 are described in this manuscript. The combination of MiSeq and de novo PacBio sequencing revealed a 6.38 Mbp chromosome containing 6254 genomic objects. Three Mobile Genetic Elements (MGE) were also detected: a linear double stranded DNA bacteriophage (ϕ6423) and two plasmids (pNF1 and pNF2) highlighting the genomic complexity of this strain. A first RNA-seq transcriptomic study was then performed on 3 independent glucose fermentations. Clustering analysis allowed us to detect some key gene clusters involved in the main life cycle steps (acidogenesis, solvantogenesis and sporulation) and differentially regulated among the fermentation. These putative clusters included some putative metabolic operons comparable to those found in other reference strains such as C. beijerinckii NCIMB 8052 or C. acetobutylicum ATCC 824. Interestingly, only one gene was encoding for an alcohol dehydrogenase converting acetone into isopropanol, suggesting a single genomic event occurred on this strain to produce isopropanol. CONCLUSIONS: We present the full genome sequence of Clostridium beijerinckii DSM 6423, providing a complete genetic background of this strain. This offer a great opportunity for the development of dedicated genetic tools currently lacking for this strain. Moreover, a first RNA-seq analysis allow us to better understand the global metabolism of this natural isopropanol producer, opening the door to future targeted engineering approaches.

Transcriptome analysis of Clostridium beijerinckii adaptation mechanisms in response to ferulic acid.

Clostridium beijerinckii 4693:int with high ferulic acid (FA) tolerance was engineered and characterized in our lab. In this study, the minimum inhibition concentrations of FA against C. beijerinckii NCIMB 8052 (wild-type) and 4693:int were 1.0 and 1.5g/l, respectively; cell viability was 18.5% and 106.7%, respectively, in the presence of 0.5g/l FA. A comparative transcriptome analysis was carried out at two different growth stages to evaluate sensitivity to FA. Genes that were differentially expressed included those related to redox and associated cofactors, riboflavin metabolism, two-component system, glycolysis and butanoate metabolism, and DNA replication as well as those encoding ATP-binding cassette transporters. Cbei_2134 and Cbei_2135 encoding alkyl hydroperoxide reductases are thought to be involved in antibacterial and adaptation mechanisms in C. beijerinckii in the presence of FA.

Interactions between Bacillus cereus CGMCC 1.895 and Clostridium beijerinckii NCIMB 8052 in coculture for butanol production under nonanaerobic conditions.

Low oxygen tolerance and substrate restriction continues to hamper the process of biobutanol industrialization. In this work, butanol fermentation with cocultures of Bacillus cereus China General Microbiological Culture Collection Center (CGMCC) 1.895 and Clostridium beijerinckii NCIMB 8052 under nonanaerobic conditions was investigated, and the interactions between these two strains were examined. The addition of B. cereus CGMCC 1.895 resulted in higher oxygen tolerance and a wider range of substrate utilization, compared with the pure culture of C. beijerinckii NCIMB 8052. Butanol concentration reached 10.49 g/L with an optimized inoculation size of 90% under nonanaerobic conditions, and this concentration was close to that of pure C. beijerinckii NCIMB 8052 culture under anaerobic conditions. Dynamic relative abundance analysis demonstrated that the ratio of C. beijerinckii NCIMB 8052 accounted for nearly 99% of the cocultured cells. Furthermore, the substrate utilization range was expanded, allowing the use of corn mash for butanol production. The final concentration of butanol and total solvents was 6.78 and 10.52 g/L, respectively. Coculture also was performed successfully in a 5-L fermenter and 8.75 g/L butanol was obtained. Dynamic dissolved oxygen analysis demonstrated that B. cereus consumed the dissolved oxygen in the broth and resulted in the anaerobic condition for C. beijerinckii.

Butanol production by a Clostridium beijerinckii mutant with high ferulic acid tolerance.

A mutant strain of Clostridium beijerinckii, with high tolerance to ferulic acid, was generated using atmospheric pressure glow discharge and high-throughput screening of C. beijerinckii NCIMB 8052. The mutant strain M11 produced 7.24 g/L of butanol when grown in P2 medium containing 30 g/L of glucose and 0.5 g/L of ferulic acid, which is comparable to the production from non-ferulic acid cultures (8.11 g/L of butanol). When 0.8 g/L of ferulic acid was introduced into the P2 medium, C. beijerinckii M11 grew well and produced 4.91 g/L of butanol. Both cell growth and butanol production of C. beijerinckii M11 were seriously inhibited when 0.9 g/L of ferulic acid was added into the P2 medium. Furthermore, C. beijerinckii M11 could produce 6.13 g/L of butanol using non-detoxified hemicellulosic hydrolysate from diluted sulfuric acid-treated corn fiber (SAHHC) as the carbon source. These results demonstrate that C. beijerinckii M11 has a high ferulic acid tolerance and is able to use non-detoxified SAHHC for butanol production.

Clostridium beijerinckii mutant obtained atmospheric pressure glow discharge generates enhanced electricity in a microbial fuel cell.

A Clostridium beijerinckii mutant M13 was derived from C. beijerinckii NCIMB 8052 by atmospheric pressure glow discharge. C. beijerinckii M13 generated a maximum output power density of 79.2 mW m(-2) and a maximum output voltage of 230 mV in a microbial fuel cell containing 1 g glucose l(-1) as carbon source and 0.15 g methyl viologen l(-1) as an electron carrier.

Process development for biological production of butanol from Eastern redcedar.

Eastern redcedar is an invasive softwood species in Oklahoma and across grasslands in the Central Plains of the United States and potential feedstock for butanol production. Butanol has higher energy content than ethanol and can be upgraded to jet and diesel fuels. The objective of this study was to develop a process for production of butanol from redcedar. Results showed that Clostridium acetobutylicum ATCC 824 and Clostridium beijerinckii NCIMB 8052 did not grow in fermentation medium with citrate buffer. However, both strains grew in the medium with acetate buffer, resulting in 3-4g/L greater butanol than without acetate. Detoxification of redcedar hydrolyzate was required to increase butanol concentration from 1 to 13g/L. Hydrolyzate was detoxified by activated carbon to remove inhibitors. Fermentations in detoxified redcedar hydrolyzate reached 13g/L butanol and 19g/L total ABE, comparable to glucose control. This shows the potential for redcedar use in butanol production.

Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq.

BACKGROUND: Clostridium beijerinckii is a prominent solvent-producing microbe that has great potential for biofuel and chemical industries. Although transcriptional analysis is essential to understand gene functions and regulation and thus elucidate proper strategies for further strain improvement, limited information is available on the genome-wide transcriptional analysis for C. beijerinckii. RESULTS: The genome-wide transcriptional dynamics of C. beijerinckii NCIMB 8052 over a batch fermentation process was investigated using high-throughput RNA-Seq technology. The gene expression profiles indicated that the glycolysis genes were highly expressed throughout the fermentation, with comparatively more active expression during acidogenesis phase. The expression of acid formation genes was down-regulated at the onset of solvent formation, in accordance with the metabolic pathway shift from acidogenesis to solventogenesis. The acetone formation gene (adc), as a part of the sol operon, exhibited highly-coordinated expression with the other sol genes. Out of the > 20 genes encoding alcohol dehydrogenase in C. beijerinckii, Cbei_1722 and Cbei_2181 were highly up-regulated at the onset of solventogenesis, corresponding to their key roles in primary alcohol production. Most sporulation genes in C. beijerinckii 8052 demonstrated similar temporal expression patterns to those observed in B. subtilis and C. acetobutylicum, while sporulation sigma factor genes sigE and sigG exhibited accelerated and stronger expression in C. beijerinckii 8052, which is consistent with the more rapid forespore and endspore development in this strain. Global expression patterns for specific gene functional classes were examined using self-organizing map analysis. The genes associated with specific functional classes demonstrated global expression profiles corresponding to the cell physiological variation and metabolic pathway switch. CONCLUSIONS: The results from this work provided insights for further C. beijerinckii strain improvement employing system biology-based strategies and metabolic engineering approaches.

Clostridium beijerinckii mutant with high inhibitor tolerance obtained by low-energy ion implantation.

Clostridium beijerinckii mutant strain IB4, which has a high level of inhibitor tolerance, was screened by low-energy ion implantation and used for butanol fermentation from a non-detoxified hemicellulosic hydrolysate of corn fiber treated with dilute sulfuric acid (SAHHC). Evaluation of toxicity showed C. beijerinckii IB4 had a higher level of tolerance than parent strain C. beijerinckii NCIMB 8052 for five out of six phenolic compounds tested (the exception was vanillin). Using glucose as carbon source, C. beijerinckii IB4 produced 9.1 g l(-1) of butanol with an acetone/butanol/ethanol (ABE) yield of 0.41 g g(-1). When non-detoxified SAHHC was used as carbon source, C. beijerinckii NCIMB 8052 grew well but ABE production was inhibited. By contrast, C. beijerinckii IB4 produced 9.5 g l(-1) of ABE with a yield of 0.34 g g(-1), including 2.2 g l(-1) acetone, 6.8 g l(-1) butanol, and 0.5 g l(-1) ethanol. The remarkable fermentation and inhibitor tolerance of C. beijerinckii IB4 appears promising for ABE production from lignocellulosic materials.

Clostridium beijerinckii mutant obtained by atmospheric pressure glow discharge producing high proportions of butanol and solvent yields.

With 30 g glucose/l as carbon source, Clostridium beijerinckii ART124, a mutant created by atmospheric pressure glow discharge, produced 13.7 g total solvent/l (containing 3.1 g acetone/l, 10.4 g butanol/l and 0.2 g ethanol/l) in 72 h. The mutant could also use sucrose or xylose or a mixture of glucose/xylose/arabinose with nearly equal yields.

Performance of batch, fed-batch, and continuous A-B-E fermentation with pH-control.

Batch, fed-batch, and continuous A-B-E fermentations were conducted and compared with pH controlled at 4.5, the optimal range for solvent production. While the batch mode provides the highest solvent yield, the continuous mode was preferred in terms of butanol yield and productivity. The highest butanol yield and productivity found in the continuous fermentation at dilution rate of 0.1h(-1) were 0.21 g-butanol/g-glucose and 0.81 g/L/h, respectively. In the continuous and fed-batch fermentation, the time needed for passing acidogenesis to solventogenesis was an intrinsic hindrance to higher butanol productivity. Therefore, a low dilution rate is suggested for the continuous A-B-E fermentation, while the fed-batch mode is not suggested for solvent production. While 3:6:1 ratio of acetone, butanol, and ethanol is commonly observed from A-B-E batch fermentation by Clostridium acetobutylicum when the pH is uncontrolled, up to 94% of the produced solvent was butanol in the chemostat with pH controlled at 4.5.

Influence of reduced electron shuttling compounds on biological H2 production in the fermentative pure culture Clostridium beijerinckii.

Several reports suggest that extracellular electron shuttles influence fermentative metabolism in a beneficial manner for bioremediation and biotechnology strategies. The focus of this research was to characterize the effects of reduced electron shuttling molecules on fermentative H(2) production. Reduced electron shuttles may provide reducing equivalents to generate H(2), which influences alternate cellular processes. Electron shuttling compounds cycle between reduced-oxidized states and influence fermentative physiology. Clostridium beijerinckii fermentation was altered using a physiological approach that resulted in H(2) production with the reduced extracellular electron shuttle anthrahydroquinone-2,6,-disulfonate (AH(2)QDS) and biologically reduced humic substances as the primary electron donors. Cells were suspended in a buffer with an excess of the biological electron transfer molecule NAD(+), with AH(2)QDS (100-1000 microM) or biologically reduced humic substances (0.01-0.025 g/L) as the sole electron source. Increasing concentrations of AH(2)QDS and reduced humics increased H(2) production, while H(2) production was suppressed by Fe(III) hydroxides, which outcompeted the cells for electrons from the reduced shuttles, suggesting that the shuttles are in fact electron donors for H(2) production. Oxidized AQDS/humics did not increase H(2) production. Organic acid production shifted toward butyric acid in the presence of reduced electron shuttles, particularly with growing cells. Growth and hydrogen production rates in growing cells were initially faster in the presence of the reduced electron shuttles; however, the final biomass yield was inversely proportional to the starting AH(2)QDS concentration, which suggests that reduced shuttles may compete with anabolic cell processes for available energetic resources or that the shift to excess butyrate becomes toxic to the cells.

Contribution of C. beijerinckii and C. sporogenes in association with C. tyrobutyricum to the butyric fermentation in Emmental type cheese.

The relationship between C. tyrobutyricum, C. sporogenes and C. beijerinckii in experimental cheese conditions, and their influences on late-blowing and butyric fermentation, have been investigated. A molecular approach using a PCR-TTGE method in combination with conventional methods, such as microbiological and physico-chemical analysis, was performed to monitor the evolution of these clostridial species, simultaneously with the occurrence of cheese defects. Sixteen Emmental type cheeses were produced from milk inoculated with different clostridial spore associations. In all cheeses inoculated with C. tyrobutyricum, obvious signs of late blowing were detected. In cheeses inoculated with C. beijerinckii or C. sporogenes, a formation of holes in cheese body was observed, with a concomitant slight amount of butyric acid production. Even though C. beijerinckii and C. sporogenes were less metabolically active and less numerically important than C. tyrobutyricum in cheese as shown by TTGE profiles, the association of these species to C. tyrobutyricum enhanced the butyric fermentation and the cheese defects. The level of butyric content in ripened cheese increased to 268 mg 100 g(-1) in presence of C. tyrobutyricum, and reached a maximum of 414 mg 100 g(-1) in presence of the C. beijerinckii-C. tyrobutyricum (1:10) association. The propionic fermentation was also higher in cheese inoculated with C. tyrobutyricum, and was slowed down in presence of C. beijerinckii and C. sporogenes. From 30 days of ripening, a strong correlation between the chemical contents and the intensity of cheese defects was demonstrated. A chemical analysis of cheese associated with a molecular method for microbial spoilage investigation allows the prediction of the level of late blowing at early stages of ripening, and the understanding of the origin of the defect.

Maintenance of DeltapH by a butanol-tolerant mutant of Clostridium beijerinckii.

The isolation of Clostridium beijerinckii mutants that are more tolerant of butanol than the wild-type offered the opportunity to investigate whether the membrane activities which are required for maintaining the transmembrane DeltapH (the difference in pH between the cellular interior and exterior) are sensitive targets of butanol toxicity. The DeltapH was measured by the accumulation of [14C]benzoate using late-exponential-phase cells which were suspended in citrate/phosphate buffer at pH 5 (to maximize the DeltapH component of the protonmotive force) and supplemented with glucose and Mg2+. The DeltapH of the butanol-tolerant tolerant mutant, strain BR54, of C. beijerinckii NCIMB 8052 was found to be significantly more tolerant of added butanol than the wild-type. Thus, in potassium citrate/phosphate buffer the mutant cells maintained a DeltapH of 1.4 when butanol was added to a concentration of 1.5 % (w/v), while the wild-type DeltapH was reduced to 0.1. The DeltapH of both strains was completely dissipated with 1.75 % butanol, an effect attributed to a chaotropic effect on the membrane phospholipids. Similar results were obtained in sodium citrate/phosphate buffer. In the absence of added Mg2+, the DeltapH of the mutant decreased in both sodium and potassium citrate/phosphate buffer, but more rapidly in the former. Interestingly, the addition of butanol at low concentrations (0.8 %) prevented this DeltapH dissipation, but only in cells suspended in sodium citrate/phosphate buffer, and not in potassium citrate/phosphate buffer. In wild-type cells the decrease in DeltapH occurred more slowly than in the mutant, and sparing of the DeltapH by 0.8 % butanol was less pronounced. The authors interpret these data to mean that the DeltapH is dissipated in the absence of Mg2+ by a Na+- or K+-linked process, possibly by a Na+/H+ or a K+/H+ antiporter, and that the former is inhibited by butanol. Apparently, butanol can selectively affect a membrane-associated function at concentrations lower than required for the complete dissipation of transmembrane ion gradients. Additionally, since the butanol-tolerant mutant BR54 is deficient in the ability to detoxify methylglyoxal (MG) and contains higher levels of MG than the wild-type, the higher Na+/H+ antiporter activity of the mutant may be due to the greater degree of protein glycation by MG in the mutant cells. The mechanism of butanol tolerance may be an indirect result of the elevated glycation of cell proteins in the mutant strain. Analysis of membrane protein fractions revealed that mutant cells contained significantly lower levels of unmodified arginine residues than those of the wild-type cells, and that unmodified arginine residues of the wild-type were decreased by exposure of the growing cells to added MG.