Fermentation characteristics ofClostridium pasteurianumLMG 3285 grown on glucose and mannitol

Sustainable Production of Biofuels and Biochemicals via Electro-Fermentation Technology

The energy crisis and climate change are two of the most concerning issues for human beings nowadays. For that reason, the scientific community is focused on the search for alternative biofuels to conventional fossil fuels as well as the development of sustainable processes to develop a circular economy. Bioelectrochemical processes have been demonstrated to be useful for producing bioenergy and value-added products from several types of waste. Electro-fermentation has gained great attention in the last few years due to its potential contribution to biofuel and biochemical production, e.g., hydrogen, methane, biopolymers, etc. Conventional fermentation processes pose several limitations in terms of their practical and economic feasibility. The introduction of two electrodes in a bioreactor allows the regulation of redox instabilities that occur in conventional fermentation, boosting the overall process towards a high biomass yield and enhanced product formation. In this regard, key parameters such as the type of culture, the nature of the electrodes as well as the operating conditions are crucial in order to maximize the production of biofuels and biochemicals via electro-fermentation technology. This article comprises a critical overview of the benefits and limitations of this emerging bio-electrochemical technology and its contribution to the circular economy.

Measurement of fasting breath hydrogen concentration as a simple diagnostic method for pancreatic exocrine insufficiency

Background

Pancreatic exocrine insufficiency (PEI) is associated with the outcome of pancreatic disease. However, there is no method for assessing PEI that can be used noninvasively and easily for outpatient. It has been reported that changes in intestinal bacteria caused by PEI may increase breath hydrogen concentration (BHC) levels during glucose or lactose loading. We have evaluated the usefulness of fasting breath hydrogen concentration (FBHC) measurement without glucose loading for the evaluation of PEI.

Methods

Sixty patients underwent FBHC measurement, BT-PABA testing, and microbiome analysis. They were classified into PEI group (PABA excretion rate < 73.4%, n = 30) and non-PEI group (n = 30). The FBHC of the two groups were compared, and the diagnostic ability of PEI by them was evaluated. The 16 s rRNA (V3–V4) from fecal samples was analyzed by MiSeq.

Results

FBHC levels was higher in the PEI group 15.70 (1.4 to 77.0) ppm than in the non-PEI group 2.80 (0.7 to 28.2) ppm (P < 0.0001). FBHC was negatively correlated with PABA excretion rate (r =  − 0.523, P < 0.001). The cutoff value of FBHC of 10.7 ppm (95% CI: 0.678–0.913, P < 0.001) showed a sensitivity of 73.3% and specificity of 83.3% for PEI diagnosis. In the PEI group, there was a significant increase of relative abundance of phylum Firmicutes (P < 0.05) and the genus Clostridium (P < 0.05).

Conclusion

FBHC shows good potential as a simple and repeatable test for the diagnosis of PEI. The elevated FBHC levels may be caused by hydrogen-producing bacteria such as Clostridium.

Bioengineering of anaerobic digestion for volatile fatty acids, hydrogen or methane production: A critical review

Anaerobic digestion (AD) is a well-established technology used for producing biogas or biomethane alongside the slurry used as biofertilizer. However, using a variety of wastes and residuals as substrate and mixed cultures in the bioreactor makes AD as one of the most complicated biochemical processes employing hydrolytic, acidogenic, hydrogen-producing, acetate-forming bacteria as well as acetoclastic and hydrogenoclastic methanogens. Hydrogen and volatile fatty acids (VFAs) including acetic, propionic, isobutyric, butyric, isovaleric, valeric and caproic acid and other carboxylic acids such as succinic and lactic acids are formed as intermediate products. As these acids are important precursors for various industries as mixed or purified chemicals, the AD process can be bioengineered to produce VFAs alongside hydrogen and therefore biogas plants can become biorefineries. The current review paper provides the theory and means to produce and accumulate VFAs and hydrogen, inhibit their conversion to methane and to extract them as the final products. The effects of pretreatment, pH, temperature, hydraulic retention time (HRT), organic loading rate (OLR), chemical methane inhibitions, and heat shocking of the inoculum on VFAs accumulation, hydrogen production, VFAs composition, and the microbial community were discussed. Furthermore, this paper highlights the possible techniques for recovery of VFAs from the fermentation media in order to minimize product inhibition as well as to supply the carboxylates for downstream procedures.

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.

Genetic relatedness of faecal coliforms and enterococci bacteria isolated from water and sediments of the Apies River, Gauteng, South Africa

To date, the microbiological quality of river sediments and its impact on water resources are not included in the water quality monitoring assessment. Therefore, the aim of this study was to establish genetic relatedness between faecal coliforms and enterococci isolated from the river water and riverbed sediments of Apies River to better understand the genetic similarity of microorganisms between the sediment and water phases. Indicator bacteria were subjected to a molecular study, which consisted of PCR amplification and sequence analysis of the 16S rRNA and 23S rRNA gene using specific primers for faecal coliforms and enterococci, respectively. Results revealed that the Apies River had high faecal pollution levels with enterococci showing low to moderate correlation coefficient (r² values ranged from 0.2605 to 0.7499) compared to the faecal coliforms which showed zero to low correlation (r² values ranged from 0.0027 to 0.1407) indicating that enterococci may be better indicator than faecal coliforms for detecting faecal contamination in riverbed sediments. The phylogenetic tree of faecal coliforms revealed a 98% homology among their nucleotide sequences confirming the close genetic relatedness between river water and riverbed sediment isolates. The phylogenetic tree of the enterococci showed that Enterococcus faecalis and Enterococcus faecium are the predominant species found in both river water and riverbed sediments with bootstrap values of ≥99%. A high degree of genetic relatedness between sediment and water isolates indicated a possible common ancestry and transmission pathway. We recommend the microbial monitoring of riverbed sediments as it harbours more diverse microbial community and once resuspended may cause health and environmental problems.

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.

Influence of pH Regulation Mode in Glucose Fermentation on Product Selection and Process Stability

Mixed culture anaerobic fermentation generates a wide range of products from simple sugars, and is potentially an effective process for producing renewable commodity chemicals. However it is difficult to predict product spectrum, and to control the process. One of the key control handles is pH, but the response is commonly dependent on culture history. In this work, we assess the impact of pH regulation mode on the product spectrum. Two regulation modes were applied: in the first, pH was adjusted from 4.5 to 8.5 in progressive steps of 0.5 and in the second, covered the same pH range, but the pH was reset to 5.5 before each change. Acetate, butyrate, and ethanol were produced throughout all pH ranges, but there was a shift from butyrate at pH < 6.5 to ethanol at pH > 6.5, as well as a strong and consistent shift from hydrogen to formate as pH increased. Microbial analysis indicated that progressive pH resulted in dominance by Klebsiella, while reset pH resulted in a bias towards Clostridium spp., particularly at low pH, with higher variance in community between different pH levels. Reset pH was more responsive to changes in pH, and analysis of Gibbs free energy indicated that the reset pH experiments operated closer to thermodynamic equilibrium, particularly with respect to the formate/hydrogen balance. This may indicate that periodically resetting pH conforms better to thermodynamic expectations.

Antisense-RNA-Mediated Gene Downregulation in Clostridium pasteurianum

Clostridium pasteurianum is receiving growing attention for its unique metabolic properties, particularly its ability to convert waste glycerol and glycerol-rich byproducts into butanol, a prospective biofuel. Genetic tool development and whole genome sequencing have recently been investigated to advance the genetic tractability of this potential industrial host. Nevertheless, methodologies for tuning gene expression through plasmid-borne expression and chromosomal gene downregulation are still absent. Here we demonstrate plasmid-borne heterologous gene expression and gene knockdown using antisense RNA in C. pasteurianum. We first employed a common thermophilic β-galactosidase (lacZ) gene reporter system from Thermoanaerobacterium thermosulfurogenes to characterize two promoters involved in the central fermentative metabolism of C. pasteurianum. Due to a higher level of constitutive lacZ expression compared to the ferredoxin gene (fdx) promoter, the thiolase (thl) promoter was selected to drive expression of asRNA. Expression of a lacZ asRNA resulted in 52%–58% downregulation of β-galactosidase activity compared to the control strain throughout the duration of culture growth. Subsequent implementation of our asRNA approach for downregulation of the native hydrogenase I gene (hydA) in C. pasteurianum resulted in altered end product distribution, characterized by an increase in production of reduced metabolites, particularly butyrate (40% increase) and ethanol (25% increase). Knockdown of hydA was also accompanied by increased acetate formation and lower levels of 1,3-propanediol, signifying a dramatic shift in cellular metabolism in response to inhibition of the hydrogenase enzyme. The methodologies described herein for plasmid-based heterologous gene expression and antisense-RNA-mediated gene knockdown should promote rational metabolic engineering of C. pasteurianum for enhanced production of butanol as a prospective biofuel.

Production of hydrogen, ethanol and volatile fatty acids from the seaweed carbohydrate mannitol

Fermentative hydrogen from seaweed is a potential biofuel of the future. Mannitol, which is a typical carbohydrate component of seaweed, was used as a substrate for hydrogen fermentation. The theoretical specific hydrogen yield (SHY) of mannitol was calculated as 5 mol H2/mol mannitol (615.4 mL H2/g mannitol) for acetic acid pathway, 3 mol H2/mol mannitol (369.2 mL H2/g mannitol) for butyric acid pathway and 1 mol H2/mol mannitol (123.1 mL H2/g mannitol) for lactic acid and ethanol pathways. An optimal SHY of 1.82 mol H2/mol mannitol (224.2 mL H2/g mannitol) was obtained by heat pre-treated anaerobic digestion sludge under an initial pH of 8.0, NH4Cl concentration of 25 mM, NaCl concentration of 50mM and mannitol concentration of 10 g/L. The overall energy conversion efficiency achieved was 96.1%. The energy was contained in the end products, hydrogen (17.2%), butyric acid (38.3%) and ethanol (34.2%).

Oral administration of mannitol may be an effective treatment for ischemia-reperfusion injury

Inhalation of hydrogen gas has been proved to be an effective treatment for ischemia-reperfusion injury. There has been considerable evidence of hydrogen's protective effect to diseases related to oxidative injury, such as the ischemia-reperfusion injury of the brain, liver and heart. Our previous studies demonstrated that intraperitoneal injection of hydrogen-rich saline protected hypoxic-ischemic brain injury, myocardial and intestine ischemia-reperfusion injury in rats. Bacteria in the large intestinal can produce endogenous hydrogen, and our preliminary experiments revealed that oral administration of mannitol in humans and animals can significantly increase the level of endogenous hydrogen. Therefore, we speculated that oral administration of mannitol may be effective against ischemia-reperfusion injury, which is a convenient, effective and unique treatment for ischemia-reperfusion injury.

Clostridium arbusti sp. nov., an anaerobic bacterium isolated from pear orchard soil

An obligately anaerobic, Gram-positive, spore-forming bacterial strain, designated SL206T, was isolated from pear orchard soils. Strain SL206T cells were straight or slightly curved rods, with motility by peritrichate flagella. Cell walls contained meso-diaminopimelic acid; wall sugars were glucose, rhamnose and mannose. The major fatty acids were C16 : 0, C18 : 1 ω9c and summed feature 10 (containing C18 : 1 ω11c/9t/6t). API 20A reactions were negative for oxidase, catalase and acid production from l-rhamnose, sucrose, trehalose, d-xylose, melezitose, salicin and d-sorbitol, and positive for acid production from d-glucose, sucrose, maltose, d-mannose and raffinose. Glucose was fermented to acetate, butyrate, CO2, H2 and ethanol in culture. The G+C content of the genomic DNA was 31.1 mol%. Based on comparative 16S rRNA gene sequence analysis, the isolate belonged to the genus Clostridium and formed a clade with Clostridium pasteurianum. The species most closely related to strain SL206T were C. pasteurianum (98.6 % similarity) and Clostridium acidisoli (97.8 % similarity). In DNA–DNA relatedness studies, the isolate had 59.5 % relatedness with C. pasteurianum and thus represented a unique species. On the basis of these studies, strain SL206T (=KCTC 5449T =JCM 14858T) is proposed to represent the type strain of a novel species, Clostridium arbusti sp. nov.

Performance assessment of malolactic fermenting bacteria Oenococcus oeni and Lactobacillus brevis in continuous culture

The growth performance of malolactic fermenting bacteria Oenococcus oeni NCIMB 11648 and Lactobacillus brevis X(2) was assessed in continuous culture. O. oeni grew at a dilution rate range of 0.007 to 0.052 h(-1) in a mixture of 5:6 (g l(-1)) of glucose/fructose at an optimal pH of 4.5, and L. brevis X(2) grew at 0.010 to 0.089 h(-1) in 10 g l(-1) glucose at an optimal pH of 5.5 in a simple and safe medium. The cell dry weight, substrate uptake and product formation were monitored, as well as growth kinetics, yield parameters and fermentation balances were also evaluated under pH control conditions. A comparison of growth characteristics of two strains was made, and this showed significantly different performance. O. oeni has lower maximum specific growth rate (mu(max)=0.073 h(-1)), lower maximum cell productivity (Q (x) (max)=17.6 mg cell l(-1) h(-1)), lower maximum biomass yield (Y (x/s) (max)=7.93 g cell mol(-1) sugar) and higher maintenance coefficient (m (s)=0.45 mmol(-1) sugar g(-1) cell h(-1)) as compared with L. brevis X(2) (mu(max)=0.110 h(-1); Q (x) (max)=93.2 g(-1) cell mol(-1) glucose; Y (x/s) (max)=22.3 g cell mol(-1) glucose; m (s)=0.21 mmol(-1) glucose g(-1) cell h(-1)). These data suggest a possible more productive strategy for their combined use in maturation of cider and wine.

Effect of pH on hydrogen production from glucose by a mixed culture

The effect of pH on the conversion of glucose to hydrogen by a mixed culture of fermentative bacteria was evaluated. At 36 degrees C, six hours hydraulic retention, over 90% of glucose was degraded at pH ranging 4.0-7.0, producing biogas and an effluent comprising mostly fatty acids. At the optimal pH of 5.5, the biogas comprised 64 +/- 2% of hydrogen with a yield of 2.1 +/- 0.1 mol-H2/mol-glucose and a specific production rate of 4.6 +/- 0.4 l-H2/(g-VSS day). The effluent was composed of acetate (15.3-34.1%) and butyrate (31.2-45.6%), plus smaller quantities of other volatile fatty acids and alcohols. The diversity of microbial communities increased with pH, based on 16S rDNA analysis by denaturing gradient gel electrophoresis (DGGE).

Physiology of carbohydrate to solvent conversion by clostridia

The solvent-forming clostridia have attracted interest because of their ability to convert a range of carbohydrates to end-products such as acetone, butanol and ethanol. Polymeric substrates such as cellulose, hemicellulose and starch are degraded by extracellular enzymes. The majority of cellulolytic clostridia, typified by Clostridium thermocellum, produce a multi-enzyme cellulase complex in which the organization of components is critical for activity against the crystalline substrate. A variety of enzymes involved in degradation of hemicellulose and starch have been identified in different strains. The products of degradation, and other soluble substrates, are accumulated via membrane-bound transport systems which are generally poorly characterized. It is clear, however, that the phosphoenolpyruvate-dependent phosphotransferase system (PTS) plays a major role in solute uptake in several species. Accumulated substrates are converted by intracellular enzymes to end-products characteristic of the organism, with production of ATP to support growth. The metabolic pathways have been described, but understanding of mechanisms of regulation of metabolism is incomplete. Synthesis of extracellular enzymes and membrane-bound transport systems is commonly subject to catabolite repression in the presence of a readily metabolized source of carbon and energy. While many genes encoding cellulases, xylanases and amylases have been cloned and sequenced, little is known of control of their expression. Although the mechanism of catabolite repression in clostridia is not understood, some recent findings implicate a role for the PTS as in other low G-C Gram-positive bacteria. Emphasis has been placed on describing the mechanisms underlying the switch of C. acetobutylicum fermentations from acidogenic to solventogenic metabolism at the end of the growth phase. Factors involved include a lowered pH and accumulation of undissociated butyric acid, intracellular concentration of ATP and reduced pyridine nucleotides, nutrient limitation, and the interplay between pathways of carbon and electron flow. Genes encoding enzymes of solvent pathways have been cloned and sequenced, and their expression correlated with the pattern of end-product formation in fermentations. There is evidence that the initiation of solvent formation may be subject to control mechanisms similar to other stationary-phase phenomena, including sporulation. The application of recently developed techniques for genetic manipulation of the bacterium is improving understanding of the regulatory circuits, but a complete molecular description of the control of solvent formation remains elusive. Experimental manipulation of the pathways of electron flow in other species has been shown to influence the range and yield of fermentation end-products. Acid-forming clostridia can, under appropriate conditions, be induced to form atypical solvents as products. While the mechanisms of regulation of gene expression are not at all understood, the capacity to adapt in this way further illustrates the metabolic flexibility of clostridial strains.

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

The metabolism of Clostridium butyricum DSM 5431 was studied in chemostat culture under carbon limitation using either glucose or glycerol. On glycerol, the enzymes glycerol dehydrogenase, diol dehydratase and 1,3-propanediol (1,3-PD) dehydrogenase constitute the branch point that partitions the carbon flux between the competing pathways, i.e. formation of either 1,3-PD or acetate and butyrate. The increasing levels of these enzyme activities with increasing dilution rates (D) explained the constant proportion of glycerol conversion into 1,3-PD. The production of acetate or butyrate constitutes another important branch point and when D increased (i) large amounts of intracellular acetyl-CoA accumulated, (ii) the carbon flux switched from butyric acid to acetic acid, (iii) the specific activity of thiolase was not affected, suggesting this enzyme may be the bottleneck for carbon flux to butyrate biosynthesis providing an explanation for the accumulation of large amounts of intracellular acetyl-CoA, and (iv) high levels of NADH were found in the cell. Oxidation of NADH by 1,3-PD dehydrogenase was linked to the production of 3-hydroxypropionaldehyde (3-HPA) by glycerol dehydratase. The fact that high intracellular concentrations of NADH were found means that diol dehydratase activity is the rate-limiting step in 1,3-PD formation, avoiding the accumulation of 3-HPA which is a very toxic compound. The specific rate of glucose catabolism (q glucose = 11.1 mmol h-1 g-1) was around four times lower than the specific rate of glycerol catabolism (q glucose = 57.4 mmol h-1 g-1). On glucose-grown cells, reducing equivalents which are released in the glycolytic pathway were reoxidized by the butyric pathway and the low specific formation rate of butyric acid led to an increase in the intracellular level of acetyl-CoA and NADH. Carbon flow was higher on glycerol due to the reoxidation of NADH by both butyric and PD pathways.