Engineering Clostridium for improved solvent production: recent progress and perspective

Stirring the hydrogen and butanol production from Enset fiber via simultaneous saccharification and fermentation (SSF) process

Enset fiber is a promising feedstock for biofuel production with the potential to reduce carbon emissions and improve the sustainability of the energy system. This study aimed to maximize hydrogen and butanol production from Enset fiber through simultaneous saccharification and fermentation (SSF) process in bottles as well as in bioreactor. The SSF process in bottles resulted in a higher butanol concentration of 11.36 g/L with a yield of 0.23 g/g and a productivity of 0.16 g/(L h) at the optimal process parameters of 5% (w/v) substrate loading, 16 FPU/g cellulase loading, and 100 rpm agitation speed from pretreated Enset fiber. Moreover, a comparable result to the bottle experiment was observed in the bioreactor with pH-uncontrolled SSF process, although with a decreased in butanol productivity to 0.095 g/(L h). However, using the pre-hydrolysis simultaneous saccharification and fermentation (PSSF) process in the bioreactor with a 7% (w/v) substrate loading led to the highest butanol concentration of 12.84 g/L with a productivity of 0.104 g/(L h). Furthermore, optimizing the SSF process parameters to favor hydrogen resulted in an increased hydrogen yield of 198.27 mL/g-Enset fiber at atmospheric pressure, an initial pH of 8.0, and 37 °C. In general, stirring the SSF process to shift the product ratio to either hydrogen or butanol was possible by adjusting temperature and pressure. At 37 °C and atmospheric pressure, the process resulted in an e-mol yield of 12% for hydrogen and 38% for butanol. Alternatively, at 30 °C and 0.55 bar overpressure, the process achieved a yield of 6% e-mol of hydrogen and 48% e-mol of butanol. This is the first study to produce hydrogen and butanol from Enset fiber using the SSF process and contributes to the development of a circular bioeconomy.

Revisiting Solar Energy Flow in Nanomaterial-Microorganism Hybrid Systems

Nanomaterial-microorganism hybrid systems (NMHSs), integrating semiconductor nanomaterials with microorganisms, present a promising platform for broadband solar energy harvesting, high-efficiency carbon reduction, and sustainable chemical production. While studies underscore its potential in diverse solar-to-chemical energy conversions, prevailing NMHSs grapple with suboptimal energy conversion efficiency. Such limitations stem predominantly from an insufficient systematic exploration of the mechanisms dictating solar energy flow. This review provides a systematic overview of the notable advancements in this nascent field, with a particular focus on the discussion of three pivotal steps of energy flow: solar energy capture, cross-membrane energy transport, and energy conversion into chemicals. While key challenges faced in each stage are independently identified and discussed, viable solutions are correspondingly postulated. In view of the interplay of the three steps in affecting the overall efficiency of solar-to-chemical energy conversion, subsequent discussions thus take an integrative and systematic viewpoint to comprehend, analyze and improve the solar energy flow in the current NMHSs of different configurations, and highlighting the contemporary techniques that can be employed to investigate various aspects of energy flow within NMHSs. Finally, a concluding section summarizes opportunities for future research, providing a roadmap for the continued development and optimization of NMHSs.

Positive effect of phasin in biohydrogen production of non polyhydroxybutyrate-producing Clostridium acetobutylicum ATCC 824

In this study, the goal was to enhance the tolerance of Clostridium acetobutylicum ATCC 824 to biomass-based inhibitory compounds for biohydrogen production and evaluate various known genes that enhance the production of biochemicals in various hosts. The introduction of phaP, the major polyhydroxyalkanoate granule-associated protein that has been reported as a chaperone-like protein resulted in increased tolerance to inhibitors and leads to higher levels of hydrogen production, cell growth, and glucose consumption in the presence of these inhibitors. It was observed that the introduction of phaP led to an increase in the transcription of the hydrogenase gene, whereas transcription of the chaperone functional genes decreased compared to the wild type. Finally, the introduction of phaP could significantly enhance biohydrogen production by 2.6-fold from lignocellulosic hydrolysates compared to that of wild type. These findings suggested that the introduction of phaP could enhance growth and biohydrogen production, even in non-polyhydroxyalkanoate-producing strains.

Harnessing lignocellulosic biomass for butanol production through clostridia for sustainable waste management: recent advances and perspectives

The escalating waste generation rates, driven by population growth, urbanization, and consumption patterns, have made waste management a critical global concern with significant environmental, social, and economic repercussions. Among the various waste sources, lignocellulosic biomass represents a significant proportion of agricultural, agro-industrial, and municipal wastes. Biofuels are gaining attention as a promising substitute to fossil fuels, and butanol is one such biofuel that has been identified as a potential candidate due to its compatibility with existing fuel infrastructure, lower volatility, and higher energy density. Sustainable management of lignocellulosic biomass waste and its utilization in fermentation are viable alternatives to produce butanol via the promising microbial catalyst clostridia. This review provides an overview of lignocellulosic biomass waste management, focusing on recent advances in strain development for butanol production from renewable biomass with an emphasis on future perspectives.

Enhancement of biohydrogen production in Clostridium acetobutylicum ATCC 824 by overexpression of glyceraldehyde-3-phosphate dehydrogenase gene

In the dark fermentation of hydrogen, development of production host is crucial as bacteria act on substrates and produce hydrogen. The present study aimed to improve hydrogen production through the development of Clostridium acetobutylicum as a superior biohydrogen producer. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which produces NADH/NADPH for metabolites and energy in primary pathways, was introduced to enhance hydrogen production. The strain CAC824-G containing gapC that encodes GAPDH showed a 66.3 % higher hydrogen production than the wild-type strain, with increased NADH and NADPH pools. Glucose consumption and other byproducts, such as acetone, butanol, and ethanol, were also high in CAC824-G. Overexpression of gapC resulted in increased hydrogen production with sugars obtained from different biomass, even in the presence of inhibitors such as vanillin, 5-hydroxymethylfufural, acetic acid, and formic acid. Our results imply that overexpression of gapC in Clostridium is possible to expand the production of the reported biochemicals to produce hydrogen.

Elucidating dynamic anaerobe metabolism with HRMAS 13C NMR and genome-scale modeling

Anaerobic microbial metabolism drives critical functions within global ecosystems, host-microbiota interactions, and industrial applications, yet remains ill-defined. Here we advance a versatile approach to elaborate cellular metabolism in obligate anaerobes using the pathogen Clostridioides difficile, an amino acid and carbohydrate-fermenting Clostridia. High-resolution magic angle spinning nuclear magnetic resonance (NMR) spectroscopy of C. difficile, grown with fermentable 13C substrates, informed dynamic flux balance analysis (dFBA) of the pathogen's genome-scale metabolism. Analyses identified dynamic recruitment of oxidative and supporting reductive pathways, with integration of high-flux amino acid and glycolytic metabolism at alanine's biosynthesis to support efficient energy generation, nitrogen handling and biomass generation. Model predictions informed an approach leveraging the sensitivity of 13C NMR spectroscopy to simultaneously track cellular carbon and nitrogen flow from [U-13C]glucose and [15N]leucine, confirming the formation of [13C,15N]alanine. Findings identify metabolic strategies used by C. difficile to support its rapid colonization and expansion in gut ecosystems.

Production of acetone, butanol, and ethanol by electro-fermentation with Clostridium saccharoperbutylacetonicum N1-4

This manuscript describes the effect of altering the extracellular redox potential during the production of acetone, butanol, and ethanol on a dual chamber H-type microbial fuel cell by fermenting glucose with Clostridium saccharoperbutylacetonicum N1-4. Extracellular redox potential modification was achieved by either supplementing the microbial broth with the redox agent NADH or by poising the cathode potential at -600 mV vs. Ag/AgCl. The addition of NADH was found to foment the production of acetone via fermentation of glucose. The addition of 200 mM of NADH to the catholyte rendered the highest production of acetone (2.4 g L^-1), thus outperforming the production of acetone by conventional fermentation means (control treatment) by a factor of 2.2. The experimental evidence gathered here, indicates that cathodic electro-fermentation of glucose favors the production of butanol. When poising the cathode potential at -600 mV vs Ag/AgCl (electro-fermentation), the largest production of butanol was achieved (5.8 g L^-1), outperforming the control treatment by a factor of 1.5. The production of ABE solvents and the electrochemical measurements demonstrate the electroactive properties of C. saccharoperbutylacetonicum N1-4 and illustrates the usefulness of bio-electrochemical systems to improve conventional fermentative processes.

Synthetic metabolism for in vitro acetone biosynthesis driven by ATP regeneration

In vitro ketone production continues to be a challenge due to the biochemical features of the enzymes involved-even when some of them have been extensively characterized (e.g. thiolase from Clostridium acetobutylicum), the assembly of synthetic enzyme cascades still face significant limitations (including issues with protein aggregation and multimerization). Here, we designed and assembled a self-sustaining enzyme cascade with acetone yields close to the theoretical maximum using acetate as the only carbon input. The efficiency of this system was further boosted by coupling the enzymatic sequence to a two-step ATP-regeneration system that enables continuous, cost-effective acetone biosynthesis. Furthermore, simple methods were implemented for purifying the enzymes necessary for this synthetic metabolism, including a first-case example on the isolation of a heterotetrameric acetate:coenzyme A transferase by affinity chromatography.

Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks

The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.

Current progress on engineering microbial strains and consortia for production of cellulosic butanol through consolidated bioprocessing

In the last decades, fermentative production of n-butanol has regained substantial interest mainly owing to its use as drop-in-fuel. The use of lignocellulose as an alternative to traditional acetone-butanol-ethanol fermentation feedstocks (starchy biomass and molasses) can significantly increase the economic competitiveness of biobutanol over production from non-renewable sources (petroleum). However, the low cost of lignocellulose is offset by its high recalcitrance to biodegradation which generally requires chemical-physical pre-treatment and multiple bioreactor-based processes. The development of consolidated processing (i.e., single-pot fermentation) can dramatically reduce lignocellulose fermentation costs and promote its industrial application. Here, strategies for developing microbial strains and consortia that feature both efficient (hemi)cellulose depolymerization and butanol production will be depicted, that is, rational metabolic engineering of native (hemi)cellulolytic or native butanol-producing or other suitable microorganisms; protoplast fusion of (hemi)cellulolytic and butanol-producing strains; and co-culture of (hemi)cellulolytic and butanol-producing microbes. Irrespective of the fermentation feedstock, biobutanol production is inherently limited by the severe toxicity of this solvent that challenges process economic viability. Hence, an overview of strategies for developing butanol hypertolerant strains will be provided.

Conversion of Syngas from Entrained Flow Gasification of Biogenic Residues with Clostridium carboxidivorans and Clostridium autoethanogenum

Synthesis gas fermentation is a microbial process, which uses anaerobic bacteria to convert CO-rich gases to organic acids and alcohols and thus presents a promising technology for the sustainable production of fuels and platform chemicals from renewable sources. Clostridium carboxidivorans and Clostridium autoethanogenum are two acetogenic bacteria, which have shown their high potential for these processes by their high tolerance toward CO and in the production of industrially relevant products such as ethanol, 1-butanol, 1-hexanol, and 2,3-butanediol. A promising approach is the coupling of gasification of biogenic residues with a syngas fermentation process. This study investigated batch processes with C. carboxidivorans and C. autoethanogenum in fully controlled stirred-tank bioreactors and continuous gassing with biogenic syngas produced by an autothermal entrained flow gasifier on a pilot scale >1200 °C. They were then compared to the results of artificial gas mixtures of pure gases. Because the biogenic syngas contained 2459 ppm O2 from the bottling process after gasification of torrefied wood and subsequent syngas cleaning for reducing CH4, NH3, H2S, NOX, and HCN concentrations, the oxygen in the syngas was reduced to 259 ppm O2 with a Pd catalyst before entering the bioreactor. The batch process performance of C. carboxidivorans in a stirred-tank bioreactor with continuous gassing of purified biogenic syngas was identical to an artificial syngas mixture of the pure gases CO, CO2, H2, and N2 within the estimation error. The alcohol production by C. autoethanogenum was even improved with the purified biogenic syngas compared to reference batch processes with the corresponding artificial syngas mixture. Both acetogens have proven their potential for successful fermentation processes with biogenic syngas, but full carbon conversion to ethanol is challenging with the investigated biogenic syngas.

High-rate continuous n-butanol production by Clostridium acetobutylicum from glucose and butyric acid in a single-pass fibrous bed bioreactor

Biobutanol produced in acetone-butanol-ethanol (ABE) fermentation at batch mode cannot compete with chemically derived butanol because of the low reactor productivity. Continuous fermentation can dramatically enhance productivity and lower capital and operating costs but are rarely used in industrial fermentation because of increased risks in culture degeneration, cell washout, and contamination. In this study, cells of the asporogenous Clostridium acetobutylicum ATCC55025 were immobilized in a single-pass fibrous-bed bioreactor (FBB) for continuous production of butanol from glucose and butyrate at various dilution rates. Butyric acid in the feed medium helped maintaining cells in the solventogenic phase for stable continuous butanol production. At the dilution rate of 1.88 h^-1 , butanol was produced at 9.55 g/L with a yield of 0.24 g/g and productivity of 16.8 g/L/h, which was the highest productivity ever achieved for biobutanol fermentation and an 80-fold improvement over the conventional ABE fermentation. The extremely high productivity was attributed to the high density of viable cells (~100 g/L at >70% viability) immobilized in the fibrous matrix, which also enabled the cells to better tolerate butanol and butyric acid. The FBB was stable for continuous operation for an extended period of over one month. This article is protected by copyright. All rights reserved.

Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools

Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.

Potentials of bio-butanol conversion to valuable products

In the last decade, there was observed a growing demand for both n-butanol as a potential fuel or fuel additive, and propylene as the only raw material for production of alcohol and other more bulky propylene chemical derivatives with faster growing outputs (polymers, propylene oxide, and acrylic acid). The predictable oilfield depletion and the European Green Deal adoption stimulated interest in alternative processes for n-butanol production, especially those involving bio-based materials. Their commercialization will promote additional market penetration of n-butanol for its application as a basic chemical. We analyze briefly the current status of two most advanced bio-based processes, i.e. ethanol–to-n-butanol and acetone–butanol–ethanol (ABE) fermentation. In the second part of the review, studies of n-butanol and ABE conversion to valuable products are considered with an emphasis on the most perspective catalytic systems and variants of the future processes realization.

ACETONE-BUTYL FERMENTATION PECULIARITIES OF THE BUTANOL STRAINS -PRODUCER

The aim of this review was to generalize and analyze the features of acetone-butyl fermentation as a type of butyric acid fermentation in the process of obtaining butanol as an alternative biofuel. Methods. The methods of analysis and generalization of analytical information and literature sources were used in the review. The results were obtained using the following methods such as microbiological (morphological properties of strains), chromatographic (determination of solvent concentration), spectrophotometric (determination of bacterial concentration), and molecular genetic (phylogenetic analysis of strains). Results. The process of acetone-butyl fermentation was analyzed, the main producer strains were considered, the features of the relationship between alcohol formation and sporulation were described, the possibility of butanol obtaining from synthesis gas was shown, and the features of the industrial production of butanol were considered. Conclusions. The features of the mechanism of acetone-butyl fermentation (the relationships between alcohol formation and sporulation, the duration of the acid-forming and alcohol-forming stages during batch fermentation depending on the change in the concentration of H2, CO, partial pressure, organic acids and mineral additives) and obtaining an enrichment culture during the production of butanol as an alternative fuel were shown. The possibility of using synthesis gas as a substrate for reducing atmospheric emissions during the fermentation process was shown. The direction of increasing the productivity of butanol-producing strains to create a competitive industrial biofuel technology was proposed.

Bioprocesses for the recovery of bioenergy and value-added products from wastewater: A review

Wastewater and activated sludge present a major challenge worldwide. Wastewater generated from large and small-scale industries, laundries, human residential areas and other sources is emerging as a main problem in sanitation and maintenance of smart/green cities. During the last decade, different technologies and processes have been developed to recycle and purify the wastewater. Currently, identification and fundamental consideration of development of more advanced microbial-based technologies that enable wastewater treatment and simultaneous resource recovery to produce bioenergy, biofuels and other value-added compounds (organic acids, fatty acids, bioplastics, bio-pesticides, bio-surfactants and bio-flocculants etc.) became an emerging topic. In the last several decades, significant development of bioprocesses and techniques for the extraction and recovery of mentioned valuable molecules and compounds from wastewater, waste biomass or sludge has been made. This review presents different microbial-based process routes related to resource recovery and wastewater application for the production of value-added products and bioenergy. Current process limitations and insights for future research to promote more efficient and sustainable routes for this under-utilized and continually growing waste stream are also discussed.

Effects of orphan histidine kinases on clostridial sporulation progression and metabolism

Solventogenesis and sporulation of clostridia are the main responsive adaptations to the acidic environment during acetone-butanol-ethanol (ABE) fermentation. It was hypothesized that five orphan histidine kinases (HKs) including Cac3319, Cac0323, Cac0903, Cac2730, and Cac0437 determined the cell fates between sporulation and solventogenesis. In this study, the comparative genomic analysis revealed that a mutation in cac0437 appeared to contribute to the nonsporulating feature of ATCC 55025. Hence, the individual and interactive roles of five HKs in regulating cell growth, metabolism, and sporulation were investigated. The fermentation results of mutants with different HK expression levels suggested that cac3319 and cac0437 played critical roles in regulating sporulation and acids and butanol biosynthesis. Morphological analysis revealed that cac3319 knockout abolished sporulation (Stage 0) whereas cac3319 overexpression promoted spore development (Stage VII), and cac0437 knockout initiated but blocked sporulation before Stage II, indicating the progression of sporulation was altered through engineering HKs. By combinatorial HKs knockout, the interactive effects between two different HKs were investigated. This study elucidated the regulatory roles of HKs in clostridial differentiation and demonstrated that HK engineering can be effectively used to control sporulation and enhance butanol biosynthesis.

Physiological limitations and opportunities in microbial metabolic engineering

Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.

Enforcing ATP hydrolysis enhanced anaerobic glycolysis and promoted solvent production in Clostridium acetobutylicum

Background

The intracellular ATP level is an indicator of cellular energy state and plays a critical role in regulating cellular metabolism. Depletion of intracellular ATP in (facultative) aerobes can enhance glycolysis, thereby promoting end product formation. In the present study, we examined this s trategy in anaerobic ABE (acetone-butanol-ethanol) fermentation using Clostridium acetobutylicum DSM 1731.

Results

Following overexpression of atpAGD encoding the subunits of water-soluble, ATP-hydrolyzing F₁-ATPase, the intracellular ATP level of 1731(pITF₁) was significantly reduced compared to control 1731(pIMP1) over the entire batch fermentation. The glucose uptake was markedly enhanced, achieving a 78.8% increase of volumetric glucose utilization rate during the first 18 h. In addition, an early onset of acid re-assimilation and solventogenesis in concomitant with the decreased intracellular ATP level was evident. Consequently, the total solvent production was significantly improved with remarkable increases in yield (14.5%), titer (9.9%) and productivity (5.3%). Further genome-scale metabolic modeling revealed that many metabolic fluxes in 1731(pITF₁) were significantly elevated compared to 1731(pIMP1) in acidogenic phase, including those from glycolysis, tricarboxylic cycle, and pyruvate metabolism; this indicates significant metabolic changes in response to intracellular ATP depletion.

Conclusions

In C. acetobutylicum DSM 1731, depletion of intracellular ATP significantly increased glycolytic rate, enhanced solvent production, and resulted in a wide range of metabolic changes. Our findings provide a novel strategy for engineering solvent-producing C. acetobutylicum, and many other anaerobic microbial cell factories.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01639-7.

Sporulation in solventogenic and acetogenic clostridia

The Clostridium genus harbors compelling organisms for biotechnological production processes; while acetogenic clostridia can fix C1-compounds to produce acetate and ethanol, solventogenic clostridia can utilize a wide range of carbon sources to produce commercially valuable carboxylic acids, alcohols, and ketones by fermentation. Despite their potential, the conversion by these bacteria of carbohydrates or C1 compounds to alcohols is not cost-effective enough to result in economically viable processes. Engineering solventogenic clostridia by impairing sporulation is one of the investigated approaches to improve solvent productivity. Sporulation is a cell differentiation process triggered in bacteria in response to exposure to environmental stressors. The generated spores are metabolically inactive but resistant to harsh conditions (UV, chemicals, heat, oxygen). In Firmicutes, sporulation has been mainly studied in bacilli and pathogenic clostridia, and our knowledge of sporulation in solvent-producing or acetogenic clostridia is limited. Still, sporulation is an integral part of the cellular physiology of clostridia; thus, understanding the regulation of sporulation and its connection to solvent production may give clues to improve the performance of solventogenic clostridia. This review aims to provide an overview of the triggers, characteristics, and regulatory mechanism of sporulation in solventogenic clostridia. Those are further compared to the current knowledge on sporulation in the industrially relevant acetogenic clostridia. Finally, the potential applications of spores for process improvement are discussed.Key Points• The regulatory network governing sporulation initiation varies in solventogenic clostridia.• Media composition and cell density are the main triggers of sporulation.• Spores can be used to improve the fermentation process.

Engineering Clostridium cellulovorans for highly selective n-butanol production from cellulose in consolidated bioprocessing

Cellulosic n-butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans, a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adhE2 from C. acetobutylicum for n-butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl-CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adhE2 would enhance n-butanol production. In this study, thiolase (thlA^CA ) from C. acetobutylicum and 3-hydroxybutyryl-CoA dehydrogenase (hbd^CT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adhE2 to increase the flux from acetyl-CoA to butyryl-CoA. In addition, ferredoxin-NAD(P)⁺ oxidoreductase (fnr), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl-CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n-butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adhE2-fnr^CA -thlA^CA -hbd^CT produced n-butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n-butanol production from cellulosic biomass in consolidated bioprocessing.

Recent advances in the valorization of plant biomass

Plant biomass is a highly abundant renewable resource that can be converted into several types of high-value-added products, including chemicals, biofuels and advanced materials. In the last few decades, an increasing number of biomass species and processing techniques have been developed to enhance the application of plant biomass followed by the industrial application of some of the products, during which varied technologies have been successfully developed. In this review, we summarize the different sources of plant biomass, the evolving technologies for treating it, and the various products derived from plant biomass. Moreover, the challenges inherent in the valorization of plant biomass used in high-value-added products are also discussed. Overall, with the increased use of plant biomass, the development of treatment technologies, and the solution of the challenges raised during plant biomass valorization, the value-added products derived from plant biomass will become greater in number and more valuable.

Increasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics

Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.

Changes in efflux pump activity of Clostridium beijerinckii throughout ABE fermentation

Pumping toxic substances through a cytoplasmic membrane by protein transporters known as efflux pumps represents one bacterial mechanism involved in the stress response to the presence of toxic compounds. The active efflux might also take part in exporting low-molecular-weight alcohols produced by intrinsic cell metabolism; in the case of solventogenic clostridia, predominantly acetone, butanol and ethanol (ABE). However, little is known about this active efflux, even though some evidence exists that membrane pumps might be involved in solvent tolerance. In this study, we investigated changes in overall active efflux during ABE fermentation, employing a flow cytometric protocol adjusted for Clostridia and using ethidium bromide (EB) as a fluorescence marker for quantification of direct efflux. A fluctuation in efflux during the course of standard ABE fermentation was observed, with a maximum reached during late acidogenesis, a high efflux rate during early and mid-solventogenesis and an apparent decrease in EB efflux rate in late solventogenesis. The fluctuation in efflux activity was in accordance with transcriptomic data obtained for various membrane exporters in a former study. Surprisingly, under altered cultivation conditions, when solvent production was attenuated, and extended acidogenesis was promoted, stable low efflux activity was reached after an initial peak that appeared in the stage comparable to standard ABE fermentation. This study confirmed that efflux pump activity is not constant during ABE fermentation and suggests that undisturbed solvent production might be a trigger for activation of pumps involved in solvent efflux. KEY POINTS: • Flow cytometric assay for efflux quantification in Clostridia was established. • Efflux rate peaked in late acidogenesis and in early solventogenesis. • Impaired solventogenesis led to an overall decrease in efflux.

Using Co-Culture to Functionalize Clostridium Fermentation

Clostridium fermentations have been developed for producing butanol and other value-added chemicals, but their development is constrained by some limitations, such as relatively high substrate cost and the need to maintain an anaerobic condition. Recently, co-culture is emerging as a popular way to address these limitations by introducing a partner strain with Clostridium. Generally speaking, the co-culture strategy enables the use of a cheaper substrate, maintains the growth of Clostridium without any anaerobic treatment, improves product yields, and/or widens the product spectrum. Herein, we review recent developments of co-culture strategies involving Clostridium species according to their partner stains' functions with representative examples. We also discuss research challenges that need to be addressed for the future development of Clostridium co-cultures.

The effect of corn syrup and whey on the conversion process of CO to ethanol using Clostridium ljungdahlii

CO is one of the toxic components of syngas, which is the major source of air pollution. Syngas fermentation technology has the ability to convert toxic gases into valuable biofuels, such as ethanol. Fermentative ethanol production is an important method that can be used to promote environmental protection. CO can be converted into ethanol, via the Wood-Ljungdahl pathway, using Clostridium ljungdahlii. The components of the growing medium--especially the trace-element solution and yeast extract--are the main reasons for the high costs associated with this process, however, and this especially impacts scaled-up operations. In this study, cheaper substitutes for these components were used in order to determine their effect on ethanol production. The study comprised three main parts--the optimization of CO concentration, and the substitution of corn syrup and whey powder in the process. The optimum volume of CO for ethanol production was found to be 10 mL. Corn syrup can be used instead of trace-element solution, but the use of yeast extract with the corn syrup was determined to be essential. Up to 1.4 g/L ethanol production was observed with the addition of 15 mL corn syrup. Whey powder had the advantage of being usable without yeast extract, with up to 2.5 g/L ethanol being produced from a 30-g/L concentration. The main finding was that either corn syrup or whey powder can be used as substitutes for expensive basal-medium components.

Advances and Applications of Clostridium Co-culture Systems in Biotechnology

Clostridium spp. are important microorganisms that can degrade complex biomasses such as lignocellulose, which is a widespread and renewable natural resource. Co-culturing Clostridium spp. and other microorganisms is considered to be a promising strategy for utilizing renewable feed stocks and has been widely used in biotechnology to produce bio-fuels and bio-solvents. In this review, we summarize recent progress on the Clostridium co-culture system, including system unique advantages, composition, products, and interaction mechanisms. In addition, biochemical regulation and genetic modifications used to improve the Clostridium co-culture system are also summarized. Finally, future prospects for Clostridium co-culture systems are discussed in light of recent progress, challenges, and trends.

Bacteria associated with cockroaches: health risk or biotechnological opportunity?

Abstract

Cockroaches have existed for 300 million years and more than 4600 extant species have been described. Throughout their evolution, cockroaches have been associated with bacteria, and today Blattabacterium species flourish within specialized bacteriocytes, recycling nitrogen from host waste products. Cockroaches can disseminate potentially pathogenic bacteria via feces and other deposits, particularly members of the family Enterobacteriaceae, but also Staphylococcus and Mycobacterium species, and thus, they should be cleared from sites where hygiene is essential, such as hospitals and kitchens. On the other hand, cockroaches also carry bacteria that may produce metabolites or proteins with potential industrial applications. For example, an antibiotic-producing Streptomyces strain was isolated from the gut of the American cockroach Periplaneta americana. Other cockroach-associated bacteria, including but not limited to Bacillus, Enterococcus, and Pseudomonas species, can also produce bioactive metabolites that may be suitable for development as pharmaceuticals or plant protection products. Enzymes that degrade industrially relevant substrates, or that convert biomasses into useful chemical precursors, are also expressed in cockroach-derived bacteria and could be deployed for use in the food/feed, paper, oil, or cosmetics industries. The analysis of cockroach gut microbiomes has revealed a number of lesser-studied bacteria that may form the basis of novel taxonomic groups. Bacteria associated with cockroaches can therefore be dangerous or useful, and this review explores the bacterial clades that may provide opportunities for biotechnological exploitation.

Key points

• Members of the Enterobacteriaceae are the most frequently cultivated bacteria from cockroaches.

• Cultivation-independent studies have revealed a diverse community, led by the phyla Bacteroidetes and Firmicutes.

• Although cockroaches may carry pathogenic bacteria, most strains are innocuous and may be useful for biotechnological applications.

Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives

The sustainable production of solvents from above ground carbon is highly desired. Several clostridia naturally produce solvents and use a variety of renewable and waste-derived substrates such as lignocellulosic biomass and gas mixtures containing H2/CO2 or CO. To enable economically viable production of solvents and biofuels such as ethanol and butanol, the high productivity of continuous bioprocesses is needed. While the first industrial-scale gas fermentation facility operates continuously, the acetone-butanol-ethanol (ABE) fermentation is traditionally operated in batch mode. This review highlights the benefits of continuous bioprocessing for solvent production and underlines the progress made towards its establishment. Based on metabolic capabilities of solvent producing clostridia, we discuss recent advances in systems-level understanding and genome engineering. On the process side, we focus on innovative fermentation methods and integrated product recovery to overcome the limitations of the classical one-stage chemostat and give an overview of the current industrial bioproduction of solvents.

Recent advances in n-butanol and butyrate production using engineered Clostridium tyrobutyricum

Acidogenic clostridia naturally producing acetic and butyric acids has attracted high interest as a novel host for butyrate and n-butanol production. Among them, Clostridium tyrobutyricum is a hyper butyrate-producing bacterium, which re-assimilates acetate for butyrate biosynthesis by butyryl-CoA/acetate CoA transferase (CoAT), rather than the phosphotransbutyrylase-butyrate kinase (PTB-BK) pathway widely found in clostridia and other microbial species. To date, C. tyrobutyricum has been engineered to overexpress a heterologous alcohol/aldehyde dehydrogenase, which converts butyryl-CoA to n-butanol. Compared to conventional solventogenic clostridia, which produce acetone, ethanol, and butanol in a biphasic fermentation process, the engineered C. tyrobutyricum with a high metabolic flux toward butyryl-CoA produced n-butanol at a high yield of > 0.30 g/g and titer of > 20 g/L in glucose fermentation. With no acetone production and a high C4/C2 ratio, butanol was the only major fermentation product by the recombinant C. tyrobutyricum, allowing simplified downstream processing for product purification. In this review, novel metabolic engineering strategies to improve n-butanol and butyrate production by C. tyrobutyricum from various substrates, including glucose, xylose, galactose, sucrose, and cellulosic hydrolysates containing the mixture of glucose and xylose, are discussed. Compared to other recombinant hosts such as Clostridium acetobutylicum and Escherichia coli, the engineered C. tyrobutyricum strains with higher butyrate and butanol titers, yields and productivities are the most promising hosts for potential industrial applications.

Characterization of sporulation dynamics of Pseudoclostridium thermosuccinogenes using flow cytometry

Single-cell analysis of microbial population heterogeneity is a fast growing research area in microbiology due to its potential to identify and quantify the impact of subpopulations on microbial performance in, for example, industrial biotechnology, environmental biology, and pathogenesis. Although several tools have been developed, determination of population heterogenity in anaerobic bacteria, especially spore-forming clostridia species has been amply studied. In this study we applied single cell analysis techniques such as flow cytometry (FCM) and fluorescence-assisted cell sorting (FACS) on the spore-forming succinate producer Pseudoclostridium thermosuccinogenes. By combining FCM and FACS with fluorescent staining, we differentiated and enriched all sporulation-related morphologies of P. thermosuccinogenes. To evaluate the presence of metabolically active vegetative cells, a blend of the dyes propidium iodide (PI) and carboxy fluorescein diacetate (cFDA) tested best. Side scatter (SSC-H) in combination with metabolic indicator cFDA dye provided the best separation of sporulation populations. Based on this protocol, we successfully determined culture heterogeneity of P. thermosuccinogenes by discriminating between mature spores, forespores, dark and bright phase endospores, and vegetative cells populations. Henceforth, this methodology can be applied to further study sporulation dynamics and its impact on fermentation performance and product formation by P. thermosuccinogenes.

Metabolic Engineering of Histidine Kinases in Clostridium beijerinckii for Enhanced Butanol Production

Clostridium beijerinckii, a promising industrial microorganism for butanol production, suffers from low butanol titer and lack of high-efficiency genetical engineering toolkit. A few histidine kinases (HKs) responsible for Spo0A phosphorylation have been demonstrated as functionally important components in regulating butanol biosynthesis in solventogenic clostridia such as C. acetobutylicum, but no study about HKs has been conducted in C. beijerinckii. In this study, six annotated but uncharacterized candidate HK genes sharing partial homologies (no less than 30%) with those in C. acetobutylicum were selected based on sequence alignment. The encoding region of these HK genes were deleted with CRISPR-Cas9n-based genome editing technology. The deletion of cbei2073 and cbei4484 resulted in significant change in butanol biosynthesis, with butanol production increased by 40.8 and 17.3% (13.8 g/L and 11.5 g/L vs. 9.8 g/L), respectively, compared to the wild-type. Faster butanol production rates were observed, with butanol productivity greatly increased by 40.0 and 20.0%, respectively, indicating these two HKs are important in regulating cellular metabolism in C. beijerinckii. In addition, the sporulation frequencies of two HKs inactivated strains decreased by 96.9 and 77.4%, respectively. The other four HK-deletion (including cbei2087, cbei2435, cbei4925, and cbei1553) mutant strains showed few phenotypic changes compared with the wild-type. This study demonstrated the role of HKs on sporulation and solventogenesis in C. beijerinckii, and provided a novel engineering strategy of HKs for improving metabolite production. The hyper-butanol-producing strains generated in this study have great potentials in industrial biobutanol production.

Butanol production by Saccharomyces cerevisiae: perspectives, strategies and challenges

The search for gasoline substitutes has grown in recent decades, leading to the increased production of ethanol as viable alternative. However, research in recent years has shown that butanol exhibits various advantages over ethanol as a biofuel. Furthermore, butanol can also be used as a chemical platform, serving as an intermediate product and as a solvent in industrial reactions. This alcohol is naturally produced by some Clostridium species; however, Clostridial fermentation processes still have inherent problems, which focuses the interest on Saccharomyces cerevisiae for butanol production, as an alternative organism for the production of this alcohol. S. cerevisiae exhibits great adaptability to industrial conditions and can be modified with a wide range of genetic tools. Although S. cerevisiae is known to naturally produce isobutanol, the n-butanol synthesis pathway has not been well established in wild S. cerevisiae strains. Two strategies are most commonly used for of S. cerevisiae butanol production: the heterologous expression of the Clostridium pathway or the amino acid uptake pathways. However, butanol yields produced from S. cerevisiae are lower than ethanol yield. Thus, there are still many challenges needed to be overcome, which can be minimized through genetic and evolutive engineering, for butanol production by yeast to become a reality.

Control of solvent production by sigma-54 factor and the transcriptional activator AdhR in Clostridium beijerinckii

Clostridia are obligate anaerobic bacteria that can produce solvents such as acetone, butanol and ethanol. Alcohol dehydrogenases (ADHs) play a key role in solvent production; however, their regulatory mechanisms remain largely unknown. In this study, we characterized the regulatory mechanisms of two ADH-encoding genes in C. beijerinckii. SigL (sigma factor σ⁵⁴ ) was found to be required for transcription of adhA1 and adhA2 genes. Moreover, a novel transcriptional activator AdhR was identified, which binds to the σ⁵⁴ promoter and activates σ⁵⁴ -dependent transcription of adhA1 and adhA2. Clostridia beijerinckii mutants deficient in SigL or AdhR showed severely impaired butanol and ethanol production as well as altered acetone and butyrate synthesis. Overexpression of SigL resulted in significantly improved solvent production by C. beijerinckii when butyrate was added to cultures. Our results reveal SigL as a novel engineering target for improving solvent production by C. beijerinckii and other solvent-producing clostridia. Moreover, this study gains an insight into regulation of alcohol metabolism in diverse clostridia.

Production of n-butanol from cassava bagasse hydrolysate by engineered Clostridium tyrobutyricum overexpressing adhE2: Kinetics and cost analysis

The production of biofuels such as butanol is usually limited by the availability of inexpensive raw materials and high substrate cost. Using food crops as feedstock in the biorefinery industry has been criticized for its competition with food supply, causing food shortage and increased food prices. In this study, cassava bagasse as an abundant, renewable, and inexpensive byproduct from the cassava starch industry was used for n-butanol production. Cassava bagasse hydrolysate containing mainly glucose was obtained after treatments with dilute acid and enzymes (glucoamylases and cellulases) and then supplemented with corn steep liquor for use as substrate in repeated-batch fermentation with engineered Clostridium tyrobutyricum CtΔack-adhE2 in a fibrous-bed bioreactor. Stable butanol production with high titer (>15.0 g/L), yield (>0.30 g/g), and productivity (~0.3 g/L∙h) was achieved, demonstrating the feasibility of an economically competitive process for n-butanol production from cassava bagasse for industrial application.

Development of an in vivo fluorescence based gene expression reporter system for Clostridium tyrobutyricum

C. tyrobutyricum, an acidogenic Clostridium, has aroused increasing interest due to its potential to produce biofuel efficiently. However, construction of recombinant C. tyrobutyricum for enhanced biofuel production has been impeded by the limited genetic engineering tools. In this study, a flavin mononucleotide (FMN)-dependent fluorescent protein Bs2-based gene expression reporter system was developed to monitor transformation and explore in vivo strength and regulation of various promoters in C. tyrobutyricum and C. acetobutylicum. Unlike green fluorescent protein (GFP) and its variants, Bs2 can emit green light without oxygen, which makes it extremely suitable for promoter screening and transformation confirmation in organisms grown anaerobically. The expression levels of bs2 under thiolase promoters from C. tyrobutyricum and C. acetobutylicum were measured and compared based on fluorescence intensities. The capacities of the two promoters in driving secondary alcohol dehydrogenase (adh) gene for isopropanol production in C. tyrobutyricum were distinguished, confirming that this reporter system is a convenient, effective and reliable tool for promoter strength assay and real time monitoring in C. tyrobutyricum, while demonstrating the feasibility of producing isopropanol in C. tyrobutyricum for the first time.