Developing a coculture for enhanced butanol production by Clostridium beijerinckii and Saccharomyces cerevisiae

Synthetic microbial ecology: engineering habitats for modular consortia

Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.

Biobutanol production from underutilized substrates using Clostridium: Unlocking untapped potential for sustainable energy development

The increasing demand for sustainable energy has brought biobutanol as a potential substitute for fossil fuels. The Clostridium genus is deemed essential for biobutanol synthesis due to its capability to utilize various substrates. However, challenges in maintaining fermentation continuity and achieving commercialization persist due to existing barriers, including butanol toxicity to Clostridium, low substrate utilization rates, and high production costs. Proper substrate selection significantly impacts fermentation efficiency, final product quality, and economic feasibility in Clostridium biobutanol production. This review examines underutilized substrates for biobutanol production by Clostridium, which offer opportunities for environmental sustainability and a green economy. Extensive research on Clostridium, focusing on strain development and genetic engineering, is essential to enhance biobutanol production. Additionally, critical suggestions for optimizing substrate selection to enhance Clostridium biobutanol production efficiency are also provided in this review. In the future, cost reduction and advancements in biotechnology may make biobutanol a viable alternative to fossil fuels.

Lignocellulosic ethanol and butanol production by Saccharomyces cerevisiae and Clostridium beijerinckii co-culture using non-detoxified corn stover hydrolysate

Considering global economic and environmental -benefits, green renewable biofuels such as ethanol and butanol are considered as sustainable alternatives to fossil fuels. Thus, developing a co-culture strategy for ethanol and butanol production by Saccharomyces cerevisiae and Clostridium beijerinckii has emerged as a promising approach for biofuel production from lignocellulosic biomass. This study developed a co-culture of S. cerevisiae and C. beijerinckii for ethanol and butanol production from non-detoxified corn stover hydrolysate. By firstly inoculating 3 % S. cerevisiae and then 7 % C. beijerinckii with 8-10 h time intervals, the optimized co-culture process gave 24.0 g/L ABE (20.8 g/L ethanol and 2.4 g/L butanol), obtaining ABE yield and productivity of 0.421 g/g and 0.55 g/L/h. The demonstrated co-culture strategy made full use of hexose and pentose in hydrolysate and contributed to total yield and efficiency compared to conventional ethanol or ABE fermentation, indicating its great potential for developing economically feasible and sustainable bioalcohols production.

Unraveling the unique butyrate re-assimilation mechanism of Clostridium sp. strain WK and the application of butanol production from red seaweed Gelidium amansii through a distinct acidolytic pretreatment

Exploration of the algae-derived biobutanol synthesis has become one of the hotspots due to its highly cost-effective and environment-friendly features. In this study, a solventogenic strain Clostridium sp. strain WK produced 13.96 g/L butanol with a maximal yield of 0.41 g/g from glucose in the presence of 24 g/L butyrate. Transcriptional analysis indicated that the acid re-assimilation of this strain was predominantly regulated by genes buk-ptb rather than ctfAB, explaining its special phenotypes including high butyrate tolerance and the pH-independent fermentation. In addition, a butyric acid-mediated hydrolytic system was established for the first time to release a maximal yield of 0.35 g/g reducing sugars from the red algal biomass (Gelidium amansii). Moreover, 4.48 g/L of butanol was finally achieved with a significant enhancement by 29.9 folds. This work reveals an unconventional metabolic pathway for butanol synthesis in strain WK, and demonstrates the feasibility to develop renewable biofuels from marine resources.

Harnessing the yeast Saccharomyces cerevisiae for the production of fungal secondary metabolites

Fungal secondary metabolites (FSMs) represent a remarkable array of bioactive compounds, with potential applications as pharmaceuticals, nutraceuticals, and agrochemicals. However, these molecules are typically produced only in limited amounts by their native hosts. The native organisms may also be difficult to cultivate and genetically engineer, and some can produce undesirable toxic side-products. Alternatively, recombinant production of fungal bioactives can be engineered into industrial cell factories, such as aspergilli or yeasts, which are well amenable for large-scale manufacturing in submerged fermentations. In this review, we summarize the development of baker's yeast Saccharomyces cerevisiae to produce compounds derived from filamentous fungi and mushrooms. These compounds mainly include polyketides, terpenoids, and amino acid derivatives. We also describe how native biosynthetic pathways can be combined or expanded to produce novel derivatives and new-to-nature compounds. We describe some new approaches for cell factory engineering, such as genome-scale engineering, biosensor-based high-throughput screening, and machine learning, and how these tools have been applied for S. cerevisiae strain improvement. Finally, we prospect the challenges and solutions in further development of yeast cell factories to more efficiently produce FSMs.

Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791T

Clostridium beijerinckii is a relatively widely studied, yet non-model, bacterium. While 246 genome assemblies of its various strains are available currently, the diversity of the whole species has not been studied, and it has only been analyzed in part for a missing genome of the type strain. Here, we sequenced and assembled the complete genome of the type strain Clostridium beijerinckii DSM 791T, composed of a circular chromosome and a circular megaplasmid, and used it for a comparison with other genomes to evaluate diversity and capture the evolution of the whole species. We found that strains WB53 and HUN142 were misidentified and did not belong to the Clostridium beijerinckii species. Additionally, we filtered possibly misassembled genomes, and we used the remaining 237 high-quality genomes to define the pangenome of the whole species. By its functional annotation, we showed that the core genome contains genes responsible for basic metabolism, while the accessory genome has genes affecting final phenotype that may vary among different strains. We used the core genome to reconstruct the phylogeny of the species and showed its great diversity, which complicates the identification of particular strains, yet hides possibilities to reveal hitherto unreported phenotypic features and processes utilizable in biotechnology.

Modelling microbial communities: Harnessing consortia for biotechnological applications

Microbes propagate and thrive in complex communities, and there are many benefits to studying and engineering microbial communities instead of single strains. Microbial communities are being increasingly leveraged in biotechnological applications, as they present significant advantages such as the division of labour and improved substrate utilisation. Nevertheless, they also present some interesting challenges to surmount for the design of efficient biotechnological processes. In this review, we discuss key principles of microbial interactions, followed by a deep dive into genome-scale metabolic models, focussing on a vast repertoire of constraint-based modelling methods that enable us to characterise and understand the metabolic capabilities of microbial communities. Complementary approaches to model microbial communities, such as those based on graph theory, are also briefly discussed. Taken together, these methods provide rich insights into the interactions between microbes and how they influence microbial community productivity. We finally overview approaches that allow us to generate and test numerous synthetic community compositions, followed by tools and methodologies that can predict effective genetic interventions to further improve the productivity of communities. With impending advancements in high-throughput omics of microbial communities, the stage is set for the rapid expansion of microbial community engineering, with a significant impact on biotechnological processes.

Comparative transcriptome analysis of Clostridium tyrobutyricum expressing a heterologous uptake hydrogenase

Clostridium tyrobutyricum is a promising microbial cell factory to produce biofuels. In this study, an uptake hydrogenase (hyd2293) from Ethanoligenens harbinense was overexpressed in C. tyrobutyricum and significantly affected the redox reactions and metabolic profiles. Compared to the parental strain (Ct-WT), the mutant strain Ct-Hyd2293 produced ~34% less butyrate, ~148% more acetate, and ~11% less hydrogen, accompanied by the emerging genesis of butanol. Comparative transcriptome analysis revealed that 666 genes were significantly differentially expressed after the overexpression of hyd2293, including 82 up-regulated genes and 584 down-regulated genes. The up-regulated genes were mainly involved in carbohydrate and energy metabolisms while the down-regulated genes were distributed in nearly all pathways. Genes involved in glucose transportation, glycolysis, different fermentation pathways and hydrogen metabolism were studied and the gene expression changes showed the mechanism of the metabolic flux redistribution in Ct-Hyd2293. The overexpression of uptake hydrogenase redirected electrons from hydrogen and butyrate to butanol. The key enzymes participating in the energy conservation and sporulation were also identified and their transcription levels were generally reduced. This study demonstrated the transcriptomic responses of C. tyrobutyricum to the expression of a heterologous uptake hydrogenase, which provided a better understanding of the metabolic characteristics of C. tyrobutyricum and demonstrated the potential role of redox manipulation in metabolic engineering for biofuel productions.

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.

A novel integrated process to convert cellulose and hemicellulose in rice straw to biobutanol

A novel integrated process was established in this study to produce butanol from rice straw. In the first pretreatment, an alternative NaOH/Urea preatment operated at -12 ^oC efficiently removed 10.9 g lignin and preserved 91.54% cellulose and hemicellulose in 100 g rice straw. Subsequently, crude cellulase produced from Trichoderma viride was used to convert pretreated rice straw to mono-sugars for fermentation. The yields of glucose, xylose and arabiose obtained from 100 g rice straw were 31 g, 13.4 g and 0.48 g, respectively, resulting in a 69.45% saccharification efficiency of crude enzyme. Finally, to alleviate the carbon catabolite repression (CCR) and enhance butanol production, the coculture system of Clostridium beijerinckii and Saccharomyces cerevisiae was applied. Compared to monoculture of C. beijerinckii F-6, more sugars were consumed, especially the reduction rate of xylose reached to 81.87%, 32.99% higher than that in monoculture system. With more substrate facilitied into metabolism, the butanol concentration reached to 10.62 g/L corresponding to 0.28 g/g substrate, 115.38% higher than that in monoculture system. Overall, this integrated process was a low-energy consumption and efficient method for butanol production from rice straw.

Butanol production from cellulosic material by anaerobic co-culture of white-rot fungus Phlebia and bacterium Clostridium in consolidated bioprocessing

Butanol production from lignocelluloses is desirable. Unfortunately, the known wild-types of butanol fermenting Clostridium bacteria are not capable of delignification and saccharification. Here we analyzed butanol production from cellulosic material using anaerobic co-culture of C. saccharoperbutylacetonicum with the white-rot fungus Phlebia sp. MG-60-P2. In consolidated bioprocessing, the co-culture synergistically produced butanol and enhanced saccharification. Knockout of the pyruvate decarboxylase gene from MG-60-P2 to produce transformant line KO77 led to inhibition of ethanol fermentation and high accumulation of saccharified cellobiose and glucose from cellulose. In co-culture of KO77 with C. saccharoperbutylacetonicum, enhanced butanol production was observed (3.2 g/L, compared with 2.5 g/L in co-culture of MG-60-P2 and C. saccharoperbutylacetonicum). We believe this is the first application of co-culture between white-rot fungus and Clostridium to produce butanol from cellulose; butanol production from lignocellulose by co-culture of C. saccharoperbutylacetonicum with Phlebia sp. MG-60-P2 and its transformant should be pursued.

Effects of biochar on ethanol-type and butyrate-type fermentative hydrogen productions

Low hydrogen yield was the bottleneck of dark fermentative hydrogen production. To solve this problem, the effects of rice straw-derived biochar on hydrogen production was investigated in different fermentation types. Ethanol-type and butyrate-type fermentations, two dominant types of dark fermentation, were carried out in batch fermentations with different concentrations of biochar. The results revealed that 3 g/L was the best concentration for both types of fermentations. Hydrogen production increased by 118.4% and 79.6% in ethanol-type and butyrate-type fermentations, respectively. The maximal hydrogen yields of ethanol-type and butyrate-type fermentations were 1.34 and 2.36 mol/mol-glucose, respectively. The addition of biochar buffered the broth pH, lowered the redox potential, and released mineral nutrients. The porosity of biochar boosted cell immobilization and thus improved the H2 productivity. This study demonstrated the enhancement effect of biochar on ethanol- and butyrate-type fermentative hydrogen productions, and enhanced the understanding of the functional mechanisms of biochar.

Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia

The global energy crisis and limited supply of petroleum fuels have rekindled the interest in utilizing a sustainable biomass to produce biofuel. Butanol, an advanced biofuel, is a superior renewable resource as it has a high energy content and is less hygroscopic than other candidates. At present, the biobutanol route, employing acetone-butanol-ethanol (ABE) fermentation in Clostridium species, is not economically competitive due to the high cost of feedstocks, low butanol titer, and product inhibition. Based on an analysis of the physiological characteristics of solventogenic clostridia, current advances that enhance ABE fermentation from strain improvement to product separation were systematically reviewed, focusing on: (1) elucidating the metabolic pathway and regulation mechanism of butanol synthesis; (2) enhancing cellular performance and robustness through metabolic engineering, and (3) optimizing the process of ABE fermentation. Finally, perspectives on engineering and exploiting clostridia as cell factories to efficiently produce various chemicals and materials are also discussed.

Enhanced butanol-hydrogen coproduction by Clostridium beijerinckii with biochar as cell's carrier

In this study, the effects of biochar on the fermentation performance of butanol-hydrogen coproduction by Clostridium beijerinckii F-6 were investigated. Results showed that the biochar with rich porous and graphitized structure can significantly promote the coproduction of butanol and hydrogen. The productivity of butanol and hydrogen reached 0.148 g/L/h and 0.299 mmol/L/h with biochar addition which were 20.23% and 48.76% higher than that in control without biochar addition, respectively. Moreover, the whole energy conversion efficiency calculated based on the heat value showed increment from 43.69% to 51.75% with biochar addition. Combined analysis of organic acids accumulation and oxidation-reduction potential fluctuation proved that biochar can regulate reducing power during fermentation and accelerate the conversion of acid phase to solvent phase. Scanning electron microscope images showed that biochar acted as carriers for cells absorption. Confirmation experiment further proved that biochar enhanced the butanol tolerant ability of Clostridium beijerinckii F-6.

Enhanced Biobutanol Production in Folic Acid-Induced Medium by Using Clostridium acetobutylicum NRRL B-527

The conventional acetone-butanol-ethanol fermentation process suffers from several key hurdles viz. low solvent titer, insufficient yield and productivity, and solvent intolerance which largely affect butanol commercialization. To counteract these issues, the effect of stimulator, namely, folic acid was investigated in the present study to improve butanol titer. Folic acid is involved in biosynthesis of a diverse range of cellular components, which subsequently alter the amino acid balance. Therefore, different concentrations of folic acid were screened, and 10 mg/L supplementation resulted in a maximum butanol production of 10.78 ± 0.09 g/L with total solvents of 18.91 ± 0.21 g/L. Folic acid addition at different time intervals was also optimized to get additional improvements in final butanol concentration. Overall, folic acid supplementation resulted in two-fold increase in butanol concentration and thus could be considered as a promising strategy to enhance solvent titers.