From pre-culture to solvent: current trends in Clostridium acetobutylicum cultivation

The biological production of butanol via ABE (acetone-butanol-ethanol) fermentation using Clostridium acetobutylicum has a storied history of over 100 years, initially driven by the demand for synthetic rubber during World War I and later for industrial applications. Despite its decline due to the rise of petrochemical alternatives, renewed interest has emerged due to the global shift towards sustainable energy sources and rising oil prices. This review highlights the challenges in the cultivation process of C. acetobutylicum, such as strain degeneration, solvent toxicity, and substrate costs, and presents recent advancements aimed at overcoming these issues. Detailed documentation of the entire cultivation process including cell conservation, pre-culture, and main culture is seen as a fundamental step to facilitate further progress in research. Key strategies to improve production efficiency were identified as controlling pH to facilitate the metabolic shift from acidogenesis to solventogenesis, employing in situ product removal techniques, and advancing metabolic engineering for improved solvent tolerance of C. acetobutylicum. Furthermore, the use of renewable resources, particularly lignocellulosic biomass, positions ABE fermentation as a viable solution for sustainable solvent production. By focusing on innovative research avenues, including co-cultivation and bioelectrochemical systems, the potential for C. acetobutylicum to contribute significantly to a bio-based economy can be realized. KEY POINTS: • Historical significance and revival of ABE fermentation with Clostridium acetobutylicum • Current challenges and innovative solutions in cultivating C. acetobutylicum • New avenues for enhancing productivity and sustainability.

New insights into the influence of pre-culture on robust solvent production of C. acetobutylicum

Clostridia are known for their solvent production, especially the production of butanol. Concerning the projected depletion of fossil fuels, this is of great interest. The cultivation of clostridia is known to be challenging, and it is difficult to achieve reproducible results and robust processes. However, existing publications usually concentrate on the cultivation conditions of the main culture. In this paper, the influence of cryo-conservation and pre-culture on growth and solvent production in the resulting main cultivation are examined. A protocol was developed that leads to reproducible cultivations of Clostridium acetobutylicum. Detailed investigation of the cell conservation in cryo-cultures ensured reliable cell growth in the pre-culture. Moreover, a reason for the acid crash in the main culture was found, based on the cultivation conditions of the pre-culture. The critical parameter to avoid the acid crash and accomplish the shift to the solventogenesis of clostridia is the metabolic phase in which the cells of the pre-culture were at the time of inoculation of the main culture; this depends on the cultivation time of the pre-culture. Using cells from the exponential growth phase to inoculate the main culture leads to an acid crash. To achieve the solventogenic phase with butanol production, the inoculum should consist of older cells which are in the stationary growth phase. Considering these parameters, which affect the entire cultivation process, reproducible results and reliable solvent production are ensured. KEY POINTS: • Both cryo- and pre-culture strongly impact the cultivation of C. acetobutylicum • Cultivation conditions of the pre-culture are a reason for the acid crash • Inoculum from cells in stationary growth phase ensures shift to solventogenesis.

Dark-fermentative hydrogen production from synthetic lignocellulose hydrolysate by a mixed bacterial culture: The relationship between hydraulic retention time and pH conditions

This study assessed the effect of hydraulic retention time (HRT) ranging from 24 to 3 h on continuous dark-fermentative H₂ production in four bioreactors operated at pH 5.0, 5.5, 6.0 and 6.5. A mixture of cellobiose, xylose and arabinose was used as the substrate. The highest hydrogen production rate between HRTs of 24 and 12 h was observed at pH 6.5, while at HRT below 12 h at pH 6.0. At a HRT of 3 h it reached 11.4 L H₂/L-d. Thus, the optimum pH for H₂ production depends on the HRT. The highest sugar utilization was obtained at pH 6.0 and 6.5 and decreased in the following order: cellobiose > xylose > arabinose. The pH conditions, in contrast to HRT, were found to have a significant influence on the bacterial composition. Low diversity in bacterial culture dominated by the Clostridium genus allows for stable and high H₂ production performance.

Bacillus sp. isolated from banana waste and analysis of metabolic pathways in acidogenic systems in hydrogen production

The autochthonous bacterial strain was isolated from banana waste (BW) for hydrogen production and organic acids from different pure substrates and BW. The potential production of H₂ and metabolic pathways were analyzed at pH 7.0 at 37 °C. Facultative anaerobic bacterium similar to Bacillus sp. was identified, with generation time (Tg) and growth rate (μ) of 0.43 h and 1.60 h^-1, respectively, from glucose. The hydrogen production (P) using pure substrates was observed between 10.81 mmol.L^-1 and 17.75 mmol.L^-1 from xylose and maltose, respectively. The biggest and smallest hydrogen P of 18.77 mmol.L^-1 and 1.72 mmol.L^-1, were obtained with 3.5 and 0.5 g.L^-1 of cellobiose, respectively. The highest hydrogen yield (126.93 mL.g^-1_{carbohydrates added}) was obtained with 2 g.L^-1 cellobiose. In the assay using banana waste (5 g.L^-1) the maximum P and yield (YH₂) of 31.7 mmol.L^-1 and 94.66 mL H₂ g^-1_{carbohydrates added}, was obtained respectively. The main metabolic pathway of hydrogen production by Bacillus sp. RM1 from banana waste was acetic-butyric acid of 487.69 g.L^-1 and 535.88 g.L^-1, respectively. The accessibility of various carbon sources by Bacillus sp. RM1 in fermentation can benefit the hydrogen production from complex organic substrates in the bioaugmentation process.

Solvent production from xylose

Xylose is the second most abundant sugar derived from lignocellulose; it is considered less desirable than glucose for fermentation, and strategies that specifically increase xylose utilization in wild type or engineered cells are goals for biofuel production. Issues arise with xylose utilization because of carbohydrate catabolite repression, which is the preferential utilization of glucose relative to xylose in fermentations with both pure and mixed cultures. Taken together the low substrate utilization rates and solvent yields with xylose compared to glucose, many industrial fermentations ignore the xylolytic portion of the reaction in lieu of methods to maintain high glucose. This is shortsighted given the massive potential for xylose generation from a number of sustainable biomass feedstocks, based on utilization of the hemicellulose fraction(s) that enter pretreatment. A number of strategies have been developed in recent years to address xylose utilization and solvent production from xylose in systems with just xylose, or in systems with mixtures of glucose plus xylose, which are more typical of pretreated lignocellulose. The approaches vary in terms of complexity, stability, and ease of introduction to existing fermentation infrastructure (i.e., so-called drop-in fermentation strategies). Some approaches can be considered traditional engineering approaches (e.g., change the reaction conditions), while others are more subtle cellular approaches to eliminate the impacts of catabolite repression. Finally, genetic engineering has been used to increase xylose utilization, although this can be considered a relatively nascent approach compared to manipulations completed to date for glucose utilization.

Evidence of mixotrophic carbon-capture by n-butanol-producer Clostridium beijerinckii

Recent efforts to combat increasing greenhouse gas emissions include their capture into advanced biofuels, such as butanol. Traditionally, biobutanol research has been centered solely on its generation from sugars. Our results show partial re-assimilation of CO₂ and H₂ by n-butanol-producer C. beijerinckii. This was detected as synchronous CO₂/H₂ oscillations by direct (real-time) monitoring of their fermentation gasses. Additional functional analysis demonstrated increased total carbon recovery above heterotrophic values associated to mixotrophic assimilation of synthesis gas (H₂, CO₂ and CO). This was further confirmed using ¹³C-Tracer experiments feeding ¹³CO₂ and measuring the resulting labeled products. Genome- and transcriptome-wide analysis revealed transcription of key C-1 capture and additional energy conservation genes, including partial Wood-Ljungdahl and complete reversed pyruvate ferredoxin oxidoreductase / pyruvate-formate-lyase-dependent (rPFOR/Pfl) pathways. Therefore, this report provides direct genetic and physiological evidences of mixotrophic inorganic carbon-capture by C. beijerinckii.

The pangenome of the genus Clostridium

The pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species is presented; some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair. The GS-GOGAT may represent the central pathway for generating organic nitrogen from inorganic nitrogen sources. Glycerol and glucose metabolism genes are well represented in the core genome together with a set of energy conservation systems. A metabolic network comprising proteins/enzymes, RNAs and metabolites, whose topological structure is a non-random and scale-free network with hierarchically structured modules was built. These modules shed light on the interactions between RNAs, proteins and metabolites, revealing biological features of transcription and translation, cell wall biosynthesis, C1 metabolism and N metabolism. Network analysis identified four nodes that function as hubs and bottlenecks, namely, coenzyme A, HPr kinases, S-adenosylmethionine and the ribonuclease P-protein, suggesting pivotal roles for them in Clostridium.

Industrial production of acetone and butanol by fermentation-100 years later

Microbial production of acetone and butanol was one of the first large-scale industrial fermentation processes of global importance. During the first part of the 20th century, it was indeed the second largest fermentation process, superseded in importance only by the ethanol fermentation. After a rapid decline after the 1950s, acetone-butanol-ethanol (ABE) fermentation has recently gained renewed interest in the context of biorefinery approaches for the production of fuels and chemicals from renewable resources. The availability of new methods and knowledge opens many new doors for industrial microbiology, and a comprehensive view on this process is worthwhile due to the new interest. This thematic issue of FEMS Microbiology Letters, dedicated to the 100th anniversary of the first industrial exploitation of Chaim Weizmann's ABE fermentation process, covers the main aspects of old and new developments, thereby outlining a model development in biotechnology. All major aspects of industrial microbiology are exemplified by this single process. This includes new technologies, such as the latest developments in metabolic engineering, the exploitation of biodiversity and discoveries of new regulatory systems such as for microbial stress tolerance, as well as technological aspects, such as bio- and down-stream processing.

Industrial production of acetone and butanol by fermentation—100 years later.