Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum

Power-to-vitamins: producing folate (vitamin B9) from renewable electric power and CO2 with a microbial protein system

We recently proposed a two-stage Power-to-Protein technology to produce microbial protein from renewable electric power and CO2. Two stages were operated in series: Clostridium ljungdahlii in Stage A to reduce CO2 with H2 into acetate, and Saccharomyces cerevisiae in Stage B to utilize O2 and produce microbial protein from acetate. Renewable energy can be used to power water electrolysis to produce H2 and O2. A drawback of Stage A was the need for continuous vitamin supplementation. In this study, by using the more robust thermophilic acetogen Thermoanaerobacter kivui instead of C. ljungdahlii, vitamin supplementation was no longer needed. Additionally, S. cerevisiae produced folate when grown with acetate as a sole carbon source, achieving a total folate concentration of 6.7 mg per 100 g biomass with an average biomass concentration of 3 g l-1. The developed Power-to-Vitamin system enables folate production from renewable power and CO2 with zero or negative net-carbon emissions.

Engineered acetogenic bacteria as microbial cell factory for diversified biochemicals

Acetogenic bacteria (acetogens) are a class of microorganisms with conserved Wood-Ljungdahl pathway that can utilize CO and CO2/H2 as carbon source for autotrophic growth and convert these substrates to acetate and ethanol. Acetogens have great potential for the sustainable production of biofuels and bulk biochemicals using C1 gases (CO and CO2) from industrial syngas and waste gases, which play an important role in achieving carbon neutrality. In recent years, with the development and improvement of gene editing methods, the metabolic engineering of acetogens is making rapid progress. With introduction of heterogeneous metabolic pathways, acetogens can improve the production capacity of native products or obtain the ability to synthesize non-native products. This paper reviews the recent application of metabolic engineering in acetogens. In addition, the challenges of metabolic engineering in acetogens are indicated, and strategies to address these challenges are also discussed.

Optimization of CO fermentation by Clostridium carboxidivorans in batch reactors: Effects of the medium composition

OBJECTIVES

The objective of this study was to investigate the effects of medium composition on CO fermentation by Clostridium carboxidivorans. The focus was to reduce the medium cost preserving acceptable levels of solvent production.

METHODS

Yeast extract (YE) concentration was set in the range of 0-3 g/L. Different reducing agents were investigated, including cysteine-HCl 0.6 g/L, pure cysteine 0.6 g/L, sodium sulphide (Na2S) 0.6 g/L, cysteine-sodium sulphide 0.6 g/L and cysteine-sodium sulphide 0.72 g/L. The concentration of the metal solution was decreased down to 25 % of the standard value. Fermentation tests were also carried out with and without tungsten or selenium.

RESULTS

The results demonstrated that under optimized conditions, namely yeast extract (YE) concentration set at 1 g/L, pure cysteine as the reducing agent and trace metal concentration reduced to 75 % of the standard value, reasonable solvent production was achieved in less than 150 h. Under these operating conditions, the production levels were found to be 1.39 g/L of ethanol and 0.27 g/L of butanol. Furthermore, the study revealed that selenium was not necessary for C. carboxidivorans fermentation, whereas the presence of tungsten played a crucial role in both cell growth and solvent production.

CONCLUSIONS

The optimization of the medium composition in CO fermentation by Clostridium carboxidivorans is crucial for cost-effective solvent production. Tuning the yeast extract (YE) concentration, using pure cysteine as the reducing agent and reducing trace metal concentration contribute to reasonable solvent production within a relatively short fermentation period. Tungsten is essential for cell growth and solvent production, while selenium is not required.

Development of a genetic engineering toolbox for syngas-utilizing acetogen Clostridium sp. AWRP

BACKGROUND

Clostridium sp. AWRP (AWRP) is a novel acetogenic bacterium isolated under high partial pressure of carbon monoxide (CO) and can be one of promising candidates for alcohol production from carbon oxides. Compared to model strains such as C. ljungdahlii and C. autoethanogenum, however, genetic manipulation of AWRP has not been established, preventing studies on its physiological characteristics and metabolic engineering.

RESULTS

We were able to demonstrate the genetic domestication of AWRP, including transformation of shuttle plasmids, promoter characterization, and genome editing. From the conjugation experiment with E. coli S17-1, among the four replicons tested (pCB102, pAMβ1, pIP404, and pIM13), three replicated in AWRP but pCB102 was the only one that could be transferred by electroporation. DNA methylation in E. coli significantly influenced transformation efficiencies in AWRP: the highest transformation efficiencies (102-103 CFU/µg) were achieved with unmethylated plasmid DNA. Determination of strengths of several clostridial promoters enabled the establishment of a CRISPR/Cas12a genome editing system based on Acidaminococcus sp. BV3L6 cas12a gene; interestingly, the commonly used CRISPR/Cas9 system did not work in AWRP, although it expressed the weakest promoter (C. acetobutylicum Pptb) tested. This system was successfully employed for the single gene deletion (xylB and pyrE) and double deletion of two prophage gene clusters.

CONCLUSIONS

The presented genome editing system allowed us to achieve several genome manipulations, including double deletion of two large prophage groups. The genetic toolbox developed in this study will offer a chance for deeper studies on Clostridium sp. AWRP for syngas fermentation and carbon dioxide (CO2) sequestration.

Identification of Bacteria Associated with Tobacco Mildew and Tobacco-Specific Nitrosamines During Tobacco Fermentation

Tobacco mildew and tobacco-specific nitrosamines (TSNAs) affect the quality of tobacco products during fermentation. Microbes are thought to play key roles in the development of specific properties of fermented tobacco; however, little is known about the bacteria involved in the fermentation process. This study aims to identify key microbes related to mildew and TSNA formation. Tobacco was fermented at 25 °C, 35 °C, and 45 °C for 2, 4, and 6 weeks, with unfermented samples used as controls. Our preliminary exploration found that TSNAs content elevated with the increase of temperature and period, and mildew was easy to occur at low temperature with short period. Hence, samples were divided into three groups: the temperature gradient group (25 °C, 35 °C, and 45 °C for 6 weeks); the low-temperature group (control, 25 °C for 2, 4, and 6 weeks); and the high-temperature group (control, 45 °C for 2, 4, and 6 weeks). After collecting fermented tobacco leaves, 16S rRNA gene sequencing was used to explore the structure and dynamic changes of bacterial community during fermentation. Methylobacterium and Deinococcus were shared between the temperature gradient and high-temperature groups and showed a linear downward trend; these might play a role in the production of TSNAs. Massilia, Ruminiclostridium, and Cellulosilyticum species increased with prolonged fermentation time in the low-temperature group; this might be associated with tobacco mildew. In summary, the microbial diversity of fermented tobacco was explored under different conditions. These findings might provide data and material support to improve the quality of fermented tobacco products; however, further omics based studies are warranted to analysis the gene and protein expression patter in the identified bacteria.

Developing a genetic engineering method for Acetobacterium wieringae to expand one-carbon valorization pathways

BACKGROUND

Developing new bioprocesses to produce chemicals and fuels with reduced production costs will greatly facilitate the replacement of fossil-based raw materials. In most fermentation bioprocesses, the feedstock usually represents the highest cost, which becomes the target for cost reduction. Additionally, the biorefinery concept advocates revenue growth from the production of several compounds using the same feedstock. Taken together, the production of bio commodities from low-cost gas streams containing CO, CO₂, and H₂, obtained from the gasification of any carbon-containing waste streams or off-gases from heavy industry (steel mills, processing plants, or refineries), embodies an opportunity for affordable and renewable chemical production. To achieve this, by studying non-model autotrophic acetogens, current limitations concerning low growth rates, toxicity by gas streams, and low productivity may be overcome. The Acetobacterium wieringae strain JM is a novel autotrophic acetogen that is capable of producing acetate and ethanol. It exhibits faster growth rates on various gaseous compounds, including carbon monoxide, compared to other Acetobacterium species, making it potentially useful for industrial applications. The species A. wieringae has not been genetically modified, therefore developing a genetic engineering method is important for expanding its product portfolio from gas fermentation and overall improving the characteristics of this acetogen for industrial demands.

RESULTS

This work reports the development and optimization of an electrotransformation protocol for A. wieringae strain JM, which can also be used in A. wieringae DSM 1911, and A. woodii DSM 1030. We also show the functionality of the thiamphenicol resistance marker, catP, and the functionality of the origins of replication pBP1, pCB102, pCD6, and pIM13 in all tested Acetobacterium strains, with transformation efficiencies of up to 2.0 × 10³ CFU/μg_DNA. Key factors affecting electrotransformation efficiency include OD₆₀₀ of cell harvesting, pH of resuspension buffer, the field strength of the electric pulse, and plasmid amount. Using this method, the acetone production operon from Clostridium acetobutylicum was efficiently introduced in all tested Acetobacterium spp., leading to non-native biochemical acetone production via plasmid-based expression.

CONCLUSIONS

A. wieringae can be electrotransformed at high efficiency using different plasmids with different replication origins. The electrotransformation procedure and tools reported here unlock the genetic and metabolic manipulation of the biotechnologically relevant A. wieringae strains. For the first time, non-native acetone production is shown in A. wieringae.

Enabling Ethanologenesis in Moorella thermoacetica through Construction of a Replicating Shuttle Vector

Replicating plasmid shuttle vectors are key tools for efficient genetic and metabolic engineering applications, allowing the development of sustainable bioprocesses using non-model organisms with unique metabolic capabilities. To date, very limited genetic manipulation has been achieved in the thermophilic acetogen, Moorella thermoacetica, partly due to the lack of suitable shuttle vectors. However, M. thermoacetica has considerable potential as an industrial chassis organism, which can only be unlocked if reliable and effective genetic tools are in place. This study reports the construction of a replicating shuttle vector for M. thermoacetica through the identification and implementation of a compatible Gram-positive replicon to allow plasmid maintenance within the host. Although characterisation of plasmid behaviour proved difficult, the designed shuttle vector was subsequently applied for ethanologenesis, i.e., ethanol production in this organism. The non-native ethanologenesis in M. thermoacetica was achieved via plasmid-borne overexpression of the native aldh gene and heterologous expression of Clostridium autoethanogenum adhE1 gene. This result demonstrates the importance of the developed replicating plasmid vector for genetic and metabolic engineering efforts in industrially important M. thermoacetica.

Design, Analysis, and Implementation of a Novel Biochemical Pathway for Ethylene Glycol Production in Clostridium autoethanogenum

The platform chemical ethylene glycol (EG) is used to manufacture various commodity chemicals of industrial importance, but largely remains synthesized from fossil fuels. Although several novel metabolic pathways have been reported for its bioproduction in model organisms, none has been reported for gas-fermenting, non-model acetogenic chassis organisms. Here, we describe a novel, synthetic biochemical pathway to convert acetate into EG in the industrially important gas-fermenting acetogen,Clostridium autoethanogenum. We not only developed a computational workflow to design and analyze hundreds of novel biochemical pathways for EG production but also demonstrated a successful pathway construction in the chosen host. The EG production was achieved using a two-plasmid system to bypass unfeasible expression levels and potential toxic enzymatic interactions. Although only a yield of 0.029 g EG/g fructose was achieved and therefore requiring further strain engineering efforts to optimize the designed strain, this work demonstrates an important proof-of-concept approach to computationally design and experimentally implement fully synthetic metabolic pathways in a metabolically highly specific, non-model host organism.

Engineering Acetogenic Bacteria for Efficient One-Carbon Utilization

C1 gases, including carbon dioxide (CO₂) and carbon monoxide (CO), are major contributors to climate crisis. Numerous studies have been conducted to fix and recycle C1 gases in order to solve this problem. Among them, the use of microorganisms as biocatalysts to convert C1 gases to value-added chemicals is a promising solution. Acetogenic bacteria (acetogens) have received attention as high-potential biocatalysts owing to their conserved Wood–Ljungdahl (WL) pathway, which fixes not only CO₂ but also CO. Although some metabolites have been produced via C1 gas fermentation on an industrial scale, the conversion of C1 gases to produce various biochemicals by engineering acetogens has been limited. The energy limitation of acetogens is one of the challenges to overcome, as their metabolism operates at a thermodynamic limit, and the low solubility of gaseous substrates results in a limited supply of cellular energy. This review provides strategies for developing efficient platform strains for C1 gas conversion, focusing on engineering the WL pathway. Supplying liquid C1 substrates, which can be obtained from CO₂, or electricity is introduced as a strategy to overcome the energy limitation. Future prospective approaches on engineering acetogens based on systems and synthetic biology approaches are also discussed.

Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences

RNA-guided nucleases from CRISPR-Cas systems expand opportunities for precise, targeted genome modification. Endogenous CRISPR-Cas systems in many prokaryotes are attractive to circumvent expression, functionality, and unintended activity hurdles posed by heterologous CRISPR-Cas effectors. However, each CRISPR-Cas system recognizes a unique set of protospacer adjacent motifs (PAMs), which requires identification by extensive screening of randomized DNA libraries. This challenge hinders development of endogenous CRISPR-Cas systems, especially those based on multi-protein effectors and in organisms that are slow-growing or have transformation idiosyncrasies. To address this challenge, we present Spacer2PAM, an easy-to-use, easy-to-interpret R package built to predict and guide experimental determination of functional PAM sequences for any CRISPR-Cas system given its corresponding CRISPR array as input. Spacer2PAM can be used in a 'Quick' method to generate a single PAM prediction or in a 'Comprehensive' method to inform targeted PAM libraries small enough to screen in difficult to transform organisms. We demonstrate Spacer2PAM by predicting PAM sequences for industrially relevant organisms and experimentally identifying seven PAM sequences that mediate interference from the Spacer2PAM-informed PAM library for the type I-B CRISPR-Cas system from Clostridium autoethanogenum. We anticipate that Spacer2PAM will facilitate the use of endogenous CRISPR-Cas systems for industrial biotechnology and synthetic biology.

Agr Quorum Sensing influences the Wood-Ljungdahl pathway in Clostridium autoethanogenum

Acetogenic bacteria are capable of fermenting CO2 and carbon monoxide containing waste-gases into a range of platform chemicals and fuels. Despite major advances in genetic engineering and improving these biocatalysts, several important physiological functions remain elusive. Among these is quorum sensing, a bacterial communication mechanism known to coordinate gene expression in response to cell population density. Two putative agr systems have been identified in the genome of Clostridium autoethanogenum suggesting bacterial communication via autoinducing signal molecules. Signal molecule-encoding agrD1 and agrD2 genes were targeted for in-frame deletion. During heterotrophic growth on fructose as a carbon and energy source, single deletions of either gene did not produce an observable phenotype. However, when both genes were simultaneously inactivated, final product concentrations in the double mutant shifted to a 1.5:1 ratio of ethanol:acetate, compared to a 0.2:1 ratio observed in the wild type control, making ethanol the dominant fermentation product. Moreover, CO2 re-assimilation was also notably reduced in both hetero- and autotrophic growth conditions. These findings were supported through comparative proteomics, which showed lower expression of carbon monoxide dehydrogenase, formate dehydrogenase A and hydrogenases in the ∆agrD1∆agrD2 double mutant, but higher levels of putative alcohol and aldehyde dehydrogenases and bacterial micro-compartment proteins. These findings suggest that Agr quorum sensing, and by inference, cell density play a role in carbon resource management and use of the Wood-Ljungdahl pathway as an electron sink.

Multiple analysis of root exudates and microbiome in rice (Oryza sativa) under low P conditions

Plants release various metabolites from roots and root exudates contribute to differences in stress tolerance among plant species. Plant and soil microbes have complex interactions that are affected by biotic and abiotic factors. The purpose of this study was to examine the differences in metabolites in root exudates of rice (Oryza sativa) cultivars and their correlation with bacterial populations in the rhizosphere. Two rice cultivars (O. sativa cv. Akamai and O. sativa cv. Koshihikari) were grown in soils fertilized with 0 g P kg^-1 (- P) or 4.8 g P kg^-1 (+ P). Root exudates and root-attached soil were collected at 13 and 20 days after transplanting (DAT) and their metabolites and bacterial community structure were determined. The exudation of proline, serine, threonine, valine and 4-coumarate were increased under low P conditions in both cultivars. There was a positive correlation between the concentration of pantothenate in root exudates and the representation of members of the genera Clostridium and Sporosarcina, which were negatively correlated with root dry weight. Gracilibacter, Opitutus, Pelotomaculum, Phenylobacterium and Oxobacter were positively correlated with root dry weight and presence of allantoin, 2-aminobtyrate and GlcNac. This study provides new information about the response of plants and rhizosphere soil bacteria to low P conditions.

Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation

Owing to rising levels of greenhouse gases in our atmosphere and oceans, climate change poses significant environmental, economic, and social challenges globally. Technologies that enable carbon capture and conversion of greenhouse gases into useful products will help mitigate climate change by enabling a new circular carbon economy. Gas fermentation usingcarbon-fixing microorganisms offers an economically viable and scalable solution with unique feedstock and product flexibility that has been commercialized recently. We review the state of the art of gas fermentation and discuss opportunities to accelerate future development and rollout. We discuss the current commercial process for conversion of waste gases to ethanol, including the underlying biology, challenges in process scale-up, and progress on genetic tool development and metabolic engineering to expand the product spectrum. We emphasize key enabling technologies to accelerate strain development for acetogens and other nonmodel organisms.

Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms

Unabated mining and utilisation of petroleum and petroleum resources and their conversion to essential fuels and chemicals have drastic environmental consequences, contributing to global warming and climate change. In addition, fossil fuels are finite resources, with a fast-approaching shortage. Accordingly, research efforts are increasingly focusing on developing sustainable alternatives for chemicals and fuels production. In this context, bioprocesses, relying on microorganisms, have gained particular interest. For example, acetogens use the Wood-Ljungdahl pathway to grow on single carbon C1-gases (CO2 and CO) as their sole carbon source and produce valuable products such as acetate or ethanol. These autotrophs can, therefore, be exploited for large-scale fermentation processes to produce industrially relevant chemicals from abundant greenhouse gases. In addition, genetic tools have recently been developed to improve these chassis organisms through synthetic biology approaches. This review will focus on the challenges of genetically and metabolically modifying acetogens. It will first discuss the physical and biochemical obstacles complicating successful DNA transfer in these organisms. Current genetic tools developed for several acetogens, crucial for strain engineering to consolidate and expand their catalogue of products, will then be described. Recent tool applications for metabolic engineering purposes to allow redirection of metabolic fluxes or production of non-native compounds will lastly be covered.

Online monitoring applying the anaerobic respiratory monitoring system reveals iron(II) limitation in YTF medium for Clostridium ljungdahlii

Online monitoring of microbial cultures is an effective approach for studying both aerobic and anaerobic microorganisms. Especially in small-scale cultivations, several parallel online monitored experiments can generate a detailed understanding of the cultivation, compared to a situation where a few data points are generated from time course sampling and offline analysis. However, the availability of small-scale online monitoring devices for acetogenic organisms is limited. In this study, the previously reported anaerobic Respiration Activity MOnitoring System (anaRAMOS) device was adapted for online monitoring of Clostridium ljungdahlii (C. ljungdahlii) cultures with fructose as the carbon source. The anaRAMOS was applied to identify conversion of different carbon sources present in commonly used YTF medium. An iron(II) deficiency was discovered in this medium for C. ljungdahlii. Addition of iron(II) to the YTF medium reduced the cultivation time and increased biomass yield of C. ljungdahlii cultures by 50% and 40%, respectively. The measurement of the carbon dioxide transfer rate was used to calculated the iron(II) contained in complex components. By demonstrating the application of the anaRAMOS device for medium optimization, it is proven that the described online monitoring device has potential for use in process development.

Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals

Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.

Evaluation of Media Components and Process Parameters in a Sensitive and Robust Fed-Batch Syngas Fermentation System with Clostridium ljungdahlii

The fermentation of synthesis gas, or syngas, by acetogenic bacteria can help in transitioning from a fossil-fuel-based to a renewable bioeconomy. The main fermentation products of Clostridium ljungdahlii, one of such microorganisms, are acetate and ethanol. A sensitive, robust and reproducible system was established for C. ljungdahlii syngas fermentation, and several process parameters and medium components (pH, gas flow, cysteine and yeast extract) were investigated to assess its impact on the fermentation outcomes, as well as real time gas consumption. Moreover, a closed carbon balance could be achieved with the data obtained. This system is a valuable tool to detect changes in the behavior of the culture. It can be applied for the screening of strains, gas compositions or media components, for a better understanding of the physiology and metabolic regulation of acetogenic bacteria. Here, it was shown that neither yeast extract nor cysteine was a limiting factor for cell growth since their supplementation did not have a noticeable impact on product formation or overall gas consumption. By combining the lowering of both the pH and the gas flow after 24 h, the highest ethanol to acetate ratio was achieved, but with the caveat of lower productivity.

Effect of pH, yeast extract and inorganic carbon on chain elongation for hexanoic acid production

Several anaerobic bioconversion technologies produce short chain volatile fatty acids and sometimes ethanol, which can together be elongated to hexanoic acid (C6 acid) by Clostridium kluyveri in a secondary fermentation process. Initiatives are needed to further optimize the process. Therefore, five strategies were tested aiming at elucidating their influence on hexanoic acid production from mixtures of acetic acid, butyric acid and ethanol. pH-regulated bioreactors, maintained at pH 7.5, 6.8 or 6.4 led to maximum C6 acid concentrations of, respectively, 19.4, 18.3 and 13.3 g L^-1. At pH 6.8, yeast extract omission resulted in a decrease of the hexanoic acid concentration to 12.0 g L^-1 while the addition of an inorganic carbon source, such as bicarbonate, for pH control, increased the C6 acid concentration up to 21.4 g L^-1. This research provides guidelines for efficient improved production of hexanoic acid by pure cultures of C. kluyveri, contributing to the state of art.