Gas Fermentation-A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks

Methane production from syngas using a trickle-bed reactor setup

Syngas from gasification of waste biomass is a mixture of carbon monoxide (CO), carbon dioxide (CO₂), and hydrogen (H₂), which can be utilized for the synthesis of biofuels such as methane (CH₄). The aim of the study research work was to demonstrate how syngas could be methanated and upgraded to natural gas quality (biomethane) in a fed-batch trickle-bed reactor system using either manure - (AD-M) or sludge-based (AD-WW) inoculum as microbial basis. The methanated syngas had a high concentration of CO₂ and did not fulfil the criteria for natural gas quality biomethane. Further upgrading of syngas to biomethane could be achieved simultaneously in the same reactors by addition of exogenous H_2, resulting in CH₄ concentrations up to 91.0 ± 3.5% (AD-WW) and 95.3 ± 1.0% (AD-M). Microbial analysis indicated that the communities differed between AD-M and AD-WW demonstrating functional redundancy among the microbial communities of different inocula.

Strategies to improve viability of a circular carbon bioeconomy-A techno-economic review of microbial electrosynthesis and gas fermentation

A circular carbon bioeconomy has potential to halt atmospheric accumulation of greenhouse gases causing climate change and sustainably produce chemical, agricultural and fuel products. Here, we report application of a simplified technoeconomic assessment to critically review two approaches in this space - microbial electrosynthesis and gas fermentation. For microbial electrosynthesis, decoupling of surface-dependant abiotic process for electron delivery from volume-dependant biotic carbon fixation, is shown as the only economically viable strategy to scale-up due to comparatively low biofilm electron consumption rate. This is effectively an electrolyser-assisted gas fermentation system. Targeting high-value products, such as protein for human food consumption is one of the few pathways forward for electrolyser-assisted gas fermentation. Alternatively, gas fermentation of reformed biogas presents an interesting and potentially more sustainable implementation pathway to improve economic viability of chemicals. This critical review suggests linking water treatment resource recovery with gas fermentation is attractive for bioplastics and butanol in terms of competitiveness and market demand.

Process Engineering Aspects for the Microbial Conversion of C1 Gases

Industrially applied bioprocesses for the reduction of C1 gases (CO₂ and/or CO) are based in particular on (syn)gas fermentation with acetogenic bacteria and on photobioprocesses with microalgae. In each case, process engineering characteristics of the autotrophic microorganisms are specified and process engineering aspects for improving gas and electron supply are summarized before suitable bioreactor configurations are discussed for the production of organic products under given economic constraints. Additionally, requirements for the purity of C1 gases are summarized briefly. Finally, similarities and differences in microbial CO₂ valorization are depicted comparing gas fermentations with acetogenic bacteria and photobioprocesses with microalgae.

Engineering Cupriavidus necator H16 for the autotrophic production of (R)-1,3-butanediol

Butanediols are widely used in the synthesis of polymers, specialty chemicals and important chemical intermediates. Optically pure R-form of 1,3-butanediol (1,3-BDO) is required for the synthesis of several industrial compounds and as a key intermediate of β-lactam antibiotic production. The (R)-1,3-BDO can only be produced by application of a biocatalytic process. Cupriavidus necator H16 is an established production host for biosynthesis of biodegradable polymer poly-3-hydroxybutryate (PHB) via acetyl-CoA intermediate. Therefore, the utilisation of acetyl-CoA or its upstream precursors offers a promising strategy for engineering biosynthesis of value-added products such as (R)-1,3-BDO in this bacterium. Notably, C. necator H16 is known for its natural capacity to fix carbon dioxide (CO₂) using hydrogen as an electron donor. Here, we report engineering of this facultative lithoautotrophic bacterium for heterotrophic and autotrophic production of (R)-1,3-BDO. Implementation of (R)-3-hydroxybutyraldehyde-CoA- and pyruvate-dependent biosynthetic pathways in combination with abolishing PHB biosynthesis and reducing flux through the tricarboxylic acid cycle enabled to engineer strain, which produced 2.97 g/L of (R)-1,3-BDO and achieved production rate of nearly 0.4 Cmol Cmol⁻¹ h⁻¹ autotrophically. This is first report of (R)-1,3-BDO production from CO₂.

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Engineering of chemolithoautotroph C. necator H16 for (R)-1,3-butanediol production.

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Implementation of (R)-3-hydroxybutyraldehyde-CoA- and pyruvate-dependent pathways for (R)-1,3-butanediol biosynthesis.

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Redirecting carbon flux for (R)-1,3-butanediol biosynthesis.

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Achieved 2.97 g/L of (R)-1,3-butanediol with production rate of nearly 0.4 Cmol/(Cmol h) autotrophically.

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First report of (R)-1,3-butanediol production from carbon dioxide.

Propionate Production from Carbon Monoxide by Synthetic Cocultures of Acetobacterium wieringae and Propionigenic Bacteria

Gas fermentation is a promising way to convert CO-rich gases to chemicals. We studied the use of synthetic cocultures composed of carboxydotrophic and propionigenic bacteria to convert CO to propionate. So far, isolated carboxydotrophs cannot directly ferment CO to propionate, and therefore, this cocultivation approach was investigated. Four distinct synthetic cocultures were constructed, consisting of Acetobacterium wieringae (DSM 1911^T) and Pelobacter propionicus (DSM 2379^T), Ac. wieringae (DSM 1911^T) and Anaerotignum neopropionicum (DSM 3847^T), Ac. wieringae strain JM and P. propionicus (DSM 2379^T), and Ac. wieringae strain JM and An. neopropionicum (DSM 3847^T). Propionate was produced by all the cocultures, with the highest titer (∼24 mM) being measured in the coculture composed of Ac. wieringae strain JM and An. neopropionicum, which also produced isovalerate (∼4 mM), butyrate (∼1 mM), and isobutyrate (0.3 mM). This coculture was further studied using proteogenomics. As expected, enzymes involved in the Wood-Ljungdahl pathway in Ac. wieringae strain JM, which are responsible for the conversion of CO to ethanol and acetate, were detected; the proteome of An. neopropionicum confirmed the conversion of ethanol to propionate via the acrylate pathway. In addition, proteins related to amino acid metabolism and stress response were highly abundant during cocultivation, which raises the hypothesis that amino acids are exchanged by the two microorganisms, accompanied by isovalerate and isobutyrate production. This highlights the importance of explicitly looking at fortuitous microbial interactions during cocultivation to fully understand coculture behavior. IMPORTANCE Syngas fermentation has great potential for the sustainable production of chemicals from wastes (via prior gasification) and flue gases containing CO/CO₂. Research efforts need to be directed toward expanding the product portfolio of gas fermentation, which is currently limited to mainly acetate and ethanol. This study provides the basis for a microbial process to produce propionate from CO using synthetic cocultures composed of acetogenic and propionigenic bacteria and elucidates the metabolic pathways involved. Furthermore, based on proteomics results, we hypothesize that the two bacterial species engage in an interaction that results in amino acid exchange, which subsequently promotes isovalerate and isobutyrate production. These findings provide a new understanding of gas fermentation and a coculturing strategy for expanding the product spectrum of microbial conversion of CO/CO₂.

Growth Enhancement Facilitated by Gaseous CO2 through Heterologous Expression of Reductive Tricarboxylic Acid Cycle Genes in Escherichia coli

The enzymatic mechanisms of carbon fixation by autotrophs, such as the reductive tricarboxylic acid cycle (rTCA), have inspired biotechnological approaches to producing bio-based chemicals directly through CO2. To explore the possibility of constructing an rTCA cycle in Escherichia coli and to investigate their potential for CO2 assimilation, a total of ten genes encoding the key rTCA cycle enzymes, including α-ketoglutarate:ferredoxin oxidoreductase, ATP-dependent citrate lyase, and fumarate reductase/succinate dehydrogenase, were cloned into E. coli. The transgenic E. coli strain exhibited enhanced growth and the ability to assimilate external inorganic carbon with a gaseous CO2 supply. Further experiments conducted in sugar-free medium containing hydrogen as the electron donor and dimethyl sulfoxide (DMSO) as the electron acceptor proved that the strain is able to undergo anaerobic respiration, using CO2 as the major carbon source. The transgenic stain demonstrated CO2-enhanced growth, whereas the genes involved in chemotaxis, flagellar assembly, and acid-resistance were upregulated under the anaerobic respiration. Furthermore, metabolomic analysis demonstrated that the total concentrations of ATP, ADP, and AMP in the transgenic strain were higher than those in the vector control strain and these results coincided with the enhanced growth. Our approach offers a novel strategy to engineer E. coli for assimilating external gaseous CO2.

Addressing the post‐COVID era through engineering biology

Currently, the world is faced with two fundamental issues of great importance, namely climate change and the coronavirus pandemic. These are intimately involved with the need to control climate change and the need to switch from high carbon, unsustainable economies to low carbon economies. Inherent in this approach are the concepts of the bioeconomy and the Green Industrial Revolution. The article addresses both issues, but it, principally, focusses on the development of the bioeconomy. It considers how nations are divided in relation to the use of biotechnology and synthetic biology in terms of their bioeconomy strategies. The article addresses, as a central theme, the nature and role of engineering biology in these developments. Engineering biology is addressed in terms of BioDesign, coupled with high levels of automation (including AI and machine learning) to increase reproducibility and reliability to meet industrial standards. This lends itself to distributed manufacturing of products in a range of fields. Engineering biology is a platform technology that can be applied in a range of sectors. The bioeconomy, as an engine for economic growth is addressed—in terms of moving from oil‐based economies to bio‐based economies—using biomass, for example, using selected lignocellulosic waste as a feedstock.

Dynamic metabolic modelling predicts efficient acetogen-gut bacterium cocultures for CO-to-butyrate conversion

AIMS

While gas-fermenting acetogens have been engineered to secrete non-native metabolites such as butyrate, acetate remains the most thermodynamically favourable product. An alternative to metabolic engineering is to exploit native capabilities for CO-to-acetate conversion by coculturing an acetogen with a second bacterium that provides efficient acetate-butyrate conversion.

METHODS AND RESULTS

We used dynamic metabolic modelling to computationally evaluate the CO-to-butyrate conversion capabilities of candidate coculture systems by exploiting the diversity of human gut bacteria for anaerobic synthesis of butyrate from acetate and ethanol. A preliminary screening procedure based on flux balance analysis was developed to identify 48 gut bacteria which satisfied minimal growth rate and acetate-to-butyrate conversion requirements when cultured on minimal medium containing acetate and a simple sugar not consumed by the paired acetogen. A total of 170 acetogen/gut bacterium/sugar combinations were dynamically simulated for continuous growth using a 70/30 CO/CO₂ feed gas mixture and minimal medium computationally determined for each combination.

CONCLUSIONS

While coculture systems involving the acetogens Eubacterium limosum or Blautia producta yielded low butyrate productivities and CO-to-ethanol conversion had minimal impact on system performance, dynamic simulations predicted a large number of promising coculture designs with Clostridium ljungdahlii or C. autoethanogenum as the CO-to-acetate converter. Pairings with the gut bacterium Clostridium hylemonae or Roseburia hominis were particularly promising due to their ability to generate high butyrate productivities over a range of dilution rates with a variety of sugars. The higher specific acetate secretion rate of C. ljungdahlii proved more beneficial than the elevated growth rate of C. autoethanogenum for coculture butyrate productivity.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study demonstrated that metabolic modelling could provide useful insights into coculture design that can guide future experimental studies. More specifically, our predictions generated several favourable designs, which could serve as the first coculture systems realized experimentally.

Transcriptional control of Clostridium autoethanogenum using CRISPRi

Gas fermentation by Clostridium autoethanogenum is a commercial process for the sustainable biomanufacturing of fuels and valuable chemicals using abundant, low-cost C1 feedstocks (CO and CO₂) from sources such as inedible biomass, unsorted and nonrecyclable municipal solid waste, and industrial emissions. Efforts toward pathway engineering and elucidation of gene function in this microbe have been limited by a lack of genetic tools to control gene expression and arduous genome engineering methods. To increase the pace of progress, here we developed an inducible CRISPR interference (CRISPRi) system for C. autoethanogenum and applied that system toward transcriptional repression of genes with ostensibly crucial functions in metabolism.

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.

Capture and Reuse of Carbon Dioxide (CO2) for a Plastics Circular Economy: A Review

Plastic production has been increasing at enormous rates. Particularly, the socioenvironmental problems resulting from the linear economy model have been widely discussed, especially regarding plastic pieces intended for single use and disposed improperly in the environment. Nonetheless, greenhouse gas emissions caused by inappropriate disposal or recycling and by the many production stages have not been discussed thoroughly. Regarding the manufacturing processes, carbon dioxide is produced mainly through heating of process streams and intrinsic chemical transformations, explaining why first-generation petrochemical industries are among the top five most greenhouse gas (GHG)-polluting businesses. Consequently, the plastics market must pursue full integration with the circular economy approach, promoting the simultaneous recycling of plastic wastes and sequestration and reuse of CO2 through carbon capture and utilization (CCU) strategies, which can be employed for the manufacture of olefins (among other process streams) and reduction of fossil-fuel demands and environmental impacts. Considering the previous remarks, the present manuscript’s purpose is to provide a review regarding CO2 emissions, capture, and utilization in the plastics industry. A detailed bibliometric review of both the scientific and the patent literature available is presented, including the description of key players and critical discussions and suggestions about the main technologies. As shown throughout the text, the number of documents has grown steadily, illustrating the increasing importance of CCU strategies in the field of plastics manufacture.

Metabolic engineering of Moorella thermoacetica for thermophilic bioconversion of gaseous substrates to a volatile chemical

Gas fermentation is one of the promising bioprocesses to convert CO₂ or syngas to important chemicals. Thermophilic gas fermentation of volatile chemicals has the potential for the development of consolidated bioprocesses that can simultaneously separate products during fermentation. This study reports the production of acetone from CO₂ and H₂, CO, or syngas by introducing the acetone production pathway using acetyl–coenzyme A (Ac-CoA) and acetate produced via the Wood–Ljungdahl pathway in Moorella thermoacetica. Reducing the carbon flux from Ac-CoA to acetate through genetic engineering successfully enhanced acetone productivity, which varied on the basis of the gas composition. The highest acetone productivity was obtained with CO–H₂, while autotrophic growth collapsed with CO₂–H₂. By adding H₂ to CO, the acetone productivity from the same amount of carbon source increased compared to CO gas only, and the maximum specific acetone production rate also increased from 0.04 to 0.09 g-acetone/g-dry cell/h. Our development of the engineered thermophilic acetogen M. thermoacetica, which grows at a temperature higher than the boiling point of acetone (58 °C), would pave the way for developing a consolidated process with simplified and cost-effective recovery via condensation following gas fermentation.

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.

Blending industrial blast furnace gas with H2 enables Acetobacterium woodii to efficiently co-utilize CO, CO2 and H2

In this study, the impact of gas composition (i.e. CO, CO₂ and H₂ partial pressures) on CO₂ utilization, growth, and acetate production was investigated in batch and continuous cultures of A. woodii. Based on an industrial blast furnace gas, H₂ blending was used to study the impact of H₂ availability on CO₂ fixation alone and together with CO using idealized gas streams. With H₂ available as an additional energy source, net CO₂ fixation and CO, CO₂ and H₂ co-utilization was achieved in gas-limited fermentations. Using industrial blast furnace gas, up to 15.1 g l^-1 acetate were produced in continuous cultures. Flux balance analysis showed that intracellular fluxes and total ATP production were dependent on the availability of H₂ and CO. Overall, H₂ blending was shown to be a suitable control strategy for gas fermentations and demonstrated that A. woodii is an interesting host for CO₂ fixation from industrial gas streams.

Design of mutualistic microbial consortia for stable conversion of carbon monoxide to value-added chemicals

Carbon monoxide (CO) is a promising carbon source for producing value-added biochemicals via microbial fermentation. However, its microbial conversion has been challenging because of difficulties in genetic engineering of CO-utilizing microorganisms and, more importantly, maintaining CO consumption which is negatively affected by the toxicity of CO and accumulated byproducts. To overcome these issues, we devised mutualistic microbial consortia, co-culturing Eubacterium limosum and genetically engineered Escherichia coli for the production of 3-hydroxypropionic acid (3-HP) and itaconic acid (ITA). During the co-culture, E. limosum assimilated CO and produced acetate, a toxic by-product, while E. coli utilized acetate as a sole carbon source. We found that this mutualistic interaction dramatically stabilized and improved CO consumption of E. limosum compared to monoculture. Consequently, the improved CO consumption allowed successful production of 3-HP and ITA from CO. This study is the first demonstration of value-added biochemical production from CO using a microbial consortium. Moreover, it suggests that synthetic mutualistic microbial consortium can serve as a powerful platform for the valorization of CO.

Unlocking Nature's Biosynthetic Power-Metabolic Engineering for the Fermentative Production of Chemicals

Fermentation as a production method for chemicals is especially attractive, as it is based on cheap renewable raw materials and often exhibits advantages in terms of costs and sustainability. The tremendous development of technology in bioscience has resulted in an exponentially increasing knowledge about biological systems and has become the main driver for innovations in the field of metabolic engineering. Progress in recombinant DNA technology, genomics, and computational methods open new, cheaper, and faster ways to metabolically engineer microorganisms. Existing biosynthetic pathways for natural products, such as vitamins, organic acids, amino acids, or secondary metabolites, can be discovered and optimized efficiently, thereby enabling competitive commercial production processes. Novel biosynthetic routes can now be designed by the rearrangement of nature's unlimited number of enzymes and metabolic pathways in microbial strains. This expands the range of chemicals accessible by biotechnology and has yielded the first commercial products, while new fermentation technologies targeting novel active ingredients, commodity chemicals, and CO₂ -fixation methods are on the horizon.

Improved robustness of microbial electrosynthesis by adaptation of a strict anaerobic microbial catalyst to molecular oxygen

Microbial electrosynthesis (MES) and other bioprocesses such as syngas fermentation developed for energy storage and the conversion of carbon dioxide into valuable chemicals often employs acetogens as microbial catalysts. Acetogens are sensitive to molecular oxygen, which means that bioproduction reactors must be maintained under strict anaerobic conditions. This requirement increases cost and does not eliminate the possibility of O₂ leakage. For MES, the risk is even greater since the system generates O₂ when water splitting is the anodic reaction. Here, we show that O₂ from the anode of a MES reactor diffuses into the cathode chamber where strict anaerobes reduce CO₂. To overcome this drawback, a stepwise adaptive laboratory evolution (ALE) strategy is used to develop the O₂ tolerance of the acetogen Sporomusa ovata. Two heavily-mutated S. ovata strains growing well autotrophically in the presence of 0.5 to 5% O₂ were obtained. The adapted strains were more performant in the MES system than the wild type converting electrical energy and CO₂ into acetate 1.5 fold faster. This study shows that the O₂ tolerance of acetogens can be increased, which leads to improvement of the performance and robustness of energy-storage bioprocesses such as MES where O₂ is an inhibitor.

Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2

Decelerating global warming is one of the predominant challenges of our time and will require conversion of CO₂ to usable products and commodity chemicals. Of particular interest is the production of fuels, because the transportation sector is a major source of CO₂ emissions. Here, we review recent technological advances in metabolic engineering of the hydrogen-oxidizing bacterium Cupriavidus necator H16, a chemolithotroph that naturally consumes CO₂ to generate biomass. We discuss recent successes in biofuel production using this organism, and the implementation of electrolysis/artificial photosynthesis approaches that enable growth of C. necator using renewable electricity and CO₂. Last, we discuss prospects of improving the nonoptimal growth of C. necator in ambient concentrations of CO₂.

Toward sustainable, cell-free biomanufacturing

Industrial biotechnology is an attractive approach to address the need for low-cost fuels and products from sustainable resources. Unfortunately, cells impose inherent limitations on the effective synthesis and release of target products. One key constraint is that cellular survival objectives often work against the production objectives of biochemical engineers. Additionally, industrial strains release CO₂ and struggle to utilize sustainable, potentially profitable feedstocks. Cell-free biotechnology, which uses biological machinery harvested from cells, can address these challenges with advantages including: (i) shorter development times, (ii) higher volumetric production rates, and (iii) tolerance to otherwise toxic molecules. In this review, we highlight recent advances in cell-free technologies toward the production of non-protein products beyond lab-scale demonstrations and describe guiding principles for designing cell-free systems. Specifically, we discuss carbon and energy sources, reaction homeostasis, and scale-up. Expanding the scope of cell-free biomanufacturing practice could enable innovative approaches for the industrial production of green chemicals.

Direct utilization of industrial carbon dioxide with low impurities for acetate production via microbial electrosynthesis

The present study aimed to demonstrate the utilization of unpurified industrial CO₂ with low impurities for acetate production via microbial electrosynthesis (MES) for the first time. In MES experiments with CO₂-rich brewery gas, the enriched mixed culture dominated by Acetobacterium produced 1.8 ± 0.2 g/L acetic acid at 0.26 ± 0.03 g/L_catholyte/d rate and outperformed a pure culture of Clostridium ljungdahlii (1.1 ± 0.02 g/L; 0.138 ± 0.004 g/L_catholyte/d). The electron recovery in acetic acid was also more for mixed culture (84 ± 13%) than C. ljungdahlii (42 ± 14%). Electrochemical analysis of biocathodes suggested the role of microbial biofilm in improved hydrogen electrocatalysis. In comparative gas fermentation tests, the mixed culture outperformed C. ljungdahlii and produced acetic acid at a similar level with both industrial and pure CO₂ feedstocks. These results suggest the robustness and capability of the mixed microbial community for utilizing slightly impure industrial CO₂ for bioproduction and presents a major advancement in MES technology.

Overcoming Energetic Barriers in Acetogenic C1 Conversion

Currently one of the biggest challenges for society is to combat global warming. A solution to this global threat is the implementation of a CO₂-based bioeconomy and a H₂-based bioenergy economy. Anaerobic lithotrophic bacteria such as the acetogenic bacteria are key players in the global carbon and H₂ cycle and thus prime candidates as driving forces in a H₂- and CO₂-bioeconomy. Naturally, they convert two molecules of CO₂via the Wood-Ljungdahl pathway (WLP) to one molecule of acetyl-CoA which can be converted to different C2-products (acetate or ethanol) or elongated to C4 (butyrate) or C5-products (caproate). Since there is no net ATP generation from acetate formation, an electron-transport phosphorylation (ETP) module is hooked up to the WLP. ETP provides the cell with additional ATP, but the ATP gain is very low, only a fraction of an ATP per mol of acetate. Since acetogens live at the thermodynamic edge of life, metabolic engineering to obtain high-value products is currently limited by the low energy status of the cells that allows for the production of only a few compounds with rather low specificity. To set the stage for acetogens as production platforms for a wide range of bioproducts from CO₂, the energetic barriers have to be overcome. This review summarizes the pathway, the energetics of the pathway and describes ways to overcome energetic barriers in acetogenic C1 conversion.

Carbon Allocation in Multi-Product Steel Mills That Co‐process Biogenic and Fossil Feedstocks and Adopt Carbon Capture Utilization and Storage Technologies

This work investigates the effects of carbon allocation on the emission intensities of low-carbon products cogenerated in facilities that co‐process biogenic and fossil feedstocks and apply the carbon capture utilization and storage technology. Thus, these plants simultaneously sequester CO2 and synthesize fuels or chemicals. We consider an integrated steel mill that injects biomass into the blast furnace, captures CO2 for storage, and ferments CO into ethanol from the blast furnace gas. We examine two schemes to allocate the CO2 emissions avoided [due to the renewable feedstock share (biomass) and CO2 capture and storage (CCS)] to the products of steel, ethanol, and electricity (generated through the combustion of steel mill waste gases): 1) allocation by (carbon) mass, which represents actual carbon flows, and 2) a free-choice attribution that maximizes the renewable content allocated to electricity and ethanol. With respect to the chosen assumptions on process performance and heat integration, we find that allocation by mass favors steel and is unlikely to yield an ethanol product that fulfills the Renewable Energy Directive (RED) biofuel criterion (65% emission reduction relative to a fossil comparator), even when using renewable electricity and applying CCS to the blast furnace gas prior to CO conversion into ethanol and electricity. In contrast, attribution fulfills the criterion and yields bioethanol for electricity grid intensities <180 gCO2/kWhel without CCS and yields bioethanol for grid intensities up to 800 gCO2/kWhel with CCS. The overall emissions savings are up to 27 and 47% in the near-term and long-term future, respectively. The choice of the allocation scheme greatly affects the emissions intensities of cogenerated products. Thus, the set of valid allocation schemes determines the extent of flexibility that manufacturers have in producing low-carbon products, which is relevant for industries whose product target sectors that value emissions differently. We recommend that policymakers consider the emerging relevance of co‐processing in nonrefining facilities. Provided there is no double-accounting of emissions, policies should contain a reasonable degree of freedom in the allocation of emissions savings to low-carbon products, so as to promote the sale of these savings, thereby making investments in mitigation technologies more attractive to stakeholders.

Alternative Extraction and Characterization of Nitrogen-Containing Azaphilone Red Pigments and Ergosterol Derivatives from the Marine-Derived Fungal Talaromyces sp. 30570 Strain with Industrial Relevance

Many species of Talaromyces of marine origin could be considered as non-toxigenic fungal cell factory. Some strains could produce water-soluble active biopigments in submerged cultures. These fungal pigments are of interest due to their applications in the design of new pharmaceutical products. In this study, the azaphilone red pigments and ergosterol derivatives produced by a wild type of Talaromyces sp. 30570 (CBS 206.89 B) marine-derived fungal strain with industrial relevance were described. The strain was isolated from the coral reef of the Réunion island. An alternative extraction of the fungal pigments using high pressure with eco-friendly solvents was studied. Twelve different red pigments were detected, including two pigmented ergosterol derivatives. Nine metabolites were identified using HPLC-PDA-ESI/MS as Monascus-like azaphilone pigments. In particular, derivatives of nitrogen-containing azaphilone red pigment, like PP-R, 6-[(Z)-2-Carboxyvinyl]-N-GABA-PP-V, N-threonine-monascorubramin, N-glutaryl-rubropunctamin, monascorubramin, and presumed N-threonyl-rubropunctamin (or acid form of the pigment PP-R) were the major pigmented compounds produced. Interestingly, the bioproduction of these red pigments occurred only when complex organic nitrogen sources were present in the culture medium. These findings are important for the field of the selective production of Monascus-like azaphilone red pigments for the industries.

Syngas Derived from Lignocellulosic Biomass Gasification as an Alternative Resource for Innovative Bioprocesses

A hybrid system based on lignocellulosic biomass gasification and syngas fermentation represents a second-generation biorefinery approach that is currently in the development phase. Lignocellulosic biomass can be gasified to produce syngas, which is a gas mixture consisting mainly of H2, CO, and CO2. The major challenge of biomass gasification is the syngas’s final quality. Consequently, the development of effective syngas clean-up technologies has gained increased interest in recent years. Furthermore, the bioconversion of syngas components has been intensively studied using acetogenic bacteria and their Wood–Ljungdahl pathway to produce, among others, acetate, ethanol, butyrate, butanol, caproate, hexanol, 2,3-butanediol, and lactate. Nowadays, syngas fermentation appears to be a promising alternative for producing commodity chemicals in comparison to fossil-based processes. Research studies on syngas fermentation have been focused on process design and optimization, investigating the medium composition, operating parameters, and bioreactor design. Moreover, metabolic engineering efforts have been made to develop genetically modified strains with improved production. In 2018, for the first time, a syngas fermentation pilot plant from biomass gasification was built by LanzaTech Inc. in cooperation with Aemetis, Inc. Future research will focus on coupling syngas fermentation with additional bioprocesses and/or on identifying new non-acetogenic microorganisms to produce high-value chemicals beyond acetate and ethanol.

Revealing formate production from carbon monoxide in wild type and mutants of Rnf- and Ech-containing acetogens, Acetobacterium woodii and Thermoanaerobacter kivui

Acetogenic bacteria have gained much attraction in recent years as they can produce different biofuels and biochemicals from H2 plus CO2 or even CO alone, therefore opening a promising alternative route for the production of biofuels from renewable sources compared to existing sugar-based routes. However, CO metabolism still raises questions concerning the biochemistry and bioenergetics in many acetogens. In this study, we focused on the two acetogenic bacteria Acetobacterium woodii and Thermoanaerobacter kivui which, so far, are the only identified acetogens harbouring a H2 -dependent CO2 reductase and furthermore belong to different classes of 'Rnf'- and 'Ech-acetogens'. Both strains catalysed the conversion of CO into the bulk chemical acetate and formate. Formate production was stimulated by uncoupling the energy metabolism from the Wood-Ljungdahl pathway, and specific rates of 1.44 and 1.34 mmol g-1  h-1 for A. woodii ∆rnf and T. kivui wild type were reached. The demonstrated CO-based formate production rates are, to the best of our knowledge, among the highest rates ever reported. Using mutants of ∆hdcr, ∆cooS, ∆hydBA, ∆rnf and ∆ech2 with deficiencies in key enzyme activities of the central metabolism enabled us to postulate two different CO utilization pathways in these two model organisms.

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.

Parameters influencing the development of highly conductive and efficient biofilm during microbial electrosynthesis: the importance of applied potential and inorganic carbon source

Cathode-driven applications of bio-electrochemical systems (BESs) have the potential to transform CO2 into value-added chemicals using microorganisms. However, their commercialisation is limited as biocathodes in BESs are characterised by slow start-up and low efficiency. Understanding biosynthesis pathways, electron transfer mechanisms and the effect of operational variables on microbial electrosynthesis (MES) is of fundamental importance to advance these applications of a system that has the capacity to convert CO2 to organics and is potentially sustainable. In this work, we demonstrate that cathodic potential and inorganic carbon source are keys for the development of a dense and conductive biofilm that ensures high efficiency in the overall system. Applying the cathodic potential of -1.0 V vs. Ag/AgCl and providing only gaseous CO2 in our system, a dense biofilm dominated by Acetobacterium (ca. 50% of biofilm) was formed. The superior biofilm density was significantly correlated with a higher production yield of organic chemicals, particularly acetate. Together, a significant decrease in the H2 evolution overpotential (by 200 mV) and abundant nifH genes within the biofilm were observed. This can only be mechanistically explained if intracellular hydrogen production with direct electron uptake from the cathode via nitrogenase within bacterial cells is occurring in addition to the commonly observed extracellular H2 production. Indeed, the enzymatic activity within the biofilm accelerated the electron transfer. This was evidenced by an increase in the coulombic efficiency (ca. 69%) and a 10-fold decrease in the charge transfer resistance. This is the first report of such a significant decrease in the charge resistance via the development of a highly conductive biofilm during MES. The results highlight the fundamental importance of maintaining a highly active autotrophic Acetobacterium population through feeding CO2 in gaseous form, which its dominance in the biocathode leads to a higher efficiency of the system.

From Acetate to Bio-Based Products: Underexploited Potential for Industrial Biotechnology

Currently, most biotechnological products are based on microbial conversion of carbohydrate substrates that are predominantly generated from sugar- or starch-containing plants. However, direct competitive uses of these feedstocks in the food and feed industry represent a dilemma, so using alternative carbon sources has become increasingly important in industrial biotechnology. A promising alternative carbon source that may be generated in substantial amounts from lignocellulosic biomass and C1 gases is acetate. This review discusses the underexploited potential of acetate to become a next-generation platform substrate in future industrial biotechnology and summarizes alternative sources and routes for acetate production. Furthermore, biotechnological aspects of microbial acetate utilization and the state of the art of biotechnological acetate conversion into value-added bioproducts are highlighted.

Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1

One primary objective of synthetic biology is to improve the sustainability of chemical manufacturing. Naturally occurring biological systems can utilize a variety of carbon sources, including waste streams that pose challenges to traditional chemical processing, such as lignin biomass, providing opportunity for remediation and valorization of these materials. Success, however, depends on identifying micro-organisms that are both metabolically versatile and engineerable. Identifying organisms with this combination of traits has been a historic hindrance. Here, we leverage the facile genetics of the metabolically versatile bacterium Acinetobacter baylyi ADP1 to create easy and rapid molecular cloning workflows, including a Cas9-based single-step marker-less and scar-less genomic integration method. In addition, we create a promoter library, ribosomal binding site (RBS) variants and test an unprecedented number of rationally integrated bacterial chromosomal protein expression sites and variants. At last, we demonstrate the utility of these tools by examining ADP1’s catabolic repression regulation, creating a strain with improved potential for lignin bioprocessing. Taken together, this work highlights ADP1 as an ideal host for a variety of sustainability and synthetic biology applications.

High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure

The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline “AcetoScan” presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.

Ethanol Metabolism Dynamics in Clostridium ljungdahlii Grown on Carbon Monoxide

Bioethanol production from syngas using acetogenic bacteria has attracted considerable attention in recent years. However, low ethanol yield is the biggest challenge that prevents the commercialization of syngas fermentation into biofuels using microbial catalysts. The present study demonstrated that ethanol metabolism plays an important role in recycling NADH/NAD⁺ during autotrophic growth. Deletion of bifunctional aldehyde/alcohol dehydrogenase (adhE) genes leads to significant growth deficiencies in gas fermentation. Using specific fermentation technology in which the gas pressure and pH were constantly controlled at 0.1 MPa and 6.0, respectively, we revealed that ethanol was formed during the exponential phase, closely accompanied by biomass production. Then, ethanol was oxidized to acetate via the aldehyde ferredoxin oxidoreductase pathway in Clostridium ljungdahlii A metabolic experiment using ¹³C-labeled ethanol and acetate, redox balance analysis, and comparative transcriptomic analysis demonstrated that ethanol production and reuse shared the metabolic pathway but occurred at different growth phases.IMPORTANCE Ethanol production from carbon monoxide (CO) as a carbon and energy source by Clostridium ljungdahlii and "Clostridium autoethanogenum" is currently being commercialized. During gas fermentation, ethanol synthesis is NADH-dependent. However, ethanol oxidation and its regulatory mechanism remain incompletely understood. Energy metabolism analysis demonstrated that reduced ferredoxin is the sole source of NADH formation by the Rnf-ATPase system, which provides ATP for cell growth during CO fermentation. Therefore, ethanol production is tightly linked to biomass production (ATP production). Clarification of the mechanism of ethanol oxidation and biosynthesis can provide an important reference for generating high-ethanol-yield strains of C. ljungdahlii in the future.

Homoacetogenesis and microbial community composition are shaped by pH and total sulfide concentration

Biological CO2 sequestration through acetogenesis with H2 as electron donor is a promising technology to reduce greenhouse gas emissions. Today, a major issue is the presence of impurities such as hydrogen sulfide (H2 S) in CO2 containing gases, as they are known to inhibit acetogenesis in CO2 -based fermentations. However, exact values of toxicity and inhibition are not well-defined. To tackle this uncertainty, a series of toxicity experiments were conducted, with a mixed homoacetogenic culture, total dissolved sulfide concentrations ([TDS]) varied between 0 and 5 mM and pH between 5 and 7. The extent of inhibition was evaluated based on acetate production rates and microbial growth. Maximum acetate production rates of 0.12, 0.09 and 0.04 mM h-1 were achieved in the controls without sulfide at pH 7, pH 6 and pH 5. The half-maximal inhibitory concentration (IC50 qAc ) was 0.86, 1.16 and 1.36 mM [TDS] for pH 7, pH 6 and pH 5. At [TDS] above 3.33 mM, acetate production and microbial growth were completely inhibited at all pHs. 16S rRNA gene amplicon sequencing revealed major community composition transitions that could be attributed to both pH and [TDS]. Based on the observed toxicity levels, treatment approaches for incoming industrial CO2 streams can be determined.

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.

Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways

Gas fermentation by autotrophic bacteria, such as clostridia, offers a sustainable path to numerous bioproducts from a range of local, highly abundant, waste and low-cost feedstocks, such as industrial flue gases or syngas generated from biomass or municipal waste. Unfortunately, designing and engineering clostridia remains laborious and slow. The ability to prototype individual genetic part function, gene expression patterns, and biosynthetic pathway performance in vitro before implementing designs in cells could help address these bottlenecks by speeding up design. Unfortunately, a high-yielding cell-free gene expression (CFE) system from clostridia has yet to be developed. Here, we report the development and optimization of a high-yielding (236 ± 24 μg/mL) batch CFE platform from the industrially relevant anaerobe, Clostridium autoethanogenum. A key feature of the platform is that both circular and linear DNA templates can be applied directly to the CFE reaction to program protein synthesis. We demonstrate the ability to prototype gene expression, and quantitatively map aerobic cell-free metabolism in lysates from this system. We anticipate that the C. autoethanogenum CFE platform will not only expand the protein synthesis toolkit for synthetic biology, but also serve as a platform in expediting the screening and prototyping of gene regulatory elements in non-model, industrially relevant microbes.

Energy Conservation and Carbon Flux Distribution During Fermentation of CO or H2/CO2 by Clostridium ljungdahlii

Both CO and H₂ can be utilized as energy sources during the autotrophic growth of Clostridium ljungdahlii. In principle, CO is a more energetically and thermodynamically favorable energy source for gas fermentation in comparison to H₂. Therefore, metabolism may vary during growth under different energy sources. In this study, C. ljungdahlii was fed with CO and/or CO₂/H₂ at pH 6.0 with a gas pressure of 0.1 MPa. C. ljungdahlii primarily produced acetate in the presence of H₂ as an energy source, but produced alcohols with CO as an energy source under the same fermentation conditions. A key enzyme activity assay, metabolic flux analysis, and comparative transcriptomics were performed for investigating the response mechanism of C. ljungdahlii under different energy sources. A CO dehydrogenase and an aldehyde:ferredoxin oxidoreductase were found to play important roles in CO utilization and alcohol production. Based on these findings, novel metabolic schemes are proposed for C. ljungdahlii growing on CO and/or CO₂/H₂. These schemes indicate that more ATP is produced during CO-fermentation than during H₂-fermentation, leading to increased alcohol production.

Enhancing CO2-Valorization Using Clostridium autoethanogenum for Sustainable Fuel and Chemicals Production

Acetogenic bacteria can convert waste gases into fuels and chemicals. Design of bioprocesses for waste carbon valorization requires quantification of steady-state carbon flows. Here, steady-state quantification of autotrophic chemostats containing Clostridium autoethanogenum grown on CO2 and H2 revealed that captured carbon (460 ± 80 mmol/gDCW/day) had a significant distribution to ethanol (54 ± 3 C-mol% with a 2.4 ± 0.3 g/L titer). We were impressed with this initial result, but also observed limitations to biomass concentration and growth rate. Metabolic modeling predicted culture performance and indicated significant metabolic adjustments when compared to fermentation with CO as the carbon source. Moreover, modeling highlighted flux to pyruvate, and subsequently reduced ferredoxin, as a target for improving CO2 and H2 fermentation. Supplementation with a small amount of CO enabled co-utilization with CO2, and enhanced CO2 fermentation performance significantly, while maintaining an industrially relevant product profile. Additionally, the highest specific flux through the Wood-Ljungdahl pathway was observed during co-utilization of CO2 and CO. Furthermore, the addition of CO led to superior CO2-valorizing characteristics (9.7 ± 0.4 g/L ethanol with a 66 ± 2 C-mol% distribution, and 540 ± 20 mmol CO2/gDCW/day). Similar industrial processes are commercial or currently being scaled up, indicating CO-supplemented CO2 and H2 fermentation has high potential for sustainable fuel and chemical production. This work also provides a reference dataset to advance our understanding of CO2 gas fermentation, which can contribute to mitigating climate change.