Continuous gas fermentation by Acetobacterium woodii in a submerged membrane reactor with full cell retention

Two-stage conversion of syngas and pyrolysis aqueous condensate into L-malate

Hybrid thermochemical-biological processes have the potential to enhance the carbon and energy recovery from organic waste. This work aimed to assess the carbon and energy recovery potential of multifunctional processes to simultaneously sequestrate syngas and detoxify pyrolysis aqueous condensate (PAC) for short-chain carboxylates production. To evaluate relevant process parameters for mixed culture co-fermentation of syngas and PAC, two identical reactors were run under mesophilic (37 °C) and thermophilic (55 °C) conditions at increasing PAC loading rates. Both the mesophilic and the thermophilic process recovered at least 50% of the energy in syngas and PAC into short-chain carboxylates. During the mesophilic syngas and PAC co-fermentation, methanogenesis was completely inhibited while acetate, ethanol and butyrate were the primary metabolites. Over 90% of the amplicon sequencing variants based on 16S rRNA were assigned to Clostridium sensu stricto 12. During the thermophilic process, on the other hand, Symbiobacteriales, Syntrophaceticus, Thermoanaerobacterium, Methanothermobacter and Methanosarcina likely played crucial roles in aromatics degradation and methanogenesis, respectively, while Moorella thermoacetica and Methanothermobacter marburgensis were the predominant carboxydotrophs in the thermophilic process. High biomass concentrations were necessary to maintain stable process operations at high PAC loads. In a second-stage reactor, Aspergillus oryzae converted acetate, propionate and butyrate from the first stage into L-malate, confirming the successful detoxification of PAC below inhibitory levels. The highest L-malate yield was 0.26 ± 2.2 molL-malate/molcarboxylates recorded for effluent from the mesophilic process at a PAC load of 4% v/v. The results highlight the potential of multifunctional reactors where anaerobic mixed cultures perform simultaneously diverse process roles, such as carbon fixation, wastewater detoxification and carboxylates intermediate production. The recovered energy in the form of intermediate carboxylates allows for their use as substrates in subsequent fermentative stages.

Adaptive laboratory evolution of Clostridium autoethanogenum to metabolize CO2 and H2 enhances growth rates in chemostat and unravels proteome and metabolome alterations

Gas fermentation of CO2 and H2 is an attractive means to sustainably produce fuels and chemicals. Clostridium autoethanogenum is a model organism for industrial CO to ethanol and presents an opportunity for CO2-to-ethanol processes. As we have previously characterized its CO2/H2 chemostat growth, here we use adaptive laboratory evolution (ALE) with the aim of improving growth with CO2/H2. Seven ALE lineages were generated, all with improved specific growth rates. ALE conducted in the presence of 2% CO along with CO2/H2 generated Evolved lineage D, which showed the highest ethanol titres amongst all the ALE lineages during the fermentation of CO2/H2. Chemostat comparison against the parental strain shows no change in acetate or ethanol production, while Evolved D could achieve a higher maximum dilution rate. Multi-omics analyses at steady state revealed that Evolved D has widespread proteome and intracellular metabolome changes. However, the uptake and production rates and titres remain unaltered until investigating their maximum dilution rate. Yet, we provide numerous insights into CO2/H2 metabolism via these multi-omics data and link these results to mutations, suggesting novel targets for metabolic engineering in this bacterium.

Expanding the product portfolio of carbon dioxide and hydrogen-based gas fermentation with an evolved strain of Clostridium carboxidivorans

CO2:H2-based gas fermentation with acetogenic Clostridium species are at an early stage of development. This work exploited the Adaptive Laboratory Evolution technique to improve the growth of C. carboxidivorans P7 on CO2 and H2. An adapted strain with decreased growth lag phase and improved biomass production was obtained. Genomic analysis revealed a conserved frameshift mutation in the catalytic subunit of the hexameric hydrogenase gene. The resulted truncated protein variant, most likely lacking its functionality, suggests that other hydrogenases might be more efficient for H2-based growth of this strain. Furthermore, the adapted strain generated hexanol as primary fermentation product. For the first time, hexanol was produced directly from CO2:H2 blend, achieving the highest maximum productivity reported so far via gas fermentation. Traces of valerate, pentanol, eptanol and octanol were observed in the fermentation broth. The adapted strain shows promising to enrich the product spectrum targetable by future gas fermentation processes.

Alternative carbon sources for the production of plant cellular agriculture: a case study on acetate

Plant cellular agriculture aims to disrupt the way plant derived products are produced. Plant cell cultures are typically grown with sucrose as the primary carbon and energy source, but alternative carbon sources may have advantages over sucrose including less strain on food systems, lower costs, and more sustainable sourcing. Here we review carbon and energy sources that may serve as alternatives to sucrose in the cultivation of plant cell cultures. We identified acetate as a promising candidate and took the first steps to evaluate its potential for use in growing tobacco plant cell cultures. When added to media containing sucrose, acetate concentrations above 8 mM completely inhibit growth. Lower concentrations of acetate (2-4 mM) can support an increase in dry weight without sucrose but do not provide enough energy for substantial growth. 13C labeling indicates that tobacco plant cell cultures can incorporate carbon from exogenous acetate into proteins and carbohydrates. Analysis of transcriptome data showed that genes encoding glyoxylate cycle enzymes are expressed at very low levels compared to genes from the TCA cycle and glycolysis. Adaptive laboratory evolution experiments were able to increase tobacco cell cultures tolerance to acetate, demonstrating the potential for this type of approach going forward. Overall, our results indicate that acetate can be metabolized by plant cell cultures and suggest that further adaptive laboratory evolution or strain engineering efforts may enable acetate to serve as a sole carbon and energy source for tobacco plant cell cultures. This assessment of acetate provides a framework for evaluating other carbon and energy sources for plant cell cultures, efforts that will help reduce the costs and environmental impact, and increase the commercial potential of plant cellular agriculture.

No acetogen is equal: Strongly different H2 thresholds reflect diverse bioenergetics in acetogenic bacteria

Acetogens share the capacity to convert H2 and CO2 into acetate for energy conservation (ATP synthesis). This reaction is attractive for applications, such as gas fermentation and microbial electrosynthesis. Different H2 partial pressures prevail in these distinctive applications (low concentrations during microbial electrosynthesis [<40 Pa] vs. high concentrations with gas fermentation [>9%]). Strain selection thus requires understanding of how different acetogens perform under different H2 partial pressures. Here, we determined the H2 threshold (H2 partial pressure at which acetogenesis halts) for eight different acetogenic strains under comparable conditions. We found a three orders of magnitude difference between the lowest and highest H2 threshold (6 ± 2 Pa for Sporomusa ovata vs. 1990 ± 67 Pa for Clostridium autoethanogenum), while Acetobacterium strains had intermediate H2 thresholds. We used these H2 thresholds to estimate ATP gains, which ranged from 0.16 to 1.01 mol ATP per mol acetate (S. ovata vs. C. autoethanogenum). The experimental H2 thresholds thus suggest strong differences in the bioenergetics of acetogenic strains and possibly also in their growth yields and kinetics. We conclude that no acetogen is equal and that a good understanding of their differences is essential to select the most optimal strain for different biotechnological applications.

Eight Up-Coming Biotech Tools to Combat Climate Crisis

Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood-Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.

Microbial photoelectrosynthesis: Feeding purple phototrophic bacteria electricity to produce bacterial biomass

Purple phototrophic bacteria are one of the main actors in chemolithotrophic carbon fixation and, therefore, fundamental in the biogeochemical cycle. These microbes are capable of using insoluble electron donors such as ferrous minerals or even carbon-based electrodes. Carbon fixation through extracellular electron uptake places purple phototrophic bacteria in the field of microbial electrosynthesis as key carbon capturing microorganisms. In this work we demonstrate biomass production dominated by purple phototrophic bacteria with a cathode (-0.6 V vs. Ag/AgCl) as electron donor. In addition, we compared the growth and microbial population structure with ferrous iron as the electron donor. We detect interaction between the cathode and the consortium showing a midpoint potential of 0.05 V (vs. Ag/AgCl). Microbial community analyses revealed different microbial communities depending on the electron donor, indicating different metabolic interactions. Electrochemical measurements together with population analyses point to Rhodopseudomonas genus as the key genus in the extracellular electron uptake. Furthermore, the genera Azospira and Azospirillum could play a role in the photoelectrotrophic consortium.

Leveraging substrate flexibility and product selectivity of acetogens in two-stage systems for chemical production

Carbon dioxide (CO₂ ) stands out as sustainable feedstock for developing a circular carbon economy whose energy supply could be obtained by boosting the production of clean hydrogen from renewable electricity. H₂ -dependent CO₂ gas fermentation using acetogenic microorganisms offers a viable solution of increasingly demonstrated value. While gas fermentation advances to achieve commercial process scalability, which is currently limited to a few products such as acetate and ethanol, it is worth taking the best of the current state-of-the-art technology by its integration within innovative bioconversion schemes. This review presents multiple scenarios where gas fermentation by acetogens integrate into double-stage biotechnological production processes that use CO₂ as sole carbon feedstock and H₂ as energy carrier for products' synthesis. In the integration schemes here reviewed, the first stage can be biotic or abiotic while the second stage is biotic. When the first stage is biotic, acetogens act as a biological platform to generate chemical intermediates such as acetate, formate and ethanol that become substrates for a second fermentation stage. This approach holds the potential to enhance process titre/rate/yield metrics and products' spectrum. Alternatively, when the first stage is abiotic, the integrated two-stage scheme foresees, in the first stage, the catalytic transformation of CO₂ into C₁ products that, in the second stage, can be metabolized by acetogens. This latter scheme leverages the metabolic flexibility of acetogens in efficient utilization of the products of CO₂ abiotic hydrogenation, namely formate and methanol, to synthesize multicarbon compounds but also to act as flexible catalysts for hydrogen storage or production.

Optimization of l-malic acid production from acetate with Aspergillus oryzae DSM 1863 using a pH-coupled feeding strategy

Background

Malic acid, a dicarboxylic acid mainly used in the food industry, is currently produced from fossil resources. The utilization of low-cost substrates derived from biomass could render microbial processes economic. Such feedstocks, like lignocellulosic hydrolysates or condensates of fast pyrolysis, can contain high concentrations of acetic acid. Acetate is a suitable substrate for l-malic acid production with the filamentous fungus Aspergillus oryzae DSM 1863, but concentrations obtained so far are low. An advantage of this carbon source is that it can be used for pH control and simultaneous substrate supply in the form of acetic acid. In this study, we therefore aimed to enhance l-malate production from acetate with A. oryzae by applying a pH-coupled feeding strategy.

Results

In 2.5-L bioreactor fermentations, several feeding strategies were evaluated. Using a pH-coupled feed consisting of 10 M acetic acid, the malic acid concentration was increased about 5.3-fold compared to the batch process without pH control, resulting in a maximum titer of 29.53 ± 1.82 g/L after 264 h. However, it was not possible to keep both the pH and the substrate concentration constant during this fermentation. By using 10 M acetic acid set to a pH of 4.5, or with the repeated addition of NaOH, the substrate concentration could be maintained within a constant range, but these strategies did not prove beneficial as lower maximum titers and yields were obtained. Since cessation of malic acid production was observed in later fermentation stages despite carbon availability, a possible product inhibition was evaluated in shake flask cultivations. In these experiments, malate and succinate, which is a major by-product during malic acid production, were added at concentrations of up to 50 g/L, and it was found that A. oryzae is capable of organic acid production even at high product concentrations.

Conclusions

This study demonstrates that a suitable feeding strategy is necessary for efficient malic acid production from acetate. It illustrates the potential of acetate as carbon source for microbial production of the organic acid and provides useful insights which can serve as basis for further optimization.

Modeling and assessment of the transfer effectiveness in integrated bioreactor with membrane separation

Integrating a reaction process with membrane separation allows for effective product removal, favorable shifting of the reaction equilibrium, overcoming eventual inhibitory or toxic effects of the products and has the advantage of being energy and space saving. It has found a range of applications in innovative biotechnologies, generating value-added products (exopolysaccharides, antioxidants, carboxylic acids) with high potential for separation/ concentration of thermosensitive bioactive compounds, preserving their biological activity and reducing the amount of solvents and the energy for solvent recovery. Evaluating the effectiveness of such integrated systems is based on fluid dynamics and mass transfer knowledge of flowing matter close to the membrane surface – shear deformation rates and shear stress at the membrane interface, mass transfer coefficients. A Computational Fluid Dynamics (CFD)-based approach for assessing the effectiveness of integrated stirred tank bioreactor with submerged membrane module is compiled. It is related to the hydrodynamic optimization of the selected reactor configuration in two-phase flow, as well as to the concentration profiles and analysis of the reactor conditions in terms of reaction kinetics and mass transfer.

Weak electrostimulation enhanced the microbial transformation of ibuprofen and naproxen

Ibuprofen (IBU) and naproxen (NPX) are commonly used non-steroidal anti-inflammatory drugs (NSAIDs) with high-risk quotients and are frequently detected in various aquatic environments. A weak electrostimulated biofilm not only had improved removal efficiencies to IBU and NPX, but also transformed different enantiomers with comparable efficiency and without configuration inversion. IBU was transformed mainly by oxidation (hydroxyl-IBU, carboxy-IBU), while NPX was mainly detoxified. The microbial analysis of IBU and NPX biofilm showed that the shared core consortia (> 1%) contained typical electro-active bacteria (Geobacter, Desulfovibrio), fermenters (Petrimonas, Acetobacterium) and potential degraders (Pandoraea, Nocardiaceae), which exhibited synergistic interactions by exchanging the additional electrons, H⁺, coenzyme NAD(H) or NAD(P) (H) and energy. The fungal community has a significant correlation to those core bacteria and they may also play transformation roles with their diverse enzymes. Plenty of nonspecific oxidoreductase, decarboxylase, hydrolase, cytochrome P450, and other enzymes relating to xenobiotic degradation were high-abundance encoded by the core consortia and could potentially participate in IBU and NPX biotransformation. This study offers new insights into the functional microbes and enzymes working on complex NSAIDs biotransformation and provided a feasible strategy for the enhanced removal of NSAIDs (especially IBU and NPX).

The Potential of Sequential Fermentations in Converting C1 Substrates to Higher-Value Products

Today production of (bulk) chemicals and fuels almost exclusively relies on petroleum-based sources, which are connected to greenhouse gas release, fueling climate change. This increases the urgence to develop alternative bio-based technologies and processes. Gaseous and liquid C1 compounds are available at low cost and often occur as waste streams. Acetogenic bacteria can directly use C1 compounds like CO, CO₂, formate or methanol anaerobically, converting them into acetate and ethanol for higher-value biotechnological products. However, these microorganisms possess strict energetic limitations, which in turn pose limitations to their potential for biotechnological applications. Moreover, efficient genetic tools for strain improvement are often missing. However, focusing on the metabolic abilities acetogens provide, they can prodigiously ease these technological disadvantages. Producing acetate and ethanol from C1 compounds can fuel via bio-based intermediates conversion into more energy-demanding, higher-value products, by deploying aerobic organisms that are able to grow with acetate/ethanol as carbon and energy source. Promising new approaches have become available combining these two fermentation steps in sequential approaches, either as separate fermentations or as integrated two-stage fermentation processes. This review aims at introducing, comparing, and evaluating the published approaches of sequential C1 fermentations, delivering a list of promising organisms for the individual fermentation steps and giving an overview of the existing broad spectrum of products based on acetate and ethanol. Understanding of these pioneering approaches allows collecting ideas for new products and may open avenues toward making full use of the technological potential of these concepts for establishment of a sustainable biotechnology.

Advances in cathode designs and reactor configurations of microbial electrosynthesis systems to facilitate gas electro-fermentation

In gas fermentation, a range of chemolithoautotrophs fix single-carbon (C1) gases (CO₂ and CO) when H₂ or other reductants are available. Microbial electrosynthesis (MES) enables CO₂ reduction by generating H₂ or reducing equivalents with the sole input of renewable electricity. A combined approach as gas electro-fermentation is attractive for the sustainable production of biofuels and biochemicals utilizing C1 gases. Various platform compounds such as acetate, butyrate, caproate, ethanol, butanol and bioplastics can be produced. However, technological challenges pertaining to the microbe-material interactions such as poor gas-liquid mass transfer, low biomass and biofilm coverage on cathode, low productivities still exist. We are presenting a review on latest developments in MES focusing on the configuration and design of cathodes that can address the challenges and support the gas electro-fermentation. Overall, the opportunities for advancing CO and CO₂-based biochemicals and biofuels production in MES with suitable cathode/reactor design are prospected.

Microbial Utilization of Next-Generation Feedstocks for the Biomanufacturing of Value-Added Chemicals and Food Ingredients

Global shift to sustainability has driven the exploration of alternative feedstocks beyond sugars for biomanufacturing. Recently, C1 (CO₂, CO, methane, formate and methanol) and C2 (acetate and ethanol) substrates are drawing great attention due to their natural abundance and low production cost. The advances in metabolic engineering, synthetic biology and industrial process design have greatly enhanced the efficiency that microbes use these next-generation feedstocks. The metabolic pathways to use C1 and C2 feedstocks have been introduced or enhanced into industrial workhorses, such as Escherichia coli and yeasts, by genetic rewiring and laboratory evolution strategies. Furthermore, microbes are engineered to convert these low-cost feedstocks to various high-value products, ranging from food ingredients to chemicals. This review highlights the recent development in metabolic engineering, the challenges in strain engineering and bioprocess design, and the perspectives of microbial utilization of C1 and C2 feedstocks for the biomanufacturing of value-added products.

Determining global trends in syngas fermentation research through a bibliometric analysis

Syngas fermentation, in which microorganisms convert H₂, CO, and CO₂ to acids and alcohols, is a promising alternative for carbon cycling and valorization. The intellectual landscape of the topic was characterized through a bibliometric analysis using a search query (SQ) that included all relevant documents on syngas fermentation available through the Web of Science database up to December 31st, 2021. The SQ was validated with a preliminary analysis in bibliometrix and a review of titles and abstracts of all sources. Although syngas fermentation began in the early 1980s, it grew rapidly beginning in 2008, with 92.5% of total publications and 87.3% of total citations from 2008 to 2021. The field has been steadily moving from fundamentals towards applications, suggesting that the field is maturing scientifically. The greatest number of publications and citations are from the USA, and researchers in China, Germany, and Spain also are highly active. Although collaborations have increased in the past few years, author-cluster analysis shows specialized research domains with little collaboration between groups. Based on topic trends, the main challenges to be address are related to mass-transfer limitations, and researchers are starting to explore mixed cultures, genetic engineering, microbial chain elongation, and biorefineries.

Towards new carbon-neutral food systems: Combining carbon capture and utilization with microbial protein production

Alternative protein sources such as microbial protein (MP) are currently considered to alleviate the burden that food production exerts on the environment. Even though MP production is highly efficient in land and nutrient utilization, their carbon footprint should be improved. Here we propose the use of CCU as a driver for heterotrophic MP production. By comparing different MP production routes starting from liquid substrates derived from CO2 (i.e., formate, acetate, methanol, and ethanol) and their respective metabolic pathways, the potential of this concept as a carbon-neutral food or feed production process was estimated. Acetate and ethanol appear to be the most beneficial substrates for the integrated CCU-to-MP process in terms of electricity demand (acetate: 25 - 54 kWh/kgproduct, ethanol: 28 - 56 kWh/kgproduct). Moreover, recycling CO2 enables a carbon-negative protein production process by 2030 (considering the projected CO2 emissions from electricity in the EU: 0.096 kgCO2-eq/kWh) for formate, acetate, and ethanol (-1.1 up to 13 kgCO2-eq/kgproduct).

Advanced PHB fermentation strategies with CO2-derived organic acids

Over the past decade, formic acid and acetic acid have gained increasing attention as alternative feedstocks for poly-3-hydroxybutyrate (PHB) production as these potentially CO₂-derived molecules are naturally assimilated by Cupriavidus necator. Both organic acids were individually evaluated in fed-batch fermentations at bioreactor scale. Acetic acid was revealed as the most promising carbon source yielding 42.3 g L^-1 PHB, whereas no significant amount of PHB was produced from formic acid. Hence, acetic acid was further used as the substrate during process intensification. Key performance characteristics, including process stability, PHB titer, and productivity were optimized by introducing NH₄-acetate as the nitrogen source, extending the growth phase, and implementing a repeated fed-batch procedure, respectively. These advanced fermentation strategies resulted in the establishment of a stable fermentation process reaching 58.5 g L^-1 PHB, while doubling the productivity to 0.93 g L^-1 h^-1 PHB.

Continuous H2/CO2 fermentation for acetic acid production under transient and continuous sulfide inhibition

Waste gas fermentation powered by renewable H₂ is reaching kiloton scale. The presence of sulfide, inherent to many waste gases, can cause inhibition, requiring additional gas treatment. In this work, acetogenesis and methanogenesis inhibition by sulfide were studied in a 10-L mixed-culture fermenter, supplied with CO₂ and connected with a water electrolysis unit for electricity-powered H₂ supply. Three cycles of inhibition (1.3 mM total dissolved sulfide (TDS)) and recovery were applied, then the fermenter was operated at 0.5 mM TDS for 35 days. During operation at 0.5 mM TDS the acetate production rate reached 7.1 ± 1.5 mmol C L^-1 d^-1. Furthermore, 43.7 ± 15.6% of the electrons, provided as H₂, were distributed to acetate and 7.7 ± 4.1% to butyrate, the second most abundant fermentation product. Selectivity of sulfide as inhibitor was demonstrated by a 7 days lag-phase of methanogenesis recovery, compared to 48 h for acetogenesis and by the less than 1% electrons distribution to CH₄, under 0.5 mM TDS. The microbial community was dominated by Eubacterium, Proteiniphilum and an unclassified member of the Eggerthellaceae family. The taxonomic diversity of the community decreased and conversely the phenotypic diversity increased, during operation. This work illustrated the scale-up potential of waste gas fermentations, by elucidating the effect of sulfide as a common gas impurity, and by demonstrating continuous, potentially renewable supply of electrons.

Membrane bioreactors for the production of value-added products: Recent developments, challenges and perspectives

The potential of membrane bioreactors to produce value-added products such as biofuels, biopolymers, proteins, organic acids and lipids at high productivities is emerging. Despite the promising results at laboratory scale, industrial deployment of this technology is hindered due to challenges associated with scale-up. This review aims to address these challenges and create a framework to encourage further research directed towards industrial application of membrane bioreactors to produce value-added products. This review describes the current state-of-the art in such bioreactor systems by exploiting membranes to increase the mass transfer rate of the limiting substrates, reach high cell concentrations and separate the inhibitory substances that may inhibit the bioconversion reaction. It also covers the current trends in commercialization, challenges linked with membrane usage, such as high costs and membrane fouling, and proposes possible future directions for the wider application of membrane bioreactors.

A quantitative metabolic analysis reveals Acetobacterium woodii as a flexible and robust host for formate-based bioproduction

Cheap and renewable feedstocks such as the one-carbon substrate formate are emerging for sustainable production in a growing chemical industry. We investigated the acetogen Acetobacterium woodii as a potential host for bioproduction from formate alone and together with autotrophic and heterotrophic co-substrates by quantitatively analyzing physiology, transcriptome, and proteome in chemostat cultivations in combination with computational analyses. Continuous cultivations with a specific growth rate of 0.05 h^-1 on formate showed high specific substrate uptake rates (47 mmol g^-1 h^-1). Co-utilization of formate with H₂, CO, CO₂ or fructose was achieved without catabolite repression and with acetate as the sole metabolic product. A transcriptomic comparison of all growth conditions revealed a distinct adaptation of A. woodii to growth on formate as 570 genes were changed in their transcript level. Transcriptome and proteome showed higher expression of the Wood-Ljungdahl pathway during growth on formate and gaseous substrates, underlining its function during utilization of one-carbon substrates. Flux balance analysis showed varying flux levels for the WLP (0.7-16.4 mmol g^-1 h^-1) and major differences in redox and energy metabolism. Growth on formate, H₂/CO₂, and formate + H₂/CO₂ resulted in low energy availability (0.20-0.22 ATP/acetate) which was increased during co-utilization with CO or fructose (0.31 ATP/acetate for formate + H₂/CO/CO₂, 0.75 ATP/acetate for formate + fructose). Unitrophic and mixotrophic conversion of all substrates was further characterized by high energetic efficiencies. In silico analysis of bioproduction of ethanol and lactate from formate and autotrophic and heterotrophic co-substrates showed promising energetic efficiencies (70-92%). Collectively, our findings reveal A. woodii as a promising host for flexible and simultaneous bioconversion of multiple substrates, underline the potential of substrate co-utilization to improve the energy availability of acetogens and encourage metabolic engineering of acetogenic bacteria for the efficient synthesis of bulk chemicals and fuels from sustainable one carbon substrates.

Efficient Hydrogen Delivery for Microbial Electrosynthesis via 3D-Printed Cathodes

The efficient delivery of electrochemically in situ produced H₂ can be a key advantage of microbial electrosynthesis over traditional gas fermentation. However, the technical details of how to supply large amounts of electric current per volume in a biocompatible manner remain unresolved. Here, we explored for the first time the flexibility of complex 3D-printed custom electrodes to fine tune H₂ delivery during microbial electrosynthesis. Using a model system for H₂-mediated electromethanogenesis comprised of 3D fabricated carbon aerogel cathodes plated with nickel-molybdenum and Methanococcus maripaludis, we showed that novel 3D-printed cathodes facilitated sustained and efficient electromethanogenesis from electricity and CO₂ at an unprecedented volumetric production rate of 2.2 L_CH4 /L_catholyte/day and at a coulombic efficiency of 99%. Importantly, our experiments revealed that the efficiency of this process strongly depends on the current density. At identical total current supplied, larger surface area cathodes enabled higher methane production and minimized escape of H₂. Specifically, low current density (<1 mA/cm²) enabled by high surface area cathodes was found to be critical for fast start-up times of the microbial culture, stable steady state performance, and high coulombic efficiencies. Our data demonstrate that 3D-printing of electrodes presents a promising design tool to mitigate effects of bubble formation and local pH gradients within the boundary layer and, thus, resolve key critical limitations for in situ electron delivery in microbial electrosynthesis.

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.

Investigation of putative genes for the production of medium-chained acids and alcohols in autotrophic acetogenic bacteria

Gas fermentation is a technology for producing platform chemicals as well as fuels and one of the most promising alternatives to petrochemicals. Medium-chained acids and alcohols such as hexanoate and hexanol are particularly interesting due to their versatile application. This study elucidated the pathway of chain elongation in native C6 compound-producing acetogens. Essential genes of Clostridium carboxidivorans for synthesis of medium-chained acids and alcohols were identified in order to demonstrate their catalytic activity in the acetogenic model organism Acetobacterium woodii. Two such gene clusters were identified, which are responsible for conversion of acetyl-CoA to butyryl-CoA by reverse β-oxidation. Using RT-PCR it could be demonstrated that only genes of cluster 1 are expressed constitutively with simultaneous formation of C6 compounds. Based on genes from C. carboxidivorans, a modular hexanoyl-CoA synthesis (hcs) plasmid system was constructed and transferred into A. woodii. With the recombinant A. woodii strains AWO [pPta_hcs1], AWO [pPta_hcs2], AWO [pTet_hcs1], and AWO [pTet_hcs2] butyrate and hexanoate production under heterotrophic (1.22-4.15 mM hexanoate) and autotrophic conditions (0.48-1.56 mM hexanoate) with both hcs clusters could be detected. hcs Cluster 1 from C. carboxidivorans was transferred into the ABE-fermenting strain Clostridium saccharoperbutylacetonicum as well. For further analysis, genes were also cloned into the hcs plasmid system individually. The resulting recombinant C. saccharoperbutylacetonicum strains with just individual genes neither produced hexanoate nor hexanol, but the strains containing the entire gene cluster were capable of chain elongation. A production of 0.8 mM hexanoate and 5.2 mM hexanol in the fermentation with glucose could be observed.

Microbial electrosynthesis: is it sustainable for bioproduction of acetic acid?

Microbial electrosynthesis (MES) is an innovative technology for electricity driven microbial reduction of carbon dioxide (CO2) to useful multi-carbon compounds. This study assesses the cradle-to-gate environmental burdens associated with acetic acid (AA) production via MES using graphene functionalized carbon felt cathode. The analysis shows that, though the environmental impact for the production of the functionalized cathode is substantially higher when compared to carbon felt with no modification, the improved productivity of the process helps in reducing the overall impact. It is also shown that, while energy used for extraction of AA is the key environmental hotspot, ion-exchange membrane and reactor medium (catholyte & anolyte) are other important contributors. A sensitivity analysis, describing four different scenarios, considering either continuous or fed-batch operation, is also described. Results show that even if MES productivity can be theoretically increased to match the highest space time yield reported for acetogenic bacteria in a continuous gas fermenter (148 g L-1 d-1), the environmental impact of AA produced using MES systems would still be significantly higher than that produced using a fossil-based process. Use of fed-batch operation and renewable (solar) energy sources do help in reducing the impact, however, the low production rates and overall high energy requirement makes large-scale implementation of such systems impractical. The analysis suggests a minimum threshold production rate of 4100 g m-2 d-1, that needs to be achieved, before MES could be seen as a sustainable alternative to fossil-based AA production.

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.

Acetate as substrate for L-malic acid production with Aspergillus oryzae DSM 1863

BACKGROUND

Microbial malic acid production is currently not able to compete economically with well-established chemical processes using fossil resources. The utilization of inexpensive biomass-based substrates containing acetate could decrease production costs and promote the development of microbial processes. Acetate is a by-product in lignocellulosic hydrolysates and fast pyrolysis products or can be synthesized by acetogens during syngas fermentation. For the fermentation of these substrates, a robust microorganism with a high tolerance for biomass-derived inhibitors is required. Aspergillus oryzae is a suitable candidate due to its high tolerance and broad substrate spectrum. To pave the path towards microbial malic acid production, the potential of acetate as a carbon source for A. oryzae is evaluated in this study.

RESULTS

A broad acetate concentration range was tested both for growth and malic acid production with A. oryzae. Dry biomass concentration was highest for acetic acid concentrations of 40-55 g/L reaching values of about 1.1 g/L within 48 h. Morphological changes were observed depending on the acetate concentration, yielding a pellet-like morphology with low and a filamentous structure with high substrate concentrations. For malic acid production, 45 g/L acetic acid was ideal, resulting in a product concentration of 8.44 ± 0.42 g/L after 192 h. The addition of 5-15 g/L glucose to acetate medium proved beneficial by lowering the time point of maximum productivity and increasing malic acid yield. The side product spectrum of cultures with acetate, glucose, and cultures containing both substrates was compared, showing differences especially in the amount of oxalic, succinic, and citric acid produced. Furthermore, the presence of CaCO3, a pH regulator used for malate production with glucose, was found to be crucial also for malic acid production with acetate.

CONCLUSIONS

This study evaluates relevant aspects of malic acid production with A. oryzae using acetate as carbon source and demonstrates that it is a suitable substrate for biomass formation and acid synthesis. The insights provided here will be useful to further microbial malic acid production using renewable substrates.

Increasing the Production of Volatile Fatty Acids from Corn Stover Using Bioaugmentation of a Mixed Rumen Culture with Homoacetogenic Bacteria

Volatile fatty acids (VFA) are industrially versatile chemicals and have a major market. Although currently produced from petrochemicals, chemical industries are moving towards more bio-based VFA produced from abundant, cheap and renewable sources such as lignocellulosic biomass. In this study, we examined the effect of bioaugmentation with homoacetogenic bacteria for increasing VFA production in lignocellulose fermentation process. The central hypothesis of this study was that inhibition of methanogenesis in an in vitro rumen bioreactor fed with lignocellulosic biomass hydrolysate increases the hydrogen partial pressure, which can be redirected towards increased VFA production, particularly acetic acid, through targeted bioaugmentation with known homoacetogenic bacteria. In this study, methanogenesis during ruminal fermentation of wet exploded corn stover was initially inhibited with 10 mM of 2-bromoethanesulfonate (BES), followed by bioaugmentation with either Acetitomaculum ruminis and Acetobacterium woodii in two separate bioreactors. During the inhibition phase, we found that addition of BES decreased the acetic acid yield by 24%, while increasing headspace hydrogen from 1% to 60%. After bioaugmentation, the headspace hydrogen was consumed in both bioreactors and the concentration of acetic acids increased 45% when A. ruminis was added and 70% with A. woodii added. This paper demonstrates that mixed microbial fermentation can be manipulated to increase VFA production through bioaugmentation.

Impact of substrate and growth conditions on microbial protein production and composition

Production of microbial protein (MP) from recovered resources - e.g. CO₂-sourced formate and acetate - could provide protein while enabling CO₂ capture. To assess the protein quality obtained from this process, pure cultures and enriched communities were selected and characterized kinetically, stoichiometrically and nutritionally. Growth on acetate resulted in up to 5.3 times higher maximum specific growth rate (μ_max) than formate (i.e. 0.15-0.41 h^-1 for acetate compared to 0.061-0.29 h^-1 for formate at pH = 7). The protein content was a function of the growth phase, with the highest values during stationary phase, ranging between 18 and 82%_CDW protein depending on the organism and substrate. The negative correlation between biomass productivity and protein content indicated a trade-off between production rate and product quality. The final product (i.e. dried MP) quality was in most cases superior to soybean and all cultures were rich in threonine, phenylalanine and tyrosine, regardless of the carbon source.

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.

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.

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

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

Perovskite-Based Multifunctional Cathode with Simultaneous Supplementation of Substrates and Electrons for Enhanced Microbial Electrosynthesis of Organics

Microbial electrosynthesis (MES) is an electricity-driven technology for the microbial reduction of CO₂ to organic commodities. However, the limited solubility of CO₂ in a solution and the inefficient electron transfer make it impossible for microorganisms to obtain an efficient surface for catalytic interaction, thus resulting in the low efficiency of MES. To address this, we introduce a multifunctional perovskite-based cathode material Pr_0.5(Ba_0.5Sr_0.5)_0.5Co_0.8Fe_0.2O_3-δ-carbon felt (Pr_0.5BSCF-CF), which provides a simultaneously significant increase in CO₂ absorption and hydrogen production. As a result, the volumetric acetate production rate of MES obtained by Pr_0.5BSCF-CF is 0.24 ± 0.01 g L^-1 day^-1, and it achieves a maximum acetate titer of 13.74 ± 0.20 g L^-1 within 70 days. An adequate supply of CO₂ and H₂ also provides a sufficient amount of substrates and energy for the self-replication of the biocatalysts in the MES reactor. This effect not only increases the amount of biocatalysts but also optimizes the functions of the biocatalysts; the above benefits further improve the production efficiency of the MES system. This strategy demonstrates that the development of perovskite-based multifunctional cathodes with a simultaneous supplementation of substrates and electrons is a promising approach toward improving the MES efficiency.

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.

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.

A simultaneous gas feeding and cell-recycled reaction (SGCR) system to achieve biomass boosting and high acetate titer in microbial carbon monoxide fermentation

This study employed a simultaneous gas feeding and cell-recycled reaction (SGCR) system to ferment CO using Eubacterium limosum KIST612. A bubble column reactor was equipped with an ex-situ hollow fiber membrane module to enable cell recycling. The internal gas circulation rate was adjusted by controlling the pump speed to provide sufficient gas supplement to the microorganism. Gas feedings were conducted by either the use of a gas-tight bag (Batch), a pressurized gas cylinder (Continuous), or a sequential combination of the two (Mixed feeding). Mixed feeding mode achieved higher biomass (9.7 g/L) and acetate (9.8 g/L) concentrations than Batch mode (3.2 g/L biomass and 7.0 g/L acetate) or Continuous mode (5.0 g/L biomass and 8.1 g/L acetate). The high acetate titer in Mixed feeding mode was achieved due to the high concentration of cells secured in a short time at the initial operation stage and maintaining a high specific growth rate.

Continuous conversion of CO2/H2 with Clostridium aceticum in biofilm reactors

A lab-scale stirred-tank bioreactor was reversibly retrofitted to a packed-bed and a trickle-bed biofilm reactor to study and compare the conversion of CO₂/H₂ with immobilised Clostridiumaceticum. The biofilm reactors were characterised and their functionality confirmed. Up to 8.6 g of C. aceticum were immobilised onto 300 g sintered ceramic carrier material, proving biofilm formation to be a robust means for cell retention of C. aceticum. Continuous CO₂/H₂-fermentation studies were performed with both biofilm reactor configurations as function of dilution rates, partial gas pressures and gas flow rates. The experiments showed that in the packed-bed biofilm reactor, the acetate space-time yield was independent of the dilution rate, because of low H₂ gas-liquid mass transfer rates (≤17 mmol H₂ L^-1 h^-1). The continuous operation of the trickle-bed biofilm reactor increased the gas-liquid mass transfer rates to up to 56 mmol H₂ L^-1 h^-1. Consequently, the acetate space-time yield of up to 14 mmol acetate L^-1 h^-1 was improved 3-fold at hydrogen conversions of up to 96%.

Kinetic Study on Heterotrophic Growth of Acetobacterium woodii on Lignocellulosic Substrates for Acetic Acid Production

Extensive research has been done on examining the autotrophic growth of Acetobacterium woodii with gaseous substrates (hydrogen and carbon dioxide) to produce acetic acid. However, only limited work has been performed on the heterotrophic growth of A. woodii using pure sugars or lignocellulosic feedstocks-derived sugars as substrates. In this study, we examine the growth kinetics and acetic acid production of A. woodii on glucose and xylose. While good growth was observed with glucose as substrate, no significant growth was obtained on xylose. Kinetic studies were performed in batch culture using different concentrations of glucose, ranging from 5 g/L to 40 g/L. The highest acetate production of 6.919 g/L with a product yield of 0.76 g acetic acid/g glucose was observed with 10 g/L glucose as initial substrate concentration. When testing A. woodii on corn stover hydrolysate (CSH) and wheat straw hydrolysate (WSH) formed after pretreatment and enzymatic hydrolysis, we found that A. woodii showed acetic acid production of 7.64 g/L and a product yield of 0.70 g acetic acid/g of glucose on WSH, while the acetic acid production was 7.83 g/L with a product yield of 0.65 g acetic acid/g of glucose on CSH. These results clearly demonstrate that A. woodii performed similarly on pure substrates and hydrolysates, and that the processes were not inhibited by the heterogenous components present in the lignocellulosic feedstock hydrolysates.

CO2 to succinic acid - Estimating the potential of biocatalytic routes

Microbial carbon dioxide assimilation and conversion to chemical platform molecules has the potential to be developed as economic, sustainable processes. The carbon dioxide assimilation can proceed by a variety of natural pathways and recently even synthetic CO2 fixation routes have been designed. Early assessment of the performance of the different carbon fixation alternatives within biotechnological processes is desirable to evaluate their potential. Here we applied stoichiometric metabolic modeling based on physiological and process data to evaluate different process variants for the conversion of C1 carbon compounds to the industrial relevant platform chemical succinic acid. We computationally analyzed the performance of cyanobacteria, acetogens, methylotrophs, and synthetic CO2 fixation pathways in Saccharomyces cerevisiae in terms of production rates, product yields, and the optimization potential. This analysis provided insight into the economic feasibility and allowed to estimate the future industrial applicability by estimating overall production costs. With reported, or estimated data of engineered or wild type strains, none of the simulated microbial succinate production processes showed a performance allowing competitive production. The main limiting factors were identified as gas and photon transfer and metabolic activities whereas metabolic network structure was not restricting. In simulations with optimized parameters most process alternatives reached economically interesting values, hence, represent promising alternatives to sugar-based fermentations.

Nonphotosynthetic Biological CO2 Reduction

Alarming changes in environmental conditions have prompted significant research into producing renewable commodities from sources other than fossil fuels. One such alternative is CO₂, a determinate greenhouse gas with historically high atmospheric levels. If sequestered, CO₂ could be used as a highly renewable feedstock for industrially relevant products and fuels. The vast majority of atmospheric CO₂ fixation is accomplished by photosynthetic organisms, which have unfortunately proven difficult to utilize as chassis for industrial production. Nonphotosynthetic CO₂ fixing microorganisms and pathways have recently attracted scientific and commercial interest. This Perspective will review promising alternate CO₂ fixation strategies and their potential to supply microbially produced fuels and commodity chemicals, such as higher alcohols. Acetogenic fermentation and microbial electrosynthesis are the primary focuses of this review.