Bacterial Anaerobic Synthesis Gas (Syngas) and CO2+H2 Fermentation

Isolation and characterization of novel acetogenic Moorella strains for employment as potential thermophilic biocatalysts

Thermophilic acetogenic bacteria have attracted attention as promising candidates for biotechnological applications such as syngas fermentation, microbial electrosynthesis, and methanol conversion. Here, we aimed to isolate and characterize novel thermophilic acetogens from diverse environments. Enrichment of heterotrophic and autotrophic acetogens was monitored by 16S rRNA gene-based bacterial community analysis. Seven novel Moorella strains were isolated and characterized by genomic and physiological analyses. Two Moorella humiferrea isolates showed considerable differences during autotrophic growth. The M. humiferrea LNE isolate (DSM 117358) fermented carbon monoxide (CO) to acetate, while the M. humiferrea OCP isolate (DSM 117359) transformed CO to hydrogen and carbon dioxide (H2 + CO2), employing the water-gas shift reaction. Another carboxydotrophic hydrogenogenic Moorella strain was isolated from the covering soil of an active charcoal burning pile and proposed as the type strain (ACPsT) of the novel species Moorella carbonis (DSM 116161T and CCOS 2103T). The remaining four novel strains were affiliated with Moorella thermoacetica and showed, together with the type strain DSM 2955T, the production of small amounts of ethanol from H2 + CO2 in addition to acetate. The physiological analyses of the novel Moorella strains revealed isolate-specific differences that considerably increase the knowledge base on thermophilic acetogens for future applications.

Microbial electrosynthesis from CO2 reaches productivity of syngas and chain elongation fermentations

Carbon-based products are essential to society, yet producing them from fossil fuels is unsustainable. Microorganisms have the ability to take up electrons from solid electrodes and convert carbon dioxide (CO2) to valuable carbon-based chemicals. However, higher productivities and energy efficiencies are needed to reach a viability that can make the technology transformative. Here, we show how a biofilm-based microbial porous cathode in a directed flow-through electrochemical system can continuously reduce CO2 to even-chain C2-C6 carboxylic acids over 248 days. We demonstrate a threefold higher biofilm concentration, volumetric current density, and productivity compared with the state of the art. Most notably, the volumetric productivity (VP) resembles those achieved in laboratory-scale and industrial syngas (CO-H2-CO2) fermentation and chain elongation fermentation. This work highlights key design parameters for efficient electricity-driven microbial CO2 reduction. There is need and room to improve the rates of electrode colonization and microbe-specific kinetics to scale up the technology.

Simultaneous Formate and Syngas Conversion Boosts Growth and Product Formation by Clostridium ragsdalei

Electrocatalytic CO2 reduction to CO and formate can be coupled to gas fermentation with anaerobic microorganisms. In combination with a competing hydrogen evolution reaction in the cathode in aqueous medium, the in situ, electrocatalytic produced syngas components can be converted by an acetogenic bacterium, such as Clostridium ragsdalei, into acetate, ethanol, and 2,3-butanediol. In order to study the simultaneous conversion of CO, CO2, and formate together with H2 with C. ragsdalei, fed-batch processes were conducted with continuous gassing using a fully controlled stirred tank bioreactor. Formate was added continuously, and various initial CO partial pressures (pCO0) were applied. C. ragsdalei utilized CO as the favored substrate for growth and product formation, but below a partial pressure of 30 mbar CO in the bioreactor, a simultaneous CO2/H2 conversion was observed. Formate supplementation enabled 20-50% higher growth rates independent of the partial pressure of CO and improved the acetate and 2,3-butanediol production. Finally, the reaction conditions were identified, allowing the parallel CO, CO2, formate, and H2 consumption with C. ragsdalei at a limiting CO partial pressure below 30 mbar, pH 5.5, n = 1200 min-1, and T = 32 °C. Thus, improved carbon and electron conversion is possible to establish efficient and sustainable processes with acetogenic bacteria, as shown in the example of C. ragsdalei.

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.

Steerable isobutyric and butyric acid production from CO2 and H2 by Clostridium luticellarii

Clostridium luticellarii is a recently discovered acetogen that is uniquely capable of producing butyric and isobutyric acid from various substrates (e.g. methanol), but it is unclear which factors influence its (iso)butyric acid production from H2 and CO2 . We aimed to investigate the autotrophic metabolism of C. luticellarii by identifying the necessary growth conditions and examining the effects of pH and metabolite levels on product titers and selectivity. Results show that autotrophic growth of C. luticellarii requires the addition of complex nutrient sources and the absence of shaking conditions. Further experiments combined with thermodynamic calculations identified pH as a key parameter governing the direction of metabolic fluxes. At circumneutral pH (~6.5), acetic acid is the sole metabolic end product but C. luticellarii possesses the unique ability to co-oxidize organic acids such as valeric acid under high H2 partial pressures (>1 bar). Conversely, mildly acidic pH (≤5.5) stimulates the production of butyric and isobutyric acid while partly halting the oxidation of organic acids. Additionally, elevated acetic acid concentrations stimulated butyric and isobutyric acid production up to a combined selectivity of 53 ± 3%. Finally, our results suggest that isobutyric acid is produced by a reversible isomerization of butyric acid, but valeric and caproic acid are not isomerized. These combined insights can inform future efforts to optimize and scale-up the production of valuable chemicals from CO2 using C. luticellarii.

The role of ethanol oxidation during carboxydotrophic growth of Clostridium autoethanogenum

The Wood-Ljungdahl pathway is an ancient metabolic route used by acetogenic carboxydotrophs to convert CO into acetate, and some cases ethanol. When produced, ethanol is generally seen as an end product of acetogenic metabolism, but here we show that it acts as an important intermediate and co-substrate during carboxydotrophic growth of Clostridium autoethanogenum. Depending on CO availability, C. autoethanogenum is able to rapidly switch between ethanol production and utilization, hereby optimizing its carboxydotrophic growth. The importance of the aldehyde ferredoxin:oxidoreductase (AOR) route for ethanol production in carboxydotrophic acetogens is known; however, the role of the bifunctional alcohol dehydrogenase AdhE (Ald-Adh) route in ethanol metabolism remains largely unclear. We show that the mutant strain C. autoethanogenum ∆adhE1a, lacking the Ald subunit of the main bifunctional aldehyde/alcohol dehydrogenase (AdhE, CAETHG_3747), has poor ethanol oxidation capabilities, with a negative impact on biomass yield. This indicates that the Adh-Ald route plays a major role in ethanol oxidation during carboxydotrophic growth, enabling subsequent energy conservation via substrate-level phosphorylation using acetate kinase. Subsequent chemostat experiments with C. autoethanogenum show that the wild type, in contrast to ∆adhE1a, is more resilient to sudden changes in CO supply and utilizes ethanol as a temporary storage for reduction equivalents and energy during CO-abundant conditions, reserving these 'stored assets' for more CO-limited conditions. This shows that the direction of the ethanol metabolism is very dynamic during carboxydotrophic acetogenesis and opens new insights in the central metabolism of C. autoethanogenum and similar acetogens.

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.

Predicting the performance of chain elongating microbiomes through flow cytometric fingerprinting

As part of the circular bio-economy paradigm shift, waste management and valorisation practices have moved away from sanitation and towards the production of added-value compounds. Recently, the development of mixed culture bioprocess for the conversion of waste(water) to platform chemicals, such as medium chain carboxylic acids, has attracted significant interest. Often, the microbiology of these novel bioprocesses is less diverse and more prone to disturbances, which can lead to process failure. This issue can be tackled by implementing an advanced monitoring strategy based on the microbiology of the process. In this study, flow cytometry was used to monitor the microbiology of lactic acid chain elongation for the production of caproic acid, and assess its performance both qualitatively and quantitatively. Two continuous stirred tank reactors for chain elongation were monitored flow cytometrically for over 336 days. Through community typing, four specific community types could be identified and correlated to both a specific functionality and genotypic diversity. Additionally, the machine-learning algorithms trained in this study demonstrated the ability to predict production rates of, amongst others, caproic acid with high accuracy in the present (R² > 0.87) and intermediate accuracy in the near future (R² > 0.63). The identification of specific community types and the development of predictive algorithms form the basis of advanced bioprocess monitoring based on flow cytometry, and have the potential to improve bioprocess control and optimization, leading to better product quality and yields.

Production of biofuels from C1 -gases with Clostridium and related bacteria-Recent advances

Clostridium spp. are suitable for the bioconversion of C₁ -gases (e.g., CO₂ , CO and syngas) into different bioproducts. These products can be used as biofuels and are reviewed here, focusing on ethanol, butanol and hexanol, mainly. The production of higher alcohols (e.g., butanol and hexanol) has hardly been reviewed. Parameters affecting the optimization of the bioconversion process and bioreactor performance are addressed as well as the pathways involved in these bioconversions. New aspects, such as mixotrophy and sugar versus gas fermentation, are also reviewed. In addition, Clostridia can also produce higher alcohols from the integration of the Wood-Ljungdahl pathway and the reverse ß-oxidation pathway, which has also not yet been comprehensively reviewed. In the latter process, the acetogen uses the reducing power of CO/syngas to reduce C₄ or C₆ fatty acids, previously produced by a chain elongating microorganism (commonly Clostridium kluyveri), into the corresponding bioalcohol.

Effects of Inbreeding on Microbial Community Diversity of Zea mays

Heterosis, also known as hybrid vigor, is the basis of modern maize production. The effect of heterosis on maize phenotypes has been studied for decades, but its effect on the maize-associated microbiome is much less characterized. To determine the effect of heterosis on the maize microbiome, we sequenced and compared the bacterial communities of inbred, open pollinated, and hybrid maize. Samples covered three tissue types (stalk, root, and rhizosphere) in two field experiments and one greenhouse experiment. Bacterial diversity was more affected by location and tissue type than genetic background for both within-sample (alpha) and between-sample (beta) diversity. PERMANOVA analysis similarly showed that tissue type and location had significant effects on the overall community structure, whereas the intraspecies genetic background and individual plant genotypes did not. Differential abundance analysis identified only 25 bacterial ASVs that significantly differed between inbred and hybrid maize. Predicted metagenome content was inferred with Picrust2, and it also showed a significantly larger effect of tissue and location than genetic background. Overall, these results indicate that the bacterial communities of inbred and hybrid maize are often more similar than they are different and that non-genetic effects are generally the largest influences on the maize microbiome.

Formate-induced CO tolerance and methanogenesis inhibition in fermentation of syngas and plant biomass for carboxylate production

BACKGROUND

Production of monocarboxylates using microbial communities is highly dependent on local and degradable biomass feedstocks. Syngas or different mixtures of H2, CO, and CO2 can be sourced from biomass gasification, excess renewable electricity, industrial off-gases, and carbon capture plants and co-fed to a fermenter to alleviate dependence on local biomass. To understand the effects of adding these gases during anaerobic fermentation of plant biomass, a series of batch experiments was carried out with different syngas compositions and corn silage (pH 6.0, 32 °C).

RESULTS

Co-fermentation of syngas with corn silage increased the overall carboxylate yield per gram of volatile solids (VS) by up to 29% (0.47 ± 0.07 g gVS-1; in comparison to 0.37 ± 0.02 g gVS-1 with a N2/CO2 headspace), despite slowing down biomass degradation. Ethylene and CO exerted a synergistic effect in preventing methanogenesis, leading to net carbon fixation. Less than 12% of the electrons were misrouted to CH4 when either 15 kPa CO or 5 kPa CO + 1.5 kPa ethylene was used. CO increased the selectivity to acetate and propionate, which accounted for 85% (electron equivalents) of all products at 49 kPa CO, by favoring lactic acid bacteria and actinobacteria over n-butyrate and n-caproate producers. Inhibition of n-butyrate and n-caproate production by CO happened even when an inoculum preacclimatized to syngas and lactate was used. Intriguingly, the effect of CO on n-butyrate and n-caproate production was reversed when formate was present in the broth.

CONCLUSIONS

The concept of co-fermenting syngas and plant biomass shows promise in three aspects: by making anaerobic fermentation a carbon-fixing process, by increasing the yields of short-chain carboxylates (propionate and acetate), and by minimizing electron losses to CH4. Moreover, a model was proposed for how formate can alleviate CO inhibition in certain acidogenic bacteria. Testing the fermentation of syngas and plant biomass in a continuous process could potentially improve selectivity to n-butyrate and n-caproate by enriching chain-elongating bacteria adapted to CO and complex biomass.

Mixotrophic chain elongation with syngas and lactate as electron donors

Feeding microbial communities with both organic and inorganic substrates can improve sustainability and feasibility of chain elongation processes. Sustainably produced H2 , CO2 , and CO can be co-fed to microorganisms as a source for acetyl-CoA, while a small amount of an ATP-generating organic substrate helps overcome the kinetic hindrances associated with autotrophic carboxylate production. Here, we operated two semi-continuous bioreactor systems with continuous recirculation of H2 , CO2 , and CO while co-feeding an organic model feedstock (lactate and acetate) to understand how a mixotrophic community is shaped during carboxylate production. Contrary to the assumption that H2 , CO2 , and CO support chain elongation via ethanol production in open cultures, significant correlations (p < 0.01) indicated that relatives of Clostridium luticellarii and Eubacterium aggregans produced carboxylates (acetate to n-caproate) while consuming H2 , CO2 , CO, and lactate themselves. After 100 days, the enriched community was dominated by these two bacteria coexisting in cyclic dynamics shaped by the CO partial pressure. Homoacetogenesis was strongest when the acetate concentration was low (3.2 g L-1 ), while heterotrophs had the following roles: Pseudoramibacter, Oscillibacter, and Colidextribacter contributed to n-caproate production and Clostridium tyrobutyricum and Acidipropionibacterium spp. grew opportunistically producing n-butyrate and propionate, respectively. The mixotrophic chain elongation community was more efficient in carboxylate production compared with the heterotrophic one and maintained average carbon fixation rates between 0.088 and 1.4 g CO2 equivalents L-1  days-1 . The extra H2 and CO consumed routed 82% more electrons to carboxylates and 50% more electrons to carboxylates longer than acetate. This study shows for the first time long-term, stable production of short- and medium-chain carboxylates with a mixotrophic community.

Biomass-specific rates as key performance indicators: A nitrogen balancing method for biofilm-based electrochemical conversion

Microbial electrochemical technologies (METs) employ microorganisms utilizing solid-state electrodes as either electron sink or electron source, such as in microbial electrosynthesis (MES). METs reaction rate is traditionally normalized to the electrode dimensions or to the electrolyte volume, but should also be normalized to biomass amount present in the system at any given time. In biofilm-based systems, a major challenge is to determine the biomass amount in a non-destructive manner, especially in systems operated in continuous mode and using 3D electrodes. We developed a simple method using a nitrogen balance and optical density to determine the amount of microorganisms in biofilm and in suspension at any given time. For four MES reactors converting CO₂ to carboxylates, >99% of the biomass was present as biofilm after 69 days of reactor operation. After a lag phase, the biomass-specific growth rate had increased to 0.12-0.16 days^-1. After 100 days of operation, growth became insignificant. Biomass-specific production rates of carboxylates varied between 0.08-0.37 mol_C mol_X ^-1d^-1. Using biomass-specific rates, one can more effectively assess the performance of MES, identify its limitations, and compare it to other fermentation technologies.

Model-driven approach for the production of butyrate from CO2/H2 by a novel co-culture of C. autoethanogenum and C. beijerinckii

One-carbon (C1) compounds are promising feedstocks for the sustainable production of commodity chemicals. CO₂ is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted into valuable products while reducing its atmospheric levels. Acetogens are microorganisms that can grow on CO₂/H₂ gas mixtures and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with other microbial species that can further process such products, can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone-butanol-ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of an acetogen and a solventogen in a consortium provides a potential platform to produce valuable chemicals from CO₂. In this study, metabolic modeling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO₂/H₂ mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation of Clostridium beijerinckii on these substrates in batch serum bottles and subsequently in pH-controlled bioreactors. Community modeling also suggested that a novel microbial consortium consisting of the acetogen Clostridium autoethanogenum, and the solventogen C. beijerinckii would be feasible and stable. On the basis of this prediction, a co-culture was experimentally established. C. autoethanogenum grew on CO₂/H₂ producing acetate and traces of ethanol. Acetate was in turn, consumed by C. beijerinckii together with lactate, producing butyrate. These results show that community modeling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable resources.

Metabolic changes of the acetogen Clostridium sp. AWRP through adaptation to acetate challenge

In this study, we report the phenotypic changes that occurred in the acetogenic bacterium Clostridium sp. AWRP as a result of an adaptive laboratory evolution (ALE) under the acetate challenge. Acetate-adapted strain 46 T-a displayed acetate tolerance to acetate up to 10 g L-1 and increased ethanol production in small-scale cultures. The adapted strain showed a higher cell density than AWRP even without exogenous acetate supplementation. 46 T-a was shown to have reduced gas consumption rate and metabolite production. It was intriguing to note that 46 T-a, unlike AWRP, continued to consume H2 at low CO2 levels. Genome sequencing revealed that the adapted strain harbored three point mutations in the genes encoding an electron-bifurcating hydrogenase (Hyt) crucial for autotrophic growth in CO2 + H2, in addition to one in the dnaK gene. Transcriptome analysis revealed that most genes involved in the CO2-fixation Wood-Ljungdahl pathway and auxiliary pathways for energy conservation (e.g., Rnf complex, Nfn, etc.) were significantly down-regulated in 46 T-a. Several metabolic pathways involved in dissimilation of nucleosides and carbohydrates were significantly up-regulated in 46 T-a, indicating that 46 T-a evolved to utilize organic substrates rather than CO2 + H2. Further investigation into degeneration in carbon fixation of the acetate-adapted strain will provide practical implications for CO2 + H2 fermentation using acetogenic bacteria for long-term continuous fermentation.

Impact of innovative nanoadditives on biodigesters microbiome

Nanoparticles (NPs) supplementation to biodigesters improves the digestibility of biowaste and the generation of biogas. This study investigates the impact of innovative nanoadditives on the microbiome of biodigesters. Fresh cow manure was anaerobically incubated in a water bath under mesophilic conditions for 30 days. Three different NPs (zinc ferrite, zinc ferrite with 10% carbon nanotubes and zinc ferrite with 10% C76 fullerene) were separately supplemented to the biodigesters at the beginning of the incubation period. Methane and hydrogen production were monitored daily. Manure samples were collected from the digesters at different time points and the microbial communities inside the biodigesters were investigated via real-time PCR and 16 S rRNA gene amplicon-sequencing. The results indicate that zinc ferrite NPs enhanced biogas production the most. The microbial community was significantly affected by NPs addition in terms of archaeal and bacterial 16 S rRNAgene copy numbers. The three ZF formulations NPs augmented the abundance of members within the hydrogenotrophic methanogenic phyla Methanobacteriaceae. While Methanomassiliicoccacaea were enriched in ZF/C76 supplemented biodigester due to a significant increase in hydrogen partial pressure, probably caused by the enrichment of Spirochaetaceae (genus Treponema). Overall, NPs supplementation significantly enriched acetate-producing members within Hungateiclostridiaceae in ZF/CNTs, Dysgonomonadaceae in ZF and Spirochaetaceae ZF/C76 biodigesters.

Organic carbon metabolism is a main determinant of hydrogen demand and dynamics in anaerobic soils

Hydrogen (H₂) is a crucial electron donor for many processes in the environment including nitrate-, sulfate- and, iron-reduction, homoacetogenesis, and methanogenesis, and is a major determinant of microbial competition and metabolic pathways in groundwater, sediments, and soils. Despite the importance of H₂ for many microbial processes in the environment, the total H₂ consuming capacity (or H₂ demand) of soils is generally unknown. Using soil microcosms with added H₂, the aims of this study were 1) to measure the H₂ demand of geochemically diverse soils and 2) to define the processes leading to this demand. Study results documented a large range of H₂ demand in soil (0.034-1.2 millielectron equivalents H₂ g^-1 soil). The measured H₂ demand greatly exceeded the theoretical demand predicted based on measured concentrations of common electron acceptors initially present in a library of 15 soils. While methanogenesis accounted for the largest fraction of H₂ demand, humic acid reduction and acetogenesis were also significant contributing H₂-consuming processes. Much of the H₂ demand could be attributed to CO₂ produced during incubation from fermentation and/or acetoclastic methanogenesis. The soil initial total organic carbon showed the strongest correlation to H₂ demand. Besides external additions, H₂ was likely generated or cycled in the microcosms. Apart from fermentative H₂ production, carboxylate elongation to produce C4-C7 fatty acids may have accounted for additional H₂ production in these soils. Many of these processes, especially the organic carbon contribution is underestimated in microbial models for H₂ consumption in natural soil ecosystems or during bioremediation of contaminants in soils.

Microbial community development during syngas methanation in a trickle bed reactor with various nutrient sources

Microbial community development within an anaerobic trickle bed reactor (TBR) during methanation of syngas (56% H₂, 30% CO, 14% CO₂) was investigated using three different nutrient media: defined nutrient medium (241 days), diluted digestate from a thermophilic co-digestion plant operating with food waste (200 days) and reject water from dewatered digested sewage sludge at a wastewater treatment plant (220 days). Different TBR operating periods showed slightly different performance that was not clearly linked to the nutrient medium, as all proved suitable for the methanation process. During operation, maximum syngas load was 5.33 L per L packed bed volume (pbv) & day and methane (CH₄) production was 1.26 L CH₄/L_pbv/d. Microbial community analysis with Illumina Miseq targeting 16S rDNA revealed high relative abundance (20-40%) of several potential syngas and acetate consumers within the genera Sporomusa, Spirochaetaceae, Rikenellaceae and Acetobacterium during the process. These were the dominant taxa except in a period with high flow rate of digestate from the food waste plant. The dominant methanogen in all periods was a member of the genus Methanobacterium, while Methanosarcina was also observed in the carrier community. As in reactor effluent, the dominant bacterial genus in the carrier was Sporomusa. These results show that syngas methanation in TBR can proceed well with different nutrient sources, including undefined medium of different origins. Moreover, the dominant syngas community remained the same over time even when non-sterilised digestates were used as nutrient medium. KEY POINTS: • Independent of nutrient source, syngas methanation above 1 L/L_pbv/D was achieved. • Methanobacterium and Sporomusa were dominant genera throughout the process. • Acetate conversion proceeded via both methanogenesis and syntrophic acetate oxidation.

Genome-Scale Mining of Acetogens of the Genus Clostridium Unveils Distinctive Traits in [FeFe]- and [NiFe]-Hydrogenase Content and Maturation

Knowledge of the organizational and functional properties of hydrogen metabolism is pivotal to the construction of a framework supportive of a hydrogen-fueled low-carbon economy. Hydrogen metabolism relies on the mechanism of action of hydrogenases. In this study, we investigated the genomes of several industrially relevant acetogens of the genus Clostridium (C. autoethanogenum, C. ljungdahlii, C. carboxidivorans, C. drakei, C. scatologenes, C. coskatii, C. ragsdalei, C. sp. AWRP) to systematically identify their intriguingly diversified hydrogenases’ repertoire. An entirely computational annotation pipeline unveiled common and strain-specific traits in the functional content of [NiFe]- and [FeFe]-hydrogenases. Hydrogenases were identified and categorized into functionally distinct classes by the combination of sequence homology, with respect to a database of curated nonredundant hydrogenases, with the analysis of sequence patterns characteristic of the mode of action of [FeFe]- and [NiFe]-hydrogenases. The inspection of the genes in the neighborhood of the catalytic subunits unveiled a wide agreement between their genomic arrangement and the gene organization templates previously developed for the predicted hydrogenase classes. Subunits’ characterization of the identified hydrogenases allowed us to glean some insights on the redox cofactor-binding determinants in the diaphorase subunits of the electron-bifurcating [FeFe]-hydrogenases. Finally, the reliability of the inferred hydrogenases was corroborated by the punctual analysis of the maturation proteins necessary for the biosynthesis of [NiFe]- and [FeFe]-hydrogenases.

IMPORTANCE Mastering hydrogen metabolism can support a sustainable carbon-neutral economy. Of the many microorganisms metabolizing hydrogen, acetogens of the genus Clostridium are appealing, with some of them already in usage as industrial workhorses. Having provided detailed information on the hydrogenase content of an unprecedented number of clostridial acetogens at the gene level, our study represents a valuable knowledge base to deepen our understanding of hydrogenases’ functional specificity and/or redundancy and to develop a large array of biotechnological processes. We also believe our study could serve as a basis for future strain-engineering approaches, acting at the hydrogenases’ level or at the level of their maturation proteins. On the other side, the wealth of functional elements discussed in relation to the identified hydrogenases is worthy of further investigation by biochemical and structural studies to ultimately lead to the usage of these enzymes as valuable catalysts.

Genetic Evidence Reveals the Indispensable Role of the rseC Gene for Autotrophy and the Importance of a Functional Electron Balance for Nitrate Reduction in Clostridium ljungdahlii

For Clostridium ljungdahlii, the RNF complex plays a key role for energy conversion from gaseous substrates such as hydrogen and carbon dioxide. In a previous study, a disruption of RNF-complex genes led to the loss of autotrophy, while heterotrophy was still possible via glycolysis. Furthermore, it was shown that the energy limitation during autotrophy could be lifted by nitrate supplementation, which resulted in an elevated cellular growth and ATP yield. Here, we used CRISPR-Cas12a to delete: (1) the RNF complex-encoding gene cluster rnfCDGEAB; (2) the putative RNF regulator gene rseC; and (3) a gene cluster that encodes for a putative nitrate reductase. The deletion of either rnfCDGEAB or rseC resulted in a complete loss of autotrophy, which could be restored by plasmid-based complementation of the deleted genes. We observed a transcriptional repression of the RNF-gene cluster in the rseC-deletion strain during autotrophy and investigated the distribution of the rseC gene among acetogenic bacteria. To examine nitrate reduction and its connection to the RNF complex, we compared autotrophic and heterotrophic growth of our three deletion strains with either ammonium or nitrate. The rnfCDGEAB- and rseC-deletion strains failed to reduce nitrate as a metabolic activity in non-growing cultures during autotrophy but not during heterotrophy. In contrast, the nitrate reductase deletion strain was able to grow in all tested conditions but lost the ability to reduce nitrate. Our findings highlight the important role of the rseC gene for autotrophy, and in addition, contribute to understand the connection of nitrate reduction to energy metabolism.

A functional Wood-Ljungdahl pathway devoid of a formate dehydrogenase in the gut acetogens Blautia wexlerae, Blautia luti and beyond

Species of the genus Blautia are typical inhabitants of the human gut and considered as beneficial gut microbes. However, their role in the gut microbiome and their metabolic features are poorly understood. Blautia schinkii was described as an acetogenic bacterium, characterized by a functional Wood-Ljungdahl pathway (WLP) of acetogenesis from H₂ + CO₂ . Here we report that two relatives, Blautia luti and Blautia wexlerae do not grow on H₂ + CO₂ . Inspection of the genome sequence revealed all genes of the WLP except genes encoding a formate dehydrogenase and an electron-bifurcating hydrogenase. Enzyme assays confirmed this prediction. Accordingly, resting cells neither converted H₂ + CO₂ nor H₂ + HCOOH + CO₂ to acetate. Carbon monoxide is an intermediate of the WLP and substrate for many acetogens. B. luti and B. wexlerae had an active CO dehydrogenase and resting cells performed acetogenesis from HCOOH + CO₂ + CO, demonstrating a functional WLP. Bioinformatic analyses revealed that many Blautia strains as well as other gut acetogens lack formate dehydrogenases and hydrogenases. Thus, the use of formate instead of H₂ + CO₂ as an interspecies hydrogen and electron carrier seems to be more common in the gut microbiome. This article is protected by copyright. All rights reserved.

Metabolic Engineering Interventions for Sustainable 2,3-Butanediol Production in Gas-Fermenting Clostridium autoethanogenum

Gas fermentation provides a promising platform to turn low-cost and readily available single-carbon waste gases into commodity chemicals, such as 2,3-butanediol. Clostridium autoethanogenum is usually used as a robust and flexible chassis for gas fermentation. Here, we leveraged constraint-based stoichiometric modeling and kinetic ensemble modeling of the C. autoethanogenum metabolic network to provide a systematic in silico analysis of metabolic engineering interventions for 2,3-butanediol overproduction and low carbon substrate loss in dissipated CO₂. Our analysis allowed us to identify and to assess comparatively the expected performances for a wide range of single, double, and triple interventions. Our analysis managed to individuate bottleneck reactions in relevant metabolic pathways when suggesting intervening strategies. Besides recapitulating intuitive and/or previously attempted genetic modifications, our analysis neatly outlined that interventions-at least partially-impinging on by-products branching from acetyl coenzyme A (acetyl-CoA) and pyruvate (acetate, ethanol, amino acids) offer valuable alternatives to the interventions focusing directly on the specific branch from pyruvate to 2,3-butanediol. IMPORTANCE Envisioning value chains inspired by environmental sustainability and circularity in economic models is essential to counteract the alterations in the global natural carbon cycle induced by humans. Recycling carbon-based waste gas streams into chemicals by devising gas fermentation bioprocesses mediated by acetogens of the genus Clostridium is one component of the solution. Carbon monoxide originates from multiple biogenic and abiogenic sources and bears a significant environmental impact. This study aims at identifying metabolic engineering interventions for increasing 2,3-butanediol production and avoiding carbon loss in CO₂ dissipation via C. autoethanogenum fermenting a substrate comprising CO and H₂. 2,3-Butanediol is a valuable biochemical by-product since, due to its versatility, can be transformed quite easily into chemical compounds such as butadiene, diacetyl, acetoin, and methyl ethyl ketone. These compounds are usable as building blocks to manufacture a vast range of industrially produced chemicals.

Comparison of Syngas-Fermenting Clostridia in Stirred-Tank Bioreactors and the Effects of Varying Syngas Impurities

In recent years, syngas fermentation has emerged as a promising means for the production of fuels and platform chemicals, with a variety of acetogens efficiently converting CO-rich gases to ethanol. However, the feasibility of syngas fermentation processes is related to the occurrence of syngas impurities such as NH3, H2S, and NOX. Therefore, the effects of defined additions of NH4+, H2S, and NO3− were studied in autotrophic batch processes with C. autoethanogenum, C. ljungdahlii, and C. ragsdalei while applying continuously gassed stirred-tank bioreactors. Any initial addition of ammonium and nitrate curbed the cell growth of the Clostridia being studied and reduced the final alcohol concentrations. C. ljungdahlii showed the highest tolerance to ammonium and nitrate, whereas C. ragsdalei was even positively influenced by the presence of 0.1 g L−1 H2S. Quantitative goals for the purification of syngas were identified for each of the acetogens studied in the used experimental setup. Syngas purification should in particular focus on the NOX impurities that caused the highest inhibiting effect and maintain the concentrations of NH3 and H2S within an acceptable range (e.g., NH3 < 4560 ppm and H2S < 108 ppm) in order to avoid inhibition through the accumulation of these impurities in the bioreactor.

Continuous sulfide supply enhanced autotrophic production of alcohols with Clostridium ragsdalei

Autotrophic syngas fermentation with clostridia enables the conversion of CO, CO2, and H2 into organic acids and alcohols. The batch process performance of Clostridium ragsdalei was studied in fully controlled and continuously gassed (600 mbar CO, 200 mbar H2, 200 mbar CO2) stirred-tank bioreactors. The final ethanol concentration varied as function of the reaction conditions. Decreasing the pH from pH 6.0-5.5 at a temperature of 37 °C increased the ethanol concentration from 2.33 g L-1 to 3.95 g L-1, whereas lowering the temperature from 37 to 32 °C at constant pH 6.0 resulted in a final ethanol concentration of 5.34 g L-1 after 5 days of batch operation. The sulphur availability was monitored by measuring the cysteine concentration in the medium and the H2S fraction in the exhaust gas. It was found that most of the initially added sulphur was stripped out within the first day of the batch process (first half of the exponential growth phase). A continuous sodium sulfide feed allowed ethanol concentrations to increase more than threefold to 7.67 g L-1 and the alcohol-to-acetate ratio to increase 43-fold to 17.71 g g-1.

Effect of Humin and Chemical Factors on CO2-Fixing Acetogenesis and Methanogenesis

Acetogenesis and methanogenesis have attracted attention as CO₂-fixing reactions. Humin, a humic substance insoluble at any pH, has been found to assist CO₂-fixing acetogenesis as the sole electron donor. Here, using two CO₂-fixing consortia with acetogenic and methanogenic activities, the effect of various parameters on these activities was examined. One consortium utilized humin and hydrogen (H₂) as electron donors for acetogenesis, either separately or simultaneously, but with a preference for the electron use from humin. The acetogenic activity was accelerated 14 times by FeS at 0.2 g/L as the optimal concentration, while being inhibited by MgSO₄ at concentration above 0.02 g/L and by NaCl at concentrations higher than 6 g/L. Another consortium did not utilize humin but H₂ as electron donor, suggesting that humin was not a universal electron donor for acetogenesis. For methanogenesis, both consortia did not utilize extracellular electrons from humin unless H₂ was present. The methanogenesis was promoted by FeS at 0.2 g/L or higher concentrations, especially without humin, and with NaCl at 2 g/L or higher concentrations regardless of the presence of humin, while no significant effect was observed with MgSO₄. Comparative sequence analysis of partial 16S rRNA genes suggested that minor groups were the humin-utilizing acetogens in the consortium dominated by Clostridia, while Methanobacterium was the methanogen utilizing humin with H₂.

Clostridium thailandense sp. nov., a novel CO2-reducing acetogenic bacterium isolated from peatland soil

Some species of the genus Clostridium are efficient acetate producers and have been deemed useful for upgrading industrial biogas. An acetogenic, strictly anaerobic, Gram-stain-positive, subterminal endospore-forming bacterium designated strain PL3T was isolated from peatland soil enrichments with H2 and CO2. Cells of strain PL3T were 0.8–1.0×4.0–10.0 µm in size and rod-shaped. Growth of strain PL3T occurred at pH 6.0–7.5 (optimum, pH 7.0), at 20–40 °C (optimum, 30 °C) and with 0–1.5 % (w/v) NaCl (optimum, 0.5%). Biochemical analyses revealed that strain PL3T metabolized lactose, maltose, raffinose, rhamnose, lactic acid, sorbitol, arabinose and glycerol. Acetic acid was the predominant metabolite under anaerobic respiration with H2/CO2. The major cellular fatty acids were C16 : 0, C16 : 1 cis 9 and C17 : 0 cyc. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, aminolipid and aminophospholipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PL3T belongs to the genus Clostridium with the highest sequence similarity to Clostridium aciditolerans DSM 17425T (98.6 %) followed by Clostridium nitrophenolicum (97.8 %). The genomic DNA G+C content of strain PL3T was 31.1 mol%.The genomic in silico DNA–DNA hybridization value between strain PL3T and C. aciditolerans DSM 17425T was 25.1 %, with an average nucleotide identity of 80.2 %. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain PL3T was suggested to represent a novel species of the genus Clostridium , for which the name Clostridium thailandense sp. nov. is proposed. The type strain is PL3T (=DSM 111812T=TISTR 2984T).

Biological conversion of carbon monoxide and hydrogen by anaerobic culture: Prospect of anaerobic digestion and thermochemical processes combination

Waste biomass is considered a promising renewable energy feedstock that can be converted by anaerobic digestion. However, anaerobic digestion application can be challenging due to the structural complexity of several waste biomass kinds. Therefore, coupling anaerobic digestion with thermochemical processes can offset the limitations and convert the hardly biodegradable waste biomass, including digestate residue, into value-added products: syngas and pyrogas (gaseous mixtures consisting mainly of H₂, CO, CO₂), bio-oil, and biochar for further valorisation. In this review, the utilisation boundaries and benefits of the aforementioned products by anaerobic culture are discussed. First, thermochemical process parameters for an enhanced yield of desired products are summarised. Particularly, the microbiology of CO and H₂ mixture biomethanation and fermentation in anaerobic digestion is presented. Finally, the state-of-the-art biological conversion of syngas and pyrogas to CH₄ mediated by anaerobic culture is adequately described. Extensive research shows the successful selective biological conversion of CO and H₂ to CH₄, acetic acid, and alcohols. The main bottleneck is the gas-liquid mass transfer which can be enhanced appropriately by bioreactors' configurations. A few research groups focus on bio-oil and biochar addition into anaerobic digesters. However, according to the literature review, there has been no research for utilising all value-added products at once in anaerobic digestion published so far. Although synergic effects of such can be expected. In summary, the combination of anaerobic digestion and thermochemical processes is a promising alternative for wide-scale waste biomass utilisation in practice.

Exploiting Aerobic Carboxydotrophic Bacteria for Industrial Biotechnology

Aerobic carboxydotrophic bacteria are a group of microorganisms which possess the unique trait to oxidize carbon monoxide (CO) as sole energy source with molecular oxygen (O₂) to produce carbon dioxide (CO₂) which subsequently is used for biomass formation via the Calvin-Benson-Bassham cycle. Moreover, most carboxydotrophs are also able to oxidize hydrogen (H₂) with hydrogenases to drive the reduction of carbon dioxide in the absence of CO. As several abundant industrial off-gases contain significant amounts of CO, CO₂, H₂ as well as O₂, these bacteria come into focus for industrial application to produce chemicals and fuels from such gases in gas fermentation approaches. Since the group of carboxydotrophic bacteria is rather unknown and not very well investigated, we will provide an overview about their lifestyle and the underlying metabolic characteristics, introduce promising members for industrial application, and give an overview of available genetic engineering tools. We will point to limitations and discuss challenges, which have to be overcome to apply metabolic engineering approaches and to utilize aerobic carboxydotrophs in the industrial environment.

Syngas biomethanation: effect of biomass-gas ratio, syngas composition and pH buffer

The concept of syngas biomethanation is attractive, however, it still needs improvement in optimizing the operational conditions. In the present study, syngas fermentations under different carbon monoxide (CO), carbon dioxide (CO₂) and hydrogen (H₂) compositions were conducted under two different biomass-gas ratio (BGR) systems. The results showed that high BGR enhanced the CO consumption rate, achieving a 60% enhancement with CO as the sole substrate. Stoichiometric H₂ addition could successfully convert all the CO and CO₂ to pure methane, however, higher H₂ partial pressure might decline the CO consumption due to pH inhibition from consumption of bicarbonate. Microbial analysis showed different syngas composition could affect the bacteria community, while, archaea community was only slightly affected with Methanothermobacter as the dominant methanogen. This study provided strategy for efficient syngas biomethanation and deeper insight into effect of H₂ addition on CO conversion under different BGR systems.

Conversion of Carbon Monoxide to Chemicals Using Microbial Consortia

Syngas, a gaseous mixture of CO, H₂ and CO₂, can be produced by gasification of carbon-containing materials, including organic waste materials or lignocellulosic biomass. The conversion of bio-based syngas to chemicals is foreseen as an important process in circular bioeconomy. Carbon monoxide is also produced as a waste gas in many industrial sectors (e.g., chemical, energy, steel). Often, the purity level of bio-based syngas and waste gases is low and/or the ratios of syngas components are not adequate for chemical conversion (e.g., by Fischer-Tropsch). Microbes are robust catalysts to transform impure syngas into a broad spectrum of products. Fermentation of CO-rich waste gases to ethanol has reached commercial scale (by axenic cultures of Clostridium species), but production of other chemical building blocks is underexplored. Currently, genetic engineering of carboxydotrophic acetogens is applied to increase the portfolio of products from syngas/CO, but the limited energy metabolism of these microbes limits product yields and applications (for example, only products requiring low levels of ATP for synthesis can be produced). An alternative approach is to explore microbial consortia, including open mixed cultures and synthetic co-cultures, to create a metabolic network based on CO conversion that can yield products such as medium-chain carboxylic acids, higher alcohols and other added-value chemicals.

Biofuel and chemical production from carbon one industry flux gas by acetogenic bacteria

Carbon one industry flux gas generated from fossil fuels, various industrial and domestic waste, as well as lignocellulosic biomass provides an innovative raw material to lead the sustainable development. Through the chemical and biological processing, the gas mixture composed of CO, CO₂, and H₂, also termed as syngas, is converted to biofuels and high-value chemicals. Here, the syngas fermentation process is elaborated to provide an overview. Sources of syngas are summarized and the influences of impurities on biological fermentation are exhibited. Acetogens and carboxydotrophs are the two main clusters of syngas utilizing microorganisms, their essential characters are presented, especially the energy metabolic scheme with CO, CO₂, and H₂. Synthetic biology techniques and microcompartment regulation are further discussed and proposed to create a high-efficiency cell factory. Moreover, the influencing factors in fermentation and products in carboxylic acids, alcohols, and others such like polyhydroxyalkanoate and poly-3-hydroxybutyrate are addressed. Biological fermentation from carbon one industry flux gas is a promising alternative, the latest scientific advances are expatiated hoping to inspire more creative transformation.

Reactor Designs and Configurations for Biological and Bioelectrochemical C1 Gas Conversion: A Review

Microbial C1 gas conversion technologies have developed into a potentially promising technology for converting waste gases (CO₂, CO) into chemicals, fuels, and other materials. However, the mass transfer constraint of these poorly soluble substrates to microorganisms is an important challenge to maximize the efficiencies of the processes. These technologies have attracted significant scientific interest in recent years, and many reactor designs have been explored. Syngas fermentation and hydrogenotrophic methanation use molecular hydrogen as an electron donor. Furthermore, the sequestration of CO₂ and the generation of valuable chemicals through the application of a biocathode in bioelectrochemical cells have been evaluated for their great potential to contribute to sustainability. Through a process termed microbial chain elongation, the product portfolio from C1 gas conversion may be expanded further by carefully driving microorganisms to perform acetogenesis, solventogenesis, and reverse β-oxidation. The purpose of this review is to provide an overview of the various kinds of bioreactors that are employed in these microbial C1 conversion processes.

Butyrate production in the acetogen Eubacterium limosum is dependent on the carbon and energy source

Eubacterium limosum KIST612 is one of the few acetogenic bacteria that has the genes encoding for butyrate synthesis from acetyl-CoA, and indeed, E. limosum KIST612 is known to produce butyrate from CO but not from H2  + CO2 . Butyrate production from CO was only seen in bioreactors with cell recycling or in batch cultures with addition of acetate. Here, we present detailed study on growth of E. limosum KIST612 on different carbon and energy sources with the goal, to find other substrates that lead to butyrate formation. Batch fermentations in serum bottles revealed that acetate was the major product under all conditions investigated. Butyrate formation from the C1 compounds carbon dioxide and hydrogen, carbon monoxide or formate was not observed. However, growth on glucose led to butyrate formation, but only in the stationary growth phase. A maximum of 4.3 mM butyrate was observed, corresponding to a butyrate:glucose ratio of 0.21:1 and a butyrate:acetate ratio of 0.14:1. Interestingly, growth on the C1 substrate methanol also led to butyrate formation in the stationary growth phase with a butyrate:methanol ratio of 0.17:1 and a butyrate:acetate ratio of 0.33:1. Since methanol can be produced chemically from carbon dioxide, this offers the possibility for a combined chemical-biochemical production of butyrate from H2 + CO2 using this acetogenic biocatalyst. With the advent of genetic methods in acetogens, butanol production from methanol maybe possible as well.

Synthetic co-culture of autotrophic Clostridium carboxidivorans and chain elongating Clostridium kluyveri monitored by flow cytometry

Syngas fermentation with acetogens is known to produce mainly acetate and ethanol efficiently. Co-cultures with chain elongating bacteria making use of these products are a promising approach to produce longer-chain alcohols. Synthetic co-cultures with identical initial cell concentrations of Clostridium carboxidivorans and Clostridium kluyveri were studied in batch-operated stirred-tank bioreactors with continuous CO/CO₂ -gassing and monitoring of the cell counts of both clostridia by flow cytometry after fluorescence in situ hybridization (FISH-FC). At 800 mbar CO, chain elongation activity was observed at pH 6.0, although growth of C. kluyveri was restricted. Organic acids produced by C. kluyveri were reduced by C. carboxidivorans to the corresponding alcohols butanol and hexanol. This resulted in a threefold increase in final butanol concentration and enabled hexanol production compared with a mono-culture of C. carboxidivorans. At 100 mbar CO, growth of C. kluyveri was improved; however, the capacity of C. carboxidivorans to form alcohols was reduced. Because of the accumulation of organic acids, a constant decay of C. carboxidivorans was observed. The measurement of individual cell concentrations in co-culture established in this study may serve as an effective tool for knowledge-based identification of optimum process conditions for enhanced formation of longer-chain alcohols by clostridial co-cultures.

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.

Protective effect of a reverse membrane bioreactor against toluene and naphthalene in anaerobic digestion

Raw syngas contains tar contaminants including toluene and naphthalene, which inhibit its conversion to methane. Cell encasement in a hydrophilic reverse membrane bioreactor (RMBR) could protect the cells from hydrophobic contaminants. This study aimed to investigate the inhibition of toluene and naphthalene and the effect of using RMBR. In this work, toluene and naphthalene were added at concentrations of 0.5-1.0 and 0.1-0.2 g/L in batch operation. In continuous operation, concentration of 0-6.44 g/L for toluene and 0-1.28 g/L for naphthalene were studied. The results showed that no inhibition was observed in batch operation for toluene and naphthalene at concentrations up to 1 and 0.2 g/L, respectively. In continuous operation of free cell bioreactors (FCBRs), inhibition of toluene and naphthalene started at 2.05 and 0.63 g/L, respectively. When they were present simultaneously, inhibition of toluene and naphthalene occurred at concentrations of 3.14 and 0.63 g/L, respectively. In continuous RMBRs, no inhibition for toluene and less inhibition for naphthalene were observed, resulting in higher methane production from RMBR than that of FCBR. These results indicated that RMBR system gave a better protection effect against inhibitors compared with FCBR.

A Win-Loss Interaction on Fe0 Between Methanogens and Acetogens From a Climate Lake

Diverse physiological groups congregate into environmental corrosive biofilms, yet the interspecies interactions between these corrosive physiological groups are seldom examined. We, therefore, explored Fe⁰-dependent cross-group interactions between acetogens and methanogens from lake sediments. On Fe⁰, acetogens were more corrosive and metabolically active when decoupled from methanogens, whereas methanogens were more metabolically active when coupled with acetogens. This suggests an opportunistic (win-loss) interaction on Fe⁰ between acetogens (loss) and methanogens (win). Clostridia and Methanobacterium were the major candidates doing acetogenesis and methanogenesis after four transfers (metagenome sequencing) and the only groups detected after 11 transfers (amplicon sequencing) on Fe⁰. Since abiotic H₂ failed to explain the high metabolic rates on Fe⁰, we examined whether cell exudates (spent media filtrate) promoted the H₂-evolving reaction on Fe⁰ above abiotic controls. Undeniably, spent media filtrate generated three- to four-fold more H₂ than abiotic controls, which could be partly explained by thermolabile enzymes and partly by non-thermolabile constituents released by cells. Next, we examined the metagenome for candidate enzymes/shuttles that could catalyze H₂ evolution from Fe⁰ and found candidate H₂-evolving hydrogenases and an almost complete pathway for flavin biosynthesis in Clostridium. Clostridial ferredoxin-dependent [FeFe]-hydrogenases may be catalyzing the H₂-evolving reaction on Fe⁰, explaining the significant H₂ evolved by spent media exposed to Fe⁰. It is typical of Clostridia to secrete enzymes and other small molecules for lytic purposes. Here, they may secrete such molecules to enhance their own electron uptake from extracellular electron donors but indirectly make their H₂-consuming neighbors-Methanobacterium-fare five times better in their presence. The particular enzymes and constituents promoting H₂ evolution from Fe⁰ remain to be determined. However, we postulate that in a static environment like corrosive crust biofilms in lake sediments, less corrosive methanogens like Methanobacterium could extend corrosion long after acetogenesis ceased, by exploiting the constituents secreted by acetogens.

Production of the biocommodities butanol and acetone from methanol with fluorescent FAST-tagged proteins using metabolically engineered strains of Eubacterium limosum

BACKGROUND

The interest in using methanol as a substrate to cultivate acetogens increased in recent years since it can be sustainably produced from syngas and has the additional benefit of reducing greenhouse gas emissions. Eubacterium limosum is one of the few acetogens that can utilize methanol, is genetically accessible and, therefore, a promising candidate for the recombinant production of biocommodities from this C1 carbon source. Although several genetic tools are already available for certain acetogens including E. limosum, the use of brightly fluorescent reporter proteins is still limited.

RESULTS

In this study, we expanded the genetic toolbox of E. limosum by implementing the fluorescence-activating and absorption shifting tag (FAST) as a fluorescent reporter protein. Recombinant E. limosum strains that expressed the gene encoding FAST in an inducible and constitutive manner were constructed. Cultivation of these recombinant strains resulted in brightly fluorescent cells even under anaerobic conditions. Moreover, we produced the biocommodities butanol and acetone from methanol with recombinant E. limosum strains. Therefore, we used E. limosum cultures that produced FAST-tagged fusion proteins of the bifunctional acetaldehyde/alcohol dehydrogenase or the acetoacetate decarboxylase, respectively, and determined the fluorescence intensity and product concentrations during growth.

CONCLUSIONS

The addition of FAST as an oxygen-independent fluorescent reporter protein expands the genetic toolbox of E. limosum. Moreover, our results show that FAST-tagged fusion proteins can be constructed without negatively impacting the stability, functionality, and productivity of the resulting enzyme. Finally, butanol and acetone can be produced from methanol using recombinant E. limosum strains expressing genes encoding fluorescent FAST-tagged fusion proteins.

Hydrogen as a Co-electron Donor for Chain Elongation With Complex Communities

Electron donor scarcity is seen as one of the major issues limiting economic production of medium-chain carboxylates from waste streams. Previous studies suggest that co-fermentation of hydrogen in microbial communities that realize chain elongation relieves this limitation. To better understand how hydrogen co-feeding can support chain elongation, we enriched three different microbial communities from anaerobic reactors (A, B, and C with ascending levels of diversity) for their ability to produce medium-chain carboxylates from conventional electron donors (lactate or ethanol) or from hydrogen. In the presence of abundant acetate and CO₂, the effects of different abiotic parameters (pH values in acidic to neutral range, initial acetate concentration, and presence of chemical methanogenesis inhibitors) were tested along with the enrichment. The presence of hydrogen facilitated production of butyrate by all communities and improved production of i-butyrate and caproate by the two most diverse communities (B and C), accompanied by consumption of acetate, hydrogen, and lactate/ethanol (when available). Under optimal conditions, hydrogen increased the selectivity of conventional electron donors to caproate from 0.23 ± 0.01 mol e^-/mol e^- to 0.67 ± 0.15 mol e^-/mol e^- with a peak caproate concentration of 4.0 g L^-1. As a trade-off, the best-performing communities also showed hydrogenotrophic methanogenesis activity by Methanobacterium even at high concentrations of undissociated acetic acid of 2.9 g L^-1 and at low pH of 4.8. According to 16S rRNA amplicon sequencing, the suspected caproate producers were assigned to the family Anaerovoracaceae (Peptostreptococcales) and the genera Megasphaera (99.8% similarity to M. elsdenii), Caproiciproducens, and Clostridium sensu stricto 12 (97-100% similarity to C. luticellarii). Non-methanogenic hydrogen consumption correlated to the abundance of Clostridium sensu stricto 12 taxa (p < 0.01). If a robust methanogenesis inhibition strategy can be found, hydrogen co-feeding along with conventional electron donors can greatly improve selectivity to caproate in complex communities. The lessons learned can help design continuous hydrogen-aided chain elongation bioprocesses.

Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation

Ex situ biomethanation allows the conversion of hydrogen produced from surplus electricity to methane. The flexibility of the process was recently demonstrated, yet it is unknown how intermittent hydrogen feeding impacts the functionality of the microbial communities. We investigated the effect of starvation events on the hydrogen consumption and methane production rates (MPRs) of two different methanogenic communities that were fed with hydrogen and carbon dioxide. Both communities showed functional resilience in terms of hydrogen consumption and MPRs upon starvation periods of up to 14 days. The origin of the inoculum, community structure and dominant methanogens were decisive for high gas conversion rates. Thus, pre-screening a well performing inoculum is essential to ensure the efficiency of biomethanation systems operating under flexible gas feeding regimes. Our results suggest that the type of the predominant hydrogenotrophic methanogen (here: Methanobacterium) is important for an efficient process. We also show that flexible biomethanation of hydrogen and carbon dioxide with complex microbiota is possible while avoiding the accumulation of acetate, which is relevant for practical implementation. In our study, the inoculum from an upflow anaerobic sludge blanket reactor treating wastewater from paper industry performed better compared to the inoculum from a plug flow reactor treating cow manure and corn silage. Therefore, the implementation of the power-to-gas concept in wastewater treatment plants of the paper industry, where biocatalytic biomass is readily available, may be a viable option to reduce the carbon footprint of the paper industry.

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.

Surface Analysis of Coal Indicating Neutral Red Enhances the Precursor Steps of Methanogenesis

Artificially stimulated, high-yield microbial production of methane from coal is a challenging problem that continues to generate research interest. Decomposition of organic matter and production of methane from coal are the results of multiple redox reactions carried out by different communities of bacteria and archaea. Recent work by our group (Beckmann et al., 2015) demonstrated that the presence of the redox-mediating molecule neutral red, in its crystalline form on a coal surface, can increase methane production. However, hydrolysis and the acetogenesis of the coal surface are essential precursor steps for methane production by archaea. Acetogenesis is the preparation phase of methanogenesis because methanogens can only assimilate acetate, CO₂ and H₂ among the products formed during this process. In the present study, the surface chemical analysis of neutral red treated coal using attenuated total reflectance-fourier transform infrared (ATR-FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS) demonstrate that the acetate production and resulting oxidation of the coal only occurred at few nanometers into the coal surface (at the nanoscale <5 nm). We observed that in the presence of neutral red and groundwater microbes, acetate signals in coal surface chemistry increased. This is the first evidence suggesting that neutral red enhances the biological conversion of coal into acetate. Microscopy demonstrated that neutral red crystals were co-localize with cells at the surface of coal in groundwater. This is consistent with neutral red crystals serving as a redox hub, concentrating and distributing reducing equivalents amongst the microbial community. In this study, the chemical changes of neutral red treated coal indicated that neutral red doubles the concentration of acetate over the control (coal without neutral red), emphasizing the importance of maximizing the fracture surface coverage of this redox mediator. Overall, results suggested that, neutral red not only can benefit acetoclastic methanogens, but also the fermentative and acetogenic bacteria involved in generating acetate.

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.

Combination of Trace Metal to Improve Solventogenesis of Clostridium carboxidivorans P7 in Syngas Fermentation

Higher alcohols such as butanol (C4 alcohol) and hexanol (C6 alcohol) are superior biofuels compared to ethanol. Clostridium carboxidivorans P7 is a typical acetogen capable of producing C4 and C6 alcohols natively. In this study, the composition of trace metals in culture medium was adjusted, and the effects of these adjustments on artificial syngas fermentation by C. carboxidivorans P7 were investigated. Nickel and ferrous ions were essential for growth and metabolite synthesis during syngas fermentation by P7. However, a decreased dose of molybdate improved alcohol fermentation performance by stimulating carbon fixation and solventogenesis. In response to the modified trace metal composition, cells grew to a maximum OD_{600 nm} of 1.6 and accumulated ethanol and butanol to maximum concentrations of 2.0 and 1.0 g/L, respectively, in serum bottles. These yields were ten-fold higher than the yields generated using the original composition of trace metals. Furthermore, 0.5 g/L of hexanol was detected at the end of fermentation. The results from gene expression experiments examining genes related to carbon fixation and organic acid and solvent synthesis pathways revealed a dramatic up-regulation of the Wood-Ljungdahl pathway (WLP) gene cluster, the bcs gene cluster, and a putative CoA transferase and butanol dehydrogenase, thereby indicating that both de novo synthesis and acid re-assimilation contributed to the significantly elevated accumulation of higher alcohols. The bdh35 gene was speculated to be the key target for butanol synthesis during solventogenesis.

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.