Old acetogens, new light

Carbon-wise utilization of lignin-related compounds by synergistically employing anaerobic and aerobic bacteria

BACKGROUND

Lignin is a highly abundant but strongly underutilized natural resource that could serve as a sustainable feedstock for producing chemicals by microbial cell factories. Because of the heterogeneous nature of the lignin feedstocks, the biological upgrading of lignin relying on the metabolic routes of aerobic bacteria is currently considered as the most promising approach. However, the limited substrate range and the inefficient catabolism of the production hosts hinder the upgrading of lignin-related aromatics. Particularly, the aerobic O-demethylation of the methoxyl groups in aromatic substrates is energy-limited, inhibits growth, and results in carbon loss in the form of CO2.

RESULTS

In this study, we present a novel approach for carbon-wise utilization of lignin-related aromatics by the integration of anaerobic and aerobic metabolisms. In practice, we employed an acetogenic bacterium Acetobacterium woodii for anaerobic O-demethylation of aromatic compounds, which distinctively differs from the aerobic O-demethylation; in the process, the carbon from the methoxyl groups is fixed together with CO2 to form acetate, while the aromatic ring remains unchanged. These accessible end-metabolites were then utilized by an aerobic bacterium Acinetobacter baylyi ADP1. By utilizing this cocultivation approach, we demonstrated an upgrading of guaiacol, an abundant but inaccessible substrate to most microbes, into a plastic precursor muconate, with a nearly equimolar yields (0.9 mol/mol in a small-scale cultivation and 1.0 mol/mol in a one-pot bioreactor cultivation). The process required only a minor genetic engineering, namely a single gene knock-out. Noticeably, by employing a metabolic integration of the two bacteria, it was possible to produce biomass and muconate by utilizing only CO2 and guaiacol as carbon sources.

CONCLUSIONS

By the novel approach, we were able to overcome the issues related to aerobic O-demethylation of methoxylated aromatic substrates and demonstrated carbon-wise conversion of lignin-related aromatics to products with yields unattainable by aerobic processes. This study highlights the power of synergistic integration of distinctive metabolic features of bacteria, thus unlocking new opportunities for harnessing microbial cocultures in upgrading challenging feedstocks.

Multi-approach assessment of groundwater biogeochemistry: Implications for the site characterization of prospective spent nuclear fuel repository sites

The disposal of spent nuclear fuel in deep subsurface repositories using multi-barrier systems is considered to be the most promising method for preventing radionuclide leakage. However, the stability of the barriers can be affected by the activities of diverse microbes in subsurface environments. Therefore, this study investigated groundwater geochemistry and microbial populations, activities, and community structures at three potential spent nuclear fuel repository construction sites. The microbial analysis involved a multi-approach including both culture-dependent, culture-independent, and sequence-based methods for a comprehensive understanding of groundwater biogeochemistry. The results from all three sites showed that geochemical properties were closely related to microbial population and activities. Total number of cells estimates were strongly correlated to high dissolved organic carbon; while the ratio of adenosine-triphosphate:total number of cells indicated substantial activities of sulfate reducing bacteria. The 16S rRNA gene sequencing revealed that the microbial communities differed across the three sites, with each featuring microbes performing distinctive functions. In addition, our multi-approach provided some intriguing findings: a site with a low relative abundance of sulfate reducing bacteria based on the 16S rRNA gene sequencing showed high populations during most probable number incubation, implying that despite their low abundance, sulfate reducing bacteria still played an important role in sulfate reduction within the groundwater. Moreover, a redundancy analysis indicated a significant correlation between uranium concentrations and microbial community compositions, which suggests a potential impact of uranium on microbial community. These findings together highlight the importance of multi-methodological assessments in better characterizing groundwater biogeochemical properties for the selection of potential spent nuclear fuel disposal sites.

Volatile fatty acids production from kitchen waste slurry using anaerobic membrane bioreactor via alkaline fermentation with high salinity: Evaluation on process performance and microbial succession

In this study, a pilot-scale anaerobic membrane bioreactor (AnMBR) was developed to continuously produce volatile fatty acids (VFAs) from kitchen waste slurry under an alkaline condition. The alkaline fermentation effectively suppressed methanogenesis, thus achieving high VFAs production of 60.3 g/L. Acetic acid, propionic acid, and butyric acid accounted for over 95.0 % of the total VFAs. The VFAs yield, productivity, and chemical oxygen demand (COD) recovery efficiency reached 0.5 g/g-CODinfluent, 6.0 kg/m3/d, and 62.8 %, respectively. Moreover, the CODVFAs/CODeffluent ratio exceeded 96.0 %, and the CODVFAs/NH3-N ratio through ammonia distillation reached up to 192.5. The microbial community was reshaped during the alkaline fermentation with increasing salinity. The membrane fouling of the AnMBR was alleviated by chemical cleaning and sludge discharge, and membrane modules displayed a sustained filtration performance. In conclusion, this study demonstrated that high-quality VFAs could be efficiently produced from kitchen waste slurry using an AnMBR process via alkaline fermentation.

Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer

As one of the ultimate products of hydrocarbon biodegradation, inorganic carbon always be used to evaluate hydrocarbon biodegradation rates in petroleum-hydrocarbon-contaminated (PHC) aquifers. The evaluation method was challenged because of the existence of carbon fixation microorganisms, which may uptake inorganic carbons and consequently cause the biodegradation rates to be underestimated. We wonder if there are carbon fixation microorganisms in PHC aquifers. Although an extremely limited number of carbon fixation microorganisms in PHC sites have been studied in previous studies, the vast majority of microorganisms that participate in carbon fixation have not been systematically identified. To systematically reveal carbon fixation microorganisms and their survival environmental conditions, high-throughput metagenomic sequencing technologies, which are characterized by culture-independent, unbiased, and comprehensive methods for the detection and taxonomic characterization of microorganisms, were introduced to analyze the groundwater samples collected from a PHC aquifer. Results showed that 1041 genera were annotated as carbon fixation microorganisms, which accounted for 49% of the total number of genera in the PHC aquifer. Carbon fixation genes involved in Calvin-Benson-Bassham (CBB), 3-hydroxy propionate (3HP), reductive tricarboxylic acid (rTCA), and Wood-Ljungdahl (WL) cycles accounted for 2%, 41%, 34%, and 23% of the total carbon fixation genes, respectively, and 3HP, rTCA, and WL can be deemed as the dominant carbon fixation pathways. Most of the identified carbon fixation microorganisms are potential hydrocarbon biodegraders, and the most abundant carbon fixation microorganisms, such as Microbacterium, Novosphingobium, and Reyranella, were just the most abundant microorganisms in the aquifer system. It's deduced that most of the microorganisms in the aquifer were facultative autotrophic, and undertaking the dual responsibilities of degrading hydrocarbons to inorganic carbon and uptaking inorganic carbon to biomass.

The energy-converting hydrogenase Ech2 is important for the growth of the thermophilic acetogen Thermoanaerobacter kivui on ferredoxin-dependent substrates

Thermoanaerobacter kivui is the thermophilic acetogenic bacterium with the highest temperature optimum (66°C) and with high growth rates on hydrogen (H2) plus carbon dioxide (CO2). The bioenergetic model suggests that its redox and energy metabolism depends on energy-converting hydrogenases (Ech). Its genome encodes two Echs, Ech1 and Ech2, as sole coupling sites for energy conservation during growth on H2 + CO2. During growth on other substrates, its redox activity, the (proton-gradient-coupled) oxidation of H2 may be essential to provide reduced ferredoxin (Fd) to the cell. While Ech activity has been demonstrated biochemically, the physiological function of both Ech's is unclear. Toward that, we deleted the complete gene cluster encoding Ech2. Surprisingly, the ech2 mutant grew as fast as the wild type on sugar substrates and H2 + CO2. Hence, Ech1 may be the essential enzyme for energy conservation, and either Ech1 or another enzyme may substitute for H2-dependent Fd reduction during growth on sugar substrates, putatively the H2-dependent CO2 reductase (HDCR). Growth on pyruvate and CO, substrates that are oxidized by Fd-dependent enzymes, was significantly impaired, but to a different extent. While ∆ech2 grew well on pyruvate after four transfers, ∆ech2 did not adapt to CO. Cell suspensions of ∆ech2 converted pyruvate to acetate, but no acetate was produced from CO. We analyzed the genome of five T. kivui strains adapted to CO. Strikingly, all strains carried mutations in the hycB3 subunit of HDCR. These mutations are obviously essential for the growth on CO but may inhibit its ability to utilize Fd as substrate.

IMPORTANCE

Acetogens thrive by converting H2+CO2 to acetate. Under environmental conditions, this allows for only very little energy to be conserved (∆G'<-20 kJ mol-1). CO2 serves as a terminal electron acceptor in the ancient Wood-Ljungdahl pathway (WLP). Since the WLP is ATP neutral, energy conservation during growth on H2 + CO2 is dependent on the redox metabolism. Two types of acetogens can be distinguished, Rnf- and Ech-type. The function of both membrane-bound enzyme complexes is twofold-energy conversion and redox balancing. Ech couples the Fd-dependent reduction of protons to H2 to the formation of a proton gradient in the thermophilic bacterium Thermoanaerobacter kivui. This bacterium may be utilized in gas fermentation at high temperatures, due to very high conversion rates and the availability of genetic tools. The physiological function of an Ech hydrogenase in T. kivui was studied to contribute an understanding of its energy and redox metabolism, a prerequisite for future industrial applications.

Metaproteomic assessment of gut microbial and host functional perturbations in Helicobacter pylori-infected patients subjected to an antimicrobial protocol

The impact of therapeutic interventions on the human gut microbiota (GM) is a clinical issue of paramount interest given the strong interconnection between microbial dynamics and human health. Orally administered antibiotics are known to reduce GM biomass and modify GM taxonomic profile. However, the impact of antimicrobial therapies on GM functions and biochemical pathways has scarcely been studied. Here, we characterized the fecal metaproteome of 10 Helicobacter pylori-infected patients before (T0) and after 10 days (T1) of a successful quadruple therapy (bismuth, tetracycline, metronidazole, and rabeprazole) and 30 days after therapy cessation (T2), to investigate how GM and host functions change during the eradication and healing processes. At T1, the abundance ratio between microbial and host proteins was reversed compared with that at T0 and T2. Several pathobionts (including Klebsiella, Proteus, Enterococcus, Muribaculum, and Enterocloster) were increased at T1. Therapy reshaped the relative contributions of the functions required to produce acetate, propionate, and butyrate. Proteins related to the uptake and processing of complex glycans were increased. Microbial cross-feeding with sialic acid, fucose, and rhamnose was enhanced, whereas hydrogen sulfide production was reduced. Finally, microbial proteins involved in antibiotic resistance and inflammation were more abundant after therapy. Moreover, a reduction in host proteins with known roles in inflammation and H. pylori-mediated carcinogenesis was observed. In conclusion, our results support the use of metaproteomics to monitor drug-induced remodeling of GM and host functions, opening the way for investigating new antimicrobial therapies aimed at preserving gut environmental homeostasis.

Heterologous Production of Isopropanol Using Metabolically Engineered Acetobacterium woodii Strains

The depletion of fossil fuel resources and the CO2 emissions coupled with petroleum-based industrial processes present a relevant issue for the whole of society. An alternative to the fossil-based production of chemicals is microbial fermentation using acetogens. Acetogenic bacteria are able to metabolize CO or CO2 (+H2) via the Wood-Ljungdahl pathway. As isopropanol is widely used in a variety of industrial branches, it is advantageous to find a fossil-independent production process. In this study, Acetobacterium woodii was employed to produce isopropanol via plasmid-based expression of the enzymes thiolase A, CoA-transferase, acetoacetate decarboxylase and secondary alcohol dehydrogenase. An examination of the enzymes originating from different organisms led to a maximum isopropanol production of 5.64 ± 1.08 mM using CO2 + H2 as the carbon and energy source. To this end, the genes thlA (encoding thiolase A) and ctfA/ctfB (encoding CoA-transferase) of Clostridium scatologenes, adc (encoding acetoacetate decarboxylase) originating from C. acetobutylicum and sadH (encoding secondary alcohol dehydrogenase) of C. beijerinckii DSM 6423 were employed. Since bottlenecks in the isopropanol production pathway are known, optimization of the strain was investigated, resulting in a 2.5-fold increase in isopropanol concentration.

Assessing feasible H2-CO2 sources in the US as Feedstocks for Sustainable Aviation Fuel Precursors: Acetic Acid and Ethanol Production via Hydrogenotrophic Pathways

The environmental impact of carbon dioxide emissions is significant, and research is focused on mitigating these emissions and developing eco-friendly technologies in line with green chemistry principles. Waste-to-energy technologies play a crucial role in converting waste into renewable energy and valuable biofuels and bioproducts. This study specifically explores the utilization of waste gas emissions, particularly carbon dioxide, from various sources in the United States for the production of sustainable aviation fuel (SAF) precursors, such as ethanol and acetic acid. The study categorizes and quantifies the volumes of carbon dioxide emissions into three types: non-biogenic, biogenic, and biogenic emissions from ethanol production facilities. Stoichiometric calculations are applied to compare the amounts of carbon dioxide from each category with the available hydrogen production capacity, determining if sufficient hydrogen is present for converting carbon dioxide into SAF precursors. The study reveals two key findings. Firstly, there is a significant reserve of carbon dioxide, approximately 1648 million metric tons per year (MMTy), combining all three categories, which would require a substantial increase of approximately 35-40 times in the existing hydrogen production capacity of 4.988 MMTy. This increased hydrogen production has the potential to yield approximately 1067.82 MMTy of acetic acid and 189.19 MMTy of ethanol annually. Secondly, upon analyzing the quality and application of the three sources of carbon dioxide with the currently available hydrogen production capacity, it is found that biogenic carbon dioxide from ethanol plants is the most suitable choice for immediate production of SAF precursors. This would theoretically result in an annual production of 1.36 MMTy of ethanol and 1.772 MMTy of acetic acid. The other two sources of carbon dioxide can be considered potential reserves for future utilization when additional hydrogen production facilities are established. The study provides a foundation for assessing the aggregation potential required for acetic acid and ethanol production. By optimizing the use of waste gases as raw materials, the study not only enables the production of SAF precursors but also contributes to the passive reduction of greenhouse gas emissions.

Genomic potential and physiological characteristics of C1 metabolism in novel acetogenic bacteria

Acetogenic bacteria can utilize C1 compounds, such as carbon monoxide (CO), formate, and methanol, via the Wood-Ljungdahl pathway (WLP) to produce biofuels and biochemicals. Two novel acetogenic bacteria of the family Eubacteriaceae ES2 and ES3 were isolated from Eulsukdo, a delta island in South Korea. We conducted whole genome sequencing of the ES strains and comparative genome analysis on the core clusters of WLP with Acetobacterium woodii DSM1030T and Eubacterium limosum ATCC8486T. The methyl-branch cluster included a formate transporter and duplicates or triplicates copies of the fhs gene, which encodes formyl-tetrahydrofolate synthetase. The formate dehydrogenase cluster did not include the hydrogenase gene, which might be replaced by a functional complex with a separate electron bifurcating hydrogenase (HytABCDE). Additionally, duplicated copies of the acsB gene, encoding acetyl-CoA synthase, are located within or close to the carbonyl-branch cluster. The serum bottle culture showed that ES strains can utilize a diverse range of C1 compounds, including CO, formate, and methanol, as well as CO2. Notably, ES2 exhibited remarkable resistance to high concentrations of C1 substrates, such as 100% CO (200 kPa), 700 mM formate, and 500 mM methanol. Moreover, ES2 demonstrated remarkable growth rates under 50% CO (0.45 h-1) and 200 mM formate (0.34 h-1). These growth rates are comparable to or surpassing those previously reported in other acetogenic bacteria. Our study introduces novel acetogenic ES strains and describes their genetic and physiological characteristics, which can be utilized in C1-based biomanufacturing.

A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii

To inactivate the Wood-Ljungdahl pathway in the acetogenic model bacterium Acetobacterium woodii, the genes metVF encoding two of the subunits of the methylene-tetrahydrofolate reductase were deleted. As expected, the mutant did not grow on C1 compounds and also not on lactate, ethanol or butanediol. In contrast to a mutant in which the first enzyme of the pathway (hydrogen-dependent CO2 reductase) had been genetically deleted, cells were able to grow on fructose, albeit with lower rates and yields than the wild-type. Growth was restored by addition of an external electron sink, glycine betaine + CO2 or caffeate. Resting cells pre-grown on fructose plus an external electron acceptor fermented fructose to two acetate and four hydrogen, that is, performed hydrogenogenesis. Cells pre-grown under fermentative conditions on fructose alone redirected carbon and electrons to form lactate, formate, ethanol as well as hydrogen. Apparently, growth on fructose alone induced enzymes for mixed acid fermentation (MAF). Transcriptome analyses revealed enzymes potentially involved in MAF and a quantitative model for MAF from fructose in A. woodii is presented.

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.

Thermophilic Moorella thermoacetica as a platform microorganism for C1 gas utilization: physiology, engineering, and applications

In the context of the rapid development of low-carbon economy, there has been increasing interest in utilizing naturally abundant and cost-effective one-carbon (C1) substrates for sustainable production of chemicals and fuels. Moorella thermoacetica, a model acetogenic bacterium, has attracted significant attention due to its ability to utilize carbon dioxide (CO2) and carbon monoxide (CO) via the Wood-Ljungdahl (WL) pathway, thereby showing great potential for the utilization of C1 gases. However, natural strains of M. thermoacetica are not yet fully suitable for industrial applications due to their limitations in carbon assimilation and conversion efficiency as well as limited product range. Over the past decade, progresses have been made in the development of genetic tools for M. thermoacetica, accelerating the understanding and modification of this acetogen. Here, we summarize the physiological and metabolic characteristics of M. thermoacetica and review the recent advances in engineering this bacterium. Finally, we propose the future directions for exploring the real potential of M. thermoacetica in industrial applications.

Isolation and characterization of reductive acetogens from rumen fluid samples of Murrah buffaloes

In the present study, attempts have been made to isolate reductive acetogens from the rumen fluid samples of Murrah buffaloes (Bubalus bubalis). Out of 32 rumen samples 51 isolates were isolated, and based on autotrophic growth for production of acetate and presence of formyltetrahydrofolate synthetase gene (FTHFS) 12 isolates were confirmed as reductive acetogens. Microscopic observations showed that ten isolates as Gram-positive rods (ACB28, ACB29, ACB66, ACB73, ACB81, ACB91, ACB133, ACB229, ACB52, ACB95) and two isolates as Gram-positive cocci (ACB19, ACB89). All isolates tested negative for catalase, oxidase, and gelatin liquefaction, whereas the production of H2S was detected for two (ACB52 and ACB95) of the above isolates. All these isolates showed autotrophic growth from H2 and CO2, and heterotrophic growth with different fermentable sugars, viz., d-glucose, D-fructose, and D-trehalose but failed to grow on salicin, raffinose, and l-rhamnose. Out of the isolates, two showed amylase activity (ACB28 and ACB95), five showed CMCase activity (ACB19, ACB28, ACB29, ACB73 and ACB91), three showed pectinase activity (ACB29, ACB52 and ACB89), whereas none of the isolates was found positive for avicellase and xylanase activity. Based on 16S rDNA gene sequence analysis, the isolates showed their phylogenetic relationship with maximum similarity up to 99% to different strains of earlier reported known acetogens of clostridia group including Clostridium sp. (6), Eubacterium limosum (1), Ruminococcus sp. (1) and Acetobacterium woodii (1) except one, i.e., Vagococcus fluvialis. The results indicate that reductive acetogens isolated from the rumen fluid samples of Murrah buffalos are both autotrophic and heterotrophic in nature and further investigations are required to exploit and explore their potential as an alternate hydrogen sink.

Lactate based caproate production with Clostridium drakei and process control of Acetobacterium woodii via lactate dependent in situ electrolysis

Syngas fermentation processes with acetogens represent a promising process for the reduction of CO₂ emissions alongside bulk chemical production. However, to fully realize this potential the thermodynamic limits of acetogens need to be considered when designing a fermentation process. An adjustable supply of H₂ as electron donor plays a key role in autotrophic product formation. In this study an anaerobic laboratory scale continuously stirred tank reactor was equipped with an All-in-One electrode allowing for in-situ H₂ generation via electrolysis. Furthermore, this system was coupled to online lactate measurements to control the co-culture of a recombinant lactate-producing Acetobacterium woodii strain and a lactate-consuming Clostridium drakei strain to produce caproate. When C. drakei was grown in batch cultivations with lactate as substrate, 1.6 g·L^-1 caproate were produced. Furthermore, lactate production of the A. woodii mutant strain could manually be stopped and reinitiated by controlling the electrolysis. Applying this automated process control, lactate production of the A. woodii mutant strain could be halted to achieve a steady lactate concentration. In a co-culture experiment with the A. woodii mutant strain and the C. drakei strain, the automated process control was able to dynamically react to changing lactate concentrations and adjust H₂ formation respectively. This study confirms the potential of C. drakei as medium chain fatty acid producer in a lactate-mediated, autotrophic co-cultivation with an engineered A. woodii strain. Moreover, the monitoring and control strategy presented in this study reinforces the case for autotrophically produced lactate as a transfer metabolite in defined co-cultivations for value-added chemical production.

Acetogen and acetogenesis for biological syngas valorization

The bioconversion of syngas using (homo)acetogens as biocatalysts shows promise as a viable option due to its higher selectivity and milder reaction conditions compared to thermochemical conversion. The current bioconversion process operates primarily to produce C2 chemicals (e.g., acetate and ethanol) with sufficient technology readiness levels (TRLs) in process engineering (as midstream) and product purification (as downstream). However, the economic feasibility of this process could be improved with greater biocatalytic options in the upstream phase. This review focuses on the Wood-Ljungdahl pathway (WLP) which is a biological syngas-utilization pathway, redox balance and ATP generation, suggesting that the use of a specific biocatalysts including Eubacterium limosum could be advantageous in syngas valorization. A pertinent strategy to mainly produce chemicals with a high degree of reduction is also provided with examples of flux control, mixed cultivation and mixotrophy. Finally, this article presents future direction of industrial utilization of syngas fermentation.

Obligate autotrophy at the thermodynamic limit of life in a new acetogenic bacterium

One of the important current issues of bioenergetics is the establishment of the thermodynamic limits of life. There is still no final understanding of what is the minimum value of the energy yield of a reaction that is sufficient to be used by an organism (the so-called "biological quantum of energy"). A reasonable model for determination of the minimal energy yield would be microorganisms capable of living on low-energy substrates, such as acetogenic prokaryotes. The most prominent metabolic feature of acetogens is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates, which is hardly competitive in environments. Most probably, that is why only facultative autotrophic acetogens have been known so far. Here, we describe the first obligately autotrophic acetogenic bacterium Aceticella autotrophica gen. nov., sp. nov., strain 3443-3Ac^T. Phylogenetically, the new genus falls into a monophyletic group of heterotrophic bacteria of the genera Thermoanaerobacterium, Thermoanaerobacter, and Caldanaerobacter (hereinafter referred to as TTC group), where the sole acetogenic representative has so far been the facultatively autotrophic Thermoanaerobacter kivui. A. autotrophica and T. kivui both are acetogens employing energy-converting hydrogenase (Ech-acetogens) that are likely to have inherited the acetogenesis capacity vertically from common ancestor. However, their acetogenic machineries have undergone different adjustments by gene replacements due to horizontal gene transfers from different donors. Obligate autotrophy of A. autotrophica is associated with the lack of many sugar transport systems and carbohydrate catabolism enzymes that are present in other TTC group representatives, including T. kivui.

Exploitation of a Type 1 Toxin-Antitoxin System as an Inducible Counter-Selective Marker for Genome Editing in the Acetogen Eubacterium limosum

Targeted mutations in the anaerobic methylotroph Eubacterium limosum have previously been obtained using CRISPR-based mutagenesis methods. In this study, a RelB-family toxin from Eubacterium callanderi was placed under the control of an anhydrotetracycline-sensitive promoter, forming an inducible counter-selective system. This inducible system was coupled with a non-replicative integrating mutagenesis vector to create precise gene deletions in Eubacterium limosum B2. The genes targeted in this study were those encoding the histidine biosynthesis gene hisI, the methanol methyltransferase and corrinoid protein mtaA and mtaC, and mtcB, encoding an Mttb-family methyltransferase which has previously been shown to demethylate L-carnitine. A targeted deletion within hisI brought about the expected histidine auxotrophy, and deletions of mtaA and mtaC both abolished autotrophic growth on methanol. Deletion of mtcB was shown to abolish the growth of E. limosum on L-carnitine. After an initial selection step to isolate transformant colonies, only a single induction step was required to obtain mutant colonies for the desired targets. The combination of an inducible counter-selective marker and a non-replicating integrative plasmid allows for quick gene editing of E. limosum.

Enhancing acetone production from H2 and CO2 using supplemental electron acceptors in an engineered Moorella thermoacetica

Acetogens grow autotrophically and use hydrogen (H₂) as the energy source to fix carbon dioxide (CO₂). This feature can be applied to gas fermentation, contributing to a circular economy. A challenge is the gain of cellular energy from H₂ oxidation, which is substantially low, especially when acetate formation coupled with ATP production is diverted to other chemicals in engineered strains. Indeed, an engineered strain of the thermophilic acetogen Moorella thermoacetica that produces acetone lost autotrophic growth on H₂ and CO₂. We aimed to recover autotrophic growth and enhance acetone production, in which ATP production was assumed to be a limiting factor, by supplementing with electron acceptors. Among the four selected electron acceptors, thiosulfate and dimethyl sulfoxide (DMSO) enhanced both bacterial growth and acetone titers. DMSO was the most effective and was further analyzed. We showed that DMSO supplementation enhanced intracellular ATP levels, leading to increased acetone production. Although DMSO is an organic compound, it functions as an electron acceptor, not a carbon source. Thus, supplying electron acceptors is a potential strategy to complement the low ATP production caused by metabolic engineering and to improve chemical production from H₂ and CO₂.

Reduction, evolutionary pattern and positive selection of genes encoding formate dehydrogenase in Wood-Ljungdahl pathway of gastrointestinal acetogens suggests their adaptation to formate-rich habitats

Acetogens are anaerobes using Wood-Ljungdahl pathway (WLP) as the terminal electron acceptor for both assimilation and dissimilation of CO₂ and widely distributed in diverse habitats. However, their habitat adaptation is often unclear. Given that bacterial genome evolution is often the result of environmental selective pressure, hereby we analysed gene copy number, phylogeny and selective pressure of genes involved in WLP within known genomes of 43 species to study the habitat adaption of gastrointestinal acetogens. The gene copy number of formate dehydrogenase (FDH) in gastrointestinal acetogens was much lower than that of non-gastrointestinal acetogens, and in five cases, no FDH genes were found in the genomes of five gastrointestinal acetogens, but that of the other WLP genes showed no difference. The evolutionary pattern of FDH genes was significantly different from that of the other enzymes. Additionally, seven positively selected sites were only identified in the fdhF genes, which means fdhF mutations favoured their adaptation. Collectively, reduction or loss of FDH genes and their evolutionary pattern as well as positive selection in gastrointestinal acetogens indicated their adaptation to formate-rich habitats, implying that FDH genes catalysing CO₂ reduction to formate as the first step of methyl branch of WLP may have evolved independently.

Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae

Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome-assembled genome (MAG) of the most abundant (89% relative abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and reverse transcription-PCR (RT-PCR) identified a putative five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 × HypA, HypB), and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, flavin adenine dinucleotide (FAD), two pairs of canonical [4Fe-4S] clusters, and a putative iron-sulfur cluster site in a Cys₆-bonding environment. Well-studied Acetobacterium strains, such as A. woodii DSM 1030, A. wieringae DSM 1911, or A. malicum DSM 4132, do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (~47 to 49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes, and Proteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons. IMPORTANCE Isoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene-reducing enrichment culture, dominated by Acetobacterium wieringae, with genomes of other Acetobacterium lineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription-PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.

Metatranscriptomic insights into the microbial electrosynthesis of acetate by Fe2+/Ni2+ addition

As important components of enzymes and coenzymes involved in energy transfer and Wood-Ljungdahl (WL) pathways, Fe²⁺ and Ni²⁺ supplementation may promote the acetate synthesis through CO₂ reduction by the microbial electrosynthesis (MES). However, the effect of Fe²⁺ and Ni²⁺ addition on acetate production in MES and corresponding microbial mechanisms have not been fully studied. Therefore, this study investigated the effect of Fe²⁺ and Ni²⁺ addition on acetate production in MES, and explored the underlying microbial mechanism from the metatranscriptomic perspective. Both Fe²⁺ and Ni²⁺ addition enhanced acetate production of the MES, which was 76.9% and 110.9% higher than that of control, respectively. Little effect on phylum level and small changes in genus-level microbial composition was caused by Fe²⁺ and Ni²⁺ addition. Gene expression of 'Energy metabolism', especially in 'Carbon fixation pathways in prokaryotes' was up-regulated by Fe²⁺ and Ni²⁺ addition. Hydrogenase was found as an important energy transfer mediator for CO₂ reduction and acetate synthesis. Fe²⁺ addition and Ni²⁺ addition respectively enhanced the expression of methyl branch and carboxyl branch of the WL pathway, and thus promoted acetate production. The study provided a metatranscriptomic insight into the effect of Fe²⁺ and Ni²⁺ on acetate production by CO₂ reduction in MES.

Embracing a low-carbon future by the production and marketing of C1 gas protein

Food scarcity and environmental deterioration are two major problems that human populations currently face. Fortunately, the disruptive innovation of raw food materials has been stimulated by the rapid evolution of biomanufacturing. Therefore, it is expected that the new trends in technology will not only alter the natural resource-dependent food production systems and the traditional way of life but also reduce and assimilate the greenhouse gases released into the atmosphere. This review article summarizes the metabolic pathways associated with C1 gas conversion and the production of single-cell protein for animal feed. Moreover, the protein function, worldwide authorization, market access, and methods to overcome challenges in C1 gas assimilation microbial cell factory construction are also provided. With widespread attention and increasing policy support, the production of C1 gas protein will bring more opportunities and make tremendous contributions to our sustainable future.

Anaerobic digestion of fruit and vegetable waste: a critical review of associated challenges

The depletion of fossil fuels coupled with stringent environmental laws has encouraged us to develop sustainable renewable energy. Due to its numerous benefits, anaerobic digestion (AD) has emerged as an environment-friendly technology. Biogas generated during AD is primarily a mixture of CH₄ (65-70%) and CO₂ (20-25%) and a potent energy source that can combat the energy crisis in today's world. Here, an attempt has been made to provide a broad understanding of AD and delineate the effect of various operational parameters influencing AD. The characteristics of fruit and vegetable waste (FVW) and its feasibility as a potent substrate for AD have been studied. This review also covers traditional challenges in managing FVW via AD, the implementation of various bioreactor systems to manage large amounts of organic waste and their operational boundaries, microbial consortia involved in each phase of digestion, and various strategies to increase biogas production.

Microbial electrosynthesis of acetate from CO2 under hypersaline conditions

Microbial electrosynthesis (MES) enables the bioproduction of multicarbon compounds from CO₂ using electricity as the driver. Although high salinity can improve the energetic performance of bioelectrochemical systems, acetogenic processes under elevated salinity are poorly known. Here MES under 35-60 g L^-1 salinity was evaluated. Acetate production in two-chamber MES systems at 35 g L^-1 salinity (seawater composition) gradually decreased within 60 days, both under -1.2 V cathode potential (vs. Ag/AgCl) and -1.56 A m^-2 reductive current. Carbonate precipitation on cathodes (mostly CaCO₃) likely declined the production through inhibiting CO₂ supply, the direct electrode contact for acetogens and H₂ production. Upon decreasing Ca²⁺ and Mg²⁺ levels in three-chamber reactors, acetate was stably produced over 137 days along with a low cathode apparent resistance at 1.9 ± 0.6 mΩ m² and an average production rate at 3.80 ± 0.21 g m^-2 d^-1. Increasing the salinity step-wise from 35 to 60 g L^-1 gave the most efficient acetate production at 40 g L^-1 salinity with average rates of acetate production and CO₂ consumption at 4.56 ± 3.09 and 7.02 ± 4.75 g m^-2 d^-1, respectively. The instantaneous coulombic efficiency for VFA averaged 55.1 ± 31.4%. Acetate production dropped at higher salinity likely due to the inhibited CO₂ dissolution and acetogenic metabolism. Acetobacterium up to 78% was enriched on cathodes as the main acetogen at 35 g L^-1. Under high-salinity selection, 96.5% Acetobacterium dominated on the cathode along with 34.0% Sphaerochaeta in catholyte. This research provides a first proof of concept that MES starting from CO₂ reduction can be achieved at elevated salinity.

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

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

Temporary Survival Increasing the Diversity of Culturable Heterotrophic Bacteria in the Newly Exposed Moraine at a Glacier Snout

Laohugou Glacier No. 12 is located on the northern slope of the western Qilian Mountains with a temperate continental wet climate and an extremely cold winter. Bacteria in a newly exposed moraine have to cope with various pressures owing to deglaciation at the glacier snout. However, limited information is available regarding the high diversity and temporary survival of culturable heterotrophic bacteria under various environmental stresses. To examine the tolerance of extremophiles against varying environmental conditions in a newly exposed moraine, we simulated environmental stress in bacterial cultures. The results showed that the isolated strains belonged to actinobacteria, Proteobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes. Actinobacteria was the most abundant phylum, followed by Proteobacteria, at both high and low temperatures. Pseudarthrobacter was the most abundant genus, accounting for 14.2% of the total isolates. Although several microorganisms grew at 10 °C, the proportion of microorganisms that grew at 25 °C was substantially higher. In particular, 50% of all bacterial isolates grew only at a high temperature (HT), whereas 21.4% of the isolates grew at a low temperature (LT), and 38.6% of the isolates grew at both HT and LT. In addition, many radiation-resistant extremophiles were identified, which adapted to both cold and oxidative conditions. The nearest neighbors of approximately >90% of bacteria belonged to a nonglacial environment, such as oil-contaminated soil, rocks, and black sand, instead of glacial niches. This study provides insights into the ecological traits, stress responses, and temporary survival of culturable heterotrophic bacteria in a newly exposed moraine with variable environmental conditions and the relationship of these communities with the non-glacial environment. This study may help to understand the evolution, competition, and selective growth of bacteria in the transition regions between glaciers and retreats in the context of glacier melting and retreat owing to global warming.

Biosynthesis of L-5-methyltetrahydrofolate by genetically engineered Escherichia coli

L-5-Methyltetrahydrofolate (L-5-MTHF) is the only biologically active form of folate in the human body. Production of L-5-MTHF by using microbes is an emerging consideration for green synthesis. However, microbes naturally produce only a small amount of L-5-MTHF. Here, Escherichia coli BL21(DE3) was engineered to increase the production of L-5-MTHF by overexpressing the intrinsic genes of dihydrofolate reductase and methylenetetrahydrofolate (methylene-THF) reductase, introducing the genes encoding formate-THF ligase, formyl-THF cyclohydrolase and methylene-THF dehydrogenase from the one-carbon metabolic pathway of Methylobacterium extorquens or Clostridium autoethanogenum and disrupting the gene of methionine synthase involved in the consumption and synthesis inhibition of the target product. Thus, upon its native pathway, an additional pathway for L-5-MTHF synthesis was developed in E. coli, which was further analysed and confirmed by qRT-PCR, enzyme assays and metabolite determination. After optimizing the conditions of induction time, temperature, cell density and concentration of IPTG and supplementing exogenous substances (folic acid, sodium formate and glucose) to the culture, the highest yield of 527.84 μg g^-1 of dry cell weight for L-5-MTHF was obtained, which was about 11.8 folds of that of the original strain. This study paves the way for further metabolic engineering to improve the biosynthesis of L-5-MTHF in E. coli.

The root zone of graminoids: A niche for H2-consuming acetogens in a minerotrophic peatland

The importance of acetogens for H2 turnover and overall anaerobic degradation in peatlands remains elusive. In the well-studied minerotrophic peatland fen Schlöppnerbrunnen, H2-consuming acetogens are conceptualized to be largely outcompeted by iron reducers, sulfate reducers, and hydrogenotrophic methanogens in bulk peat soil. However, in root zones of graminoids, fermenters thriving on rhizodeposits and root litter might temporarily provide sufficient H2 for acetogens. In the present study, root-free peat soils from around the roots of Molinia caerulea and Carex rostrata (i.e., two graminoids common in fen Schlöpnnerbrunnen) were anoxically incubated with or without supplemental H2 to simulate conditions of high and low H2 availability in the fen. In unsupplemented soil treatments, H2 concentrations were largely below the detection limit (∼10 ppmV) and possibly too low for acetogens and methanogens, an assumption supported by the finding that neither acetate nor methane substantially accumulated. In the presence of supplemental H2, acetate accumulation exceeded CH4 accumulation in Molinia soil whereas acetate and methane accumulated equally in Carex soil. However, reductant recoveries indicated that initially, additional unknown processes were involved either in H2 consumption or the consumption of acetate produced by H2-consuming acetogens. 16S rRNA and 16S rRNA gene analyses revealed that potential acetogens (Clostridium, Holophagaceae), methanogens (Methanocellales, Methanobacterium), iron reducers (Geobacter), and physiologically uncharacterized phylotypes (Acidobacteria, Actinobacteria, Bacteroidetes) were stimulated by supplemental H2 in soil treatments. Phylotypes closely related to clostridial acetogens were also active in soil-free Molinia and Carex root treatments with or without supplemental H2. Due to pronounced fermentation activities, H2 consumption was less obvious in root treatments, and acetogens likely thrived on root organic carbon and fermentation products (e.g., ethanol) in addition to H2. Collectively, the data highlighted that in fen Schlöppnerbrunnen, acetogens are associated to graminoid roots and inhabit the peat soil around the roots, where they have to compete for H2 with methanogens and iron reducers. Furthermore, the study underscored that the metabolically flexible acetogens do not rely on H2, potentially a key advantage over other H2 consumers under the highly dynamic conditions characteristic for the root-zones of graminoids in peatlands.

Genomic insights into versatile lifestyle of three new bacterial candidate phyla

Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance. Here, we retrieved 11 metagenomic-assembled genomes (MAGs) affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench. Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum, subsequently named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle, with the potential to utilize various types of sugars, proteins, and/or short-chain fatty acids through anaerobic pathways. This was further confirmed by a global distribution map of the three phyla, indicating a preference for oxygen-limited or particle-attached niches, such as anoxic sedimentary environments. Of note, Candidatus Canglongiota genomes harbor genes for the complete Wood- Ljungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria. Evolutionary analysis indicated that gene gain and loss events, and horizontal gene transfer (HGT) play important roles in shaping the genomic and metabolic features of the three new phyla. This study presents the genomic insight into the ecology, metabolism, and evolution of three new phyla, which broadens the phylum-level diversity within the domain Bacteria.

AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters

AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was also the first database to establish connections between the FTHFS gene, the Wood–Ljungdahl pathway and 16S ribosomal RNA genes. Since the publication of AcetoBase, there have been significant improvements in the taxonomy of many bacterial lineages and accessibility/availability of public genomics and metagenomics data. The update to the AcetoBase reference database described here (Version 2) provides new sequence data and taxonomy, along with improvements in web functionality and user interface. The evaluation of this latest update by re-analysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase Version 1 revealed significant improvements in the taxonomic assignment of FTHFS sequences.

Database URL: https://acetobase.molbio.slu.se

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.

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

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

Photosynthesis of Acetate by Sporomusa ovata-CdS Biohybrid System

Sporomusa ovata, a typical electroautotrophic microorganism, has been utilized in bioelectrosynthesis for carbon dioxide fixation to multicarbon organic chemicals. However, additional photovoltaic devices are normally needed to convert photo energy to electric energy to power the carbon dioxide fixation, which restricts the overall energy conversion efficiency. Herein, we report Sporomusa ovata-CdS biohybrids for artificial photosynthesis driven by light without any other power source. The quantum yield can reach 16.8 ± 9%, and the active duration time of the system can last for 5 days. During the artificial photosynthesis, carbon dioxide is first reduced to formate and finally converted to acetate via the Wood-Ljungdahl pathway. The carbon dioxide fixation, electron transfer, energy metabolism, and reactive oxygen species damage repair processes in the biohybrid system were characterized by proteomic analysis. Key enzymes, e.g., flavoprotein, ferredoxin, formate-tetrahydrofolate ligase, 5-methyltetrahydrofolate:corrinoid iron-sulfur protein methyltransferase, thioredoxin, and rubrerythrin, were found up-regulated in the biohybrid system. The findings are helpful in understanding the mechanism of the artificial photosynthesis and useful for the development of new biohybrid systems using genetically engineered microbes in the future. The study is expected to boost the development of bioabiotic hybrid system in solar energy harvest.

Ecological variability based on lipid biomarkers in astrobiologically interesting wetlands from the Argentinian central Andes

Andean wetlands hold extremophilic communities adapted to live in harsh conditions. Here, we investigated the microbial ecology of three high-altitude hypersaline ponds from La Puna region (Argentina) showing an increasing extent of desiccation by analyzing their lipid sedimentary record. We recreated the microbial community structure and the carbon metabolisms in each lacustrine system based on the molecular distribution of lipid biomarkers and their compound-specific carbon and hydrogen isotopic signatures. We detected lipid compounds considered to be biomarkers of cyanobacteria, sulfate-reducing bacteria, purple sulfur bacteria, and archaea in the three Andean ponds, as well as diatoms in the intermediate salinity system. The relative abundance of purple sulfur and sulfate-reducing bacteria decreased with salinity, whereas cyanobacteria and archaea decreased their relative abundance in the mid-saline pond to increase it again and became both prevailing at the highest salinity. Carbon fixation in the three ponds was driven by a combination of the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle, and the reductive acetyl-CoA pathway. This work is the first to describe molecular and isotopic lipid fingerprints in wetlands from the central Andean Puna, and serves as a basis for further biogeochemical studies in the area.

Reversible Hydrogenase Activity Confers Flexibility to Balance Intracellular Redox in Moorella thermoacetica

Hydrogen (H₂) converted to reducing equivalents is used by acetogens to fix and metabolize carbon dioxide (CO₂) to acetate. The utilization of H₂ enables not only autotrophic growth, but also mixotrophic metabolism in acetogens, enhancing carbon utilization. This feature seems useful, especially when the carbon utilization efficiency of organic carbon sources is lowered by metabolic engineering to produce reduced chemicals, such as ethanol. The potential advantage was tested using engineered strains of Moorella thermoacetica that produce ethanol. By adding H₂ to the fructose-supplied culture, the engineered strains produced increased levels of acetate, and a slight increase in ethanol was observed. The utilization of a knockout strain of the major acetate production pathway, aimed at increasing the carbon flux to ethanol, was unexpectedly hindered by H₂-mediated growth inhibition in a dose-dependent manner. Metabolomic analysis showed a significant increase in intracellular NADH levels due to H₂ in the ethanol-producing strain. Higher NADH level was shown to be the cause of growth inhibition because the decrease in NADH level by dimethyl sulfoxide (DMSO) reduction recovered the growth. When H₂ was not supplemented, the intracellular NADH level was balanced by the reversible electron transfer from NADH oxidation to H₂ production in the ethanol-producing strain. Therefore, reversible hydrogenase activity confers the ability and flexibility to balance the intracellular redox state of M. thermoacetica. Tuning of the redox balance is required in order to benefit from H₂-supplemented mixotrophy, which was confirmed by engineering to produce acetone.

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.

Fate of Clostridia and other spore-forming Firmicute bacteria during feedstock anaerobic digestion and aerobic composting

Pathogenic spore-forming Firmicutes are commonly present in animal and human wastes that are used as fertilizers in crop production. Pre-treatments of organic waste prior to land application offer the potential to abate enteric microorganisms, and therefore reduce the risk of contamination of crops or adjacent water resources with pathogens carried in these materials. The inactivation and reduction of gram-positive spore formers such as Clostridium spp., Clostridioides spp. and Bacillus spp. from animal and human waste can be challenging given the recalcitrance of the spores these bacteria produce. Given the significance of these organisms to human and animal health, information concerning spore-forming bacteria inactivation during anaerobic digestion (AD) and aerobic composting (AC) is required as the basis for recommending safe organic waste management practices. In this review, an assessment of the inactivation of spore-forming Firmicutes during AD and AC was conducted to provide guidance for practical management of organic matrices of animal or human origin. Temperature and pH may be the main factors contributing to the inactivation of spore-forming Firmicutes during batch lab-scale AD (log reduction <0.5-5 log). In continuous digesters, wet AD systems do not effectively inactivate spore-forming Firmicutes even under thermopholic conditions (log reduction -1.09 - 0.98), but dry AD systems could be a feasible management practice to inactivate spore-forming Firmicutes from organic materials with high solid content (log reduction 1.77-3.1). In contrast, composting is an effective treatment to abate spore-forming Firmicutes (log reduction 1.7-6.5) when thermophilic conditions last at least six consecutive days. Temperature, moisture content and composting scale are the key operating conditions influencing the inactivation of spore-forming Firmicutes during composting. Where possible, undertaking AD with subsequent composting to ensure the biosafety of digestate before its downstream processing and recycling is recommended to abate recalcitrant bacteria in digestate.

Visualizing the gas channel of a monofunctional carbon monoxide dehydrogenase

Carbon monoxide dehydrogenase (CODH) plays an important role in the processing of the one‑carbon gases carbon monoxide and carbon dioxide. In CODH enzymes, these gases are channeled to and from the Ni-Fe-S active sites using hydrophobic cavities. In this work, we investigate these gas channels in a monofunctional CODH from Desulfovibrio vulgaris, which is unusual among CODHs for its oxygen-tolerance. By pressurizing D. vulgaris CODH protein crystals with xenon and solving the structure to 2.10 Å resolution, we identify 12 xenon sites per CODH monomer, thereby elucidating hydrophobic gas channels. We find that D. vulgaris CODH has one gas channel that has not been experimentally validated previously in a CODH, and a second channel that is shared with Moorella thermoacetica carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS). This experimental visualization of D. vulgaris CODH gas channels lays groundwork for further exploration of factors contributing to oxygen-tolerance in this CODH, as well as study of channels in other CODHs. We dedicate this publication to the memory of Dick Holm, whose early studies of the Ni-Fe-S clusters of CODH inspired us all.

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.

Impact of different trace elements on metabolic routes during heterotrophic growth of C. ljungdahlii investigated through online measurement of the carbon dioxide transfer rate

Synthesis gas fermentation using acetogenic clostridia is a rapidly increasing research area. It offers the possibility to produce platform chemicals from sustainable C1 carbon sources. The Wood-Ljungdahl pathway (WLP), which allows acetogens to grow autotrophically, is also active during heterotrophic growth. It acts as an electron sink and allows for the utilization of a wide variety of soluble substrates and increases ATP yields during heterotrophic growth. While glycolysis leads to CO₂ evolution, WLP activity results in CO₂ fixation. Thus, a reduction of net CO₂ emissions during growth with sugars is an indicator of WLP activity. To study the effect of trace elements and ventilation rates on the interaction between glycolysis and the WLP, the model acetogen Clostridium ljungdahlii was cultivated in YTF medium, a complex medium generally employed for heterotrophic growth, with fructose as growth substrate. The recently reported anaRAMOS device was used for online measurement of metabolic activity, in form of CO₂ evolution. The addition of multiple trace elements (iron, cobalt, manganese, zinc, nickel, copper, selenium, and tungsten) was tested, to study the interaction between glycolysis and the Wood ljungdahl pathway. While the addition of iron(II) increased growth rates and ethanol production, added nickel(II) increased WLP activity and acetate formation, reducing net CO₂ production by 28%. Also, higher CO₂ availability through reduced volumetric gas flow resulted in 25% reduction of CO₂ evolution. These online metabolic data demonstrate that the anaRAMOS is a valuable tool in the investigation of metabolic responses i.e. to determine nutrient requirements that results in reduced CO₂ production. Thereby the media composition can be optimized depending on the specific goal. This article is protected by copyright. All rights reserved.

One substrate, many fates: different ways of methanol utilization in the acetogen Acetobacterium woodii

Acetogenic bacteria such as Acetobacterium woodii use the Wood-Ljungdahl pathway (WLP) for fixation of CO₂ and energy conservation. This pathway enables conversion of diverse substrates to the main product of acetogenesis, acetate. Methyl group containing substrates such as methanol or methylated compounds, derived from pectin, are abundant in the environment and a source for CO₂ . Methyl groups enter the WLP at the level of methyltetrahydrofolic acid (methyl-THF). For methyl transfer from methanol to THF a substrate specific methyltransferase system is required. In this study, we used genetic methods to identify mtaBC2A (Awo_c22760- Awo_c22740) as the methanol specific methyltransferase system of A. woodii. After methyl transfer, methyl-THF serves as carbon and/or electron- source and the respiratory Rnf complex is required for redox homeostasis if methanol+CO₂ is the substrate. Resting cells fed with methanol+CO₂ , indeed converted methanol to acetate in a 4:3 stoichiometry. When methanol was fed in combination with other electron sources such as H₂ + CO₂ or CO, methanol was converted Rnf-independently and the methyl group was condensed with CO to build acetate. When fed in combination with alternative electron sinks such as caffeate methanol was oxidized only and resulting electrons were used for non-acetogenic growth. These different pathways for the conversion of methyl-group containing substrates enable acetogens to adapt to various ecological niches and to syntrophic communities. This article is protected by copyright. All rights reserved.

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.

Clostridium muellerianum sp. nov., a carbon monoxide-oxidizing acetogen isolated from old hay

An acid/alcohol-producing, Gram-stain-positive, obligately anaerobic, rod-shaped, non-motile, non-spore forming acetogen, designated as strain P21T, was isolated from old hay after enrichment with CO as the substrate. Spores not observed even after prolonged incubation (30 days). Phylogenetic analysis of the 16S rRNA gene sequence of strain P21T showed it was closely related to Clostridium carboxidivorans DSM 15243T (97.9%), Clostridium scatologenes DSM 757T (97.7 %) and Clostridium drakei DSM 12750T (97.7 %). The genome is 5.6 Mb and the G+C content is 29.4 mol%. Average nucleotide identity between strain P21T, C. carboxidivorans , C. scatologenes and C. drakei was 87.1, 86.4, 86.4 %, respectively. Strain P21T grew on CO:CO2, H2:CO2, l-arabinose, ribose, xylose, fructose, galactose, glucose, lactose, mannose, cellobiose, sucrose, cellulose, starch, pyruvate, choline, glutamate, histidine, serine, threonine and casamino acids. End products of metabolism were acetate, butyrate, caproate, ethanol and hexanol. Dominant cellular fatty acids (>10 %) were C16 : 0 (41.5 %), C16 : 1 ω7c/C16 : 1 ω6c (10.0 %), and a summed feature containing cyclo C17 : 1/C18 : 0 (17.3 %). Based on the phenotypic, chemotaxonomic, phylogenetic and phylogenomic analyses, strain P21T represents a new species in the genus Clostridium , for which the name Clostridium muellerianum sp. nov. is proposed. The type strain is P21T (=DSM 111390T=NCIMB 15261T).

Strategies to Mitigate Enteric Methane Emissions from Ruminant Animals

Human activities account for approximately two-thirds of global methane emissions, wherein the livestock sector is the single massive methane emitter. Methane is a potent greenhouse gas of over 21 times the warming effect of carbon dioxide. In the rumen, methanogens produce methane as a by-product of anaerobic fermentation. Methane released from ruminants is considered as a loss of feed energy that could otherwise be used for productivity. Economic progress and growing population will inflate meat and milk product demands, causing elevated methane emissions from this sector. In this review, diverse approaches from feed manipulation to the supplementation of organic and inorganic feed additives and direct-fed microbial in mitigating enteric methane emissions from ruminant livestock are summarized. These approaches directly or indirectly alter the rumen microbial structure thereby reducing rumen methanogenesis. Though many inorganic feed additives have remarkably reduced methane emissions from ruminants, their usage as feed additives remains unappealing because of health and safety concerns. Hence, feed additives sourced from biological materials such as direct-fed microbials have emerged as a promising technique in mitigating enteric methane emissions.

Insights into carbon-fixation pathways through metagonomics in the sediments of deep-sea cold seeps

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior. At present, six pathways of autotrophic carbon fixation have been found: the Calvin cycle, the reductive Acetyl-CoA or Wood-Ljungdahl pathway (rAcCoA), the reductive tricarboxylic acid cycle (rTCA), the 3-hydroxypropionate bicycle (3HP), the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB), and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB). Although our knowledge about carbon fixation pathways in the ocean has increased significantly, carbon fixation pathways in the cold seeps are still unknown. In this study, we collected sediment samples from two cold seeps and one trough in the south China sea (SCS), and investigated with metagenomic and metagenome assembled genomes (MAGs). We found that six autotrophic carbon fixation pathways present in the cold seeps and trough with rTCA cycle was the most common pathway, whose genes were particularly high in the cold seeps and increased with sediment depths; the rAcCoA cycle mainly occurred in the cold seep regions, and the abundance of module genes increased with sediment depths. We also elucidated members of chemoautotrophic microorganisms involved in these six carbon-fixation pathways. The rAcCoA, rTCA and DC/4-HB cycles required significantly less energy probably play an important role in the deep-sea environments, especially in the cold seeps. This study provided metabolic insights into the carbon fixation pathways in the cold seeps, and laid the foundation for future detailed study on processes and rates of carbon fixation in the deep-sea ecosystems.