One-carbon substrate-based biohydrogen production: Microbes, mechanism, and productivity

Methane emission mitigation of Paenibacillus yonginensis DCY84T incorporated with silicate on paddy rice (Oryzae sativa L.) plantation revealed in soil microbiome profiling

Anthropogenic methane emissions from paddy cultivation contribute to greenhouse gas levels owing to the anaerobic conditions in flooded rice fields, which promotes the activity of methanogenic bacteria. This study explored bioremediation strategies to mitigate methane release through the application of plant growth-promoting rhizobacteria combined with silicate in rice cultivation. Rice seeds were coated with Paenibacillus yonginensis DCY84T, with and without the addition of silicate, prior to sowing. Results revealed notable reduction in methane flux during the peak growth stage of rice in seeds treated with DCY84T (27.215 ± 1.975 mg m-2 h-1), with a further reduction observed when silicate was also applied (23.592 ± 3.112 mg m-2 h-1), compared to untreated seeds (37.305 ± 2.990 mg m-2 h-1). Additionally, treatment with DCY84T (28.24 ± 0.55 g) resulted in an increase in rice yield (p < 0.05), as evidenced by a greater 1000-grain weight compared to both the control group (26.91 ± 0.09 g) and the application of silicate (27.37 ± 0.57 g). The beta diversity of the soil microbial community highlighted distinct differences between the treated and control groups, indicating DCY84T inoculation with or without silicate altered the soil microbial structure. Particularly, the treated groups showed dominance of the phylum Proteobacteria, especially the classes Alphaproteobacteria and Deltaproteobacteria. Furthermore, the addition of silicate to DCY84T-coated rice seeds resulted in a higher abundance of bacterial families, such as Anaerolinaceae, Clostridiceae, and Nitrospirae which compete with methanogens for organic substrates, thereby reducing their methane production. Notably, the DCY84T-silicate treatment group showed higher levels of methane metabolism biomarkers such as formate dehydrogenase within the soil microbiome, which correlated with the observed reduction in methane emissions. These findings suggest that coating rice seeds with DCY84T and silicate prior to sowing effectively mediates methane production and release during rice cultivation by promoting beneficial soil bacterial communities.

Exploring the Potential of Syngas Fermentation for Recovery of High-Value Resources: A Comprehensive Review

Synthesis gas (syngas) fermentation represents a promising biological method for converting industrial waste gases, particularly carbon monoxide (CO) and carbon dioxide (CO₂) from industrial sources (e.g. steel production or municipal waste gasification), into high-value products such as biofuels, chemicals, and animal feed using acetogenic bacteria. This review identifies and addresses key challenges that hinder the large-scale adoption of this technology, including limitations in gas mass transfer, an incomplete understanding of microbial metabolic pathways, and suboptimal bioprocess conditions. Our findings emphasize the critical role of microbial strain selection and bioprocess optimization to enhance productivity and scalability, with a focus on utilizing diverse microbial consortia and efficient reactor systems. By examining recent advancements in microbial conditioning, operational parameters, and reactor design, this study provides actionable insights to improve syngas fermentation efficiency, suggesting pathways towards overcoming current technical barriers for its broader industrial application beyond the production of bulk chemicals.

Conventional and biodegradable microplastics affected arsenic mobility and methylation in paddy soils through distinct chemical-microbial pathways

The presence of microplastics (MPs) in paddy soil has become a growing concern, yet the influence of MPs on arsenic (As) dynamics in paddy soil remains largely unexplored. A 98-day microcosm experiment was conducted to investigate the impact of MPs on As behavior in As-contaminated paddy soil. The results revealed that conventional microplastics (CMPs) reduced As concentration in porewater by 25-38 %, but substantially increased the percentage of methylated As (% MeAs) in soil by 8-23 times under 5 % dosages after 98-day incubation. In contrast, at the end of incubation, biodegradable microplastics (BMPs) at 5 % dosages notably increased As concentration in porewater and % MeAs in soil by 2-9 times and 11-395 times, respectively. The combination of network analysis and Random-Forest analysis implied that CMPs might inhibit As mobility through enhancing microbial As(III) oxidation and promote As methylation by enriching arsM-carrying microbes. However, BMPs promoted As release mainly accompanying with microbial iron reduction, and enhanced As methylation through enriching fermenting bacteria (i.e., Clostridiaceae) and arsM-carrying organic matter degrading bacteria (i.e., Gemmatimonas and Nocardia). These findings might provide broaden insights into As cycling induced by MPs and contribute to the prevention of combined pollution from As and MPs in paddy soil.

Industrial biotechnology goes thermophilic: Thermoanaerobes as promising hosts in the circular carbon economy

Transitioning away from fossil feedstocks is imperative to mitigate climate change, and necessitates the utilization of renewable, alternative carbon and energy sources to foster a circular carbon economy. In this context, lignocellulosic biomass and one-carbon compounds emerge as promising feedstocks that could be renewably upgraded by thermophilic anaerobes (thermoanaerobes) via gas fermentation or consolidated bioprocessing to value-added products. In this review, the potential of thermoanaerobes for cost-efficient, effective and sustainable bioproduction is discussed. Metabolic and bioprocess engineering approaches are reviewed to draw a comprehensive picture of current developments and future perspectives for the conversion of renewable feedstocks to chemicals and fuels of interest. Selected bioprocessing scenarios are outlined, offering practical insights into the applicability of thermoanaerobes at a large scale. Collectively, the potential advantages of thermoanaerobes regarding process economics could facilitate an easier transition towards sustainable bioprocesses with renewable feedstocks.

Harnessing recalcitrant lignocellulosic biomass for enhanced biohydrogen production: Recent advances, challenges, and future perspective

Biohydrogen (Bio-H2) is widely recognized as a sustainable and environmentally friendly energy source, devoid of any detrimental impact on the environment. Lignocellulosic biomass (LB) is a readily accessible and plentiful source material that can be effectively employed as a cost-effective and sustainable substrate for Bio-H2 production. Despite the numerous challenges, the ongoing progress in LB pretreatment technology, microbial fermentation, and the integration of molecular biology techniques have the potential to enhance Bio-H2 productivity and yield. Consequently, this technology exhibits efficiency and the capacity to meet the future energy demands associated with the valorization of recalcitrant biomass. To date, several pretreatment approaches have been investigated in order to improve the digestibility of feedstock. Nevertheless, there has been a lack of comprehensive systematic studies examining the effectiveness of pretreatment methods in enhancing Bio-H2 production through dark fermentation. Additionally, there is a dearth of economic feasibility evaluations pertaining to this area of research. Thus, this review has conducted comparative studies on the technological and economic viability of current pretreatment methods. It has also examined the potential of these pretreatments in terms of carbon neutrality and circular economy principles. This review paves the way for a new opportunity to enhance Bio-H2 production with technological approaches.

NADP+ or CO2 reduction by frhAGB-encoded hydrogenase through interaction with formate dehydrogenase 3 in the hyperthermophilic archaeon Thermococcus onnurineus NA1

IMPORTANCE

The strategy using structural homology with the help of structure prediction by AlphaFold was very successful in finding potential targets for the frhAGB-encoded hydrogenase of Thermococcus onnurineus NA1. The finding that the hydrogenase can interact with FdhB to reduce the cofactor NAD(P)+ is significant in that the enzyme can function to supply reducing equivalents, just as F420-reducing hydrogenases in methanogens use coenzyme F420 as an electron carrier. Additionally, it was identified that T. onnurineus NA1 could produce formate from H2 and CO2 by the concerted action of frhAGB-encoded hydrogenase and formate dehydrogenase Fdh3.

Renewable Hydrogen Production and Storage Via Enzymatic Interconversion of CO2 and Formate with Electrochemical Cofactor Regeneration

The urgent need to reduce CO2 emissions has motivated the development of CO2 capture and utilization technologies. An emerging application is CO2 transformation into storage chemicals for clean energy carriers. Formic acid (FA), a valuable product of CO2 reduction, is an excellent hydrogen carrier. CO2 conversion to FA, followed by H2 release from FA, are conventionally chemically catalyzed. Biocatalysts offer a highly specific and less energy-intensive alternative. CO2 conversion to formate is catalyzed by formate dehydrogenase (FDH), which usually requires a cofactor to function. Several FDHs have been incorporated in bioelectrochemical systems where formate is produced by the biocathode and the cofactor is electrochemically regenerated. H2 production from formate is also catalyzed by several microorganisms possessing either formate hydrogenlyase or hydrogen-dependent CO2 reductase complexes. Combination of these two processes can lead to a CO2 -recycling cycle for H2 production, storage, and release with potentially lower environmental impact than conventional methods.

Eight Up-Coming Biotech Tools to Combat Climate Crisis

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

Biological treatment of biowaste as an innovative source of CO-The role of composting process

Carbon monoxide (CO) is an essential "building block" for producing everyday chemicals on industrial scale. Carbon monoxide can also be generated though a lesser-known and sometimes forgotten biorenewable pathways that could be explored to advance biobased production from large and more sustainable sources such as bio-waste treatment. Organic matter decomposition can generate carbon monoxide both under aerobic and anaerobic conditions. While anaerobic carbon monoxide generation is relatively well understood, the aerobic is not. Yet many industrial-scale bioprocesses involve both conditions. This review summarizes the necessary basic biochemistry knowledge needed for realization of initial steps towards biobased carbon monoxide production. We analyzed for the first time, the complex information about carbon monoxide production during aerobic, anaerobic bio-waste treatment and storage, carbon monoxide-metabolizing microorganisms, pathways, and enzymes with bibliometric analysis of trends. The future directions recognizing limitations of combined composting and carbon monoxide production have been discussed in greater detail.

Formate-driven H2 production by whole cells of Thermoanaerobacter kivui

Background

In times of global warming there is an urgent need to replace fossil fuel-based energy vectors by less carbon dioxide (CO2)-emitting alternatives. One attractive option is the use of molecular hydrogen (H2) since its combustion emits water (H2O) and not CO2. Therefore, H2 is regarded as a non-polluting fuel. The ways to produce H2 can be diverse, but steam reformation of conventional fossil fuel sources is still the main producer of H2 gas up to date. Biohydrogen production via microbes could be an alternative, environmentally friendly and renewable way of future H2 production, especially when the flexible and inexpensive C1 compound formate is used as substrate.

Results

In this study, the versatile compound formate was used as substrate to drive H2 production by whole cells of the thermophilic acetogenic bacterium Thermoanaerobacter kivui which harbors a highly active hydrogen-dependent CO2 reductase (HDCR) to oxidize formate to H2 and CO2 and vice versa. Under optimized reaction conditions, T. kivui cells demonstrated the highest H2 production rates (qH2 = 685 mmol g−1 h−1) which were so far reported in the literature for wild-type organisms. Additionally, high yields (Y(H2/formate)) of 0.86 mol mol−1 and a hydrogen evolution rate (HER) of 999 mmol L−1 h−1 were observed. Finally, stirred-tank bioreactor experiments demonstrated the upscaling feasibility of the applied whole cell system and indicated the importance of pH control for the reaction of formate-driven H2 production.

Conclusions

The thermophilic acetogenic bacterium T. kivui is an efficient biocatalyst for the oxidation of formate to H2 (and CO2). The existing genetic tool box of acetogenic bacteria bears further potential to optimize biohydrogen production in future and to contribute to a future sustainable formate/H2 bio-economy.

Thermophilic Water Gas Shift Reaction at High Carbon Monoxide and Hydrogen Partial Pressures in Parageobacillus thermoglucosidasius KP1013

The facultatively anaerobic Parageobacillus thermoglucosidasius oxidizes carbon monoxide to produce hydrogen via the water gas shift (WGS) reaction. In the current work, we examined the influence of carbon monoxide (CO) and hydrogen (H2) on the WGS reaction in the thermophilic P. thermoglucosidasius by cultivating two hydrogenogenic strains under varying CO and H2 compositions. Microbial growth and dynamics of the WGS reaction were monitored by evaluating parameters such as pressure, headspace composition, metabolic intermediates, pH, and optical density. Our analyses revealed that compared to the previously studied P. thermoglucosidasius strains, the strain KP1013 demonstrated higher CO tolerance and improved WGS reaction kinetics. Under anaerobic conditions, the lag phase before the WGS reaction shortened to 8 h, with KP1013 showing no hydrogen-induced product inhibition at hydrogen partial pressures up to 1.25 bar. The observed lack of product inhibition and the reduced lag phase of the WGS reaction support the possibility of establishing an industrial process for biohydrogen production with P. thermoglucosidasius.

Thermal Design of a Biohydrogen Production System Driven by Integrated Gasification Combined Cycle Waste Heat Using Dynamic Simulation

Utilizing biological processes for hydrogen production via gasification is a promising alternative method to coal gasification. The present study proposes a dynamic simulation model that uses a one-dimensional heat-transfer analysis method to simulate a biohydrogen production system. The proposed model is based on an existing experimental design setup. It is used to simulate a biohydrogen production system driven by the waste heat from an integrated gasification combined cycle (IGCC) power plant equipped with carbon capture and storage technologies. The data from the simulated results are compared with the experimental measurement data to validate the developed model’s reliability. The results show good agreement between the experimental data and the developed model. The relative root-mean-square error for the heat storage, feed-mixing, and bioreactor tanks is 1.26%, 3.59%, and 1.78%, respectively. After the developed model’s reliability is confirmed, it is used to simulate and optimize the biohydrogen production system inside the IGCC power plant. The bioreactor tank’s time constant can be improved when reducing the operating volume of the feed-mixing tank by the scale factors of 0.75 and 0.50, leading to a 15.76% and 31.54% faster time constant, respectively, when compared with the existing design.

A Novel NADP-Dependent Formate Dehydrogenase From the Hyperthermophilic Archaeon Thermococcus onnurineus NA1

The genome of the hyperthermophilic archaeon Thermococcus onnurineus NA1 contains three copies of the formate dehydrogenase (FDH) gene, fdh1, fdh2, and fdh3. Previously, we reported that fdh2, clustered with genes encoding the multimeric membrane-bound hydrogenase and cation/proton antiporter, was essential for formate-dependent growth with H2 production. However, the functionality of the other two FDH-coding genes has not yet been elucidated. Herein, we purified and characterized cytoplasmic Fdh3 to understand its functionality. The purified Fdh3 was identified to be composed of a tungsten-containing catalytic subunit (Fdh3A), an NAD(P)-binding protein (Fdh3B), and two Fe-S proteins (Fdh3G1 and Fdh3G2). Fdh3 oxidized formate with specific activities of 241.7 U/mg and 77.4 U/mg using methyl viologen and NADP+ as electron acceptors, respectively. While most FDHs exhibited NAD+-dependent formate oxidation activity, the Fdh3 of T. onnurineus NA1 showed a strong preference for NADP+ over NAD+ as a cofactor. The catalytic efficiency (k cat /K m) of Fdh3 for NADP+ was measured to be 5,281 mM-1 s-1, which is the highest among NADP-dependent FDHs known to date. Structural modeling suggested that Arg204 and Arg205 of Fdh3B may contribute to the stabilization of the 2'-phosphate of NADP(H). Fdh3 could also use ferredoxin as an electron acceptor to oxidize formate with a specific activity of 0.83 U/mg. Furthermore, Fdh3 showed CO2 reduction activity using reduced ferredoxin or NADPH as an electron donor with a specific activity of 0.73 U/mg and 1.0 U/mg, respectively. These results suggest a functional role of Fdh3 in disposing of reducing equivalents by mediating electron transfer between formate and NAD(P)H or ferredoxin.

The Historical Development of Cultivation Techniques for Methanogens and Other Strict Anaerobes and Their Application in Modern Microbiology

The cultivation and investigation of strictly anaerobic microorganisms belong to the fields of anaerobic microbial physiology, microbiology, and biotechnology. Anaerobic cultivation methods differ from classic microbiological techniques in several aspects. The requirement for special instruments, which are designed to prevent the contact of the specimen with air/molecular oxygen by different means of manipulation, makes this field more challenging for general research compared to working with aerobic microorganisms. Anaerobic microbiological methods are required for many purposes, such as for the isolation and characterization of new species and their physiological examination, as well as for anaerobic biotechnological applications or medical indications. This review presents the historical development of methods for the cultivation of strictly anaerobic microorganisms focusing on methanogenic archaea, anaerobic cultivation methods that are still widely used today, novel methods for anaerobic cultivation, and almost forgotten, but still relevant, techniques.

Selective butanol production from carbon monoxide by an enriched anaerobic culture

An anaerobic mixed culture able to grow on pure carbon monoxide (CO) as well as syngas (CO, CO₂ and H₂), that produced unusual high concentrations of butanol, was enriched in a bioreactor with intermittent CO gas feeding. At pH 6.2, it mainly produced acids, generally acetic and butyric acid. After adaptation, under stress conditions of CO exposure at a partial pressure of 1.8 bar and low pH (e.g., 5.7), the enrichment accumulated ethanol, but also high amounts of butanol, up to 6.8 g/L, never reported before, with a high butanol/butyric acid molar ratio of 12.6, highlighting the high level of acid to alcohol conversion. At the end of the assay, both the acetic acid and ethanol concentrations decreased, with concomitant butyric acid production, suggesting C₂ to C₄ acid bioconversion, though this was not a dominant bioconversion process. The reverse reaction of ethanol oxidation to acetic acid was observed in the presence of CO₂ produced during CO fermentation. Interestingly, butanol oxidation with simultaneous butyric acid production occurred upon production of CO₂ from CO, which has to the best of our knowledge never been reported. Although the sludge inoculum contained a few known solventogenic Clostridia, the relative taxonomic abundance of the enriched sludge was diverse in Clostridia and Bacilli classes, containing known solventogens, e.g., Clostridium ljungdhalii, Clostridium ragsdalei and Clostridium coskatii, confirming their efficient enrichment. The relative abundance of unassigned Clostridium species amounted to 27% with presumably novel ethanol/butanol producers.

Levulinic Acid-Inducible and Tunable Gene Expression System for Methylorubrum extorquens

Methylorubrum extorquens AM1 is an efficient platform strain possessing biotechnological potential in formate- and methanol-based single carbon (C1) bioeconomy. Constitutive expression or costly chemical-inducible expression systems are not always desirable. Here, several glucose-, xylose-, and levulinic acid (LA)-inducible promoter systems were assessed for the induction of green fluorescent protein (GFP) as a reporter protein. Among them, the LA-inducible gene expression system (HpdR/P _hpdH ) showed a strong expression of GFP (51-fold) compared to the control. The system was induced even at a low concentration of LA (0.1 mM). The fluorescence intensity increased with increasing concentrations of LA up to 20 mM. The system was tunable and tightly controlled with meager basal expression. The maximum GFP yield obtained using the system was 42 mg/g biomass, representing 10% of the total protein content. The efficiency of the proposed system was nearly equivalent (90%-100%) to that of the widely used strong promoters such as P _mxaF and P _L/O4 . The HpdR/P _hpdH system worked equally efficiently in five different strains of M. extorquens. LA is a low-cost, renewable, and sustainable platform chemical that can be used to generate a wide range of products. Hence, the reported system in potent strains of M. extorquens is highly beneficial in the C1-biorefinery industry to produce value-added products and bulk chemicals.

Biomethanation of Carbon Monoxide by Hyperthermophilic Artificial Archaeal Co-Cultures

Climate neutral and sustainable energy sources will play a key role in future energy production. Biomethanation by gas to gas conversion of flue gases is one option with regard to renewable energy production. Here, we performed the conversion of synthetic carbon monoxide (CO)-containing flue gases to methane (CH4) by artificial hyperthermophilic archaeal co-cultures, consisting of Thermococcus onnurineus and Methanocaldococcus jannaschii, Methanocaldococcus vulcanius, or Methanocaldococcus villosus. Experiments using both chemically defined and complex media were performed in closed batch setups. Up to 10 mol% CH4 was produced by converting pure CO or synthetic CO-containing industrial waste gases at a high rate using a co-culture of T. onnurineus and M. villosus. These findings are a proof of principle and advance the fields of Archaea Biotechnology, artificial microbial ecosystem design and engineering, industrial waste-gas recycling, and biomethanation.

Resource recovery from sugarcane vinasse by anaerobic digestion - A review

The increase in biofuel production by 2030, driven by the targets set at the 21st United Nations Framework Convention on Climate Change (COP21), will promote an increase in ethanol production, and consequently more vinasse generation. Sugarcane vinasse, despite having a high polluting potential due to its high concentration of organic matter and nutrients, has the potential to produce value-added resources such as volatile fatty acids (VFA), biohydrogen (bioH₂) and biomethane (bioCH₄) from anaerobic digestion. The objective of this paper is to present a critical review on the vinasse treatment by anaerobic digestion focusing on the final products. Effects of operational parameters on production and recovery of these resources, such as pH, temperature, retention time and type of inoculum were addressed. Given the importance of treating sugarcane vinasse due to its complex composition and high volume generated in the ethanol production process, this is the first review that evaluates the production of VFAs, bioH₂ and bioCH₄ in the treatment of this organic residue. Also, the challenges of the simultaneous production of VFA, bioH₂ and bioCH₄ and resources recovery in the wastewater streams generated in flex-fuel plants, using sugarcane and corn as raw material in ethanol production, are presented. The installation of flex-fuel plants was briefly discussed, with the main impacts on the treatment process of these effluents either jointly or simultaneously, depending on the harvest season.

Archaea Biotechnology

Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are historically overshadowed by bacteria and eukaryotes in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Today, the majority of microbial cell factories utilized for the production of value-added and high value compounds on an industrial scale are bacterial, fungal or algae based. Nevertheless, archaea are becoming ever more relevant for biotechnology as their cultivation and genetic systems improve. Some of the main advantages of archaeal cell factories are the ability to cultivate many of these often extremophilic organisms under non-sterile conditions, and to utilize inexpensive feedstocks often toxic to other microorganisms, thus drastically reducing cultivation costs. Currently, the only commercially available products of archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin and diether-/tetraether-lipids, all of which are produced utilizing halophiles. Other archaeal products, such as carotenoids and biohydrogen, as well as polyhydroxyalkanoates and methane are in early to advanced development stages, respectively. The aim of this review is to provide an overview of the current state of Archaea Biotechnology by describing the actual state of research and development as well as the industrial utilization of archaeal cell factories, their role and their potential in the future of sustainable bioprocessing, and to illustrate their physiological and biotechnological potential.

Biological process for coproduction of hydrogen and thermophilic enzymes during CO fermentation

To develop a thermophilic cell factory system that uses CO gas, we attempted to engineer a hyperthermophilic carboxydotrophic hydrogenic archaeon Thermococcus onnurineus NA1 to be capable of producing thermophilic enzymes along with hydrogen (H2). The mutant strains 156T-AM and 156T-POL were constructed to have another copy of a gene encoding α-amylase or DNA polymerase, respectively, and exhibited growth rates and H2 production rates distinct from those of the parental strain, 156T, in gas fermentation using 100% CO or coal-gasified syngas. Purified α-amylase displayed starch-hydrolyzing activity, and whole-cell extracts of 156T-AM showed saccharifying activity for potato peel waste. PCR amplification was used to demonstrate that purified DNA polymerase was free from bacterial DNA contamination, in contrast to commercial bacteria-made enzymes. This study demonstrated that this archaeal strain could coproduce enzymes and H2 using CO-containing gas, providing a basis for cell factories to upcycle industrial waste gas.

Effects of high-level expression of A1-ATPase on H2 production in Thermococcus kodakarensis

The hyperthermophilic archaeon Thermococcus kodakarensis can grow on pyruvate or maltooligosaccharides through H₂ fermentation. H₂ production levels of members of the Thermococcales are high, and studies to improve their production potential have been reported. Although H₂ production is primary metabolism, here we aimed to partially uncouple cell growth and H₂ production of T. kodakarensis. Additional A₁-type ATPase genes were introduced into T. kodakarensis KU216 under the control of two promoters; the strong constitutive cell surface glycoprotein promoter, P_csg, and the sugar-inducible fructose-1,6-bisphosphate aldolase promoter, P_fba. Whereas cells with the A₁-type ATPase genes under the control of P_csg displayed only trace levels of growth, cells with P_fba (strain KUA-PF) displayed growth sufficient for further analysis. Increased levels of A₁-type ATPase protein were detected in KUA-PF cells grown on pyruvate or maltodextrin, when compared to the levels in the host strain KU216. The growth and H₂ production levels of strain KUA-PF with pyruvate or maltodextrin as a carbon and electron source were analyzed and compared to those of the host strain KU216. Compared to a small decrease in total H₂ production, significantly larger decreases in cell growth were observed, resulting in an increase in cell-specific H₂ production. Quantification of the substrate also revealed that ATPase overexpression led to increased cell-specific pyruvate and maltodextrin consumptions. The results clearly indicate that ATPase production results in partial uncoupling of cell growth and H₂ production in T. kodakarensis.

Formate Utilization by the Crenarchaeon Desulfurococcus amylolyticus

Formate is one of the key compounds of the microbial carbon and/or energy metabolism. It owes a significant contribution to various anaerobic syntrophic associations, and may become one of the energy storage compounds of modern energy biotechnology. Microbial growth on formate was demonstrated for different bacteria and archaea, but not yet for species of the archaeal phylum Crenarchaeota. Here, we show that Desulfurococcus amylolyticus DSM 16532, an anaerobic and hyperthermophilic Crenarchaeon, metabolises formate without the production of molecular hydrogen. Growth, substrate uptake, and production kinetics on formate, glucose, and glucose/formate mixtures exhibited similar specific growth rates and similar final cell densities. A whole cell conversion experiment on formate revealed that D. amylolyticus converts formate into carbon dioxide, acetate, citrate, and ethanol. Using bioinformatic analysis, we examined whether one of the currently known and postulated formate utilisation pathways could be operative in D. amylolyticus. This analysis indicated the possibility that D. amylolyticus uses formaldehyde producing enzymes for the assimilation of formate. Therefore, we propose that formate might be assimilated into biomass through formaldehyde dehydrogenase and the oxidative pentose phosphate pathway. These findings shed new light on the metabolic versatility of the archaeal phylum Crenarchaeota.

O2 sensitivity and H2 production activity of hydrogenases-A review

Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H₂ production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O₂ sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O₂ but proficient in H₂ production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O₂ tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O₂ sensitivity of the enzyme while it catalyzes H₂ production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H₂ production and other industrial processes, as well as our own perspective on future applications.

Methods for quantification of growth and productivity in anaerobic microbiology and biotechnology

Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies and utilizable as microbial cell factories. To investigate the physiological characteristics of an anaerobic microbial population, yield, productivity, specific growth rate, biomass production, substrate uptake, and product formation are regarded as essential variables. The determination of those variables in distinct cultivation systems may be achieved by using different techniques for sampling, measuring of growth, substrate uptake, and product formation kinetics. In this review, a comprehensive overview of methods is presented, and the applicability is discussed in the frame of anaerobic microbiology and biotechnology.

Biohydrogen production of obligate anaerobic archaeon Thermococcus onnurineus NA1 under oxic conditions via overexpression of frhAGB-encoding hydrogenase genes

BACKGROUND

The production of biohydrogen (H₂) as a promising future fuel in anaerobic hyperthermophiles has attracted great attention because H₂ formation is more thermodynamically feasible at elevated temperatures and fewer undesired side products are produced. However, these microbes require anoxic culture conditions for growth and H₂ production, thereby necessitating costly and time-consuming physical or chemical methods to remove molecular oxygen (O₂). Therefore, the development of an O₂-tolerant strain would be useful for industrial applications.

RESULTS

In this study, we found that the overexpression of frhAGB-encoding hydrogenase genes in Thermococcus onnurineus NA1, an obligate anaerobic archaeon and robust H₂ producer, enhanced O₂ tolerance. When the recombinant FO strain was exposed to levels of O₂ up to 20% in the headspace of a sealed bottle, it showed significant growth. Whole transcriptome analysis of the FO strain revealed that several genes involved in the stress response such as chaperonin β subunit, universal stress protein, peroxiredoxin, and alkyl hydroperoxide reductase subunit C, were significantly up-regulated. The O₂ tolerance of the FO strain enabled it to grow on formate and produce H₂ under oxic conditions, where prior O₂-removing steps were omitted, such as the addition of reducing agent Na₂S, autoclaving, and inert gas purging.

CONCLUSIONS

Via the overexpression of frhAGB genes, the obligate anaerobic archaeon T. onnurineus NA1 gained the ability to overcome the inhibitory effect of O₂. This O₂-tolerant property of the strain may provide another advantage to this hyperthermophilic archaeon as a platform for biofuel H₂ production.

Biotechnology of extremely thermophilic archaea

Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.

Efficient whole cell biocatalyst for formate-based hydrogen production

BACKGROUND

Molecular hydrogen (H₂) is an attractive future energy carrier to replace fossil fuels. Biologically and sustainably produced H₂ could contribute significantly to the future energy mix. However, biological H₂ production methods are faced with multiple barriers including substrate cost, low production rates, and low yields. The C1 compound formate is a promising substrate for biological H₂ production, as it can be produced itself from various sources including electrochemical reduction of CO₂ or from synthesis gas. Many microbes that can produce H₂ from formate have been isolated; however, in most cases H₂ production rates cannot compete with other H₂ production methods.

RESULTS

We established a formate-based H₂ production method utilizing the acetogenic bacterium Acetobacterium woodii. This organism can use formate as sole energy and carbon source and possesses a novel enzyme complex, the hydrogen-dependent CO₂ reductase that catalyzes oxidation of formate to H₂ and CO₂. Cell suspensions reached specific formate-dependent H₂ production rates of 71 mmol g_protein^-1 h^-1 (30.5 mmol g_CDW^-1 h^-1) and maximum volumetric H₂ evolution rates of 79 mmol L^-1 h^-1. Using growing cells in a two-step closed batch fermentation, specific H₂ production rates reached 66 mmol g_CDW^-1 h^-1 with a volumetric H₂ evolution rate of 7.9 mmol L^-1 h^-1. Acetate was the major side product that decreased the H₂ yield. We demonstrate that inhibition of the energy metabolism by addition of a sodium ionophore is suitable to completely abolish acetate formation. Under these conditions, yields up to 1 mol H₂ per mol formate were achieved. The same ionophore can be used in cultures utilizing formate as specific switch from a growing phase to a H₂ production phase.

CONCLUSIONS

Acetobacterium woodii reached one of the highest formate-dependent specific H₂ productivity rates at ambient temperatures reported so far for an organism without genetic modification and converted the substrate exclusively to H₂. This makes this organism a very promising candidate for sustainable H₂ production and, because of the reversibility of the A. woodii enzyme, also a candidate for reversible H₂ storage.

Adaptive evolution of a hyperthermophilic archaeon pinpoints a formate transporter as a critical factor for the growth enhancement on formate

Previously, we reported that the hyperthermophilic archaeon Thermococcus onnurineus NA1 could grow on formate and produce H₂. Formate conversion to hydrogen was mediated by a formate-hydrogen lyase complex and was indeed a part of chemiosmotic coupling to ATP generation. In this study, we employed an adaptation approach to enhance the cell growth on formate and investigated molecular changes. As serial transfer continued on formate-containing medium at the serum vial, cell growth, H₂ production and formate consumption increased remarkably. The 156 times transferred-strain, WTF-156T, was demonstrated to enhance H₂ production using formate in a bioreactor. The whole-genome sequencing of the WTF-156T strain revealed eleven mutations. While no mutation was found among the genes encoding formate hydrogen lyase, a point mutation (G154A) was identified in a formate transporter (TON_1573). The TON_1573 (A52T) mutation, when introduced into the parent strain, conferred increase in formate consumption and H₂ production. Another adaptive passage, carried out by culturing repeatedly in a bioreactor, resulted in a strain, which has a mutation in TON_1573 (C155A) causing amino acid change, A52E. These results implicate that substitution of A52 residue of a formate transporter might be a critical factor to ensure the increase in formate uptake and cell growth.

The renaissance of life near the boiling point - at last, genetics and metabolic engineering

We discuss here the prospects for biotechnology of extreme thermophilic microorganisms.

Stoichiometry evaluation of biohydrogen production from various carbohydrates

In this paper, biochemical hydrogen potential (BHP) tests were conducted to investigate H₂ production from different substrate with acid-treated anaerobic digested sludge at the mesophilic range. The sludge was collected from an anaerobic digester and was subjected to sulfuric acid pretreatments at pH 3 for 24 h. The effects of substrate type (glucose, fructose, and sucrose as carbon source) were investigated in batch experiments. Results showed that substrate degradation rate for all of the substrates was up 95 % and the electron equivalent balance showed good closure for glucose and sucrose. Batch experiments showed that the maximum molar hydrogen yield with glucose, fructose, and sucrose was 3.27, 3.16, and 6.46 mol H₂/mol of substrate. The maximum cumulative biohydrogen production was 1552, 1487, and 1366 mL and maximum hydrogen production rate was 308, 279, and 275 mL/h for glucose, sucrose, and fructose, respectively. The experimental results suggest that the formation of hydrogen associates with the main aqueous products, i.e., acetate butyrate.

A biological process effective for the conversion of CO-containing industrial waste gas to acetate

Acetogens have often been observed to be inhibited by CO above an inhibition threshold concentration. In this study, a two-stage culture consisting of carboxydotrophic archaea and homoacetogenic bacteria is found to be effective in converting industrial waste gas derived from a steel mill process. In the first stage, Thermococcus onnurineus could grow on the Linz-Donawitz converter gas (LDG) containing ca. 56% CO as a sole energy source, converting the CO into H2 and CO2. Then, in the second stage, Thermoanaerobacter kivui could grow on the off-gas from the first stage culture, consuming the H2 and CO in the off-gas completely and producing acetate as a main product. T. kivui alone could not grow on the LDG gas. This work represents the first demonstration of acetate production using steel mill waste gas by a two-stage culture of carboxydotrophic hydrogenogenic microbes and homoacetogenic bacteria.

Adaptive engineering of a hyperthermophilic archaeon on CO and discovering the underlying mechanism by multi-omics analysis

The hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H₂ on carbon monoxide (CO) and its H₂ production rates have been improved through metabolic engineering. In this study, we applied adaptive evolution to enhance H₂ productivity. After over 150 serial transfers onto CO medium, cell density, CO consumption rate and H₂ production rate increased. The underlying mechanism for those physiological changes could be explained by using multi-omics approaches including genomic, transcriptomic and epigenomic analyses. A putative transcriptional regulator was newly identified to regulate the expression levels of genes related to CO oxidation. Transcriptome analysis revealed significant changes in the transcript levels of genes belonging to the categories of transcription, translation and energy metabolism. Our study presents the first genome-scale methylation pattern of hyperthermophilic archaea. Adaptive evolution led to highly enhanced H₂ productivity at high CO flow rates using synthesis gas produced from coal gasification.

Heterologous Production of an Energy-Conserving Carbon Monoxide Dehydrogenase Complex in the Hyperthermophile Pyrococcus furiosus

Carbon monoxide (CO) is an important intermediate in anaerobic carbon fixation pathways in acetogenesis and methanogenesis. In addition, some anaerobes can utilize CO as an energy source. In the hyperthermophilic archaeon Thermococcus onnurineus, which grows optimally at 80°C, CO oxidation and energy conservation is accomplished by a respiratory complex encoded by a 16-gene cluster containing a CO dehydrogenase, a membrane-bound [NiFe]-hydrogenase and a Na⁺/H⁺ antiporter module. This complex oxidizes CO, evolves CO₂ and H₂, and generates a Na⁺ motive force that is used to conserve energy by a Na⁺-dependent ATP synthase. Herein we used a bacterial artificial chromosome to insert the 13.2 kb gene cluster encoding the CO-oxidizing respiratory complex of T. onnurineus into the genome of the heterotrophic archaeon, Pyrococcus furiosus, which grows optimally at 100°C. P. furiosus is normally unable to utilize CO, however, the recombinant strain readily oxidized CO and generated H₂ at 80°C. Moreover, CO also served as an energy source and allowed the P. furiosus strain to grow with a limiting concentration of sugar or with peptides as the carbon source. Moreover, CO oxidation by P. furiosus was also coupled to the re-utilization, presumably for biosynthesis, of acetate generated by fermentation. The functional transfer of CO utilization between Thermococcus and Pyrococcus species demonstrated herein is representative of the horizontal gene transfer of an environmentally relevant metabolic capability. The transfer of CO utilizing, hydrogen-producing genetic modules also has applications for biohydrogen production and a CO-based industrial platform for various thermophilic organisms.

Desulfovibrio vulgaris Growth Coupled to Formate-Driven H2 Production

Formate is recognized as a superior substrate for biological H2 production by several bacteria. However, the growth of a single organism coupled to this energetic pathway has not been shown in mesophilic conditions. In the present study, a bioreactor with gas sparging was used, where we observed for the first time that H2 production from formate can be coupled with growth of the model sulfate-reducing bacterium Desulfovibrio vulgaris in the absence of sulfate or a syntrophic partner. In these conditions, D. vulgaris had a maximum growth rate of 0.078 h(-1) and a doubling time of 9 h, and the ΔG of the reaction ranged between -21 and -18 kJ mol(-1). This is the first report of a single mesophilic organism that can grow while catalyzing the oxidation of formate to H2 and bicarbonate. Furthermore, high volumetric and specific H2 production rates (125 mL L(-1) h(-1) and 2500 mL gdcw(-1) h(-1)) were achieved in a new bioreactor designed and optimized for H2 production. This high H2 production demonstrates that the nonconventional H2-producing organism D. vulgaris is a good biocatalyst for converting formate to H2.

Relevance of nutrient media composition for hydrogen production in Chlamydomonas

Microalgae are capable of biological H2 photoproduction from water, solar energy, and a variety of organic substrates. Acclimation responses to different nutrient regimes finely control photosynthetic activity and can influence H2 production. Hence, nutrient stresses are an interesting scenario to study H2 production in photosynthetic organisms. In this review, we mainly focus on the H2-production mechanisms in Chlamydomonas reinhardtii and the physiological relevance of the nutrient media composition when producing H2.

Overproduction of the membrane-bound [NiFe]-hydrogenase in Thermococcus kodakarensis and its effect on hydrogen production

The hyperthermophilic archaeon Thermococcus kodakarensis can utilize sugars or pyruvate for growth. In the absence of elemental sulfur, the electrons via oxidation of these substrates are accepted by protons, generating molecular hydrogen (H₂). The hydrogenase responsible for this reaction is a membrane-bound [NiFe]-hydrogenase (Mbh). In this study, we have examined several possibilities to increase the protein levels of Mbh in T. kodakarensis by genetic engineering. Highest levels of intracellular Mbh levels were achieved when the promoter of the entire mbh operon (TK2080-TK2093) was exchanged to a strong constitutive promoter from the glutamate dehydrogenase gene (TK1431) (strain MHG1). When MHG1 was cultivated under continuous culture conditions using pyruvate-based medium, a nearly 25% higher specific hydrogen production rate (SHPR) of 35.3 mmol H₂ g-dcw⁻¹ h⁻¹ was observed at a dilution rate of 0.31 h⁻¹. We also combined mbh overexpression using an even stronger constitutive promoter from the cell surface glycoprotein gene (TK0895) with disruption of the genes encoding the cytosolic hydrogenase (Hyh) and an alanine aminotransferase (AlaAT), both of which are involved in hydrogen consumption (strain MAH1). At a dilution rate of 0.30 h⁻¹, the SHPR was 36.2 mmol H₂ g-dcw⁻¹ h⁻¹, corresponding to a 28% increase compared to that of the host T. kodakarensis strain. Increasing the dilution rate to 0.83 h⁻¹ or 1.07 h⁻¹ resulted in a SHPR of 120 mmol H₂ g-dcw⁻¹ h⁻¹, which is one of the highest production rates observed in microbial fermentation.

A Critical Assessment of Microbiological Biogas to Biomethane Upgrading Systems

Microbiological biogas upgrading could become a promising technology for production of methane (CH(4)). This is, storage of irregular generated electricity results in a need to store electricity generated at peak times for use at non-peak times, which could be achieved in an intermediate step by electrolysis of water to molecular hydrogen (H(2)). Microbiological biogas upgrading can be performed by contacting carbon dioxide (CO(2)), H(2) and hydrogenotrophic methanogenic Archaea either in situ in an anaerobic digester, or ex situ in a separate bioreactor. In situ microbiological biogas upgrading is indicated to require thorough bioprocess development, because only low volumetric CH(4) production rates and low CH(4) fermentation offgas content have been achieved. Higher volumetric production rates are shown for the ex situ microbiological biogas upgrading compared to in situ microbiological biogas upgrading. However, the ex situ microbiological biogas upgrading currently suffers from H(2) gas liquid mass transfer limitation, which results in low volumetric CH(4) productivity compared to pure H(2)/CO(2) conversion to CH(4). If waste gas utilization from biological and industrial sources can be shown without reduction in volumetric CH(4) productivity, as well as if the aim of a single stage conversion to a CH(4) fermentation offgas content exceeding 95 vol% can be demonstrated, ex situ microbiological biogas upgrading with pure or enrichment cultures of methanogens could become a promising future technology for almost CO(2)-neutral biomethane production.