Effect of the addition of an inorganic carbon source on the degradation of sotol vinasse by Rhodopseudomonastelluris

The difficulty of the microbial conversion process for the degradation of sotol vinasse due to its high acidity and organic load makes it an effluent with high potential for environmental contamination, therefore its treatment is of special interest. Calcium carbonate is found in great abundance and has the ability to act as a neutralizing agent, maintaining the alkalinity of the fermentation medium as well as, through its dissociation, releasing CO2 molecules that can be used by phototrophic CO2-fixing bacteria. This study evaluated the use of Rhodopseudomonas telluris (OR069658) for the degradation of vinasse in different concentrations of calcium carbonate (0, 2, 4, 6, 8 and 10% m/v). The results showed that calcium carbonate concentration influenced volatile fatty acids (VFA), alkalinity and pH, which in turn influenced changes in the degradation of chemical oxygen demand (COD), phenol and sulfate. Maximum COD and phenol degradation values of 83.16 ± 0.15% and 90.16 ± 0.30%, respectively, were obtained at a calcium carbonate concentration of 4%. At the same time, the lowest COD and phenol degradation values of 52.01 ± 0.38% and 68.21 ± 0.81%, respectively, were obtained at a calcium carbonate concentration of 0%. The data obtained also revealed to us that at high calcium carbonate concentrations of 6-10%, sotol vinasse can be biosynthesized by Rhodopseudomonas telluris (OR069658) to VFA, facilitating the degradation of sulfates. The findings of this study confirmed the potential for using Rhodopseudomonas telluris (OR069658) at a calcium carbonate concentration of 4% as an appropriate alternative treatment for sotol vinasse degradation.

Mitochondrial membrane transporters as attractive targets for the fermentative production of succinic acid from glycerol in Saccharomyces cerevisiae

Previously, we reported an engineered Saccharomyces cerevisiae CEN.PK113-1A derivative able to produce succinic acid (SA) from glycerol with net CO2 fixation. Apart from an engineered glycerol utilization pathway that generates NADH, the strain was equipped with the NADH-dependent reductive branch of the TCA cycle (rTCA) and a heterologous SA exporter. However, the results indicated that a significant amount of carbon still entered the CO2-releasing oxidative TCA cycle. The current study aimed to tune down the flux through the oxidative TCA cycle by targeting the mitochondrial uptake of pyruvate and cytosolic intermediates of the rTCA pathway, as well as the succinate dehydrogenase complex. Thus, we tested the effects of deletions of MPC1, MPC3, OAC1, DIC1, SFC1, and SDH1 on SA production. The highest improvement was achieved by the combined deletion of MPC3 and SDH1. The respective strain produced up to 45.5 g/L of SA, reached a maximum SA yield of 0.66 gSA/gglycerol, and accumulated the lowest amounts of byproducts when cultivated in shake-flasks. Based on the obtained data, we consider a further reduction of mitochondrial import of pyruvate and rTCA intermediates highly attractive. Moreover, the approaches presented in the current study might also be valuable for improving SA production when sugars (instead of glycerol) are the source of carbon.

Carbon efficient production of chemicals with yeasts

Microbial metabolism offers a wide variety of opportunities to produce chemicals from renewable resources. Employing such processes of industrial biotechnology provides valuable means to fight climate change by replacing fossil feedstocks by renewable substrate to reduce or even revert carbon emission. Several yeast species are well suited chassis organisms for this purpose, illustrated by the fact that the still largest microbial production of a chemical, namely bioethanol is based on yeast. Although production of ethanol and some other chemicals is highly efficient, this is not the case for many desired bulk chemicals. One reason for low efficiency is carbon loss, which decreases the product yield and increases the share of total production costs that is taken by substrate costs. Here we discuss the causes for carbon loss in metabolic processes, approaches to avoid carbon loss, as well as opportunities to incorporate carbon from CO2 , based on the electron balance of pathways. These aspects of carbon efficiency are illustrated for the production of succinic acid from a diversity of substrates using different pathways.

The oxygen-tolerant reductive glycine pathway assimilates methanol, formate and CO2 in the yeast Komagataella phaffii

The current climatic change is predominantly driven by excessive anthropogenic CO2 emissions. As industrial bioprocesses primarily depend on food-competing organic feedstocks or fossil raw materials, CO2 co-assimilation or the use of CO2-derived methanol or formate as carbon sources are considered pathbreaking contributions to solving this global problem. The number of industrially-relevant microorganisms that can use these two carbon sources is limited, and even fewer can concurrently co-assimilate CO2. Here, we search for alternative native methanol and formate assimilation pathways that co-assimilate CO2 in the industrially-relevant methylotrophic yeast Komagataella phaffii (Pichia pastoris). Using 13C-tracer-based metabolomic techniques and metabolic engineering approaches, we discover and confirm a growth supporting pathway based on native enzymes that can perform all three assimilations: namely, the oxygen-tolerant reductive glycine pathway. This finding paves the way towards metabolic engineering of formate and CO2 utilisation to produce proteins, biomass, or chemicals in yeast.

Conversion of CO2 into organic acids by engineered autotrophic yeast

The increase of CO2 emissions due to human activity is one of the preeminent reasons for the present climate crisis. In addition, considering the increasing demand for renewable resources, the upcycling of CO2 as a feedstock gains an extensive importance to establish CO2-neutral or CO2-negative industrial processes independent of agricultural resources. Here we assess whether synthetic autotrophic Komagataella phaffii (Pichia pastoris) can be used as a platform for value-added chemicals using CO2 as a feedstock by integrating the heterologous genes for lactic and itaconic acid synthesis. 13C labeling experiments proved that the resulting strains are able to produce organic acids via the assimilation of CO2 as a sole carbon source. Further engineering attempts to prevent the lactic acid consumption increased the titers to 600 mg L-1, while balancing the expression of key genes and modifying screening conditions led to 2 g L-1 itaconic acid. Bioreactor cultivations suggest that a fine-tuning on CO2 uptake and oxygen demand of the cells is essential to reach a higher productivity. We believe that through further metabolic and process engineering, the resulting engineered strain can become a promising host for the production of value-added bulk chemicals by microbial assimilation of CO2, to support sustainability of industrial bioprocesses.

Carbon dioxide fixation via production of succinic acid from glycerol in engineered Saccharomyces cerevisiae

Background

The microbial production of succinic acid (SA) from renewable carbon sources via the reverse TCA (rTCA) pathway is a process potentially accompanied by net-fixation of carbon dioxide (CO₂). Among reduced carbon sources, glycerol is particularly attractive since it allows a nearly twofold higher CO₂-fixation yield compared to sugars. Recently, we described an engineered Saccharomyces cerevisiae strain which allowed SA production in synthetic glycerol medium with a maximum yield of 0.23 Cmol Cmol⁻¹. The results of that previous study suggested that the glyoxylate cycle considerably contributed to SA accumulation in the respective strain. The current study aimed at improving the flux into the rTCA pathway accompanied by a higher CO₂-fixation and SA yield.

Results

By changing the design of the expression cassettes for the rTCA pathway, overexpressing PYC2, and adding CaCO₃ to the batch fermentations, an SA yield on glycerol of 0.63 Cmol Cmol⁻¹ was achieved (i.e. 47.1% of the theoretical maximum). The modifications in this 2nd-generation SA producer improved the maximum biomass-specific glycerol consumption rate by a factor of nearly four compared to the isogenic baseline strain solely equipped with the dihydroxyacetone (DHA) pathway for glycerol catabolism. The data also suggest that the glyoxylate cycle did not contribute to the SA production in the new strain. Cultivation conditions which directly or indirectly increased the concentration of bicarbonate, led to an accumulation of malate in addition to the predominant product SA (ca. 0.1 Cmol Cmol⁻¹ at the time point when SA yield was highest). Off-gas analysis in controlled bioreactors with CO₂-enriched gas-phase indicated that CO₂ was fixed during the SA production phase.

Conclusions

The data strongly suggest that a major part of dicarboxylic acids in our 2nd-generation SA-producer was formed via the rTCA pathway enabling a net fixation of CO₂. The greatly increased capacity of the rTCA pathway obviously allowed successful competition with other pathways for the common precursor pyruvate. The overexpression of PYC2 and the increased availability of bicarbonate, the co-substrate for the PYC reaction, further strengthened this capacity. The achievements are encouraging to invest in future efforts establishing a process for SA production from (crude) glycerol and CO₂.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01817-1.

The white koji fungus Aspergillus luchuensis mut. kawachii

The white koji fungus, Aspergillus luchuensis mut. kawachii, is used in the production of shochu, a traditional Japanese distilled spirit. White koji fungus plays an important role in the shochu production process by supplying amylolytic enzymes such as α-amylase and glucoamylase. These enzymes convert starch contained in primary ingredients such as rice, barley, buckwheat, and sweet potato into glucose, which is subsequently utilized by the yeast Saccharomyces cerevisiae to produce ethanol. White koji fungus also secretes large amounts of citric acid, which lowers the pH of the shochu mash, thereby preventing the growth of undesired microbes and enabling stable production of shochu in relatively warm regions of Japan. This review describes the historical background, research tools, and recent advances in studies of the mechanism of citric acid production by white koji fungus.

State of the Art on the Microbial Production of Industrially Relevant Organic Acids

The industrial relevance of organic acids is high; because of their chemical properties, they can be used as building blocks as well as single-molecule agents with a huge annual market. Organic acid chemical platforms can derive from fossil sources by petrochemical refining processes, but most of them also represent natural metabolites produced by many cells. They are the products, by-products or co-products of many primary metabolic processes of microbial cells. Thanks to the potential of microbial cell factories and to the development of industrial biotechnology, from the last decades of the previous century, the microbial-based production of these molecules has started to approach the market. This was possible because of a joint effort of microbial biotechnologists and biochemical and process engineers that boosted natural production up to the titer, yield and productivity needed to be industrially competitive. More recently, the possibility to utilize renewable residual biomasses as feedstock not only for biofuels, but also for organic acids production is further augmenting the sustainability of their production, in a logic of circular bioeconomy. In this review, we briefly present the latest updates regarding the production of some industrially relevant organic acids (citric fumaric, itaconic, lactic and succinic acid), discussing the challenges and possible future developments of successful production.

Prediction of Genes That Function in Methanogenesis and CO2 Pathways in Extremophiles

Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO₂ into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO₂ emissions.

Coordination of consolidated bioprocessing technology and carbon dioxide fixation to produce malic acid directly from plant biomass in Myceliophthora thermophila

BACKGROUND

Consolidated bioprocessing (CBP) technique is a promising strategy for biorefinery construction, producing bulk chemicals directly from plant biomass without extra hydrolysis steps. Fixing and channeling CO₂ into carbon metabolism for increased carbon efficiency in producing value-added compounds is another strategy for cost-effective bio-manufacturing. It has not been reported whether these two strategies can be combined in one microbial platform.

RESULTS

In this study, using the cellulolytic thermophilic fungus Myceliophthora thermophila, we designed and constructed a novel biorefinery system DMCC (Direct microbial conversion of biomass with CO₂ fixation) through incorporating two CO₂ fixation modules, PYC module and Calvin-Benson-Bassham (CBB) pathway. Harboring the both modules, the average rate of fixing and channeling ¹³CO₂ into malic acid in strain CP51 achieved 44.4, 90.7, and 80.7 mg/L/h, on xylose, glucose, and cellulose, respectively. The corresponding titers of malic acid were up to 42.1, 70.4, and 70.1 g/L, respectively, representing the increases of 40%, 10%, and 7%, respectively, compared to the parental strain possessing only PYC module. The DMCC system was further improved by enhancing the pentose uptake ability. Using raw plant biomass as the feedstock, yield of malic acid produced by the DMCC system was up to 0.53 g/g, with ¹³C content of 0.44 mol/mol malic acid, suggesting DMCC system can produce 1 t of malic acid from 1.89 t of biomass and fix 0.14 t CO₂ accordingly.

CONCLUSIONS

This study designed and constructed a novel biorefinery system named DMCC, which can convert raw plant biomass and CO₂ into organic acid efficiently, presenting a promising strategy for cost-effective production of value-added compounds in biorefinery. The DMCC system is one of great options for realization of carbon neutral economy.

Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists

Hydroxybenzoic acids, like gallic acid and protocatechuic acid, are highly abundant natural compounds. In biotechnology, they serve as critical precursors for various molecules in heterologous production pathways, but a major bottleneck is these acids’ non-oxidative decarboxylation to hydroxybenzenes. Optimizing this step by pathway and enzyme engineering is tedious, partly because of the complicating cofactor dependencies of the commonly used prFMN-dependent decarboxylases. Here, we report the crystal structures (1.5–1.9 Å) of two homologous fungal decarboxylases, AGDC1 from Arxula adenivorans, and PPP2 from Madurella mycetomatis. Remarkably, both decarboxylases are cofactor independent and are superior to prFMN-dependent decarboxylases when heterologously expressed in Saccharomyces cerevisiae. The organization of their active site, together with mutational studies, suggests a novel decarboxylation mechanism that combines acid–base catalysis and transition state stabilization. Both enzymes are trimers, with a central potassium binding site. In each monomer, potassium introduces a local twist in a β-sheet close to the active site, which primes the critical H86-D40 dyad for catalysis. A conserved pair of tryptophans, W35 and W61, acts like a clamp that destabilizes the substrate by twisting its carboxyl group relative to the phenol moiety. These findings reveal AGDC1 and PPP2 as founding members of a so far overlooked group of cofactor independent decarboxylases and suggest strategies to engineer their unique chemistry for a wide variety of biotechnological applications.

The highly-stable immobilization of enzymes on a waste mycelium carrier

Mycelium is an abundant waste from the fermentation industry, and the environmental problems associated with its required disposal seriously limited the development of fermentation industry. In China, millions of tons of various kinds of mycelium residues were produced each year. Research into providing added-value to mycelium, while avoiding its disposal, is hence of paramount importance. Mycelium can be used as carrier for enzymes, while the enzyme immobilization moreover improves their stability and lifetime performance. Carrier recycling, the natural degradation and disposal of artificial polymer carriers are critical issues in immobilization. This research investigated its use to manufacture a highly-stable immobilized enzyme. An acid pretreatment was employed to enhance the adsorption ability of mycelium, and its adsorption ability was compared with other carriers. Under the optimal conditions, a core-shell immobilized enzyme with porous structure was obtained. The stability and the recycle results of the evaluation indicated the excellent performance of the immobilized enzyme. The mycelium recycling was also investigated to verify the practicability. All the results indicated that the use of a mycelium-based carrier was a promising strategy for the reutilization of the fermentation waste, and this technique provides an alternative way to reduce the total amount of the waste mycelium. Meanwhile, the stability and reusability performance of the mycelium-based immobilization could also decrease the influence of the disposal of the solid waste from denatured enzymes to the environment.

Engineering Saccharomyces cerevisiae for Succinic Acid Production From Glycerol and Carbon Dioxide

Previously, our lab replaced the endogenous FAD-dependent pathway for glycerol catabolism in S. cerevisiae by the synthetic NAD-dependent dihydroxyacetone (DHA) pathway. The respective modifications allow the full exploitation of glycerol’s higher reducing power (compared to sugars) for the production of the platform chemical succinic acid (SA) via a reductive, carbon dioxide fixing and redox-neutral pathway in a production host robust for organic acid production. Expression cassettes for three enzymes converting oxaloacetate to SA in the cytosol (“SA module”) were integrated into the genome of UBR2_CBS-DHA, an optimized CEN.PK derivative. Together with the additional expression of the heterologous dicarboxylic acid transporter DCT-02 from Aspergillus niger, a maximum SA titer of 10.7 g/L and a yield of 0.22 ± 0.01 g/g glycerol was achieved in shake flask (batch) cultures. Characterization of the constructed strain under controlled conditions in a bioreactor supplying additional carbon dioxide revealed that the carbon balance was closed to 96%. Interestingly, the results of the current study indicate that the artificial “SA module” and endogenous pathways contribute to the SA production in a highly synergistic manner.

The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2

The methylotrophic yeast Pichia pastoris is widely used in the manufacture of industrial enzymes and pharmaceuticals. Like most biotechnological production hosts, P. pastoris is heterotrophic and grows on organic feedstocks that have competing uses in the production of food and animal feed. In a step toward more sustainable industrial processes, we describe the conversion of P. pastoris into an autotroph that grows on CO2. By addition of eight heterologous genes and deletion of three native genes, we engineer the peroxisomal methanol-assimilation pathway of P. pastoris into a CO2-fixation pathway resembling the Calvin-Benson-Bassham cycle, the predominant natural CO2-fixation pathway. The resulting strain can grow continuously with CO2 as a sole carbon source at a µmax of 0.008 h-1. The specific growth rate was further improved to 0.018 h-1 by adaptive laboratory evolution. This engineered P. pastoris strain may promote sustainability by sequestering the greenhouse gas CO2, and by avoiding consumption of an organic feedstock with alternative uses in food production.

Microbial carbon dioxide fixation: new tricks for an old game

The exploitation of petroleum as energy and material source opened unprecedented possibilities for the development of our human societies, but only now we realize that the use of fossil resources comes at devastatingly high environmental costs. Consequently, our efforts to tap other carbon sources are steadily increasing. Industrial microbiology has the potential to use carbon dioxide directly as carbon source, thereby converting a foe into a friend. This thematic issue of FEMS Microbiology Letters sheds some light on recent developments for the understanding of microbial pathways for carbon dioxide fixation and on strategies for their industrial exploitation.