Microbial CO2 fixation and biotechnology in reducing industrial CO2 emissions

Real-time monitoring method of microbial growth using a simple pressure-based respiration detection system

Dry cell weight (DCW) and optical density (OD) measurement methods provide useful data for assessing microbial growth. However, their sampling process is labor-intensive and time-consuming. Therefore, we aimed to evaluate a method for measuring microbial growth through continuous CO2 measurement under aerobic conditions using a pressure-based respiration detection system, which is traditionally used in anaerobic environments and applies measurement of reduced pressure by capturing CO2 with KOH. The pressure reduction rate, OD, and DCW values were compared during Ralstonia eutropha H16 culture, which revealed a correlation of R2 of 0.99 between the pressure reduction and DCW and a change of DCW (g/L) per pressure (1 mbar) of -0.02 g/L. It showed theoretical limit of detection at 14.67 mbar corresponding to 0.0428 g/L of DCW and theoretical limit of quantification at 48.9 mbar as lower limits. When the pressure-based method was applied to compare carbon source utilization and growth of different strains, such as E. coli sp., Pseudomonas sp., Burkholderia sp., and Bacillus sp., it showed a high correlation with DCW. Overall, these results demonstrate that the pressure-based respiration detection system is a reliable tool for microbial growth monitoring and offers significant advantages by providing real-time data with less labor.

Ancestral carbonic anhydrase with significantly enhanced stability and activity for CO2 capture and utilization

Carbonic anhydrases (CAs) has garnered increasing attention in carbon capture, utilization and storage (CCUS) due to their ecological friendliness. However, most of them suffer susceptibility to deactivation in harsh conditions. Herein, a reliable dataset was adopted for creating ancestral CAs through an optimized ancestral sequence reconstruction (ASR) method. After prescreening, the ancestor AncCA19 was obtained and successfully expressed. The hydration activity of AncCA19 was as high as 58,859 WAU/mg, with the optimum temperature and pH obtained by esterase assay at 100 ℃ and 9, respectively. AncCA19 had the longest half-life (1.7 h) at 95 ℃ compared with existing CAs. After 2 weeks' incubation in artificial seawater at 30 ℃ or 25.0 % N-methyldiethanolamine (MDEA) at 60 ℃, the activities remained above 47,370 WAU/mg and 6,596 WAU/mg, respectively. Thus, AncCA19, as a novel benchmark of CAs, exhibits exceptional stability in a variety CCUS applications, establishing a versatile candidate for effective CO2 capture.

Heterologous Expression and Functional Verification of Extracellular Carbonic Anhydrases in Bacillus safensis yw6 from Mariana Trench

The exploration and exploitation of deep-sea microbial resources is of great scientific value for understanding biological evolution under extreme conditions. Deep-sea microorganisms are critical in the ocean carbon cycle, and marine heterotrophic microorganisms secrete extracellular carbonic anhydrase (CA) to fix inorganic carbon, an important process in climate regulation. Extracellular CA provides a green method for fixing carbon dioxide into stable minerals containing Ca2+. However, studies on extracellular CA in deep-sea microorganisms are limited. In this study, Bacillus safensis yw6 was isolated from Mariana Trench sediments and three candidate extracellular CA genes (β-ca1, β-ca2, and γ-ca) were identified by whole genome sequencing. Bioinformatics analyses showed that these CAs have different structural compositions, with the β-CA having α-helix and random coiling, whereas the γ-CA has more random coiling and stretched strands. Heterologous expression in E. coli BL21 (DE3) showed that β-CA2 had the highest enzyme activity, followed by γ-CA and β-CA1. Field emission scanning electron microscopy (FESEM) observations showed that the engineered strains with β-ca2 genes produced deposits that were like those from natural sources. This finding not only provides new perspectives for the utilization of deep-sea microbial resources, but also provides an important scientific basis for the molecular mechanisms of extracellular CAs of deep-sea microbes.

Screening and characterization of integration sites based on CRISPR-Cpf1 in Pichia pastoris

Pichia pastoris, a methylotrophic yeast, can utilize methanol as a carbon source and energy source to synthesize high-value chemicals, and is an ideal host for biomanufacturing. Constructing the P. pastoris cell factory is somewhat impeded due to the absence of genetic tools for manipulating multi-gene biosynthetic pathways. To broaden its application in the field of metabolic engineering, this study identified and screened 15 novel integration sites in P. pastoris using CRISPR-Cpf1 genome editing technology, with EGFP serving the reporter protein. These integration sites have integration efficiencies of 10-100 % and varying expression strengths, which allow for selection based on the expression levels of genes as needed. Additionally, these integrated sites are applied in the heterologous biosynthesis of P. pastoris, such as the astaxanthin biosynthetic pathway and the carbon dioxide fixation pathway of the Calvin-Benson-Bassham (CBB) cycle. During the three-site integration process, the 8 genes of the CBB cycle were integrated into the genome of P. pastoris. This indicates the potential of these integration sites for integrating large fragments and suggests their successful application in metabolic engineering of P. pastoris. This may lead to improved efficiency of genetic engineering in P. pastoris.

Production of succinate with two CO2 fixation reactions from fatty acids in Cupriavidus necator H16

BACKGROUND

Biotransformation of CO2 into high-value-added carbon-based products is a promising process for reducing greenhouse gas emissions. To realize the green transformation of CO2, we use fatty acids as carbon source to drive CO2 fixation to produce succinate through a portion of the 3-hydroxypropionate (3HP) cycle in Cupriavidus necator H16.

RESULTS

This work can achieve the production of a single succinate molecule from one acetyl-CoA molecule and two CO2 molecules. It was verified using an isotope labeling experiment utilizing NaH13CO3. This implies that 50% of the carbon atoms present in succinate are derived from CO2, resulting in a twofold increase in efficiency compared to prior methods of succinate biosynthesis that relied on the carboxylation of phosphoenolpyruvate or pyruvate. Meanwhile, using fatty acid as a carbon source has a higher theoretical yield than other feedstocks and also avoids carbon loss during acetyl-CoA and succinate production. To further optimize succinate production, different approaches including the optimization of ATP and NADPH supply, optimization of metabolic burden, and optimization of carbon sources were used. The resulting strain was capable of producing succinate to a level of 3.6 g/L, an increase of 159% from the starting strain.

CONCLUSIONS

This investigation established a new method for the production of succinate by the implementation of two CO2 fixation reactions and demonstrated the feasibility of ATP, NADPH, and metabolic burden regulation strategies in biological carbon fixation.

Optimization strategies for CO2 biological fixation

Global sustainable development faces a significant challenge in effectively utilizing CO2. Meanwhile, CO2 biological fixation offers a promising solution. CO2 has the highest oxidation state (+4 valence state), whereas typical multi‑carbon chemicals have lower valence states. The Gibbs free energy (ΔG) changes of CO2 reductive reactions are generally positive and this renders it necessary to input different forms of energy. Although biological carbon fixation processes are friendly to operate, the thermodynamic obstacles must be overcome. To make this reaction occur favorably and efficiently, diverse strategies to enhance CO2 biological fixation efficiency have been proposed by numerous researchers. This article reviews recent advances in optimizing CO2 biological fixation and intends to provide new insights into achieving efficient biological utilization of CO2. It first outlines the thermodynamic characteristics of diverse carbon fixation reactions and proposes optimization directions for CO2 biological fixation. A comprehensive overview of the catalytic mechanisms, optimization strategies, and challenges encountered by common carbon-fixing enzymes is then provided. Subsequently, potential routes for improving the efficiency of biological carbon fixation are discussed, including the ATP supply, reducing power supply, energy supply, reactor design, and carbon enrichment system modules. In addition, effective artificial carbon fixation pathways were summarized and analyzed. Finally, prospects are made for the research direction of continuously improving the efficiency of biological carbon fixation.

Acidophilic heterotrophs: basic aspects and technological applications

Acidophiles comprise a group of microorganisms adapted to live in acidic environments. Despite acidophiles are usually associated with an autotrophic metabolism, more than 80 microorganisms capable of utilizing organic matter have been isolated from natural and man-made environments. The ability to reduce soluble and insoluble iron compounds has been described for many of these species and may be harnessed to develop new or improved mining processes when oxidative bioleaching is ineffective. Similarly, as these microorganisms grow in highly acidic media and the chances of contamination are reduced by the low pH, they may be employed to implement robust fermentation processes. By conducting an extensive literature review, this work presents an updated view of basic aspects and technological applications in biomining, bioremediation, fermentation processes aimed at biopolymers production, microbial electrochemical systems, and the potential use of extremozymes.

Tire materials disturb transformations of nitrogen compounds and affect the structure of biomass in aerobic granular sludge reactors

Tire materials (TMs) present a notable hazard due to their potential to release harmful chemicals and microplastics into the environment. They can infiltrate wastewater treatment plants, where their effects remain inadequately understood, raising concerns regarding their influence on treatment procedures. Thus, this study investigated the impact of TMs in wastewater (10, 25, 50 mg/L) on wastewater treatment efficiency, biomass morphology, and microbial composition in aerobic granular sludge (AGS) reactors. TM dosage negatively correlated with nitrification and denitrification efficiencies, reducing overall nitrogen removal, but did not affect the efficiency of chemical-oxygen-demand removal. The presence of TMs increased the diameter of the granules due to TM incorporation into the biomass. The most frequently leached additives from TMs were N-(1,3-dimethylbutyl)-N'-phenyl-1,4-phenylenediamine, benzothiazole (BTH), and 2-hydroxybenzothiazole. In the treated wastewater, only BTH and aniline were detected in higher concentrations, which indicates that tire additives were biodegraded by AGS. The microbial community within the AGS adapted to TMs and their chemicals, highlighting the potential for efficient degradation of tire additives by bacteria belonging to the genera Rubrivivax, Ferruginibacter, and Xanthomonas. Additionally, our research underscores AGS's ability to incorporate TMs into biomass and effectively biodegrade tire additives, offering a promising solution for addressing environmental concerns related to TMs.

Carbon dioxide reduction to high-value chemicals in microbial electrosynthesis system: Biological conversion and regulation strategies

Large emissions of atmospheric carbon dioxide (CO2) are causing climatic and environmental problems. It is crucial to capture and utilize the excess CO2 through diverse methods, among which the microbial electrosynthesis (MES) system has become an attractive and promising technology to mitigate greenhouse effects while reducing CO2 to high-value chemicals. However, the biological conversion and metabolic pathways through microbial catalysis have not been clearly elucidated. This review first introduces the main acetogenic bacteria for CO2 reduction and extracellular electron transfer mechanisms in MES. It then intensively analyzes the CO2 bioconversion pathways and carbon chain elongation processes in MES, together with energy supply and utilization. The factors affecting MES performance, including physical, chemical, and biological aspects, are summarized, and the strategies to promote and regulate bioconversion in MES are explored. Finally, challenges and perspectives concerning microbial electrochemical carbon sequestration are proposed, and suggestions for future research are also provided. This review provides theoretical foundation and technical support for further development and industrial application of MES for CO2 reduction.

Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications

Anthropogenic carbon dioxide (CO2) levels are rising to alarming concentrations in earth's atmosphere, causing adverse effects and global climate changes. In the last century, innovative research on CO2 reduction using chemical, photochemical, electrochemical and enzymatic approaches has been addressed. In particular, natural CO2 conversion serves as a model for many processes and extensive studies on microbes and enzymes regarding redox reactions involving CO2 have already been conducted. In this review we focus on the enzymatic conversion of CO2 to carbon monoxide (CO) as the chemical conversion downstream of CO production render CO particularly attractive as a key intermediate. We briefly discuss the different currently known natural autotrophic CO2 fixation pathways, focusing on the reversible reaction of CO2, two electrons and protons to CO and water, catalyzed by carbon monoxide dehydrogenases (CODHs). We then move on to classify the different type of CODHs, involved catalyzed chemical reactions and coupled metabolisms. Finally, we discuss applications of CODH enzymes in photochemical and electrochemical cells to harness CO2 from the environment transforming it into commodity chemicals.

Perspectives for Using CO2 as a Feedstock for Biomanufacturing of Fuels and Chemicals

Microbial cell factories offer an eco-friendly alternative for transforming raw materials into commercially valuable products because of their reduced carbon impact compared to conventional industrial procedures. These systems often depend on lignocellulosic feedstocks, mainly pentose and hexose sugars. One major hurdle when utilizing these sugars, especially glucose, is balancing carbon allocation to satisfy energy, cofactor, and other essential component needs for cellular proliferation while maintaining a robust yield. Nearly half or more of this carbon is inevitably lost as CO2 during the biosynthesis of regular metabolic necessities. This loss lowers the production yield and compromises the benefit of reducing greenhouse gas emissions-a fundamental advantage of biomanufacturing. This review paper posits the perspectives of using CO2 from the atmosphere, industrial wastes, or the exhausted gases generated in microbial fermentation as a feedstock for biomanufacturing. Achieving the carbon-neutral or -negative goals is addressed under two main strategies. The one-step strategy uses novel metabolic pathway design and engineering approaches to directly fix the CO2 toward the synthesis of the desired products. Due to the limitation of the yield and efficiency in one-step fixation, the two-step strategy aims to integrate firstly the electrochemical conversion of the exhausted CO2 into C1/C2 products such as formate, methanol, acetate, and ethanol, and a second fermentation process to utilize the CO2-derived C1/C2 chemicals or co-utilize C5/C6 sugars and C1/C2 chemicals for product formation. The potential and challenges of using CO2 as a feedstock for future biomanufacturing of fuels and chemicals are also discussed.

Will tomorrow's mineral materials be grown?

Biomineralization, the capacity to form minerals, has evolved in a great diversity of bacterial lineages as an adaptation to different environmental conditions and biological functions. Microbial biominerals often display original properties (morphology, composition, structure, association with organics) that significantly differ from those of abiotically formed counterparts, altogether defining the 'mineral phenotype'. In principle, it should be possible to take advantage of microbial biomineralization processes to design and biomanufacture advanced mineral materials for a range of technological applications. In practice, this has rarely been done so far and only for a very limited number of biomineral types. This is mainly due to our poor understanding of the underlying molecular mechanisms controlling microbial biomineralization pathways, preventing us from developing bioengineering strategies aiming at improving biomineral properties for different applications. Another important challenge is the difficulty to upscale microbial biomineralization from the lab to industrial production. Addressing these challenges will require combining expertise from environmental microbiologists and geomicrobiologists, who have historically been working at the forefront of research on microbe-mineral interactions, alongside bioengineers and material scientists. Such interdisciplinary efforts may in the future allow the emergence of a mineral biomanufacturing industry, a critical tool towards the development more sustainable and circular bioeconomies.

Extremophiles: the species that evolve and survive under hostile conditions

Extremophiles possess unique cellular and molecular mechanisms to assist, tolerate, and sustain their lives in extreme habitats. These habitats are dominated by one or more extreme physical or chemical parameters that shape existing microbial communities and their cellular and genomic features. The diversity of extremophiles reflects a long list of adaptations over millions of years. Growing research on extremophiles has considerably uncovered and increased our understanding of life and its limits on our planet. Many extremophiles have been greatly explored for their application in various industrial processes. In this review, we focused on the characteristics that microorganisms have acquired to optimally thrive in extreme environments. We have discussed cellular and molecular mechanisms involved in stability at respective extreme conditions like thermophiles, psychrophiles, acidophiles, barophiles, etc., which highlight evolutionary aspects and the significance of extremophiles for the benefit of mankind.

Production of sustainable biofuels from microalgae with CO2 bio-sequestration and life cycle assessment

Due to anthropogenic emissions, there is an increase in the concentration of carbon dioxide (CO₂) in the atmosphere. Microalgae are versatile, universal, and photosynthetic microorganisms present in nature. Biological CO₂ sequestration using microalgae is a novel concept in CO₂ mitigation strategies. In the current review, the difference between carbon capture and storage (CCS), carbon capture utilization and storage (CCUS), and carbon capture and utilization (CCU) is clarified. The current status of CO₂ sequestration techniques is discussed, including various methods and a comparative analysis of abiotic and biotic sequestration. Particular focus is given to sequestration methods associated with microalgae, including advantages of CO₂ bio-sequestration using microalgae, a summary of microalgae species that tolerate high CO₂ concentrations, biochemistry of microalgal CO₂ biofixation, and elements influencing the microalgal CO₂ sequestration. In addition, this review highlights and summarizes the research efforts made on the production of various biofuels using microalgae. Notably, Chlorella sp. is found to be the most beneficial microalgae, with a sizeable hydrogen (H₂) generation capability ranging from 6.1 to 31.2 mL H₂/g microalgae, as well as the species of C. salina, C. fusca, Parachlorella kessleri, C. homosphaera, C. vacuolate, C. pyrenoidosa, C. sorokiniana, C. lewinii, and C. protothecoides. Lastly, the technical feasibility and life cycle analysis are analyzed. This comprehensive review will pave the way for promoting more aggressive research on microalgae-based CO₂ sequestration.

Prospects for engineering Ralstonia eutropha and Zymomonas mobilis for the autotrophic production of 2,3-butanediol from CO2 and H2

The decarbonization of the chemical industry and a shift toward circular economies because of high global CO2 emissions make CO2 an attractive feedstock for manufacturing chemicals. Moreover, H2 is a low-cost and carbon-free reductant because technologies such as solar-driven electrolysis and supercritical water (scH2O) gasification enable sustainable production of molecular hydrogen (H2). We review the recent advances in engineering Ralstonia eutropha, the representative species of "Knallgas" bacteria, for utilizing CO2 and H2 to autotrophically produce 2,3-butanediol (2,3-BDO). This assessment is focused on state-of-the-art approaches for splitting H2 to supply energy in the form of ATP and NADH to power cellular reactions and employing the Calvin-Benson-Bassham cycle for CO2 fixation. Major challenges and opportunities for application and future perspectives are discussed in the context of developing other promising CO2 and H2-utilizing microorganisms, exemplified by Zymomonas mobilis.

Porous Polymer Materials for CO2 Capture and Electrocatalytic Reduction

Efficient capture of CO₂ and its conversion into other high value-added compounds by electrochemical methods is an effective way to reduce excess CO₂ in the atmosphere. Porous polymeric materials hold great promise for selective adsorption and electrocatalytic reduction of CO₂ due to their high specific surface area, tunable porosity, structural diversity, and chemical stability. Here, we review recent research advances in this field, including design of porous organic polymers (POPs), porous coordination polymers (PCPs), covalent organic frameworks (COFs), and functional nitrogen-containing polymers for capture and electrocatalytic reduction of CO₂. In addition, key issues and prospects for the optimal design of porous polymers for future development are elucidated. This review is expected to shed new light on the development of advanced porous polymer electrocatalysts for efficient CO₂ reduction.

Valorization of CO2 to β-farnesene in Rhodobacter sphaeroides

The valorization of CO₂ into valuable products is a sustainable strategy to help overcome the climate crisis. In particular, biological conversion is attractive as it can produce long-chain hydrocarbons such as terpenoids. This study reports the high yield of β-farnesene production from CO₂ by expressing heterologous β-farnesene synthase (FS) into Rhodobacter sphaeroides. To increase the expression of FS, a strong active promoter and a ribosome binding site (RBS) were engineered. Moreover, β-farnesene production was improved further through the supply of exogenous antioxidants and additional nutrients. Finally, β-farnesene was produced from CO₂ at a titer of 44.53 mg/L and yield of 234.08 mg/g, values that were correspondingly 23 times and 46 times higher than those from the initial production of β-farnesene. Altogether, the results here suggest that the autotrophic production of β-farnesene can provide a starting point for achieving a circular carbon economy.