Recent progress in the engineering of C1-utilizing microbes

Harnessing acetogenic bacteria for one-carbon valorization toward sustainable chemical production

The pressing climate change issues have intensified the need for a rapid transition towards a bio-based circular carbon economy. Harnessing acetogenic bacteria as biocatalysts to convert C1 compounds such as CO2, CO, formate, or methanol into value-added multicarbon chemicals is a promising solution for both carbon capture and utilization, enabling sustainable and green chemical production. Recent advances in the metabolic engineering of acetogens have expanded the range of commodity chemicals and biofuels produced from C1 compounds. However, producing energy-demanding high-value chemicals on an industrial scale from C1 substrates remains challenging because of the inherent energetic limitations of acetogenic bacteria. Therefore, overcoming this hurdle is necessary to scale up the acetogenic C1 conversion process and realize a circular carbon economy. This review overviews the acetogenic bacteria and their potential as sustainable and green chemical production platforms. Recent efforts to address these challenges have focused on enhancing the ATP and redox availability of acetogens to improve their energetics and conversion performances. Furthermore, promising technologies that leverage low-cost, sustainable energy sources such as electricity and light are discussed to improve the sustainability of the overall process. Finally, we review emerging technologies that accelerate the development of high-performance acetogenic bacteria suitable for industrial-scale production and address the economic sustainability of acetogenic C1 conversion. Overall, harnessing acetogenic bacteria for C1 valorization offers a promising route toward sustainable and green chemical production, aligning with the circular economy concept.

Engineering microbial metabolic homeostasis for chemicals production

Microbial-based bio-refining promotes the development of a biotechnology revolution to encounter and tackle the enormous challenges in petroleum-based chemical production by biomanufacturing, biocomputing, and biosensing. Nevertheless, microbial metabolic homeostasis is often incompatible with the efficient synthesis of bioproducts mainly due to: inefficient metabolic flow, robust central metabolism, sophisticated metabolic network, and inevitable environmental perturbation. Therefore, this review systematically summarizes how to optimize microbial metabolic homeostasis by strengthening metabolic flux for improving biotransformation turnover, redirecting metabolic direction for rewiring bypass pathway, and reprogramming metabolic network for boosting substrate utilization. Future directions are also proposed for providing constructive guidance on the development of industrial biotechnology.

Bioreduction of chromate in a syngas-based membrane biofilm reactor

This study leveraged synthesis gas (syngas), a renewable resource attainable through the gasification of biowaste, to achieve efficient chromate removal from water. To enhance syngas transfer efficiency, a membrane biofilm reactor (MBfR) was employed. Long-term reactor operation showed a stable and high-level chromate removal efficiency > 95%, yielding harmless Cr(III) precipitates, as visualised by scanning electron microscopy and energy dispersive X-ray analysis. Corresponding to the short hydraulic retention time of 0.25 days, a high chromate removal rate of 80 µmol/L/d was attained. In addition to chromate reduction, in situ production of volatile fatty acids (VFAs) by gas fermentation was observed. Three sets of in situ batch tests and two groups of ex situ batch tests jointly unravelled the mechanisms, showing that biological chromate reduction was primarily driven by VFAs produced from in situ syngas fermentation, whereas hydrogen originally present in the syngas played a minor role. 16 S rRNA gene amplicon sequencing has confirmed the enrichment of syngas-fermenting bacteria (such as Sporomusa), who performed in situ gas fermentation leading to the synthesis of VFAs, and organics-utilising bacteria (such as Aquitalea), who utilised VFAs to drive chromate reduction. These findings, combined with batch assays, elucidate the pathways orchestrating synergistic interactions between fermentative microbial cohorts and chromate-reducing microorganisms. The findings facilitate the development of cost-effective strategies for groundwater and drinking water remediation and present an alternative application scenario for syngas.

Valorization of single-carbon chemicals by using carboligases as key enzymes

Single-carbon (C1) biorefinery plays a key role in the consumption of global greenhouse gases and a circular carbon economy. Thereby, we have focused on the valorization of C1 compounds (e.g. methanol, formaldehyde, and formate) into multicarbon products, including bioplastic monomers, glycolate, and ethylene glycol. For instance, methanol, derived from the oxidation of CH4, can be converted into glycolate, ethylene glycol, or erythrulose via formaldehyde and glycolaldehyde, employing C1 and/or C2 carboligases as essential enzymes. Escherichia coli was engineered to convert formate, produced from CO via CO2 or from CO2 directly, into glycolate. Recent progress in the design of biotransformation pathways, enzyme discovery, and engineering, as well as whole-cell biocatalyst engineering for C1 biorefinery, was addressed in this review.

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.

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

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

Encapsulation of Methanotrophs within a Polymeric Matrix Containing Copper- and Iron-Based Nanoparticles to Enhance Methanol Production from a Simulated Biogas

The production of renewable energy or biochemicals is gaining more attention to minimize the emissions of greenhouse gases such as methane (CH4) and carbon dioxide for sustainable development. In the present study, the influence of copper (Cu)- and iron (Fe)-based nanoparticles (NPs), such as Cu, Fe3O4, and CuFe2O4, was evaluated during the growth of methanotrophs for inoculum preparation and on the development of a polymeric-matrix-based encapsulation system to enhance methanol production from simulated biogas (CH4 and CO2). The use of simulated biogas feed and the presence of NP-derived inoculums produce a remarkable enhancement in methanol production up to 149% and 167% for Methyloferula stellata and Methylocystis bryophila free-cells-based bioconversion, respectively, compared with the use of pure CH4 as a control feed during the growth stage. Furthermore, these methanotrophs encapsulated within a polymeric matrix and NPs-based systems exhibited high methanol production of up to 156%, with a maximum methanol accumulation of 12.8 mmol/L over free cells. Furthermore, after encapsulation, the methanotrophs improved the stability of residual methanol production and retained up to 62.5-fold higher production potential than free cells under repeated batch reusability of 10 cycles. In the presence of CH4 vectors, methanol production by M. bryophila improved up to 16.4 mmol/L and retained 20% higher recycling stability for methanol production in paraffin oil. These findings suggest that Cu and Fe NPs can be beneficially employed with a polymeric matrix to encapsulate methanotrophs and improve methanol production.

In Vivo Detection of Low Molecular Weight Platform Chemicals and Environmental Contaminants by Genetically Encoded Biosensors

Genetically encoded biosensor systems operating in living cells are versatile, cheap, and transferable tools for the detection and quantification of a broad range of small molecules. This review presents state-of-the-art biosensor designs and assemblies, featuring transcription factor-, riboswitch-, and enzyme-coupled devices, highly engineered fluorescent probes, and emerging two-component systems. Importantly, (bioinformatic-assisted) strategies to resolve contextual issues, which cause biosensors to miss performance criteria in vivo, are highlighted. The optimized biosensing circuits can be used to monitor chemicals of low molecular mass (<200 g mol^-1) and physicochemical properties that challenge conventional chromatographical methods with high sensitivity. Examples herein include but are not limited to formaldehyde, formate, and pyruvate as immediate products from (synthetic) pathways for the fixation of carbon dioxide (CO₂), industrially important derivatives like small- and medium-chain fatty acids and biofuels, as well as environmental toxins such as heavy metals or reactive oxygen and nitrogen species. Lastly, this review showcases biosensors capable of assessing the biosynthesis of platform chemicals from renewable resources, the enzymatic degradation of plastic waste, or the bioadsorption of highly toxic chemicals from the environment. These applications offer new biosensor-based manufacturing, recycling, and remediation strategies to tackle current and future environmental and socioeconomic challenges including the wastage of fossil fuels, the emission of greenhouse gases like CO₂, and the pollution imposed on ecosystems and human health.