Production of Bio-alkanes from Biomass and CO2

Leveraging Engineered Pseudomonas putida Minicells for Bioconversion of Organic Acids into Short-Chain Methyl Ketones

Methyl ketones, key building blocks widely used in diverse industrial applications, largely depend on oil-derived chemical methods for their production. Here, we investigated biobased production alternatives for short-chain ketones, adapting the solvent-tolerant soil bacterium Pseudomonas putida as a host for ketone biosynthesis either by whole-cell biocatalysis or using engineered minicells, chromosome-free bacterial vesicles. Organic acids (acetate, propanoate and butanoate) were selected as the main carbon substrate to drive the biosynthesis of acetone, butanone and 2-pentanone. Pathway optimization identified efficient enzyme variants from Clostridium acetobutylicum and Escherichia coli, tested with both constitutive and inducible expression of the cognate genes. By implementing these optimized pathways in P. putida minicells, which can be prepared through a simple three-step purification protocol, the feedstock was converted into the target short-chain methyl ketones. These results highlight the value of combining morphology and pathway engineering of noncanonical bacterial hosts to establish alternative bioprocesses for toxic chemicals that are difficult to produce by conventional approaches.

Quantitative Characterization of Gene Regulatory Circuits Associated With Fungal Secondary Metabolism to Discover Novel Natural Products

Microbial genetic circuits are vital for regulating gene expression and synthesizing bioactive compounds. However, assessing their strength and timing, especially in multicellular fungi, remains challenging. Here, an advanced microfluidic platform is combined with a mathematical model enabling precise characterization of fungal gene regulatory circuits (GRCs) at the single-cell level. Utilizing this platform, the expression intensity and timing of 30 transcription factor-promoter combinations derived from two representative fungal GRCs, using the model fungus Aspergillus nidulans are determined. As a proof of concept, the selected GRC combination is utilized to successfully refactor the biosynthetic pathways of bioactive molecules, precisely control their production, and activate the expression of the silenced biosynthetic gene clusters (BGCs). This study provides insights into microbial gene regulation and highlights the potential of platform in fungal synthetic biology applications and the discovery of novel natural products.

Beyond methane, new frontiers in anaerobic microbial hydrocarbon utilizing pathways

Alkanes, single carbon methane to long-chain hydrocarbons (e.g. hexadecane and tetradecane), are important carbon sources to anaerobic microbial communities. In anoxic environments, archaea are known to utilize and produce methane via the methyl-coenzyme M reductase enzyme (MCR). Recent explorations of new environments, like deep sea sediments, that have coupled metagenomics and cultivation experiments revealed divergent MCRs, also referred to as alkyl-coenzyme M reductases (ACRs) in archaea, with similar mechanisms as the C1 utilizing canonical MCR mechanism. These ACR enzymes have been shown to activate other alkanes such as ethane, propane and butane for subsequent degradation. The reversibility of canonical MCRs suggests that these non-methane-activating homologues (ACRs) might have similar reversibility, perhaps mediated by undiscovered lineages that produce alkanes under certain conditions. The discovery of these alternative alkane utilization pathways holds significant promise for a breadth of potential biotechnological applications in bioremediation, energy production and climate change mitigation.

Enzymatic interfacial conversion of acylglycerols in Pickering emulsions stabilized by hydrogel microparticles

HYPOTHESIS

A critical challenge in the enzymatic conversion of acylglycerols is the limited exposure of the enzyme dissolved in the aqueous solution to the hydrophobic substrate in the oil phase. Positioning the enzyme in a microenvironment with balanced hydrophobicity and hydrophilicity in Pickering emulsion will facilitate the acylglycerol-catalyzing reactions at the interface between the oil and liquid phases.

EXPERIMENTS

In this work, to overcome the challenge of biphasic catalysis, we report a method to immobilize enzymes in polyethylene glycol (PEG)-based hydrogel microparticles (HMPs) at the interface between the oil and water phases in Pickering emulsion to promote the enzymatic conversion of acylglycerols.

FINDINGS

3 wt% of HMPs can stabilize the oil-in-water Pickering emulsion for at least 14 days and increase the viscosity of emulsions. Lipase-HMP conjugates showed significantly higher hydrolytic activity in Pickering emulsion; HMP-immobilized lipase SMG1 showed an activity about three times that of free lipase SMG1. Co-immobilization of a lipase and a fatty acid photodecarboxylase from Chlorella variabilis (CvFAP) in Pickering emulsion enables light-driven cascade conversion of triacylglycerols to hydrocarbons, transforming waste oil to renewable biofuels in a green and sustainable approach. HMPs stabilize the Pickering emulsion and promote interfacial biocatalysis in converting acylglycerols to renewable biofuels.

Co-NC@Co-NP hierarchical nanoforest steering charge exchange efficiency at biotic-abiotic interface for microbial electrochemical carbon reduction

Converting anthropogenic carbon dioxide (CO2) to value-added products using bio-electrochemical conversions represents a promising strategy for producing sustainable fuel. However, the reaction kinetics are hindered by insufficient attachment of microorganisms and limited charge extraction at the bioinorganic interface. A hierarchical nanoforest with doped cobalt‑nitrogen-doped carbon covering cobalt nanoparticle (Co-NC@Co-NP) was integrated with a CO2-to-CH4 conversion microbiome for methane production to address these shortcomings. In-situ nanoforests were developed on the nanosheet by chemical vapor deposition with Co nanoparticles catalyzed. The bio-nanowire-like carbon nanotubes enhanced the electrostatic force for microbe enrichment via the tip effect, providing a maximum of 3.6-fold electron-receiving microbes to utilize reducing equivalents. The Co-NC@Co-NP enhanced the direct electron transfer between microbes and electrodes, reducing the adoption of energy barriers for heme-like proteins. Thus, the optimized electron transfer pathway improved selectivity by a factor of 2.0 compared to the pristine nanosheet biohybrid. Furthermore, the adjusted microbial community structure provided sufficient methanogenesis genes to match the strong electron flow, achieving maximal methane production rates (311.1 mmol/m2/day at -0.9 V vs. Ag/AgCl), 8.62 times higher than those of the counterpart nanosheet biohybrid (36.06 mmol/m2/day). This work demonstrates a comprehensive assessment of biotic-abiotic energy transfer, which may serve as a guiding principle for designing efficient bio-electrochemical systems.

In Situ Encapsulation of Cytochrome c within Covalent Organic Frames Using Deep Eutectic Solvents under Ambient Conditions

In situ integration of enzymes with covalent organic frameworks (COFs) to form hybrid biocatalysts is both significant and challenging. In this study, we present an innovative strategy employing deep eutectic solvents (DESs) to synergistically synthesize COFs and shield cytochrome c (Cyt c). By utilizing DESs as reaction solvents in combination with water, we successfully achieved rapid and in situ encapsulation of Cyt c within COFs (specifically COF-TAPT-TFB) under ambient conditions. The resulting Cyt c@COF-TAPT-TFB composite demonstrates a remarkable preservation of enzymatic activity. This encapsulation strategy also imparts exceptional resistance to organic solvents and exhibits impressive recycling stability. Additionally, the enhanced catalytic efficiency of Cyt c@COF-TAPT-TFB in a photoenzymatic cascade reaction is also showcased.

Photoenzymatic Decarboxylation to Produce Hydrocarbon Fuels: A Critical Review

Photoenzymatic decarboxylation shows great promise as a pathway for the generation of hydrocarbon fuels. CvFAP, which is derived from Chlorella variabilis NC64A, is a photodecarboxylase capable of converting fatty acids into hydrocarbons. CvFAP is an example of coupling biocatalysis and photocatalysis to produce alkanes. The catalytic process is mild, and it does not yield toxic substances or excess by-products. However, the activity of CvFAP can be readily inhibited by several factors, and further enhancement is required to improve the enzyme yield and stability. In this article, we will examine the latest advancements in CvFAP research, with a particular focus on the enzyme's structural and catalytic mechanism, summarized some limitations in the application of CvFAP, and laboratory-level methods for enhancing enzyme activity and stability. This review can serve as a reference for future large-scale industrial production of hydrocarbon fuels.

Immobilization of fatty acid photodecarboxylase in magnetic nickel ferrite nanoparticle

Fatty acid photodecarboxylase in Chlorella variabilis NC64A (CvFAP) performed excellent ability to exclusively decarboxylate renewable fatty acids for C1-shortened hydrocarbons fuel production under visible light. However, the large-scale application by such an approach is limited by the free state of CvFAP catalyst, which is unstable for efficient biofuel production. In this study, CvFAP was immobilized in magnetic nickel ferrite (NiFe₂O₄) nanoparticles for facile recovery by a simple procedure. The shift of Ni 2p in electron binding energy was detected to clarify the interaction between Ni²⁺ and histidine of CvFAP. The coordination of NiFe₂O₄ and CvFAP contributed to an efficient affinity binding with an immobilization capacity of 98 mg/g carrier. Hydrocarbon fuel concentration of 3.7 mM was obtained by NiFe₂O₄@CvFAP-induced photoenzymatic decarboxylation. The high stability of CvFAP in terms of residual enzyme activity of 79.7% and 68% at pH 9 and organic solvent ratio of 60%, respectively, were observed.

Lignocellulosic biomass valorization via bio-photo/electro hybrid catalytic systems

Lignocellulosic biomass valorization is regarded as a promising approach to alleviate energy crisis and achieve carbon neutrality. Bioactive enzymes have attracted great attention and been commonly applied for biomass valorization owing to their high selectivity and catalytic efficiency under environmentally benign reaction conditions. Same as biocatalysis, photo-/electro-catalysis also happens at mild conditions (i.e., near ambient temperature and pressure). Therefore, the combination of these different catalytic approaches to benefit from their resulting synergy is appealing. In such hybrid systems, harness of renewable energy from the photo-/electro-catalytic compartment can be combined with the unique selectivity of biocatalysts, therefore providing a more sustainable and greener approach to obtain fuels and value-added chemicals from biomass. In this review, we firstly introduce the pros/cons, classifications, and the applications of photo-/electro-enzyme coupled systems. Then we focus on the fundamentals and comprehensive applications of the most representative biomass-active enzymes including lytic polysaccharide monooxygenases (LPMOs), glucose oxidase (GOD)/dehydrogenase (GDH) and lignin peroxidase (LiP), together with other biomass-active enzymes in the photo-/electro- enzyme coupled systems. Finally, we propose current deficiencies and future perspectives of biomass-active enzymes to be applied in the hybrid catalytic systems for global biomass valorization.

Photoenzymatic decarboxylation: A promising way to produce sustainable aviation fuels and fine chemicals

As one of the fastest-growing carbon emission sources, the aviation sector is severely restricted by carbon emission reduction targets. Sustainable aviation fuel (SAF) has emerged as the most potential alternative to traditional aviation fuel, but harsh production technologies limit its commercialization. Fatty acids photodecarboxylase from Chlorella variabilis NC64A (CvFAP), the latest discovered photoenzyme, provides promising approaches to produce various carbon-neutral biofuels and fine chemicals. This review highlights the state-of-the-art strategies to enhance the application of CvFAP in carbon-neutral biofuel and fine chemicals production, including supplementing alkane as decoy molecular, screening efficient CvFAP variants with directed evolution, constructing genetic strains, employing biphasic catalytic system, and immobilizing CvFAP in an efficient photobioreactor. Furthermore, future opportunities are suggested to enhance photoenzymatic decarboxylation and explore the catalytic mechanism of CvFAP. This review provides a broad context to improve CvFAP catalysis and advance its potential applications.

Prospects and trends in bioelectrochemical systems: Transitioning from CO2 towards a low-carbon circular bioeconomy

Resource scarcity and climate change are the most quested topics in view of environmental sustainability. CO2 sequestration through bioelectrochemical systems is an attractive option for fostering bioeconomy development upon several value-added products generation. This review details the state-of-the-art of bioelectrochemical systems for resource recovery from CO2 along with various biocatalysts capable of utilizing CO2. Two bioprocesses (photo-electrosynthesis and chemolithoelectrosynthesis) were discussed projecting their potential for biobased economy development from CO2. Significance of adopting circular strategies for efficient resource recycling, intensifying product value, integrations/interlinking of multiple process chains for the development of circular bioeconomy were discussed. Existing constrains as well as outlook for near establishment of circular bioeconomy from CO2 is presented by weighing fore-sighted plans with current actions. Need for developing CO2-based circular bioeconomy via innovative business models by analyzing social, technical, environmental and product related aspects are also discussed providing a roadmap of gaps to pursue for attaining practicality.

Microbial fingerprints of methanation in a hybrid electric-biological anaerobic digestion

Biomethane as a sustainable, alternative, and carbon-neutral renewable energy source to fossil fuels is highly needed to alleviate the global energy crisis and climate change. The conventional anaerobic digestion (AD) process for biomethane production from waste(water) streams has been widely employed while struggling with a low production rate, low biogas qualities, and frequent instability. The electric-biologically hybrid microbial electrochemical anaerobic digestion system (MEC-AD) prospects more stable and robust biomethane generation, which facilitates complex organic substrates degradation and mediates functional microbial populations by giving a small input power (commonly voltages < 1.0 V), mainly enhancing the communication between electroactive microorganisms and (electro)methanogens. Despite numerous bioreactor tests and studies that have been conducted, based on the MEC-AD systems, the integrated microbial fingerprints, and cooperation, accelerating substrate degradation, and biomethane production, have not been fully summarized. Herein, we present a comprehensive review of this novel developing biotechnology, beginning with the principles of MEC-AD. First, we examine the fundamentals, configurations, classifications, and influential factors of the whole system's performances (reactor types, applied voltages, temperatures, conductive materials, etc.,). Second, extracellular electron transfer either between diverse microbes or between microbes and electrodes for enhanced biomethane production are analyzed. Third, we further conclude (electro)methanogenesis, and microbial interactions, and construct ecological networks of microbial consortia in MEC-AD. Finally, future development and perspectives on MEC-AD for biomethane production are proposed.

Model development of bioelectrochemical systems: A critical review from the perspective of physiochemical principles and mathematical methods

Bioelectrochemical systems (BESs) are promising devices for wastewater treatment and bio-energy production. Since various processes are interacted and affect the overall performance of the device, the development of theoretical modeling is an efficient approach to understand the fundamental mechanisms that govern the performance of the BES. This review aims to summarize the physiochemical principle and mathematical method in BES models, which is of great importance for the establishment of an accurate model while has received little attention in previous reviews. In this review, we begin with a classification of existing models including bioelectrochemical models, electronic models, and machine learning models. Subsequently, physiochemical principles and mathematical methods in models are discussed from two aspects: one is the description of methodology how to build a framework for models, and the other is to further review additional methods that can enrich model functions. Finally, the advantages/disadvantages, extended applications, and perspectives of models are discussed. It is expected that this review can provide a viewpoint from methodologies to understand BES models.

Photobiocatalytic Decarboxylation for the Synthesis of Fatty Epoxides from Renewable Fatty Acids

Fatty epoxides are unique building blocks in organic transformations and materials production; however, their synthetic methodologies are currently not accessible from renewable fatty acids. Herein, a photoenzymatic decarboxylation of epoxy fatty acids into fatty epoxides was demonstrated using fatty acid photodecarboxylase (FAP) from Chlorella variabilis NC64A (CvFAP). Various fatty epoxides were synthesized in excellent selectivity by wild-type CvFAP. The decarboxylation reaction was also achieved with four new FAP homologues, potentially suggesting a broad availability of the biocatalysts for this challenging decarboxylation reaction. By combining CvFAP with lipase and peroxygenase, a multienzymatic cascade to transform oleic acid and its triglyceride into the corresponding fatty epoxides was established. The obtained fatty epoxides were further converted into rather unusual fatty compounds including diol, alcohol, ether, and chain-shortened carboxylic acids. The present photobiocatalytic synthesis of fatty epoxides from natural starting materials excels by its intrinsic selectivity, mild conditions, and independence of nicotinamide cofactors.

Toward bioproduction of oxo chemicals from C1 feedstocks using isobutyraldehyde as an example

Oxo chemicals are valuable chemicals for synthesizing a wide array of industrial and consumer products. However, producing of oxo chemicals is predominately through the chemical process called hydroformylation, which requires petroleum-sourced materials and generates abundant greenhouse gas. Current concerns on global climate change have renewed the interest in reducing greenhouse gas emissions and recycling the plentiful greenhouse gas. A carbon–neutral manner in this regard is producing oxo chemicals biotechnologically using greenhouse gas as C1 feedstocks. Exemplifying isobutyraldehyde, this review demonstrates the significance of using greenhouse gas for oxo chemicals production. We highlight the current state and the potential of isobutyraldehyde synthesis with a special focus on the in vivo and in vitro scheme of C1-based biomanufacturing. Specifically, perspectives and scenarios toward carbon– and nitrogen–neutral isobutyraldehyde production are proposed. In addition, key challenges and promising approaches for enhancing isobutyraldehyde bioproduction are thoroughly discussed. This study will serve as a reference case in exploring the biotechnological potential and advancing oxo chemicals production derived from C1 feedstocks.

A perspective on the combination of alkali pre-treatment with bioaugmentation to improve biogas production from lignocellulose biomass

Anaerobic digestion (AD) is a bioprocess technology that integrates into circular economy systems, which produce renewable energy and biofertilizer whilst reducing greenhouse gas emissions. However, improvements in biogas production efficiency are needed in dealing with lignocellulosic biomass. The state-of-the-art of AD technology is discussed, with emphasis on feedstock digestibility and operational difficulty. Solutions to these challenges including for pre-treatment and bioaugmentation are reviewed. This article proposes an innovative integrated system combining alkali pre-treatment, temperature-phased AD and bioaugmentation techniques. The integrated system as modelled has a targeted potential to achieve a biodegradability index of 90% while increasing methane production by 47% compared to conventional AD. The methane productivity may also be improved by a target reduction in retention time from 30 to 20 days. This, if realized has the potential to lower energy production cost and the levelized cost of abatement to facilitate an increased resource of sustainable commercially viable biomethane.

Engineering microbial metabolic energy homeostasis for improved bioproduction

Metabolic energy (ME) homeostasis is essential for the survival and proper functioning of microbial cell factories. However, it is often disrupted during bioproduction because of inefficient ME supply and excessive ME consumption. In this review, we propose strategies, including reinforcement of the capacity of ME-harvesting systems in autotrophic microorganisms; enhancement of the efficiency of ME-supplying pathways in heterotrophic microorganisms; and reduction of unessential ME consumption by microbial cells, to address these issues. This review highlights the potential of biotechnology in the engineering of microbial ME homeostasis and provides guidance for the higher efficient bioproduction of microbial cell factories.

Emerging bioelectrochemical technologies for biogas production and upgrading in cascading circular bioenergy systems

Biomethane is suggested as an advanced biofuel for the hard-to-abate sectors such as heavy transport. However, future systems that optimize the resource and production of biomethane have yet to be definitively defined. This paper assesses the opportunity of integrating anaerobic digestion (AD) with three emerging bioelectrochemical technologies in a circular cascading bioeconomy, including for power-to-gas AD (P2G-AD), microbial electrolysis cell AD (MEC-AD), and AD microbial electrosynthesis (AD-MES). The mass and energy flow of the three bioelectrochemical systems are compared with the conventional AD amine scrubber system depending on the availability of renewable electricity. An energy balance assessment indicates that P2G-AD, MEC-AD, and AD-MES circular cascading bioelectrochemical systems gain positive energy outputs by using electricity that would have been curtailed or constrained (equivalent to a primary energy factor of zero). This analysis of technological innovation, aids in the design of future cascading circular biosystems to produce sustainable advanced biofuels.

Stabilisation of the Fatty Acid Decarboxylase from Chlorella variabilis by Caprylic Acid

The fatty acid photodecarboxylase from Chlorella variabilis NC64 A (CvFAP) catalyses the light-dependent decarboxylation of fatty acids. Photoinactivation of CvFAP still represents one of the major limitations of this interesting enzyme en route to practical application. In this study we demonstrate that the photostability of CvFAP can easily be improved by the administration of medium-chain length carboxylic acids such as caprylic acid indicating that the best way of maintaining CvFAP stability is 'to keep the enzyme busy'.

Anodic electro-fermentation: Empowering anaerobic production processes via anodic respiration

In nature as well as in industrial microbiology, all microorganisms need to achieve redox balance. Their redox state and energy conservation highly depend on the availability of a terminal electron acceptor, for example oxygen in aerobic production processes. Under anaerobic conditions in the absence of an electron acceptor, redox balance is achieved via the production of reduced carbon-compounds (fermentation). An alternative strategy to artificially stabilize microbial redox and energy state is the use of anodic electro-fermentation (AEF). This emerging biotechnology empowers respiration under anaerobic conditions using the anode of a bioelectrochemical system as an undepletable terminal electron acceptor. Electrochemical control of redox metabolism and energy conservation via AEF can steer the carbon metabolism towards a product of interest and avoid the need for continuous and cost-inefficient supply of oxygen as well as the production of mixed reduced by-products, as is the case in aerobic production and fermentation processes, respectively. The great challenge for AEF is to establish efficient extracellular electron transfer (EET) from the microbe to the anode and link it to central carbon metabolism to enhance the synthesis of a target product. This article reviews the advantages and challenges of AEF, EET mechanisms, microbial energy gain, and discusses the rational choice of substrate-product couple as well as the choice of microbial catalyst. Besides, it discusses the potential of the industrial model-organism Bacillus subtilis as a promising candidate for AEF, which has not been yet considered for such an application. This prospective review contributes to a better understanding of how industrial microbiology can benefit from AEF and analyses key-factors required to successfully implement AEF processes. Overall, this work aims to advance the young research field especially by critically revisiting the fundamental aspects of AEF.