Riboflavin synthesis from gaseous nitrogen and carbon dioxide by a hybrid inorganic-biological system

XanthoMoClo─A Robust Modular Cloning Genetic Toolkit for the Genera Xanthobacter and Roseixanthobacter

Interest in Xanthobacter species is increasing due to their unique metabolic capabilities. They can grow in both heterotrophic and fully autotrophic environments, including carbon dioxide, dinitrogen gas, and hydrogen as the sole carbon, nitrogen, and energy sources, respectively. Academic and industrial groups looking to leverage these metabolic properties are already using Xanthobacter strains for the sustainable production of food and commodities. However, only a handful of genetic parts and protocols exist in scattered genetic backgrounds, and there is an unmet need for reliable genetic engineering tools to manipulate Xanthobacter species. Here, we developed XanthoMoClo, a robust modular cloning genetic toolkit for Xanthobacter and Roseixanthobacter species and strains, providing extensive tools to transform them, manipulate their metabolism, and express genes of interest. The toolkit contains plasmid parts, such as replication origins, antibiotic selection markers, fluorescent proteins, constitutive and inducible promoters, a standardized framework to incorporate novel components into the toolkit, and a conjugation donor to transform Xanthobacter and Roseixanthobacter strains easily with no or minimal optimization. We validated these plasmid components in depth in three of the most commonly studied Xanthobacter strains: X. versatilis Py2, X. autotrophicus GZ29, and X. flavus GJ10, as well as in R. finlandensis VTT E-85241. Finally, we demonstrate robust toolkit functionality across 21 different species of Xanthobacter and Roseixanthobacter, comprising 23 strains in total. The XanthoMoClo genetic toolkit is available to the research community (through AddGene) and will help accelerate the genetic engineering of Xanthobacter to further their applications in sustainability and bioremediation efforts.

Powering the Future: Unveiling the Secrets of Semiconductor Biointerfaces in Biohybrids for Semiartificial Photosynthesis

Developing technology for sustainable chemical and fuel production is a key focus of scientific research. Semiartificial photosynthesis is a promising approach, pairing "electric microbes" with artificial light absorbers (semiconductors) to convert N2, CO2, and water into value-added products using sunlight. Mimicking natural photosynthesis is done with semiconductors acting as electron donors or sinks for microbes. This method enables the production of multicarbon (C2+) chemicals (e.g., ethanol and caproic acid) and ammonia with high efficiency and selectivity. Despite significant progress, commercial-scale applications remain elusive due to fundamental challenges. This Review covers advances in semiartificial photosynthesis and highlights that there is no clear mechanistic understanding underpinning the production of chemicals using the combination of light, semiconductors, and microbes. Does the mechanism rely on H2 uptake, do the microbes eat electrons directly from the light absorbers, or is it a combination of both? It focuses on overcoming bottlenecks using advanced spectroscopy, microscopy, and synthetic biology tools to study charge transfer kinetics between microbial cell membranes and semiconductors. Understanding this interaction is crucial for increasing solar-to-chemical (STC) efficiencies, necessary for industrial use. This Review also outlines future research directions and techniques to advance this field, aiming to achieve net-zero climate goals through multidisciplinary efforts.

Creating a Genetic Toolbox for the Carbon-Fixing, Nitrogen-Fixing and Dehalogenating Bacterium Xanthobacter autotrophicus

Xanthobacter autotrophicus is a metabolically flexible microorganism with two key features: (1) The organism has adapted to grow on a wide variety of carbon sources including CO2, methanol, formate, propylene, haloalkanes and haloacids; and (2) X. autotrophicus was the first chemoautotroph identified that could also simultaneously fix N2, meaning the organism can utilize CO2, N2, and H2 for growth. This metabolic flexibility has enabled use of X. autotrophicus for gas fixation, the creation of fertilizers and foods from gases, and the dehalogenation of environmental contaminants. Despite the wide variety of applications that have already been demonstrated for this organism, there are few genetic tools available to explore and exploit its metabolism. Here, we report a genetic toolbox for use in X. autotrophicus. We first identified suitable origins of replication and quantified their copy number, and identified antibiotic resistance cassettes that could be used as selectable markers. We then tested several constitutive and inducible promoters and terminators and quantified their promoter strengths and termination efficiencies. Finally, we demonstrated that gene expression tools remain effective under both autotrophic and dehalogenative metabolic conditions to show that these tools can be used in the environments that make X. autotrophicus unique. Our extensive characterization of these tools in X. autotrophicus will enable genetic and metabolic engineering to optimize production of fertilizers and foods from gases, and enable bioremediation of halogenated environmental contaminants.

Engineered Cell Elongation Promotes Extracellular Electron Transfer of Shewanella Oneidensis

To investigate how cell elongation impacts extracellular electron transfer (EET) of electroactive microorganisms (EAMs), the division of model EAM Shewanella oneidensis (S. oneidensis) MR-1 is engineered by reducing the formation of cell divisome. Specially, by blocking the translation of division proteins via anti-sense RNAs or expressing division inhibitors, the cellular length and output power density are all increased. Electrophysiological and transcriptomic results synergistically reveal that the programmed cell elongation reinforces EET by enhancing NADH oxidation, inner-membrane quinone pool, and abundance of c-type cytochromes. Moreover, cell elongation enhances hydrophobicity due to decreased cell-surface polysaccharide, thus facilitates the initial surface adhesion stage during biofilm formation. The output current and power density all increase in positive correction with cellular length. However, inhibition of cell division reduces cell growth, which is then restored by quorum sensing-based dynamic regulation of cell growth and elongation phases. The QS-regulated elongated strain thus enables a cell length of 143.6 ± 40.3 µm (72.6-fold of that of S. oneidensis MR-1), which results in an output power density of 248.0 ± 10.6 mW m-2 (3.41-fold of that of S. oneidensis MR-1) and exhibits superior potential for pollutant treatment. Engineering cellular length paves an innovate avenue for enhancing the EET of EAMs.

Enhanced Microbial Protein Production from CO2 and Air by a MoS2 Catalyzed Bioelectrochemical System

Carbon dioxide can be relatively easily reduced to organic matter in a bioelectrochemical system (BES). However, due to insufficient reduction force from in-situ hydrogen evolution, it is difficult for nitrogen reduction. In this study, MoS2 was firstly used as an electrocatalyst for the simultaneous reduction of CO2 and N2 to produce microbial protein (MP) in a BES. Cell dry weight (CDW) could reach 0.81±0.04 g/L after 14 d operation at -0.7 V (vs. RHE), which was 108±3 % higher than that from non-catalyst control group (0.39±0.01 g/L). The produced protein had a better amino acid profile in the BES than that in a direct hydrogen system (DHS), particularly for proline (Pro). Besides, MoS2 promoted the growth of bacterial cell on an electrode and improved the biofilm extracellular electron transfer (EET) by microscopic observation and electrochemical characterization of MoS2 biocathode. The composition of the microbial community and the relative abundance of functional enzymes revealed that MoS2 as an electrocatalyst was beneficial for enriching Xanthobacter and enhancing CO2 and N2 reduction by electrical energy. These results demonstrated that an efficient strategy to improve MP production of BES is to use MoS2 as an electrocatalyst to shift amino acid profile and microbial community.

Integrated Proteomics and Metabolomics Reveal Altered Metabolic Regulation of Xanthobacter autotrophicus under Electrochemical Water-Splitting Conditions

Biological-inorganic hybrid systems are a growing class of technologies that combine microorganisms with materials for a variety of purposes, including chemical synthesis, environmental remediation, and energy generation. These systems typically consider microorganisms as simple catalysts for the reaction of interest; however, other metabolic activity is likely to have a large influence on the system performance. The investigation of biological responses to the hybrid environment is thus critical to the future development and optimization. The present study investigates this phenomenon in a recently reported hybrid system that uses electrochemical water splitting to provide reducing equivalents to the nitrogen-fixing bacteria Xanthobacter autotrophicus for efficient reduction of N2 to biomass that may be used as fertilizer. Using integrated proteomic and metabolomic methods, we find a pattern of differentiated metabolic regulation under electrochemical water-splitting (hybrid) conditions with an increase in carbon fixation products glycerate-3-phosphate and acetyl-CoA that suggests a high energy availability. We further report an increased expression of proteins of interest, namely, those responsible for nitrogen fixation and assimilation, which indicate increased rates of nitrogen fixation and support previous observations of faster biomass accumulation in the hybrid system compared to typical planktonic growth conditions. This work complicates the inert catalyst view of biological-inorganic hybrids while demonstrating the power of multiomics analysis as a tool for deeper understanding of those systems.

Synthetic microbiology in sustainability applications

Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.

Glutamate production from aerial nitrogen using the nitrogen-fixing bacterium Klebsiella oxytoca

Glutamate is an essential biological compound produced for various therapeutic and nutritional applications. The current glutamate production process requires a large amount of ammonium, which is generated through the energy-consuming and CO2-emitting Haber-Bosch process; therefore, the development of bio-economical glutamate production processes is required. We herein developed a strategy for glutamate production from aerial nitrogen using the nitrogen-fixing bacterium Klebsiella oxytoca. We showed that a simultaneous supply of glucose and citrate as carbon sources enhanced the nitrogenase activity of K. oxytoca. In the presence of glucose and citrate, K. oxytoca strain that was genetically engineered to increase the supply of 2-oxoglutarate, a precursor of glutamate synthesis, produced glutamate extracellularly more than 1 g L-1 from aerial nitrogen. This strategy offers a sustainable and eco-friendly manufacturing process to produce various nitrogen-containing compounds using aerial nitrogen.

Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production

The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.

Unexpected metabolic rewiring of CO2 fixation in H2-mediated materials-biology hybrids

A hybrid approach combining water-splitting electrochemistry and H2-oxidizing, CO2-fixing microorganisms offers a viable solution for producing value-added chemicals from sunlight, water, and air. The classic wisdom without thorough examination to date assumes that the electrochemistry in such a H2-mediated process is innocent of altering microbial behavior. Here, we report unexpected metabolic rewiring induced by water-splitting electrochemistry in H2-oxidizing acetogenic bacterium Sporomusa ovata that challenges such a classic view. We found that the planktonic S. ovata is more efficient in utilizing reducing equivalent for ATP generation in the materials-biology hybrids than cells grown with H2 supply, supported by our metabolomic and proteomic studies. The efficiency of utilizing reducing equivalents and fixing CO2 into acetate has increased from less than 80% of chemoautotrophy to more than 95% under electroautotrophic conditions. These observations unravel previously underappreciated materials' impact on microbial metabolism in seemingly simply H2-mediated charge transfer between biotic and abiotic components. Such a deeper understanding of the materials-biology interface will foster advanced design of hybrid systems for sustainable chemical transformation.

Electricity-Driven Microbial Metabolism of Carbon and Nitrogen: A Waste-to-Resource Solution

Electricity-driven microbial metabolism relies on the extracellular electron transfer (EET) process between microbes and electrodes and provides promise for resource recovery from wastewater and industrial discharges. Over the past decades, tremendous efforts have been dedicated to designing electrocatalysts and microbes, as well as hybrid systems to push this approach toward industrial adoption. This paper summarizes these advances in order to facilitate a better understanding of electricity-driven microbial metabolism as a sustainable waste-to-resource solution. Quantitative comparisons of microbial electrosynthesis and abiotic electrosynthesis are made, and the strategy of electrocatalyst-assisted microbial electrosynthesis is critically discussed. Nitrogen recovery processes including microbial electrochemical N₂ fixation, electrocatalytic N₂ reduction, dissimilatory nitrate reduction to ammonium (DNRA), and abiotic electrochemical nitrate reduction to ammonia (Abio-NRA) are systematically reviewed. Furthermore, the synchronous metabolism of carbon and nitrogen using hybrid inorganic-biological systems is discussed, including advanced physicochemical, microbial, and electrochemical characterizations involved in this field. Finally, perspectives for future trends are presented. The paper provides valuable insights on the potential contribution of electricity-driven microbial valorization of waste carbon and nitrogen toward a green and sustainable society.