Establishing Mixotrophic Growth of Cupriavidus necator H16 on CO2 and Volatile Fatty Acids

Recycling Potential of Cupriavidus necator for Life support in Space: Production of SCPs from Volatile Fatty Acid and Urea mixture

The International Space Station currently requires four annual replenishments for food supply, a practice that won't be feasible for deep space missions due to the greater distances. Based on the design of closed ecological life support systems, two waste streams were identified: urea from the crew urine, volatile fatty acids (VFAs) from a first stage of anaerobic digestion of waste. The objective of this study was to assess the ability of bacterium Cupriavidus necator to produce single cell protein on urea and VFAs. Thus, the effect of carbon sources (glucose vs VFAs) and the dilution rate on the biomass composition was determined in continuous cultures. Complete transformation of the carbon source into protein-rich biomass was achieved up to 78% cell dry weight (CDW). For both carbon sources, the protein content increased from 55.0%CDW to 78%CDW with a decrease in the dilution rate. Conversely, the nucleic acid and polyhydroxyalkanoate contents decreased with the dilution rate from 8.8%CDW to 4.8%CDW and 9.8%CDW to 0.6%CDW respectively. Working at a low dilution rate seems to be a good way to maximize protein content while minimizing unwanted nucleic acids and polyhydroxyalkanoates.

From Knallgas Bacterium to Promising Biomanufacturing Host: The Evolution of Cupriavidus necator

The expanding field of synthetic biology requires diversification of microbial chassis to expedite the transition from a fossil fuel-dependent economy to a sustainable bioeconomy. Relying exclusively on established model organisms such as Escherichia coli and Saccharomyces cerevisiae may not suffice to drive the profound advancements needed in biotechnology. In this context, Cupriavidus necator, an extraordinarily versatile microorganism, has emerged as a potential catalyst for transformative breakthroughs in industrial biomanufacturing. This comprehensive book chapter offers an in-depth review of the remarkable technological progress achieved by C. necator in the past decade, with a specific focus on the fields of molecular biology tools, metabolic engineering, and innovative fermentation strategies. Through this exploration, we aim to shed light on the pivotal role of C. necator in shaping the future of sustainable bioprocessing and bioproduct development.

Synthetic biology toolkit of Ralstonia eutropha (Cupriavidus necator)

Synthetic biology encompasses many kinds of ideas and techniques with the common theme of creating something novel. The industrially relevant microorganism, Ralstonia eutropha (also known as Cupriavidus necator), has long been a subject of metabolic engineering efforts to either enhance a product it naturally makes (polyhydroxyalkanoate) or produce novel bioproducts (e.g., biofuels and other small molecule compounds). Given the metabolic versatility of R. eutropha and the existence of multiple molecular genetic tools and techniques for the organism, development of a synthetic biology toolkit is underway. This toolkit will allow for novel, user-friendly design that can impart new capabilities to R. eutropha strains to be used for novel application. This article reviews the different synthetic biology techniques currently available for modifying and enhancing bioproduction in R. eutropha. KEY POINTS: • R. eutropha (C. necator) is a versatile organism that has been examined for many applications. • Synthetic biology is being used to design more powerful strains for bioproduction. • A diverse synthetic biology toolkit is being developed to enhance R. eutropha's capabilities.

The production, recovery, and valorization of polyhydroxybutyrate (PHB) based on circular bioeconomy

As an energy-storage substance of microorganisms, polyhydroxybutyrate (PHB) is a promising alternative to petrochemical polymers. Under appropriate fermentation conditions, PHB-producing strains with metabolic diversity can efficiently synthesize PHB using various carbon sources. Carbon-rich wastes may serve as alternatives to pure sugar substrates to reduce the cost of PHB production. Genetic engineering strategies can further improve the efficiency of substrate assimilation and PHB synthesis. In the downstream link, PHB recycling strategies based on green chemistry concepts can replace PHB extraction using chlorinated solvents to enhance the economics of PHB production and reduce the potential risks of environmental pollution and health damage. To avoid carbon loss caused by biodegradation in the traditional sense, various strategies have been developed to degrade PHB waste into monomers. These monomers can serve as platform chemicals to synthesize other functional compounds or as substrates for PHB reproduction. The sustainable potential and cycling value of PHB are thus reflected. This review summarized the recent progress of strains, substrates, and fermentation approaches for microbial PHB production. Analyses of available strategies for sustainable PHB recycling were also included. Furthermore, it discussed feasible pathways for PHB waste valorization. These contents may provide insights for constructing PHB-based comprehensive biorefinery systems.

Polyhydroxyalkanoates bioproduction from bench to industry: Thirty years of development towards sustainability

The pursuit of carbon neutrality goals has sparked considerable interest in expanding bioplastics production from microbial cell factories. One prominent class of bioplastics, polyhydroxyalkanoates (PHA), is generated by specific microorganisms, serving as carbon and energy storage materials. To begin with, a native PHA producer, Cupriavidus necator (formerly Ralstonia eutropha) is extensively studied, covering essential topics such as carbon source selection, cultivation techniques, and accumulation enhancement strategies. Recently, various hosts including archaea, bacteria, cyanobacteria, yeast, and plants have been explored, stretching the limit of microbial PHA production. This review provides a comprehensive overview of current advancements in PHA bioproduction, spanning from the native to diversified cell factories. Recovery and purification techniques are discussed, and the current status of industrial applications is assessed as a critical milestone for startups. Ultimately, it concludes by addressing contemporary challenges and future prospects, offering insights into the path towards reduced carbon emissions and sustainable development goals.

Process modelling for industrial scale polyhydroxybutyrate production using fructose, formic acid and CO2: Assessing carbon sources and economic viability

Polyhydroxybutyrate (PHB) is a biodegradable polymer that has potential to replace petroleum-derived plastics. However, the commercialisation of PHB is hindered by high production costs. In this study, the material flow and economics of an industrial scale PHB production process using fructose, formic acid and carbon dioxide (CO2) as carbon sources were simulated and analysed. The lowest breakeven price of 3.64 $/kg PHB was obtained when fructose was utilized as carbon source. When formic acid and CO2 were used, the breakeven price was 10.30 and 10.24 $/kg PHB due to raw material cost, respectively. Although using formic acid and CO2 is more expensive, they meet the emerging sustainable needs for plastic production and contribute to the circular economy via CO2 fixation. This study suggests that the use of formic acid and CO2 as feedstock for PHB production has potential to become competitive in the bioplastic market with further research.

Carbon dioxide and methane as carbon source for the production of polyhydroxyalkanoates and concomitant carbon fixation

The currently used plastics are non-biodegradable, and cause greenhouse gases (GHGs) emission as they are petroleum-based. Polyhydroxyalkanoates (PHAs) are biopolymers with excellent biodegradability and biocompatibility, which can be used to replace petroleum-based plastics. A variety of microorganisms have been found to synthesize PHAs by using typical GHGs: carbon dioxide and methane as carbon sources. Converting carbon dioxide (CO2) and methane (CH4) to PHAs is an attractive option for carbon capture and biodegradable plastic production. In this review, the microorganisms capable of using CO2 and CH4 to produce PHAs were summarized. The metabolic mechanism, PHAs production process, and the factors influencing the production process are illustrated. The currently used optimization techniques to improve the yield of PHAs are discussed. The challenges and future prospects for developing economically viable PHAs production using GHGs as carbon source are identified. This work provides an insight for achieving carbon sequestration and bioplastics based circular economy.

Autotrophic production of polyhydroxyalkanoates using acidogenic-derived H2 and CO2 from fruit waste

The environmental concerns regarding fossil plastics call for alternative biopolymers such as polyhydroxyalkanoates (PHAs) whose manufacturing costs are however still too elevated. Autotrophic microbes like Cupriavidus necator, able to convert CO2 and H2 into PHAs, offer an additional strategy. Typically, the preferred source for CO2 and H2 are expensive pure gases or syngas, which has toxic compounds for most PHAs-accumulating strains. In this work, for the first time, H2 and CO2 originating from an acidogenic reactor were converted autotrophically into poly(3-hydroxybutyrate) P(3HB). During the first stage, a mixed microbial community continuously catabolized melon waste into H2 (26.7 %) and CO2 (49.2 %) that were then used in a second bioreactor by C. necator DSM 545 to accumulate 1.7 g/L P(3HB). Additionally, the VFAs (13 gCOD/L) produced during acidogenesis were processed into 2.7 g/L of P(3HB-co-3HV). This is the first proof-of-concept of using acidogenic-derived H2 and CO2 from fruit waste to produce PHAs.

Cupriavidus necator as a platform for polyhydroxyalkanoate production: An overview of strains, metabolism, and modeling approaches

Cupriavidus necator is a bacterium with a high phenotypic diversity and versatile metabolic capabilities. It has been extensively studied as a model hydrogen oxidizer, as well as a producer of polyhydroxyalkanoates (PHA), plastic-like biopolymers with a high potential to substitute petroleum-based materials. Thanks to its adaptability to diverse metabolic lifestyles and to the ability to accumulate large amounts of PHA, C. necator is employed in many biotechnological processes, with particular focus on PHA production from waste carbon sources. The large availability of genomic information has enabled a characterization of C. necator's metabolism, leading to the establishment of metabolic models which are used to devise and optimize culture conditions and genetic engineering approaches. In this work, the characteristics of available C. necator strains and genomes are reviewed, underlining how a thorough comprehension of the genetic variability of C. necator is lacking and it could be instrumental for wider application of this microorganism. The metabolic paradigms of C. necator and how they are connected to PHA production and accumulation are described, also recapitulating the variety of carbon substrates used for PHA accumulation, highlighting the most promising strategies to increase the yield. Finally, the review describes and critically analyzes currently available genome-scale metabolic models and reduced metabolic network applications commonly employed in the optimization of PHA production. Overall, it appears that the capacity of C. necator of performing CO2 bioconversion to PHA is still underexplored, both in biotechnological applications and in metabolic modeling. However, the accurate characterization of this organism and the efforts in using it for gas fermentation can help tackle this challenging perspective in the future.

Problems and corresponding strategies for converting CO2 into value-added products in Cupriavidus necator H16 cell factories

Elevated CO2 emissions have substantially altered the worldwide climate, while the excessive reliance on fossil fuels has exacerbated the energy crisis. Therefore, the conversion of CO2 into fuel, petroleum-based derivatives, drug precursors, and other value-added products is expected. Cupriavidus necator H16 is the model organism of the "Knallgas" bacterium and is considered to be a microbial cell factory as it can convert CO2 into various value-added products. However, the development and application of C. necator H16 cell factories has several limitations, including low efficiency, high cost, and safety concerns arising from the autotrophic metabolic characteristics of the strains. In this review, we first considered the autotrophic metabolic characteristics of C. necator H16, and then categorized and summarized the resulting problems. We also provided a detailed discussion of some corresponding strategies concerning metabolic engineering, trophic models, and cultivation mode. Finally, we provided several suggestions for improving and combining them. This review might help in the research and application of the conversion of CO2 into value-added products in C. necator H16 cell factories.

Minimizing the Lag Phase of Cupriavidus necator Growth under Autotrophic, Heterotrophic, and Mixotrophic Conditions

Cupriavidus necator has the unique metabolic capability to grow under heterotrophic, autotrophic, and mixotrophic conditions. In the current work, we examined the effect of growth conditions on the metabolic responses of C. necator. In our lab-scale experiments, autotrophic growth was rapid, with a short lag phase as the exponential growth stage was initiated in 6 to 12 h. The lag phase extended significantly (>22 h) at elevated O₂ and CO₂ partial pressures, while the duration of the lag phase was independent of the H₂ or N₂ partial pressure. Under heterotrophic conditions with acetate as the organic substrate, the lag phase length was short (<12 h), but it increased with increasing acetate concentrations. When glucose and glycerol were provided as the organic substrate, the lag phase was consistently long (>12 h) regardless of the examined substrate concentrations (up to 10.0 g/L). In the transition experiments, C. necator cells showed rapid transitions from autotrophic to heterotrophic growth in less than 12 h and vice versa. Our experimental results indicate that C. necator can rapidly grow with both autotrophic and heterotrophic substrates, while the lag time substantially increases with nonacetate organic substrates (e.g., glucose or glycerol), high acetate concentrations, and high O₂ and CO₂ partial pressures. IMPORTANCE The current work investigated the inhibition of organic and gaseous substrates on the microbial adaption of Cupriavidus necator under several metabolic conditions commonly employed for commercial polyhydroxyalkanoate production. We also proposed a two-stage cultivation system to minimize the lag time required to change over between the heterotrophic, autotrophic, and mixotrophic pathways.

Fermentative bioconversion of food waste into biopolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) using Cupriavidus necator

Dependency on plastic commodities has led to a recurrent increase in their global production every year. Conventionally, plastic products are derived from fossil fuels, leading to severe environmental concerns. The recent coronavirus disease 2019 pandemic has triggered an increase in medical waste. Conversely, it has disrupted the supply chain of personal protective equipment (PPE). Valorisation of food waste was performed to cultivate C. necator for fermentative production of biopolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). The increase in biomass, PHBV yield and molar 3-hydroxy valerate (3HV) content was estimated after feeding volatile fatty acids. The fed-batch fermentation strategy reported in this study produced 15.65 ± 0.14 g/L of biomass with 5.32 g/L of PHBV with 50% molar 3HV content. This is a crucial finding, as molar concentration of 3HV can be modulated to suit the specification of biopolymer (film or fabric). The strategy applied in this study addresses the issue of global food waste burden and subsequently generates biopolymer PHBV, turning waste to wealth.

Valorization of food waste fermentation liquid into single cell protein by photosynthetic bacteria via stimulating carbon metabolic pathway and environmental behaviour

Single cell protein (SCP) production by photosynthetic bacteria (PSB) is dependent on the bioavailability of carbon source, while sufficient volatile fatty acids (VFAs) in food waste fermentation liquid might be a potential alternative. It is unclear how the fermentation liquid affects the SCP biosynthesis and the related metabolic mechanism. This work demonstrated that the SCP production could be improved effectively (2088.4 mg/L) with high conversion capacity of carbon source (0.99 mg-biomass/mg-COD) by regulating carbon source level. PSB preferred to utilize the VFAs in food waste fermentation liquid. The carbon metabolic pathways (e.g., the transformation of VFAs to acetyl-CoA, and tricarboxylic acid cycle) involved in the SCP production were enhanced under optimal condition. Moreover, optimal carbon source regulation could significantly stimulate the environmental behaviour of PSB (e.g., two-component system, quorum sensing, and ATP-binding cassette transporter) involved in adaptation to external stimulus and maintaining high bacterial activity, resulting in SCP yield promotion.

Recent Trends in Biogenic Gas, Waste and Wastewater Fermentation

In recent years, the optimization of bioprocesses for the removal of pollutants from industrial biogenic gas emissions, waste and wastewater has been the focus of intensive research. Recently developed technologies not only aim to remove such pollutants, but also to valorize them, whenever possible, through their bioconversion into useful added-value products. In this domain of progressive research, lab-, pilot-, and demonstration-scale studies are dealing with the fermentation of biogenic gases (e.g., CO2, CO, and CH4), waste or wastewater to produce a range of biofuels and valuable products, based on the activity of pure or mixed cultures of native or recombinant aerobic and anaerobic bacteria, algae, or yeasts as biocatalysts. Waste can also be converted to syngas, which can subsequently be fermented as well. A broad range of bioproducts can be obtained, e.g., biofuels and several other platform chemicals and products. This environmentally-friendly biorefinery approach addresses the need to build modern societies according to the concept of a circular economy, and yields products of commercial interest. Different examples of such approaches are described in this collection of scientific reports.