Autotrophic biosynthesis of polyhydroxyalkanoate by Ralstonia eutropha from non-combustible gas mixture with low hydrogen content

Autotrophic poly-3-hydroxybutyrate accumulation in Cupriavidus necator for sustainable bioplastic production triggered by nutrient starvation

Cupriavidus necator is a facultative chemolithoautotrophic bacterium able to convert carbon dioxide into poly-3-hydroxybutyrate. This is highly promising as the conversion process allows the production of sustainable and biodegradable plastics. Poly-3-hydroxybutyrate accumulation is known to be induced by nutrient starvation, but information regarding the optimal stress conditions controlling the process is still heterogeneous and fragmentary. This study presents a comprehensive comparison of the effects of nutrient stress conditions, namely nitrogen, hydrogen, phosphorus, oxygen, and magnesium deprivation, on poly-3-hydroxybutyrate accumulation in C. necator DSM545. Nitrogen starvation exhibited the highest poly-3-hydroxybutyrate accumulation, achieving 54% of total cell dry weight after four days of nutrient stress, and a carbon conversion efficiency of 85%. The gas consumption patterns indicated flexible physiological mechanisms underlying polymer accumulation and depolymerization. These findings provide insights into strategies for efficient carbon conversion into bioplastics, and highlight the key role of C. necator for future industrial-scale applications.

Polyhydroxyalkanoate Copolymer Production by Recombinant Ralstonia eutropha Strain 1F2 from Fructose or Carbon Dioxide as Sole Carbon Source

Ralstonia eutropha strain H16 is a chemoautotrophic bacterium that oxidizes hydrogen and accumulates poly[(R)-3-hydroxybutyrate] [P(3HB)], a prominent polyhydroxyalkanoate (PHA), within its cell. R. eutropha utilizes fructose or CO2 as its sole carbon source for this process. A PHA-negative mutant of strain H16, known as R. eutropha strain PHB-4, cannot produce PHA. Strain 1F2, derived from strain PHB-4, is a leucine analog-resistant mutant. Remarkably, the recombinant 1F2 strain exhibits the capacity to synthesize 3HB-based PHA copolymers containing 3-hydroxyvalerate (3HV) and 3-hydroxy-4-methyvalerate (3H4MV) comonomer units from fructose or CO2. This ability is conferred by the expression of a broad substrate-specific PHA synthase and tolerance to feedback inhibition of branched amino acids. However, the total amount of comonomer units incorporated into PHA was up to around 5 mol%. In this study, strain 1F2 underwent genetic engineering to augment the comonomer supply incorporated into PHA. This enhancement involved several modifications, including the additional expression of the broad substrate-specific 3-ketothiolase gene (bktB), the heterologous expression of the 2-ketoacid decarboxylase gene (kivd), and the phenylacetaldehyde dehydrogenase gene (padA). Furthermore, the genome of strain 1F2 was altered through the deletion of the 3-hydroxyacyl-CoA dehydrogenase gene (hbdH). The introduction of bktB-kivd-padA resulted in increased 3HV incorporation, reaching 13.9 mol% from fructose and 6.4 mol% from CO2. Additionally, the hbdH deletion resulted in the production of PHA copolymers containing (S)-3-hydroxy-2-methylpropionate (3H2MP). Interestingly, hbdH deletion increased the weight-average molecular weight of the PHA to over 3.0 × 106 on fructose. Thus, it demonstrates the positive effects of hbdH deletion on the copolymer composition and molecular weight of PHA.

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.

Gas fermentation combined with water electrolysis for production of polyhydroxyalkanoate copolymer from carbon dioxide by engineered Ralstonia eutropha

A recycled-gas closed-circuit culture system was developed for safe autotrophic cultivation of a hydrogen-oxidizing, polyhydroxyalkanoate (PHA)-producing Ralstonia eutropha, using a non-combustible gas mixture with low-concentration of H2 supplied by water electrolysis. Automated feedback regulation of gas flow enabled input of H2, CO2, and O2 well balanced with the cellular demands, leading to constant gas composition throughout the cultivation. The engineered strain of R. eutropha produced 1.71 g/L of poly(3-hydroxybutyrate-co-12.5 mol% 3-hydroxyhexanoate) on a gas mixture of H2/CO2/O2/N2 = 4:12:7:77 vol% with a 69.2 wt% cellular content. Overexpression of can encoding cytosolic carbonic anhydrase increased the 3HHx fraction up to 19.6 mol%. The yields of biomass and PHA on input H2 were determined to be 72.9 % and 63.1 %, corresponding to 51.0 % and 44.2 % yield on electricity, respectively. The equivalent solar-to-biomass/PHA efficiencies were estimated to be 2.1-3.8 %, highlighting the high energy conversion capability of R. eutropha.

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.

Production of Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from CO2 via pH-Stat Jar Cultivation of an Engineered Hydrogen-Oxidizing Bacterium Cupriavidus necator

The copolyester of 3-hydroxybutyrate (3HB) and 3-hydoxyhexanoate (3HHx), PHBHHx, is a biodegradable plastic characterized by high flexibility, softness, a wide process window, and marine biodegradability. PHBHHx is usually produced from structurally related carbon sources, such as vegetable oils or fatty acids, but not from inexpensive carbon sources such as sugars. In previous studies, we demonstrated that engineered strains of a hydrogen-oxidizing bacterium, Cupriavidus necator, synthesized PHBHHx with a high cellular content not only from sugars but also from CO2 as the sole carbon source in the flask culture. In this study, the highly efficient production of PHBHHx from CO2 was investigated via pH-stat jar cultivation of recombinant C. necator strains while feeding the substrate gas mixture (H2/O2/CO2 = 80:10:10 v/v%) to a complete mineral medium in a recycled-gas, closed-circuit culture system. As a result, the dry cell mass and PHBHHx concentration with the strain MF01/pBPP-ccrMeJAc-emd reached up to 59.62 ± 3.18 g·L-1 and 49.31 ± 3.14 g·L-1, respectively, after 216 h of jar cultivation with limited addition of ammonia and phosphate solutions. The 3HHx composition was close to 10 mol%, which is suitable for practical applications. It is expected that the autotrophic cultivation of the recombinant C. necator can be feasible for the mass production of PHBHHx from CO2.

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.

Continuous Supply of Non-Combustible Gas Mixture for Safe Autotrophic Culture to Produce Polyhydroxyalkanoate by Hydrogen-Oxidizing Bacteria

Polyhydroxyalkanoates (PHAs) are eco-friendly plastics that are thermoplastic and biodegradable in nature. The hydrogen-oxidizing bacterium Ralstonia eutropha can biosynthesize poly[(R)-3-hydroxybutyrate] [P(3HB)], the most common PHA, from carbon dioxide using hydrogen and oxygen as energy sources. In conventional autotrophic cultivation using R. eutropha, a gas mixture containing 75−80 vol% hydrogen is supplied; however, a gas mixture with such a high hydrogen content has a risk of explosion due to gas leakage. In this study, we aimed to develop an efficient cell culture system with a continuous supply of a non-combustible gas mixture (H2: O2: CO2: N2 = 3.8: 7.3: 13.0: 75.9) for safe autotrophic culture to produce P(3HB) by hydrogen-oxidizing bacteria, with a controlled hydrogen concentration under a lower explosive limit concentration. When the gas mixture was continuously supplied to the jar fermentor, the cell growth of R. eutropha H16 significantly improved compared to that in previous studies using flask cultures. Furthermore, an increased gas flow rate and agitation speed enhanced both cell growth and P(3HB) production. Nitrogen source deficiency promoted P(3HB) production, achieving up to 2.94 g/L P(3HB) and 89 wt% P(3HB) content in the cells after 144 h cultivation. R. eutropha NCIMB 11599, recombinant R. eutropha PHB-4, and Azohydromonas lata grew in a low-hydrogen-content gas mixture. R. eutropha H16 and recombinant R. eutropha PHB-4 expressing PHA synthase from Bacillus cereus YB-4 synthesized P(3HB) with a high weight-average molecular weight of 13.5−16.9 × 105. Thus, this autotrophic culture system is highly beneficial for PHA production from carbon dioxide using hydrogen-oxidizing bacteria as the risk of explosion is eliminated.

A Review on Enhancing Cupriavidus necator Fermentation for Poly(3-hydroxybutyrate) (PHB) Production From Low-Cost Carbon Sources

In the context of a circular economy, bioplastic production using biodegradable materials such as poly(3-hydroxybutyrate) (PHB) has been proposed as a promising solution to fundamentally solve the disposal issue of plastic waste. PHB production techniques through fermentation of PHB-accumulating microbes such as Cupriavidus necator have been revolutionized over the past several years with the development of new strategies such as metabolic engineering. This review comprehensively summarizes the latest PHB production technologies via Cupriavidus necator fermentation. The mechanism of the biosynthesis pathway for PHB production was first assessed. PHB production efficiencies of common carbon sources, including food waste, lignocellulosic materials, glycerol, and carbon dioxide, were then summarized and critically analyzed. The key findings in enhancing strategies for PHB production in recent years, including pre-treatment methods, nutrient limitations, feeding optimization strategies, and metabolism engineering strategies, were summarized. Furthermore, technical challenges and future prospects of strategies for enhanced production efficiencies of PHB were also highlighted. Based on the overview of the current enhancing technologies, more pilot-scale and larger-scale tests are essential for future implementation of enhancing strategies in full-scale biogas plants. Critical analyses of various enhancing strategies would facilitate the establishment of more sustainable microbial fermentation systems for better waste management and greater efficiency of PHB production.

Microbial autotrophic biorefineries: Perspectives for biopolymer production

The use of autotrophic microorganisms to fabricate biochemical products has attracted much attention in both academia and industry. Unlike heterotrophic microorganisms that require carbohydrates and amino acids for growth, autotrophic microorganisms have evolved to utilize either light (photoautotrophs) or chemical compounds (chemolithotrophs) to fix carbon dioxide (CO2) and drive metabolic processes. Several biotechnological approaches, including synthetic biology and metabolic engineering, have been proposed to harness autotrophic microorganisms as a sustainable/green production platform for commercially essential products such as biofuels, commodity chemicals, and biopolymers. Here, we review the recent advances in natural autotrophic microorganisms (photoautotrophic and chemoautotrophic), focusing on the biopolymer production. We present current state-of-the-art technologies to engineer autotrophic microbial cell factories for efficient biopolymer production.

Lab-Scale Cultivation of Cupriavidus necator on Explosive Gas Mixtures: Carbon Dioxide Fixation into Polyhydroxybutyrate

Aerobic, hydrogen oxidizing bacteria are capable of efficient, non-phototrophic CO₂ assimilation, using H₂ as a reducing agent. The presence of explosive gas mixtures requires strict safety measures for bioreactor and process design. Here, we report a simplified, reproducible, and safe cultivation method to produce Cupriavidus necator H16 on a gram scale. Conditions for long-term strain maintenance and mineral media composition were optimized. Cultivations on the gaseous substrates H₂, O₂, and CO₂ were accomplished in an explosion-proof bioreactor situated in a strong, grounded fume hood. Cells grew under O₂ control and H₂ and CO₂ excess. The starting gas mixture was H₂:CO₂:O₂ in a ratio of 85:10:2 (partial pressure of O₂ 0.02 atm). Dissolved oxygen was measured online and was kept below 1.6 mg/L by a stepwise increase of the O₂ supply. Use of gas compositions within the explosion limits of oxyhydrogen facilitated production of 13.1 ± 0.4 g/L total biomass (gram cell dry mass) with a content of 79 ± 2% poly-(R)-3-hydroxybutyrate in a simple cultivation set-up with dissolved oxygen as the single controlled parameter. Approximately 98% of the obtained PHB was formed from CO₂.

Strategies for Biosynthesis of C1 Gas-derived Polyhydroxyalkanoates: A review

Biosynthesis of polyhydroxyalkanoates (PHAs) from C1 gases is highly desirable in solving problems such as climate change and microplastic pollution. PHAs are biopolymers synthesized in microbial cells and can be used as alternatives to petroleum-based plastics because of their biodegradability. Because 50% of the cost of PHA production is due to organic carbon sources and salts, the utilization of costless C1 gases as carbon sources is expected to be a promising approach for PHA production. In this review, strategies for PHA production using C1 gases through fermentation and metabolic engineering are discussed. In particular, autotrophs, acetogens, and methanotrophs are strains that can produce PHA from CO₂, CO, and CH₄. In addition, integrated bioprocesses for the efficient utilization of C1 gases are introduced. Biorefinery processes from C1 gas into bioplastics are prospective strategies with promising potential and feasibility to alleviate environmental issues.

A comparative analysis of biopolymer production by microbial and bioelectrochemical technologies

Production of biopolymers from renewable carbon sources provides a path towards a circular economy. This review compares several existing and emerging approaches for polyhydroxyalkanoate (PHA) production from soluble organic and gaseous carbon sources and considers technologies based on pure and mixed microbial cultures. While bioplastics are most often produced from soluble sources of organic carbon, the use of carbon dioxide (CO₂) as the carbon source for PHA production is emerging as a sustainable approach that combines CO₂ sequestration with the production of a value-added product. Techno-economic analysis suggests that the emerging approach of CO₂ conversion to carboxylic acids by microbial electrosynthesis followed by microbial PHA production could lead to a novel cost-efficient technology for production of green biopolymers.

Biopolymers production from renewable carbon sources.

A shortcut to carbon-neutral bioplastic production: Recent advances in microbial production of polyhydroxyalkanoates from C1 resources

Since the 20th century, plastics that are widely being used in general life and industries are causing enormous plastic waste problems since improperly discarded plastics barely degrade and decompose. Thus, the demand for polyhydroxyalkanoates (PHAs), biodegradable polymers with material properties similar to conventional petroleum-based plastics, has been increased so far. The microbial production of PHAs is an environment-friendly solution for the current plastic crisis, however, the carbon sources for the microbial PHA production is a crucial factor to be considered in terms of carbon-neutrality. One‑carbon (C1) resources, such as methane, carbon monoxide, and carbon dioxide, are greenhouse gases and are abundantly found in nature and industry. C1 resources as the carbon sources for PHA production have a completely closed carbon loop with much advances; i) fast carbon circulation with direct bioconversion process and ii) simple fermentation procedure without sterilization as non-preferable nutrients. This review discusses the biosynthesis of PHAs based on C1 resource utilization by wild-type and metabolically engineered microbial host strains via biorefinery processes.

Biosynthesis of Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from CO2 by a Recombinant Cupriavidusnecator

The copolyester of 3-hydroxybutyrate (3HB) and 3-hydoxyhexanoate (3HHx), PHBHHx, is one of the most practical kind of bacterial polyhydroxyalkanoates due to its high flexibility and marine biodegradability. PHBHHx is usually produced from vegetable oils or fatty acids through β-oxidation, whereas biosynthesis from sugars has been achieved by recombinant strains of hydrogen-oxidizing bacterium Cupriavidus necator. This study investigated the biosynthesis of PHBHHx from CO2 as the sole carbon source by engineered C. necator strains. The recombinant strains capable of synthesizing PHBHHx from fructose were cultivated in a flask using complete mineral medium and a substrate gas mixture (H2/O2/CO2 = 8:1:1). The results of GC and 1H NMR analyses indicated that the recombinants of C. necator synthesized PHBHHx from CO2 with high cellular content. When 1.0 g/L (NH4)2SO4 was used as a nitrogen source, the 3HHx composition of PHBHHx in the strain MF01∆B1/pBBP-ccrMeJ4a-emd was 47.7 ± 6.2 mol%. Further investigation demonstrated that the PHA composition can be regulated by using (R)-enoyl-CoA hydratase (PhaJ) with different substrate specificity. The composition of 3HHx in PHBHHx was controlled to about 11 mol%, suitable for practical applications, and high cellular content was kept in the strains transformed with pBPP-ccrMeJAc-emd harboring short-chain-length-specific PhaJ.

Recent progress and challenges in microbial polyhydroxybutyrate (PHB) production from CO2 as a sustainable feedstock: A state-of-the-art review

The recalcitrance of petroleum-based plastics causes severe environmental problems and has accelerated research into production of biodegradable polymers from inexpensive and sustainable feedstocks. Various microorganisms are capable of producing Polyhydroxybutyrate (PHB), a representative biodegradable polymer, under nutrient-limited conditions, among which CO₂-utilizing microorganisms are of primary interest. Herein, we discuss recent progress on bacterial strains including proteobacteria, purple non-sulfur bacteria, and cyanobacteria in terms of CO₂-containing carbon sources, PHB-production capability, and genetic modification. In addition, this review introduces recent technical approaches used to improve PHB production from CO₂ such as two-stage bioprocesses and bioelectrochemical systems. Challenges and future perspectives for the development of economically feasible PHB production are also discussed. Finally, this review might provide insights into the construction of a closed-carbon-loop to cope with climate change.

Isopropanol production with reutilization of glucose-derived CO2 by engineered Ralstonia eutropha

Chemolithoautotrophic bacterium Ralstonia eutropha is a versatile host for production of various useful compounds including polyhydroxyalkanoates (PHAs) under both heterotrophic and autotrophic conditions. In this bacterium, Calvin-Benson-Bassham (CBB) cycle is functional even under heterotrophic conditions on sugars and reutilizes CO₂ emitted through sugar metabolisms into PHA, leading to increase in yield of the storage polyester. This study focused on isopropanol production from glucose by engineered strains of R. eutropha. The isopropanol-producing strains were constructed by introduction of codon-optimized genes of acetoacetate decarboxylase (adc) and primary-secondary alcohol dehydrogenase (adh) from clostridia into glucose-utilizing and PHA-negative (ΔphaC1) strain of R. eutropha. Several genetic modifications showed that high expression of the isopropanol synthesis genes by using a strong synthetic promoter and deletion of NAD⁺-dependent (S)-3-hydroxybutyryl-CoA dehydrogenase genes (paaH1 and had) in addition to NADPH-dependent acetoacetyl-CoA reductase genes (phaB1 and phaB3) were effective for improving isopropanol production with low by-production of acetone. Isopropanol titer of 4.13 g/L was achieved by two-stage cultivation of the strain IP-007/pBj5c2-adh-adc, corresponding to overall yield of 0.6 mol mol-glucose^-1. The fixation of sugar-derived CO₂ during isopropanol synthesis was evaluated by ¹³C-labelling of the isopropanol produced from [1-¹³C]-glucose. The ¹³C-abundance in isopropanol synthesized by the engineered strain was significantly increased up to 4.8%, demonstrating actual reassimilation of CO₂ emitted from glucose moiety by decarboxylation and potential contribution towards increase in the carbon yield of isopropanol on glucose.