Production of poly(3-hydroxybutyric acid-co-4-hydroxybutyric acid) and poly(4-hydroxybutyric acid) without subsequent degradation by Hydrogenophaga pseudoflava

Role of sulfide on DNRA distribution and the microbial community structure in a sulfide-driven nitrate reduction process

Microbial nitrate reduction processes involve two competing pathways: denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA). This study investigated the distribution of DNRA in a sole sulfur-driven nitrogen conversion process using a laboratory-scale sequencing biofilm batch reactor (SBBR) through a series of batch tests with varying sulfide/nitrate (S/N) ratios. The results showed that DNRA became more dominant in the sulfide-oxidizing autotrophic denitrification (SOAD) process as the S/N ratio increased to 1.5:1, 1.7:1, and 2:1, reaching a peak of 35.3% at the S/N ratio of 1.5:1. Oxidation-reduction potential (ORP) patterns demonstrated distinct inflection points for nitrate and nitrite consumption under the SOAD-only conditions, whereas these points overlapped when DNRA coexisted with SOAD. Analysis of 16S ribosomal RNA identified Ignavibacterium, Hydrogenophaga, and Geobacter as the dominant genera responsible for DNRA during autotrophic nitrate reduction. The findings of the DNRA divergence investigation provided valuable insights into enhancing biological nitrogen removal processes, particularly when coupled with the anammox.

Enrichment of biofertilizer-type hydrogen-oxidizing bacteria on urea containing Cu(II)

With the utilization of pesticides and fertilizers (e.g. urea), the presence of nitrogen and heavy metals (e.g. copper) can enter and pollute the environment. Biofertilizers can be used to replace chemical fertilizers to increase crop yields and reduce environmental stress. The utilization of hydrogen-oxidizing bacteria (HOB) to be biofertilizers has recently attracted more attention. However, the enrichment of HOB on urea and the effect of copper are undetermined. HOB were successfully enriched using urea in this investigation. The average urea conversion rate (AUCR) was 180.08 mgN/L/d with a hydraulic retention time of 10 h. Microbial community (R1) was dominated by Hydrogenophaga (83.92%), a biofertilizer-type HOB. After addition of 5.47 mg/L Cu2+, the AUCR was decreased by 16%-151.18 mgN/L/d, and the growth of HOB was inhibited by 48%. Meanwhile, inhibition was also reflected by the increase of polysaccharide content (20.27 ± 0.57 to 33.45 ± 2.53 mg/gVSS) and protein content (106.19 ± 19.39 to 125.14 ± 24.73 mg/gVSS) of extracellular polymeric substances in the HOB. The resulting microbial community (R2) was changed to Azospiralium-dominated flora (91.33%). Both enriched microbial communities (R1 and R2) exhibited the abilities of ACC degradation and phosphate solubilization. This study demonstrates that employing urea can directly enrich biofertilizer-type HOB and copper-tolerant HOB can be obtained in a 5.47 mg/L Cu2+ environment. The results provide potential methods to obtain biofertilizer from copper-containing urea wastewater via HOB.

The Role of Bacterial Polyhydroalkanoate (PHA) in a Sustainable Future: A Review on the Biological Diversity

Environmental challenges related to the mismanagement of plastic waste became even more evident during the COVID-19 pandemic. The need for new solutions regarding the use of plastics came to the forefront again. Polyhydroxyalkanoates (PHA) have demonstrated their ability to replace conventional plastics, especially in packaging. Its biodegradability and biocompatibility makes this material a sustainable solution. The cost of PHA production and some weak physical properties compared to synthetic polymers remain as the main barriers to its implementation in the industry. The scientific community has been trying to solve these disadvantages associated with PHA. This review seeks to frame the role of PHA and bioplastics as substitutes for conventional plastics for a more sustainable future. It is focused on the bacterial production of PHA, highlighting the current limitations of the production process and, consequently, its implementation in the industry, as well as reviewing the alternatives to turn the production of bioplastics into a sustainable and circular economy.

Role of carbon-dioxide sequestering bacteria for clean air environment and prospective production of biomaterials: a sustainable approach

The increase in demand of fossil fuel uses for developmental activity and manufacturing of goods have resulted a huge emission of global warming gases (GWGs) in the atmosphere. Among all GWGs, CO₂ is the major contributor that inevitably causes global warming and climate change. Mitigation strategies like biological CO₂ capture through sequestration and their storage into biological organic form are used to minimize the concentration of atmospheric CO₂ with the goal to control climate change. Since increasing atmospheric CO₂ level supports microbial growth and productivity thus microbial-based CO₂ sequestration has remarkable advantages as compared to plant-based sequestration. This review focuses on CO₂ sequestration mechanism in bacteria through different carbon fixation pathways, involved enzymes, their role in calcite, and other environmentally friendly biomaterials such as biofuel, bioplastic, and biosurfactant.

Exploiting Aerobic Carboxydotrophic Bacteria for Industrial Biotechnology

Aerobic carboxydotrophic bacteria are a group of microorganisms which possess the unique trait to oxidize carbon monoxide (CO) as sole energy source with molecular oxygen (O₂) to produce carbon dioxide (CO₂) which subsequently is used for biomass formation via the Calvin-Benson-Bassham cycle. Moreover, most carboxydotrophs are also able to oxidize hydrogen (H₂) with hydrogenases to drive the reduction of carbon dioxide in the absence of CO. As several abundant industrial off-gases contain significant amounts of CO, CO₂, H₂ as well as O₂, these bacteria come into focus for industrial application to produce chemicals and fuels from such gases in gas fermentation approaches. Since the group of carboxydotrophic bacteria is rather unknown and not very well investigated, we will provide an overview about their lifestyle and the underlying metabolic characteristics, introduce promising members for industrial application, and give an overview of available genetic engineering tools. We will point to limitations and discuss challenges, which have to be overcome to apply metabolic engineering approaches and to utilize aerobic carboxydotrophs in the industrial environment.

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.

P(3HB-co-4HB) as high value polyhydroxyalkanoate: its development over recent decades and current advances

Polyhydroxyalkanoate (PHA) is a biogenic polymer that has the potential to substitute synthetic plastic in numerous applications. This is due to its unique attribute of being a biodegradable and biocompatible thermoplastic, achievable through microbial fermentation from a broad utilizable range of renewable resources. Among all the PHAs discovered, poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] stands out as a next generation healthcare biomaterial for having high biopharmaceutical and medical value since it is highly compatible to mammalian tissue. This review provides a critical assessment and complete overview of the development and trend of P(3HB-co-4HB) research over the last few decades, highlighting aspects from the microbial strain discovery to metabolic engineering and bioprocess cultivation strategies. The article also outlines the relevance of P(3HB-co-4HB) as a material for high value-added products in numerous healthcare-related applications.

In vivo and Post-synthesis Strategies to Enhance the Properties of PHB-Based Materials: A Review

The transition toward "green" alternatives to petroleum-based plastics is driven by the need for "drop-in" replacement materials able to combine characteristics of existing plastics with biodegradability and renewability features. Promising alternatives are the polyhydroxyalkanoates (PHAs), microbial biodegradable polyesters produced by a wide range of microorganisms as carbon, energy, and redox storage material, displaying properties very close to fossil-fuel-derived polyolefins. Among PHAs, polyhydroxybutyrate (PHB) is by far the most well-studied polymer. PHB is a thermoplastic polyester, with very narrow processability window, due to very low resistance to thermal degradation. Since the melting temperature of PHB is around 170-180°C, the processing temperature should be at least 180-190°C. The thermal degradation of PHB at these temperatures proceeds very quickly, causing a rapid decrease in its molecular weight. Moreover, due to its high crystallinity, PHB is stiff and brittle resulting in very poor mechanical properties with low extension at break, which limits its range of application. A further limit to the effective exploitation of these polymers is related to their production costs, which is mostly affected by the costs of the starting feedstocks. Since the first identification of PHB, researchers have faced these issues, and several strategies to improve the processability and reduce brittleness of this polymer have been developed. These approaches range from the in vivo synthesis of PHA copolymers, to the enhancement of post-synthesis PHB-based material performances, thus the addition of additives and plasticizers, acting on the crystallization process as well as on polymer glass transition temperature. In addition, reactive polymer blending with other bio-based polymers represents a versatile approach to modulate polymer properties while preserving its biodegradability. This review examines the state of the art of PHA processing, shedding light on the green and cost-effective tailored strategies aimed at modulating and optimizing polymer performances. Pioneering examples in this field will be examined, and prospects and challenges for their exploitation will be presented. Furthermore, since the establishment of a PHA-based industry passes through the designing of cost-competitive production processes, this review will inspect reported examples assessing this economic aspect, examining the most recent progresses toward process sustainability.

Exploring the Bacterial Communities of the Kaiafas Thermal Spring Anigrides Nymphes in Greece Prior to Rehabilitation Actions

Anigrides Nymphes of Lake Kaiafas is a thermal spring that is well known for its therapeutical properties, as the hot water (32-34 °C) is rich in sulfur compounds and minerals. Nowadays, efforts are made from the Hellenic Republic to modernize the existing facilities and infrastructure networks of the area. To study the complex ecosystem of the thermal spring, we collected water from four sampling points (Lake, and Caves 1, 2, and 3). Filtration method was used for microbial enumeration. In parallel, total bacterial DNA was extracted and subjected to next-generation sequencing (NGS). A total of 166 different bacterial families were detected. Differences in families, genera, and species abundances were detected between the different sampling points. Specifically, Comamonadaceae was the most common family detected in Lake and Cave 3. Similarly, in Caves 1 and 2, Rhodobacteraceae was detected at a higher percentage compared to the rest of the families. Moreover, the detection of sequences assigned to waterborne or opportunistic pathogens, i.e., Enterobacteriaceae, Legionellaceae, Coxiellaceae, and Clostridiaceae, as well as Enterococcus and Vibrio, is of great importance. Although the presence of pathogens was not examined by quantitative PCR, the detection of their sequences strengthens the need of the planned rehabilitation actions of this natural environment in order to allow human swimming.

Poly(4-Hydroxybutyrate): Current State and Perspectives

By the end of 1980s, for the first time polyhydroxyalkanoate (PHA) copolymers with incorporated 4-hydroxybutyrate (4HB) units were produced in the bacterium Cupriavidus necator (formally Ralstonia eutropha) from structurally related carbon sources. After that, production of PHA copolymers composed of 3-hydroxybutyrate (3HB) and 4HB [P(3HB-co-4HB)] was demonstrated in diverse wild-type bacteria. The P4HB homopolymer, however, was hardly synthesized because existing bacterial metabolism on 4HB precursors also generate and incorporate 3HB. The resulting material assumes the properties of thermoplastics and elastomers depending on the 4HB fraction in the copolyester. Given the fact that P4HB is biodegradable and yield 4HB, which is a normal compound in the human body and proven to be biocompatible, P4HB has become a prospective material for medical applications, which is the only FDA approved PHA for medical applications since 2007. Different from other materials used in similar applications, high molecular weight P4HB cannot be produced via chemical synthesis. Thus, aiming at the commercial production of this type of PHA, genetic engineering was extensively applied resulting in various production strains, with the ability to convert unrelated carbon sources (e.g., sugars) to 4HB, and capable of producing homopolymeric P4HB. In 2001, Metabolix Inc. filed a patent concerning genetically modified and stable organisms, e.g., Escherichia coli, producing P4HB and copolymers from inexpensive carbon sources. The patent is currently hold by Tepha Inc., the only worldwide producer of commercial P4HB. To date, numerous patents on various applications of P4HB in the medical field have been filed. This review will comprehensively cover the historical evolution and the most recent publications on P4HB biosynthesis, material properties, and industrial and medical applications. Finally, perspectives for the research and commercialization of P4HB will be presented.

Beyond Intracellular Accumulation of Polyhydroxyalkanoates: Chiral Hydroxyalkanoic Acids and Polymer Secretion

Polyhydroxyalkanoates (PHAs) are ubiquitous prokaryotic storage compounds of carbon and energy, acting as sinks for reducing power during periods of surplus of carbon source relative to other nutrients. With close to 150 different hydroxyalkanoate monomers identified, the structure and properties of these polyesters can be adjusted to serve applications ranging from food packaging to biomedical uses. Despite its versatility and the intensive research in the area over the last three decades, the market share of PHAs is still low. While considerable rich literature has accumulated concerning biochemical, physiological, and genetic aspects of PHAs intracellular accumulation, the costs of substrates and processing costs, including the extraction of the polymer accumulated in intracellular granules, still hampers a more widespread use of this family of polymers. This review presents a comprehensive survey and critical analysis of the process engineering and metabolic engineering strategies reported in literature aimed at the production of chiral (R)-hydroxycarboxylic acids (RHAs), either from the accumulated polymer or by bypassing the accumulation of PHAs using metabolically engineered bacteria, and the strategies developed to recover the accumulated polymer without using conventional downstream separations processes. Each of these topics, that have received less attention compared to PHAs accumulation, could potentially improve the economy of PHAs production and use. (R)-hydroxycarboxylic acids can be used as chiral precursors, thanks to its easily modifiable functional groups, and can be either produced de-novo or be obtained from recycled PHA products. On the other hand, efficient mechanisms of PHAs release from bacterial cells, including controlled cell lysis and PHA excretion, could reduce downstream costs and simplify the polymer recovery process.

Enriched hydrogen-oxidizing microbiomes show a high diversity of co-existing hydrogen-oxidizing bacteria

While numerous reports exist on the axenic culturing of different hydrogen-oxidizing bacteria (HOB), knowledge about the enrichment of microbial communities growing on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources remains negligible. We want to elucidate if in such enrichments, most enriched populations are HOBs or heterotrophic organisms. In the present study, bacteria enriched from a soil sample and grown over 5 transfers using a continuous supply of hydrogen, oxygen, and carbon dioxide to obtain an enriched autotrophic hydrogen-oxidizing microbiome. The success of the enrichment was evaluated by monitoring ammonium consumption and biomass concentration for 120 days. The shift in the microbial composition of the original soil inoculum and all transfers was observed based on 16S rRNA amplicon sequencing. The hydrogen-oxidizing facultative chemolithoautotroph Hydrogenophaga electricum was isolated and found to be one of the abundant species in most transfers. Moreover, Achromobacter was isolated both under heterotrophic and autotrophic conditions, which was characterized as a hydrogen-oxidizing bacterium. The HOB enrichment condition constructed in this study provided an environment for HOB to develop and conquer in all transfers. In conclusion, we showed that enrichments on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources contain a diverse mixture of HOB and heterotrophs that resulted in a collection of culturable isolates. These isolates can be useful for further investigation for industrial applications.

Polyhydroxyalkanoates based copolymers

Polyhydroxyalkanoates (PHAs) belong to a family of natural polyesters and are produced under unbalanced growth conditions as intracellular carbon and energy reserves by a wide variety of microorganisms. Being biodegradable, biocompatible and environmental friendly thermoplastics, the PHAs are considered as future polymers to replace petrochemicals based plastics. In this review, the introduction section deals with the brief discussion on PHA nature, availability, raw materials for production, processing etc. This is followed by the discussions on modifications. The copolymer syntheses by bacterial and chemical methods have been discussed. Under chemical methods, unsaturated side chains and their derivatives, oligomer, coupling, macro-initiating, trans-esterification, radiation grafting, click chemistry, ring opening and several miscellaneous polymerization methods have been elaborated. A brief discussion on applications has been incorporated. The last section includes conclusion and future perspectives.

Application of whey retentate as complex nitrogen source for growth of the polyhydroxyalkanoate producer Hydrogenophaga pseudoflava strain DSM1023

Polyhydroxyalkanoates, microbial polyesters produced in vivo starting from renewable resources, are considered the future materials of choice to compete recalcitrant petro-chemical plastic on the polymer market. In order to make polyhydroxyalkanoates market-fit, (techno)economics of their production need to be improved. Among the multifarious factors affecting costs of polyhydroxyalkanoate production, increased volumetric productivity is of utmost importance. Improving microbial growth kinetics and increasing cell density are strategies leading to a high concentration of catalytically active biomass within a short time; after changing cultivation conditions, these cells can accumulate polyhydroxyalkanoates as intracellular products. The resulting increase of volumetric productivity for polyhydroxyalkanoates can be realized by supplying complex nitrogen sources to growing microbial cultures. In the present study, the impact of different expensive and inexpensive complex nitrogen sources, in particular whey retentate, on the growth and specific growth rates of Hydrogenophaga pseudoflava was tested.

Based on a detailed kinetic process analysis, the study demonstrates that especially whole (not hydrolyzed) whey retentate, an amply available surplus material from dairy industry, displays positive effects on cultivations of H. pseudoflava in defined media (increase of concentration of catalytically active biomass after 26.25 h of cultivation by about 50%, increase of specific growth rate μ from 0.28 to 0.41 1/h during exponential growth), while inhibiting effects (inhibition constant K i = 6.1 g/L) of acidically hydrolyzed whey retentate need to be overcome. Considering the huge amounts of surplus whey accruing especially in Europe, the combined utilization of whey permeate (carbon source) and whey retentate (complex nitrogen source) for biopolyester production can be considered a viable bioeconomic strategy for the next future.

Feeding strategies for tuning poly (3-hydroxybutyrate-co-4-hydroxybutyrate) monomeric composition and productivity using Burkholderia sacchari

Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P(3HB-4HB)) co-polymers were produced at bench-scale in fed-batch cultivations by Burkholderia sacchari from glucose (main carbon-source) and gamma-butyrolactone (GBL) as co-substrate. As P(3HB-4HB) properties highly depend on the 4-hydroxybutyrate (4HB) molar fraction, it is advantageous to have a thorough knowledge of the process in order to promote the production of the targeted final product. In this work, polymers with a 4HB molar percentage ranging from 1.5 to 8.4% (mol/mol) were obtained as consequence of a fine tuning of the fed-batch operation conditions, namely regarding the co-substrate feeding rate and its addition time, as GBL is toxic to B. sacchari cells. The best results regarding both the 4HB incorporation (molar%) and the co-polymer productivity (7.1% and 1.1g/(L.h) respectively) were reached when a pulse of GBL (<10g/L) was added early in the accumulation phase followed by a constant GBL addition at a rate similar to that of consumption so that a steady co-substrate concentration in the medium was maintained.

Fed-Batch Synthesis of Poly(3-Hydroxybutyrate) and Poly(3-Hydroxybutyrate-co-4-Hydroxybutyrate) from Sucrose and 4-Hydroxybutyrate Precursors by Burkholderia sacchari Strain DSM 17165

Based on direct sucrose conversion, the bacterium Burkholderia sacchari is an excellent producer of the microbial homopolyester poly(3-hydroxybutyrate) (PHB). Restrictions of the strain’s wild type in metabolizing structurally related 3-hydroxyvalerate (3HV) precursors towards 3HV-containing polyhydroxyalkanoate (PHA) copolyester calls for alternatives. We demonstrate the highly productive biosynthesis of PHA copolyesters consisting of 3-hydroxybuytrate (3HB) and 4-hydroxybutyrate (4HB) monomers. Controlled bioreactor cultivations were carried out using saccharose from the Brazilian sugarcane industry as the main carbon source, with and without co-feeding with the 4HB-related precursor γ-butyrolactone (GBL). Without GBL co-feeding, the homopolyester PHB was produced at a volumetric productivity of 1.29 g/(L·h), a mass fraction of 0.52 g PHB per g biomass, and a final PHB concentration of 36.5 g/L; the maximum specific growth rate µ_max amounted to 0.15 1/h. Adding GBL, we obtained 3HB and 4HB monomers in the polyester at a volumetric productivity of 1.87 g/(L·h), a mass fraction of 0.72 g PHA per g biomass, a final PHA concentration of 53.7 g/L, and a µ_max of 0.18 1/h. Thermoanalysis revealed improved material properties of the second polyester in terms of reduced melting temperature T_m (161 °C vs. 178 °C) and decreased degree of crystallinity X_c (24% vs. 71%), indicating its enhanced suitability for polymer processing.

Microbial production of polyhydroxyalkanoates (PHAs) and its copolymers: A review of recent advancements

Traditional mineral oil based plastics are important commodity to enhance the comfort and quality of life but the accumulation of these plastics in the environment has become a major universal problem due to their low biodegradation. Solution to the plastic waste management includes incineration, recycling and landfill disposal methods. These processes are very time consuming and expensive. Biopolymers are important alternatives to the petroleum-based plastics due to environment friendly manufacturing processes, biodegradability and biocompatibility. Therefore use of novel biopolymers, such as polylactide, polysaccharides, aliphatic polyesters and polyhydroxyalkanoates is of interest. PHAs are biodegradable polyesters of hydroxyalkanoates (HA) produced from renewable resources by using microorganisms as intracellular carbon and energy storage compounds. Even though PHAs are promising candidate for biodegradable polymers, however, the production cost limit their application on an industrial scale. This article provides an overview of various substrates, microorganisms for the economical production of PHAs and its copolymers. Recent advances in PHAs to reduce the cost and to improve the performance of PHAs have also been discussed.

Biosynthetic enhancement of single-stage Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) production by manipulating the substrate mixtures

Two-stage fermentation was normally employed to achieve a high poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] productivity with higher 4HB molar fraction. Here, we demonstrated single-stage fermentation method which is more industrial feasible by implementing mixed-substrate cultivation strategy. Studies on bioreactor scale show a remarkably high PHA accumulation of 73 wt%, contributing to a high PHA concentration and product yield of 8.6 g/L and 2.7 g/g, respectively. This fermentation strategy has resulted in copolymers with wider range of 4HB monomer composition, which ranges from 12 to 55 mol%. These copolymers show a broad range of weight average molecular weight (M  w) from 119.5 to 407.0 kDa. The copolymer characteristics were found to be predominantly affected by the nature of the substrates and the mixture strategies, regardless of the 4HB monomer compositions. This was supported by the determination of copolymer randomness using 13C-NMR analysis. The study warrants significantly in the copolymer scale-up and modeling at industrial level.

Methane as a resource: can the methanotrophs add value?

Methane is an abundant gas used in energy recovery systems, heating, and transport. Methanotrophs are bacteria capable of using methane as their sole carbon source. Although intensively researched, the myriad of potential biotechnological applications of methanotrophic bacteria has not been comprehensively discussed in a single review. Methanotrophs can generate single-cell protein, biopolymers, components for nanotechnology applications (surface layers), soluble metabolites (methanol, formaldehyde, organic acids, and ectoine), lipids (biodiesel and health supplements), growth media, and vitamin B12 using methane as their carbon source. They may be genetically engineered to produce new compounds such as carotenoids or farnesene. Some enzymes (dehydrogenases, oxidase, and catalase) are valuable products with high conversion efficiencies and can generate methanol or sequester CO2 as formic acid ex vivo. Live cultures can be used for bioremediation, chemical transformation (propene to propylene oxide), wastewater denitrification, as components of biosensors, or possibly for directly generating electricity. This review demonstrates the potential for methanotrophs and their consortia to generate value while using methane as a carbon source. While there are notable challenges using a low solubility gas as a carbon source, the massive methane resource, and the potential cost savings while sequestering a greenhouse gas, keeps interest piqued in these unique bacteria.

Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: Controllable P(3HB-co-4HB) biosynthesis

Clustered regularly interspaced short palindromic repeats interference (CRISPRi) is used to edit eukaryotic genomes. Here, we show that CRISPRi can also be used for fine-tuning prokaryotic gene expression while simultaneously regulating multiple essential gene expression with less labor and time consumption. As a case study, CRISPRi was used to control polyhydroxyalkanoate (PHA) biosynthesis pathway flux and to adjust PHA composition. A pathway was constructed in Escherichia coli for the production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] from glucose. The native gene sad encoding E. coli succinate semi-aldehyde dehydrogenase was expressed under the control of CRISPRi using five specially designed single guide RNAs (sgRNAs) for regulating carbon flux to 4-hydroxybutyrate (4HB) biosynthesis. The system allowed formation of P(3HB-co-4HB) consisting of 1-9mol% 4HB. Additionally, succinate, generated by succinyl-coA synthetase and succinate dehydrogenase (respectively encoded by genes sucC, sucD and sdhA, sdhB) was channeled preferentially to the 4HB precursor by using selected sgRNAs such as sucC2, sucD2, sdhB2 and sdhA1 via CRISPRi. The resulting 4HB content in P(3HB-co-4HB) was found to range from 1.4 to 18.4mol% depending on the expression levels of down-regulated genes. The results show that CRISPRi is a feasible method to simultaneously manipulate multiple genes in E. coli.

Succinic semialdehyde reductase Gox1801 from Gluconobacter oxydans in comparison to other succinic semialdehyde-reducing enzymes

Gluconobacter oxydans is an industrially important bacterium that possesses many uncharacterized oxidoreductases, which might be exploited for novel biotechnological applications. In this study, gene gox1801 was homologously overexpressed in G. oxydans and it was found that the relative expression of gox1801 was 13-fold higher than that in the control strain. Gox1801 was predicted to belong to the 3-hydroxyisobutyrate dehydrogenase-type proteins. The purified enzyme had a native molecular mass of 134 kDa and forms a homotetramer. Analysis of the enzymatic activity revealed that Gox1801 is a succinic semialdehyde reductase that used NADH and NADPH as electron donors. Lower activities were observed with glyoxal, methylglyoxal, and phenylglyoxal. The enzyme was compared to the succinic semialdehyde reductase GsSSAR from Geobacter sulfurreducens and the γ-hydroxybutyrate dehydrogenase YihU from Escherichia coli K-12. The comparison revealed that Gox1801 is the first enzyme from an aerobic bacterium reducing succinic semialdehyde with high catalytic efficiency. As a novel succinic semialdehyde reductase, Gox1801 has the potential to be used in the biotechnological production of γ-hydroxybutyrate.

Poly(3-hydroxypropionate): a promising alternative to fossil fuel-based materials

Polyhydroxyalkanoates (PHAs) are storage compounds synthesized by numerous microorganisms and have attracted the interest of industry since they are biobased and biodegradable alternatives to fossil fuel-derived plastics. Among PHAs, poly(3-hydroxypropionate) [poly(3HP)] has outstanding material characteristics and exhibits a large variety of applications. As it is not brittle like, e.g., the best-studied PHA, poly(3-hydroxybutyrate) [poly(3HB)], it can be used as a plasticizer in blends to improve their properties. Furthermore, 3-hydroxypropionic acid (3HP) is considered likely to become one of the new industrial building blocks, and it can be obtained from poly(3HP) by simple hydrolysis. Unfortunately, no natural organism is known to accumulate poly(3HP) so far. Thus, several efforts have been made to engineer genetically modified organisms capable of synthesizing the homopolymer or copolymers containing 3HP. In this review, the achievements made so far in efforts to obtain biomass which has accumulated poly(3HP) or 3HP-containing copolymers, as well as the properties of these polyesters and their applications, are compiled and evaluated.

Engineering of a xylose metabolic pathway in Rhodococcus strains

The two metabolically versatile actinobacteria Rhodococcus opacus PD630 and R. jostii RHA1 can efficiently convert diverse organic substrates into neutral lipids mainly consisting of triacylglycerol (TAG), the precursor of energy-rich hydrocarbon. Neither, however, is able to utilize xylose, the important component present in lignocellulosic biomass, as the carbon source for growth and lipid accumulation. In order to broaden their substrate utilization range, the metabolic pathway of d-xylose utilization was introduced into these two strains. This was accomplished by heterogenous expression of two well-selected genes, xylA, encoding xylose isomerase, and xylB, encoding xylulokinase from Streptomyces lividans TK23, under the control of the tac promoter with an Escherichia coli-Rhodococcus shuttle vector. The recombinant R. jostii RHA1 bearing xylA could grow on xylose as the sole carbon source, and additional expression of xylB further improved the biomass yield. The recombinant could consume both glucose and xylose in the sugar mixture, although xylose metabolism was still affected by the presence of glucose. The xylose metabolic pathway was also introduced into the high-lipid-producing strain R. opacus PD630 by expression of xylA and xylB. Under nitrogen-limited conditions, the fatty acid composition was determined, and lipid produced from xylose by recombinants of R. jostii RHA1 and R. opacus PD630 carrying xylA and xylB represented up to 52.5% and 68.3% of the cell dry weight (CDW), respectively. This work demonstrates that it is feasible to produce lipid from the sugars, including xylose, derived from renewable feedstock by genetic modification of rhodococcus strains.

Hyperproduction of poly(4-hydroxybutyrate) from glucose by recombinant Escherichia coli

Background

Poly(4-hydroxybutyrate) [poly(4HB)] is a strong thermoplastic biomaterial with remarkable mechanical properties, biocompatibility and biodegradability. However, it is generally synthesized when 4-hydroxybutyrate (4HB) structurally related substrates such as γ-butyrolactone, 4-hydroxybutyrate or 1,4-butanediol (1,4-BD) are provided as precursor which are much more expensive than glucose. At present, high production cost is a big obstacle for large scale production of poly(4HB).

Results

Recombinant Escherichia coli strain was constructed to achieve hyperproduction of poly(4-hydroxybutyrate) [poly(4HB)] using glucose as a sole carbon source. An engineering pathway was established in E. coli containing genes encoding succinate degradation of Clostridium kluyveri and PHB synthase of Ralstonia eutropha. Native succinate semialdehyde dehydrogenase genes sad and gabD in E. coli were both inactivated to enhance the carbon flux to poly(4HB) biosynthesis. Four PHA binding proteins (PhaP or phasins) including PhaP1, PhaP2, PhaP3 and PhaP4 from R. eutropha were heterologously expressed in the recombinant E. coli, respectively, leading to different levels of improvement in poly(4HB) production. Among them PhaP1 exhibited the highest capability for enhanced polymer synthesis. The recombinant E. coli produced 5.5 g L-1 cell dry weight containing 35.4% poly(4HB) using glucose as a sole carbon source in a 48 h shake flask growth. In a 6-L fermentor study, 11.5 g L-1 cell dry weight containing 68.2% poly(4HB) was obtained after 52 h of cultivation. This was the highest poly(4HB) yield using glucose as a sole carbon source reported so far. Poly(4HB) was structurally confirmed by gas chromatographic (GC) as well as 1H and 13C NMR studies.

Conclusions

Significant level of poly(4HB) biosynthesis from glucose can be achieved in sad and gabD genes deficient strain of E. coli JM109 harboring an engineering pathway encoding succinate degradation genes and PHB synthase gene, together with expression of four PHA binding proteins PhaP or phasins, respectively. Over 68% poly(4HB) was produced in a fed-batch fermentation process, demonstrating the feasibility for enhanced poly(4HB) production using the recombinant strain for future cost effective commercial development.

Poly-3-hydroxybutyrate metabolism in the type II methanotroph Methylocystis parvus OBBP

Differences in carbon assimilation pathways and reducing power requirements among organisms are likely to affect the role of the storage polymer poly-3-hydroxybutyrate (PHB). Previous researchers have demonstrated that PHB functions as a sole growth substrate in aerobic cultures enriched on acetate during periods of carbon deficiency, but it is uncertain how C(1) metabolism affects the role of PHB. In the present study, the type II methanotroph Methylocystis parvus OBBP did not replicate using stored PHB in the absence of methane, even when all other nutrients were provided in excess. When PHB-rich cultures of M. parvus OBBP were deprived of carbon and nitrogen for 48 h, they did not utilize significant amounts of stored PHB, and neither cell concentrations nor concentrations of total suspended solids changed significantly. When methane and nitrogen both were present, PHB and methane were consumed simultaneously. Cells with PHB had significantly higher specific growth rates than cells lacking PHB. The addition of formate (a source of reducing power) to PHB-rich cells delayed PHB consumption, but the addition of glyoxylate (a source of C(2) units) did not. This and results from other researchers suggest that methanotrophic PHB metabolism is linked to the supply of reducing power as opposed to the supply of C(2) units for synthesis.

Efficient polyhydroxyalkanoates production from a waste-activated sludge alkaline fermentation liquid by activated sludge submitted to the aerobic feeding and discharge process

It was reported in our previous publication that the accumulation of short-chain fatty acids (SCFA) was significantly enhanced when waste-activated sludge (WAS) was anaerobically fermented at pH 10.0 (Yuan, et al., Environ. Sci. Technol. 2006, 40, 2025-2029). In this paper, the production of polyhydroxyalkanoate (PHA) by activated sludge with an aerobic feeding and discharge (AFD) process was investigated by the use of WAS alkaline fermentation liquid as the carbon source. It was observed that compared with other PHA synthesis processes reported in the literature, the AFD process showed the highest PHA production. The PHA content in sludge reached 72.9% when activated sludge was submitted to the AFD process. This was the highest PHA content obtained so far by activated sludge using wastes as the renewable carbon source. Although nitrogen and phosphorus were released into the WAS alkaline fermentation liquid, their presence did not affect PHA synthesis, which indicates that it is unnecessary to remove the released nitrogen and phosphorus, and the fermentation liquid can be used directly for PHA production. The accumulated PHAwas mainly composed of 3-hydroxybutyrate (3HB) (73.5 mmol C%), 3-hydroxyvalerate (3HV) (24.3 mmol C%), and 3-hydroxy-2-methylvalerate (3H2MV) (2.2 mmol C%). Further investigation showed that SCFA rather than protein and carbohydrate in the alkaline fermentation liquid made the main contribution to PHA production. The PHA produced from WAS alkaline fermentation liquid had a molecular weight of 8.5 x 10(5) Da and a melting point of 101.4 degrees C. Analysis using the 16S rRNA gene clone library revealed that gamma-Proteobacteria, alpha-Proteobacteria, and beta-Proteobacteria were the dominant microorganisms in the PHA production system.

Biosynthesis of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) copolymer by Cupriavidus sp. USMAA1020 isolated from Lake Kulim, Malaysia

Cupriavidus sp. USMAA1020 was isolated from Malaysian environment and able to synthesize poly(3-hydroxybutyrate-co-4-hydroxybutyrate), [P(3HB-co-4HB)] when grown on gamma-butyrolactone as the sole carbon source. The polyester was purified from freeze-dried cells and analyzed by nuclear magnetic resonance (NMR) spectroscopy. 1H and 13C NMR results confirmed the presence of 3HB and 4HB monomers. In a one-step cultivation process, P(3HB-co-4HB) accumulation by Cupriavidus sp. USMAA1020 was affected by carbon to nitrogen ratio (C/N). A two-step cultivation process accumulated P(3HB-co-4HB) copolyester with a higher 4HB fraction (53 mol%) in nitrogen-free mineral medium containing gamma-butyrolactone. The biosynthesis of P(3HB-co-4HB) was also achieved by using 4-hydroxybutyric acid and alkanediol as 1,4-butanediol. The composition of copolyesters varied from 32 to 51 mol% 4HB, depending on the carbon sources supplied. The copolyester produced by Cupriavidus sp. USMAA1020 has a random sequence distribution of 3-hydroxybutyrate (3HB) and 4-hydroxybutyrate (4HB) units when analyzed by nuclear magnetic resonance (NMR) spectroscopy. When gamma-butyrolactone was used as the sole carbon source, the 4HB fraction in copolyester increased from 25 to 60 mol% as the concentration of gamma-butyrolactone in the culture medium increased from 2.5 g/L to 20.0 g/L.