A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation

Bacterial polyhydroxyalkanoates (PHAs) have emerged as promising eco-friendly alternatives to petroleum-based plastics since they are synthesized from renewable resources and offer exceptional properties. However, their production is limited to the stationary growth phase under nutrient-limited conditions, requiring customized strategies and costly two-phase bioprocesses. In this study, we tackle these challenges by employing a model-driven approach to reroute carbon flux and remove regulatory constraints using synthetic biology. We construct a collection of Pseudomonas putida-overproducing strains at the expense of plastics and lignin-related compounds using growth-coupling approaches. PHA production was successfully achieved during growth phase, resulting in the production of up to 46% PHA/cell dry weight while maintaining a balanced carbon-to-nitrogen ratio. Our strains are additionally validated under an upcycling scenario using enzymatically hydrolyzed polyethylene terephthalate as a feedstock. These findings have the potential to revolutionize PHA production and address the global plastic crisis by overcoming the complexities of traditional PHA production bioprocesses.

High natural PHA production from acetate in Cobetia sp. MC34 and Cobetia marina DSM 4741T and in silico analyses of the genus specific PhaC2 polymerase variant

BACKGROUND

Several members of the bacterial Halomonadacea family are natural producers of polyhydroxyalkanoates (PHA), which are promising materials for use as biodegradable bioplastics. Type-strain species of Cobetia are designated PHA positive, and recent studies have demonstrated relatively high PHA production for a few strains within this genus. Industrially relevant PHA producers may therefore be present among uncharacterized or less explored members. In this study, we characterized PHA production in two marine Cobetia strains. We further analyzed their genomes to elucidate pha genes and metabolic pathways which may facilitate future optimization of PHA production in these strains.

RESULTS

Cobetia sp. MC34 and Cobetia marina DSM 4741T were mesophilic, halotolerant, and produced PHA from four pure substrates. Sodium acetate with- and without co-supplementation of sodium valerate resulted in high PHA production titers, with production of up to 2.5 g poly(3-hydroxybutyrate) (PHB)/L and 2.1 g poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)/L in Cobetia sp. MC34, while C. marina DSM 4741T produced 2.4 g PHB/L and 3.7 g PHBV/L. Cobetia marina DSM 4741T also showed production of 2.5 g PHB/L from glycerol. The genome of Cobetia sp. MC34 was sequenced and phylogenetic analyses revealed closest relationship to Cobetia amphilecti. PHA biosynthesis genes were located at separate loci similar to the arrangement in other Halomonadacea. Further genome analyses revealed some differences in acetate- and propanoate metabolism genes between the two strains. Interestingly, only a single PHA polymerase gene (phaC2) was found in Cobetia sp. MC34, in contrast to two copies (phaC1 and phaC2) in C. marina DSM 4741T. In silico analyses based on phaC genes show that the PhaC2 variant is conserved in Cobetia and contains an extended C-terminus with a high isoelectric point and putative DNA-binding domains.

CONCLUSIONS

Cobetia sp. MC34 and C. marina DSM 4741T are natural producers of PHB and PHBV from industrially relevant pure substrates including acetate. However, further scale up, optimization of growth conditions, or use of metabolic engineering is required to obtain industrially relevant PHA production titers. The putative role of the Cobetia PhaC2 variant in DNA-binding and the potential implications remains to be addressed by in vitro- or in vivo methods.

Photoautotrophic and Mixotrophic Cultivation of Polyhydroxyalkanoate-Accumulating Microalgae Consortia Selected under Nitrogen and Phosphate Limitation

Microalgae consortia were photoautotrophically cultivated in sequencing batch photobioreactors (SBPRs) with an alteration of the normal growth and starvation (nutrient limitation) phases to select consortia capable of polyhydroxyalkanoate (PHA) accumulation. At the steady state of SBPR operation, the obtained microalgae consortia, selected under nitrogen and phosphate limitation, accumulated up to 11.38% and 10.24% of PHA in their biomass, which was identified as poly(3-hydroxybutyrate) (P3HB). Photoautotrophic and mixotrophic batch cultivation of the selected microalgae consortia was conducted to investigate the potential of biomass and PHA production. Sugar source supplementation enhanced the biomass and PHA production, with the highest PHA contents of 10.94 and 6.2%, and cumulative PHA productions of 100 and 130 mg/L, with this being achieved with sugarcane juice under nitrogen and phosphate limitation, respectively. The analysis of other macromolecules during batch cultivation indicated a high content of carbohydrates and lipids under nitrogen limitation, while higher protein contents were detected under phosphate limitation. These results recommended the selected microalgae consortia as potential tools for PHA and bioresource production. The mixed-culture non-sterile cultivation system developed in this study provides valuable information for large-scale microalgal PHA production process development following the biorefinery concept.

Production of Polyhydroxyalkanoates (PHAs) by Vibrio alginolyticus Strains Isolated from Salt Fields

Vibrio alginolyticus is a halophilic organism usually found in marine environments. It has attracted attention as an opportunistic pathogen of aquatic animals and humans, but there are very few reports on polyhydroxyalkanoate (PHA) production using V. alginolyticus as the host. In this study, two V. alginolyticus strains, LHF01 and LHF02, isolated from water samples collected from salt fields were found to produce poly(3-hydroxybutyrate) (PHB) from a variety of sugars and organic acids. Glycerol was the best carbon source and yielded the highest PHB titer in both strains. Further optimization of the NaCl concentration and culture temperature improved the PHB titer from 1.87 to 5.08 g/L in V. alginolyticus LHF01. In addition, the use of propionate as a secondary carbon source resulted in the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). V. alginolyticus LHF01 may be a promising host for PHA production using cheap waste glycerol from biodiesel refining.

Biomedical Applications of Biomolecules Isolated from Methanotrophic Bacteria in Wastewater Treatment Systems

Wastewater treatment plants and other remediation facilities serve important roles, both in public health, but also as dynamic research platforms for acquiring useful resources and biomolecules for various applications. An example of this is methanotrophic bacteria within anaerobic digestion processes in wastewater treatment plants. These bacteria are an important microbial source of many products including ectoine, polyhydroxyalkanoates, and methanobactins, which are invaluable to the fields of biotechnology and biomedicine. Here we provide an overview of the methanotrophs' unique metabolism and the biochemical pathways involved in biomolecule formation. We also discuss the potential biomedical applications of these biomolecules through creation of beneficial biocompatible products including vaccines, prosthetics, electronic devices, drug carriers, and heart stents. We highlight the links between molecular biology, public health, and environmental science in the advancement of biomedical research and industrial applications using methanotrophic bacteria in wastewater treatment systems.

Established and Emerging Producers of PHA: Redefining the Possibility

The polyhydroxyalkanoate was discovered almost around a century ago. Still, all the efforts to replace the traditional non-biodegradable plastic with much more environmentally friendly alternative are not enough. While the petroleum-based plastic is like a parasite, taking over the planet rapidly and without any feasible cure, its perennial presence has made the ocean a floating island of life-threatening debris and has flooded the landfills with toxic towering mountains. It demands for an immediate solution; most resembling answer would be the polyhydroxyalkanoates. The production cost is yet one of the significant challenges that various corporate is facing to replace the petroleum-based plastic. To deal with the economic constrain better strain, better practices, and a better market can be adopted for superior results. It demands for systems for polyhydroxyalkanoate production namely bacteria, yeast, microalgae, and transgenic plants. Solely strains affect more than 40% of overall production cost, playing a significant role in both upstream and downstream processes. The highly modifiable nature of the biopolymer provides the opportunity to replace the petroleum plastic in almost all sectors from food packaging to medical industry. The review will highlight the recent advancements and techno-economic analysis of current commercial models of polyhydroxyalkanoate production. Bio-compatibility and the biodegradability perks to be utilized highly efficient in the medical applications gives ample reason to tilt the scale in the favor of the polyhydroxyalkanoate as the new conventional and sustainable plastic.

Properties of degradable polyhydroxyalkanoates with different monomer compositions

PURPOSE

To synthesize and investigate polyhydroxyalkanoates (PHAs) with different monomer composition and percentages and polymer films prepared from them.

RESULTS

Various PHAs: homopolymer poly-3-hydroxybutyrate P(3HB) and 2-, 3-, and 4-component copolymers comprising various combinations of 3-hydroxybutyrate (3HB), 3-hydroxyvalerate (3HV), 4-hydroxybutyrate (4HB), and 3-hydroxyhexanoate (3HHx) monomers were synthesized under specialized conditions. Relationships were found between the monomer composition of PHAs and their molecular-weight and thermal properties and degree of crystallinity. All copolymers had decreased weight average molecular weights, Mw (to 390-600 kDa), and increased values of polydispersity (3.2-4.6) compared to the P(3HB). PHA copolymers showed different thermal behavior: an insignificant decrease in Tmelt and the presence of the second peak in the melting region and changes in parameters of crystallization and glass transition. At the same time, they retained thermostability, and the difference between Tmelt and Tdegr was at least 100-120 °C. Incorporation of 4HB, 3HV, and 3HHx monomer units into the 3-hydroxybutyrate chain caused changes in the amorphous to crystalline ratio and decreased the degree of crystallinity (Cx) to 20-40%. According to the degree to which the monomers reduced crystallinity, they were ranked as follows: 4HB - 3HHx - 3HV. A unique set of films was produced; their surface properties and physical/mechanical properties were studied as dependent on PHA composition; monomers other than 3-hydroxybutyrate were found to enhance hydrophilicity, surface development, and elasticity of polymer films.

CONCLUSION

An innovative set of PHA copolymers was synthesized and solution-cast films were prepared from them; the copolymers and films were investigated as dependent on polymer chemical composition. Results obtained in the present study contribute to the solution of a critical issue of producing degradable polymer materials.

Cost-Effective Production of L-DOPA by Tyrosinase-Immobilized Polyhydroxyalkanoate Nanogranules in Engineered Halomonas bluephagenesis TD01

3,4-dihydroxyphenyl-L-alanine (L-DOPA) is a preferred drug for Parkinson's disease, with an increasing demand worldwide that mainly relies on costly and environmentally problematic chemical synthesis. Yet, biological L-DOPA production is unfeasible at the industrial scale due to its low L-DOPA yield and high production cost. In this study, low-cost Halomonas bluephagenesis TD01 was engineered to produce tyrosinase TyrVs-immobilized polyhydroxyalkanoate (PHA) nanogranules in vivo, with the improved PHA content and increased immobilization efficiency of TyrVs accounting for 6.85% on the surface of PHA. A higher L-DOPA-forming monophenolase activity of 518.87 U/g PHA granules and an L-DOPA concentration of 974.36 mg/L in 3 h catalysis were achieved, compared to those of E. coli. Together with the result of L-DOPA production directly by cell lysates containing PHA-TyrVs nanogranules, our study demonstrated the robust and cost-effective production of L-DOPA by H. bluephagenesis, further contributing to its low-cost industrial production based on next-generation industrial biotechnology (NGIB).

Production and characterization of poly 3-hydroxybutyrate-co-3-hydroxyvalerate in wheat starch wastewater and its potential for nanoparticle synthesis

Polyhydroxyalkanoates (PHAs) are polymers with biodegradable and biocompatible properties accumulated in a wide variety of bacterial strains. In the present study, active sludge, wheat starch wastewater (WSW), and oil wastewater were used for the isolation and screening of PHA-accumulating bacteria. WSW was then implemented as a cheap and economical culture medium for the production of PHAs by the selected isolate. The extracted PHA was characterized, and the capability of produced biopolymer for preparing nanoparticles was evaluated. Based on the results, 96 different bacterial isolates were obtained, of which the strains isolated from WSW demonstrated the highest PHA-accumulation capability. The maximum PHA content of 3.07 g/l (59.50% of dry cell weight) was obtained by strain N6 in 21 h. The selected strain was identified by molecular approaches as Bacillus cereus. Afterward, the physicochemical characterization of an accumulated biopolymer was specified as a PHBV copolymer. Finally, spherical homogenous PHBV nanoparticles with a size of 137 nm were achieved. The PHBV nanoparticles showed a suitable small size and good zeta potential for medical applications. Hence, it can be concluded that isolated wild strain (B. cereus) has the potential exploitation capability for cost-effective PHBV production using the WSW.

Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate

Polyhydroxyalkanoates (PHAs) are biodegradable bioplastics that can be manufactured sustainably and represent a promising green alternative to petrochemical-based plastics. Here, we describe the complete genome of a new marine PHA-producing bacterium-Photobacterium ganghwense (strain C2.2), which we have isolated from the Black Sea seashore. This new isolate is psychrotolerant and accumulates PHA when glycerol is provided as the main carbon source. Transmission electron microscopy, specific staining with Nile Red visualized via epifluorescence microscopy and gas chromatography analysis confirmed the accumulation of PHA. This is the only PHA-producing Photobacterium for which we now have a complete genome sequence, allowing us to investigate the pathways for PHA production and other secondary metabolite synthesis pathways. The de novo assembly genome, obtained using open-source tools, comprises two chromosomes (3.5, 2 Mbp) and a megaplasmid (202 kbp). We identify the entire PHA synthesis gene cluster that encodes a class I PHA synthase, a phasin, a 3-ketothiolase, and an acetoacetyl-CoA reductase. No conventional PHA depolymerase was identified in strain C2.2, but a putative lipase with extracellular amorphous PHA depolymerase activity was annotated, suggesting that C2.2 is unable to degrade intracellular PHA. A complete pathway for the conversion of glycerol to acetyl-CoA was annotated, in accordance with its ability to convert glycerol to PHA. Several secondary metabolite biosynthetic gene clusters and a low number of genes involved in antibiotic resistance and virulence were also identified, indicating the strain's suitability for biotechnological applications.

Microbial Polyhydroxyalkanoates Granules: An Approach Targeting Biopolymer for Medical Applications and Developing Bone Scaffolds

Microbial polyhydroxyalkanoates (PHA) are proteinaceous storage granules ranging from 100 nm to 500 nm. Bacillus sp. serve as unique bioplastic sources of short-chain length and medium-chain length PHA showcasing properties such as biodegradability, thermostability, and appreciable mechanical strength. The PHA can be enhanced by adding functional groups to make it a more industrially useful biomaterial. PHA blends with hydroxyapatite to form nanocomposites with desirable features of compressibility. The reinforced matrices result in nanocomposites that possess significantly improved mechanical and thermal properties both in solid and melt states along with enhanced gas barrier properties compared to conventional filler composites. These superior qualities extend the polymeric composites' applications to aggressive environments where the neat polymers are likely to fail. This nanocomposite can be used in different industries as nanofillers, drug carriers for packaging essential hormones and microcapsules, etc. For fabricating a bone scaffold, electrospun nanofibrils made from biocomposite of hydroxyapatite and polyhydroxy butyrate, a form of PHA, can be incorporated with the targeted tissue. The other methods for making a polymer scaffold, includes gas foaming, lyophilization, sol-gel, and solvent casting method. In this review, PHA as a sustainable eco-friendly NextGen biomaterial from bacterial sources especially Bacillus cereus, and its application for fabricating bone scaffold using different strategies for bone regeneration have been discussed.

Transcriptome Changes in Pseudomonas putida KT2440 during Medium-Chain-Length Polyhydroxyalkanoate Synthesis Induced by Nitrogen Limitation

Pseudomonas putida’s versatility and metabolic flexibility make it an ideal biotechnological platform for producing valuable chemicals, such as medium-chain-length polyhydroxyalkanoates (mcl-PHAs), which are considered the next generation bioplastics. This bacterium responds to environmental stimuli by rearranging its metabolism to improve its fitness and increase its chances of survival in harsh environments. Mcl-PHAs play an important role in central metabolism, serving as a reservoir of carbon and energy. Due to the complexity of mcl-PHAs’ metabolism, the manner in which P. putida changes its transcriptome to favor mcl-PHA synthesis in response to environmental stimuli remains unclear. Therefore, our objective was to investigate how the P. putida KT2440 wild type and mutants adjust their transcriptomes to synthesize mcl-PHAs in response to nitrogen limitation when supplied with sodium gluconate as an external carbon source. We found that, under nitrogen limitation, mcl-PHA accumulation is significantly lower in the mutant deficient in the stringent response than in the wild type or the rpoN mutant. Transcriptome analysis revealed that, under N-limiting conditions, 24 genes were downregulated and 21 were upregulated that were common to all three strains. Additionally, potential regulators of these genes were identified: the global anaerobic regulator (Anr, consisting of FnrA, Fnrb, and FnrC), NorR, NasT, the sigma⁵⁴-dependent transcriptional regulator, and the dual component NtrB/NtrC regulator all appear to play important roles in transcriptome rearrangement under N-limiting conditions. The role of these regulators in mcl-PHA synthesis is discussed.

Polyhydroxyalkanoates: Next generation natural biomolecules and a solution for the world's future economy

Petrochemical plastics have become a cause of pollution for decades and finding alternative plastics that are environmental friendly. Polyhydroxyalkanoate (PHA), a biopolyester produced by microbial cells, has characteristics (biocompatible, biodegradable, non-toxic) that make it appropriate as a biodegradable plastic substance. The different forms of PHA make it suitable to a wide choice of products, from packaging materials to biomedical applications. The major challenge in commercialization of PHA is the cost of manufacturing. There are a lot of factors that could affect the efficiency of a development method. The development of new strategic parameters for better synthesis, including consumption of low cost carbon substrates, genetic modification of PHA-producing strains, and fermentational strategies are discussed. Recently, many efforts have been made to develop a method for the cost-effective production of PHAs. The isolation, analysis as well as characterization of PHAs are significant factors for any developmental process. Due to the biodegradable and biocompatible properties of PHAs, they are majorly used in biomedical applications such as vascular grafting, heart tissue engineering, skin tissue repairing, liver tissue engineering, nerve tissue engineering, bone tissue engineering, cartilage tissue engineering and therapeutic carrier. The emerging and interesting area of research is the development of self-healing biopolymer that could significantly broaden the operational life and protection of the polymeric materials for a broad range of uses. Biodegradable and biocompatible polymers are considered as the green materials in place of petroleum-based plastics in the future.

Statistical augmentation of polyhydroxybutyrate production by Isoptericola variabilis: Characterization, moulding, in vitro cytocompatibility and biodegradability evaluation

This study aimed to explore the production of polyhydroxybutyrate (PHB), a polyhydroxyalkanoate (PHA), which has been widely considered as a potential substitute for the synthetic polymers. Among 53 actinomycete isolates, 11 of them were found to be PHB positive and the quantity of PHB from the positive isolates varied from 10.5 to 29.82 wt% on a dry cell weight basis. A strain designated as PPLAT 012, accumulated relatively higher PHB and has been identified as Isoptericola variabilis by 16S rRNA gene sequence analysis. An effort has also been made to optimize the PHB production by the hyper-producing strain using the conventional, one-factor-at-a-time, and statistical response surface methodologies and the maximum PHB production (46.18%) in DSMZ medium, amended with 12% glucose and 9% potassium nitrate with a pH of 7.0. Further, the characteristic properties such as processability, cytocompatibility and biodegradability of the extracted PHB was also demonstrated. The physical properties of the recovered PHB was further improved by blending with PLA and the resultant blends were characterized. The present investigation has demonstrated that the isolate, Isoptericola variabilis, could be utilized as a potential source for the production of PHB with desirable characteristics, suitable for biomedical applications.

Genome Mining Reveals the Biosynthetic Pathways of Polyhydroxyalkanoate and Ectoines of the Halophilic Strain Salinivibrio proteolyticus M318 Isolated from Fermented Shrimp Paste

Salinivibrio proteolyticus M318, a halophilic bacterium isolated from fermented shrimp paste, is able to produce polyhydroxyalkanoate (PHA) from different carbon sources. In this study, we report the whole-genome sequence of strain M138, which comprises 2 separated chromosomes and 2 plasmids, and the complete genome contains 3,605,935 bp with an average GC content of 49.9%. The genome of strain M318 contains 3341 genes, 98 tRNA genes, and 28 rRNA genes. The 16S rRNA gene sequence and average nucleotide identity analysis associated with morphological and biochemical tests showed that this strain has high homology to the reference strain Salinivibrio proteolyticus DSM 8285. The genes encoding key enzymes for PHA and ectoine synthesis were identified from the bacterial genome. In addition, the TeaABC transporter responsible for ectoine uptake from the environment and the operon doeABXCD responsible for the degradation of ectoine were also detected. Strain M318 was able to produce poly(3-hydroxybutyrate) [P(3HB)] from different carbon sources such as glycerol, maltose, glucose, fructose, and starch. The ability to produce ectoines at different NaCl concentrations was investigated. High ectoine content of 26.2% of cell dry weight was obtained by this strain at 18% NaCl. This report provides genetic information regarding adaptive mechanisms of strain M318 to stress conditions, as well as new knowledge to facilitate the application of this strain as a bacterial cell factory for the production of PHA and ectoine.

Cyanobacterial Polyhydroxyalkanoates: A Sustainable Alternative in Circular Economy

Conventional petrochemical plastics have become a serious environmental problem. Its unbridled use, especially in non-durable goods, has generated an accumulation of waste that is difficult to measure, threatening aquatic and terrestrial ecosystems. The replacement of these plastics with cleaner alternatives, such as polyhydroxyalkanoates (PHA), can only be achieved by cost reductions in the production of microbial bioplastics, in order to compete with the very low costs of fossil fuel plastics. The biggest costs are carbon sources and nutrients, which can be appeased with the use of photosynthetic organisms, such as cyanobacteria, that have a minimum requirement for nutrients, and also using agro-industrial waste, such as the livestock industry, which in turn benefits from the by-products of PHA biotechnological production, for example pigments and nutrients. Circular economy can help solve the current problems in the search for a sustainable production of bioplastic: reducing production costs, reusing waste, mitigating CO2, promoting bioremediation and making better use of cyanobacteria metabolites in different industries.

Microbial Polyhydroxyalkanoates and Nonnatural Polyesters

Microorganisms produce diverse polymers for various purposes such as storing genetic information, energy, and reducing power, and serving as structural materials and scaffolds. Among these polymers, polyhydroxyalkanoates (PHAs) are microbial polyesters synthesized and accumulated intracellularly as a storage material of carbon, energy, and reducing power under unfavorable growth conditions in the presence of excess carbon source. PHAs have attracted considerable attention for their wide range of applications in industrial and medical fields. Since the first discovery of PHA accumulating bacteria about 100 years ago, remarkable advances have been made in the understanding of PHA biosynthesis and metabolic engineering of microorganisms toward developing efficient PHA producers. Recently, nonnatural polyesters have also been synthesized by metabolically engineered microorganisms, which opened a new avenue toward sustainable production of more diverse plastics. Herein, the current state of PHAs and nonnatural polyesters is reviewed, covering mechanisms of microbial polyester biosynthesis, metabolic pathways, and enzymes involved in biosynthesis of short-chain-length PHAs, medium-chain-length PHAs, and nonnatural polyesters, especially 2-hydroxyacid-containing polyesters, metabolic engineering strategies to produce novel polymers and enhance production capabilities and fermentation, and downstream processing strategies for cost-effective production of these microbial polyesters. In addition, the applications of PHAs and prospects are discussed.

Biodiversity and Habitats of Polar Region Polyhydroxyalkanoic Acid-Producing Bacteria: Bioprospection by Popular Screening Methods

Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as biodegradable versions of common plastics. PHA-producing microbes are therefore in great demand and a plethora of different environments, especially extreme habitats, have been probed for the presence of PHA-accumulators. However, the polar region has been neglected in this regard, probably due to the low accessibility of the sampling material and unusual cultivation regime. Here, we present the results of a screening procedure involving 200 bacterial strains isolated from 25 habitats of both polar regions. Agar-based tests, microscopy, and genetic methods were conducted to elucidate the biodiversity and potential of polar-region PHA-accumulators. Microscopic observation of Nile Red stained cells proved to be the most reliable screening method as it allowed to confirm the characteristic bright orange glow of the Nile Red–PHA complex as well as the typical morphology of the PHA inclusions. Psychrophilic PHA-producers belonged mostly to the Comamonadaceae family (Betaproteobacteria) although actinobacterial PHA synthesizers of the families, Microbacteriaceae and Micrococcaceae also featured prominently. Glacial and postglacial habitats as well as developed polar region soils, were evaluated as promising for PHA-producer bioprospection. This study highlights the importance of psychrophiles as biodiverse and potent polyhydroxyalkanoate sources for scientific and application-aimed research.

The Degradation of Phenanthrene, Pyrene, and Fluoranthene and Its Conversion into Medium-Chain-Length Polyhydroxyalkanoate by Novel Polycyclic Aromatic Hydrocarbon-Degrading Bacteria

Screening of high-efficient polycyclic aromatic hydrocarbon (PAH)-degrading bacteria is important due to environmental contamination by PAHs. In this study, sediment contaminated with phenanthrene (Phe), pyrene (Pyr), and fluoranthene (Fluo) was used as a source of bacteria. The ability of these isolated bacteria to convert PAHs into valuable products was determined. Based on a primary screening, 20 bacterial isolates were obtained; however, only three strains showed a good PAH-degrading ability, and were identified as Pseudomonas aeruginosa, Pseudomonas sp., and Ralstonia sp. PAH-degrading genes were detected in all isolates. Notably, all selected strains could degrade PAHs using the ortho or meta cleavage pathways due to the presence of catechol dioxygenase genes. The ability of isolated strains to convert PAHs into polyhydroxyalkanoate (PHA) was also evaluated in both single and mixed cultures. Single cultures of P. aeruginosa PAH-P02 showed 100% degradation of PAHs, with the highest biomass (1.27 ± 0.02 g l^-1) and PHA content (38.20 ± 1.92% dry cell weight). However, degradative ability and PHA production were decreased when mixtures of PAHs were used. This study showed that P. aeruginosa, Pseudomonas sp., and Ralstonia sp. were able to degrade PAHs and convert them into medium-chain-length (mcl)-PHA. A high content of 3-hydroxydecanoate (3HD, C10) was observed in this study. The formation of mcl-PHA with high 3HD content from Pyr and Fluo, and the assessment of mixed cultures converting PAHs to mcl-PHA, were novel contributions.

RSM-GA Based Optimization of Bacterial PHA Production and In Silico Modulation of Citrate Synthase for Enhancing PHA Production

The inexhaustible nature and biodegradability of bioplastics like polyhydroxyalkanoates (PHAs) make them suitable assets to replace synthetic plastics. The eventual fate of these eco-friendly and non-toxic bioplastics relies upon the endeavors towards satisfying cost and, in addition, execution necessity. In this study, we utilized and statistically optimized different food (kitchen-/agro-) waste as a sole carbon/nitrogen source for the production of PHA at a reduced cost, indicating a proficient waste administration procedure. Seven different types of kitchen-/agro-waste were used as unique carbon source and four different types of nitrogen source were used to study their impact on PHA production by Bacillus subtilis MTCC 144. Among four different studied production media, mineral salt medium (MSM) (biomass: 37.7 g/L; cell dry weight: 1.8 g/L; and PHA: 1.54 g/L) was found most suitable for PHA production. Further, carbon and nitrogen components of MSM were optimized using one-factor-at-a-time experiments, and found that watermelon rind (PHA = 12.97 g/L) and pulse peel (PHA = 13.5 g/L) were the most suitable carbon and nitrogen sources, respectively, in terms of PHA (78.60%) recovery. The concentrations of these factors (sources) were statistically optimized using response surface methodology coupled with the genetic algorithm approach. Additionally, in order to enhance microbial PHA production, the interaction of citrate synthase, a key enzyme in the TCA cycle, with different known inhibitors was studied using in silico molecular docking approach. The inhibition of citrate synthase induces the blockage of the tricarboxylic cycle (TCA), thereby increasing the concentration of acetyl-CoA that helps in enhanced PHA production. Molecular docking of citrate synthase with different inhibitors of PubChem database revealed that hesperidin (PubChem compound CID ID 10621), generally present in citrus fruits, is the most efficient inhibitor of the TCA cycle with the binding score of –11.4 and warrants experimental validation. Overall, this study provides an efficient food waste management approach by reducing the production cost and enhancing the production of PHA, thereby lessening our reliance on petroleum-based plastics.

Proteomic Response of Pseudomonas putida KT2440 to Dual Carbon-Phosphorus Limitation during mcl-PHAs Synthesis

Pseudomonas putida KT2440, one of the best characterized pseudomonads, is a metabolically versatile producer of medium-chain-length polyhydroxyalkanoates (mcl-PHAs) that serves as a model bacterium for molecular studies. The synthesis of mcl-PHAs is of great interest due to their commercial potential. Carbon and phosphorus are the essential nutrients for growth and their limitation can trigger mcl-PHAs' production in microorganisms. However, the specific molecular mechanisms that drive this synthesis in Pseudomonas species under unfavorable growth conditions remain poorly understood. Therefore, the proteomic responses of Pseudomonas putida KT2440 to the limited carbon and phosphorus levels in the different growth phases during mcl-PHAs synthesis were investigated. The data indicated that biopolymers' production was associated with the cell growth of P. putida KT2440 under carbon- and phosphorus-limiting conditions. The protein expression pattern changed during mcl-PHAs synthesis and accumulation, and during the different physiological states of the microorganism. The data suggested that the majority of metabolic activities ceased under carbon and phosphorus limitation. The abundance of polyhydroxyalkanoate granule-associated protein (PhaF) involved in PHA synthesis increased significantly at 24 and 48 h of the cultivations. The activation of proteins belonging to the phosphate regulon was also detected. Moreover, these results indicated changes in the protein profiles related to amino acids metabolism, replication, transcription, translation, stress response mechanisms, transport or signal transduction. The presented data allowed the investigation of time-course proteome alterations in response to carbon and phosphorus limitation, and PHAs synthesis. This study provided information about proteins that can be potential targets in improving the efficiency of mcl-PHAs synthesis.

Design and optimization of poly(hydroxyalkanoate)s production plants using alternative substrates

In this work, we propose a Mixed Integer Nonlinear Programming (MINLP) model to determine the optimal design of a poly(hydroxyalkanoate)s (PHAs) production plant configuration. The superstructure based optimization model considers different carbon sources as raw material: glycerol (crude and purified), corn starch, cassava starch, sugarcane sucrose and sugarcane molasses. The PHA extraction section includes four alternatives: the use of enzyme, solvent, surfactant-NaOCl or surfactant-chelate. Model constraints include detailed capital cost for equipment, mass and energy balances, product specifications and operating bounds on process units. The resulting MINLP model maximizes the project net present value (NPV) as objective function and it is implemented in an equation oriented environment. Optimization results show the sugarcane-enzyme option as the most promising alternative (NPV = 75.01 million USD) for PHAs production with an energy consumption of 22.56 MJ/kg PHA and a production cost of 3.02 USD/kg PHA. Furthermore, an economic sensitivity analysis is performed.

Occurrence of non-toxic bioemulsifiers during polyhydroxyalkanoate production by Pseudomonas strains valorizing crude glycerol by-product

While screening for polyhydroxyalkanoate (PHA) producing strains, using glycerol rich by-product as carbon source, it was observed that extracellular polymers were also secreted into the culture broth. The scope of this study was to characterize both intracellular and extracellular polymers, produced by Pseudomonas putida NRRL B-14875 and Pseudomonas chlororaphis DSM 50083, mostly focusing on those novel extracellular polymers. It was found that they fall into the class of bioemulsifiers (BE), as they showed excellent emulsion stability against different hydrocarbons/oils at various pH conditions, temperature and salinity concentrations. Cytotoxicity tests revealed that BE produced by P. chlororaphis inhibited the growth of highly pigmented human melanoma cells (MNT-1) by 50% at concentrations between 150 and 200 μg/mL, while no effect was observed on normal skin primary keratinocytes and melanocytes. This is the first study reporting mcl-PHA production by P. putida NRRL B-14785 and bioemulsifier production from both P. putida and P. chlororaphis strains.

Effect of thermal hydrolysis pretreatment on volatile fatty acids production in sludge acidification and subsequent polyhydroxyalkanoates production

The study compared the differences in VFAs production between raw sludge and thermal hydrolyzed sludge (TH-sludge) at different temperature (35 °C and 55 °C) in four semi-continuous acidification reactors. Optimal VFAs yield was obtained from TH-sludge at 35 °C (0.22 gVFA_COD/gVS), 44.6% higher than raw sludge at 35 °C, since the advantage of TH-sludge in SCOD solubilization overcame its disadvantage of lower carbon biodegradability. Moreover, high temperature (55 °C) was proved to aid the acidification of raw sludge by 15.7% (in Y_VFAs), but inhibit that of TH-sludge by 12.2%, mainly due to the suppressed microbial activities under heat. Microbial community analysis showed that TH-sludge had a larger proportion of acidogenic microbes than raw sludge, mainly attributing to the increase of Selenomonadales (37.3% vs. 3.7%); high temperature enriched thermophilic proteolytic microbes, Anaerobaculum and Coprothermobacter. Finally, optimal acidified liquid from TH-sludge at 35 °C was applied for PHAs production and achieved a competitive yield of 34.6% PHAs/DCW.

Optimal iron concentrations for growth-associated polyhydroxyalkanoate biosynthesis in the marine photosynthetic purple bacterium Rhodovulum sulfidophilum under photoheterotrophic condition

Polyhydroxyalkanoates (PHAs) are a group of natural biopolyesters that resemble petroleum-derived plastics in terms of physical properties but are less harmful biologically to the environment and humans. Most of the current PHA producers are heterotrophs, which require expensive feeding materials and thus contribute to the high price of PHAs. Marine photosynthetic bacteria are promising alternative microbial cell factories for cost-effective, carbon neutral and sustainable production of PHAs. In this study, Rhodovulum sulfidophilum, a marine photosynthetic purple nonsulfur bacterium with a high metabolic versatility, was evaluated for cell growth and PHA production under the influence of various media components found in previous studies. We evaluated iron, using ferric citrate, as another essential factor for cell growth and efficient PHA production and confirmed that PHA production in R. sulfidophilum was growth-associated under microaerobic and photoheterotrophic conditions. In fact, a subtle amount of iron (1 to 2 μM) was sufficient to promote rapid cell growth and biomass accumulation, as well as a high PHA volumetric productivity during the logarithmic phase. However, an excess amount of iron did not enhance the growth rate or PHA productivity. Thus, we successfully confirmed that an optimum concentration of iron, an essential nutrient, promotes cell growth in R. sulfidophilum and also enhances PHA utilization.

Kinetic understanding of nitrogen supply condition on biosynthesis of polyhydroxyalkanoate from benzoate by Pseudomonas putida KT2440

Nitrogen supply is critical to the synthesis of intracellular PHA in various bacteria. However, the specific role of the nitrogen in synthesizing PHA from benzoate, a lignin model compound use for the study of bacteria catabolism of aromatics, is still not clear. In this study, two culture conditions were maintained for Pseudomonas putida KT2440 to produce PHA using benzoate as a carbon source. Under nitrogen-limited and surplus conditions, the accumulation of PHA was to 37.3% and 0.25% of cell dry weight, respectively. A model fit to the kinetics of biomass growth and PHA accumulation showed good agreement with data. GC-MS and NMR showed that PHA contained six hydroxyl fatty acid monomers under nitrogen-limited conditions, while two monomers were identified under nitrogen surplus conditions. The average molecular weight of PHA increased after the nitrogen source was exhausted. These results provide a promising strategy for optimization of lignin to PHA yields.

Macroalgal biomass subcritical hydrolysates for the production of polyhydroxyalkanoate (PHA) by Haloferax mediterranei

Non-conventional carbon sources, such as macroalgae, are sustainable alternatives for large-scale production of biopolymers. The present study examined macroalgae-derived carbohydrates, as carbon sources for the production of polyhydroxyalkanoates (PHAs) by Haloferax mediterranei. Simulants of the hydrolysates of seven different macroalgal biomasses were prepared and the PHA production was studied. A maximum biomass concentration with maximum PHA content was detected in medium prepared from green macroalgae. The highest cell dry weight and PHA concentrations were 3.8 ± 0.2 g·L^-1 and 2.2 ± 0.12 g·L^-1 respectively when Haloferax mediterranei was grown in 25% (w/w) of Ulva sp. hydrolysate, at 42 °C temperature and initial pH of 7.2. Poly(3-hydroxy-butyrate-co-3-hydroxyvalerate was the major PHA constituent. The present study demonstrated that Ulva sp. is a promising feedstock for PHA production.

Genome sequence of Methylocystis hirsuta CSC1, a polyhydroxyalkanoate producing methanotroph

Polyhydroxyalkanoates (PHAs) are biodegradable plastics that can be produced by some methanotrophic organisms such as those of the genus Methylocystis. This allows the conversion of a detrimental greenhouse gas into an environmentally friendly high added‐value bioproduct. This study presents the genome sequence of Methylocystis hirsuta CSC1 (a high yield PHB producer). The genome comprises 4,213,043 bp in 4 contigs, with the largest contig being 3,776,027 bp long. Two of the other contigs are likely to correspond to large size plasmids. A total of 4,664 coding sequences were annotated, revealing a PHA production cluster, two distinct particulate methane monooxygenases with active catalytic sites, as well as a nitrogen fixation operon and a partial denitrification pathway.

Biosynthesis and characterization of a novel, biocompatible medium chain length polyhydroxyalkanoate by Pseudomonas mendocina CH50 using coconut oil as the carbon source

This study validated the utilization of triacylglycerides (TAGs) by Pseudomonas mendocina CH50, a wild type strain, resulting in the production of novel mcl-PHAs with unique physical properties. A PHA yield of 58% dcw was obtained using 20 g/L of coconut oil. Chemical and structural characterisation confirmed that the mcl-PHA produced was a terpolymer comprising of three different repeating monomer units, 3-hydroxyoctanoate, 3-hydroxydecanoate and 3-hydroxydodecanoate or P(3HO-3HD-3HDD). Bearing in mind the potential of P(3HO-3HD-3HDD) in biomedical research, especially in neural tissue engineering, in vitro biocompatibility studies were carried out using NG108-15 (neuronal) cells. Cell viability data confirmed that P(3HO-3HD-3HDD) supported the attachment and proliferation of NG108-15 and was therefore confirmed to be biocompatible in nature and suitable for neural regeneration.

Tuning culturing conditions towards the production of neutral lipids from lubricant-based wastewater in open mixed bacterial communities

Production of bacterial lipid-based biofuels using inexpensive substrates, as wastes, is an emerging approach. In this work, a selective process using carbon feast-famine cycles was applied to obtain an indigenous microbial community of hydrocarbon-degrading and lipid-accumulating bacteria, using a real lubricant-based wastewater as carbon source. In the conditions applied, the enriched bacterial community, dominated by members of the genus Rhodococcus, Pseudomonas and Acinetobacter, was able to degrade almost all hydrocarbons present in the wastewater within 24 h' incubation and to accumulate, although in low levels, triacylglycerol (TAG) (<5% of cell dry weight (CDW)) and polyhydroxyalkanoates (PHA) (3.8% ± 1.1% of the CDW) as well as an unknown lipid (29% ± 6% of CDW), presumably a wax ester-like compound. The influence of culture conditions, namely carbon and nitrogen concentrations (and C/N ratio) and cultivation time, on the amount and profile of produced storage compounds was further assessed using a statistical approach based on a central composite circumscribed design and surface response methodology. The regression analysis of the experimental design revealed that only nitrogen concentration and C/N ratio are significant for neutral lipid biosynthesis (p < 0.05). Maximum neutral lipid content, i.e. 33% (CDW basis), was achieved for the lowest carbon and nitrogen concentrations evaluated (10 g COD L^-1 and 0.02 g N L^-1). PHA accounted for less than 5% of CDW. In these conditions, neutral lipid content was mainly composed by TAG, about 70% (w/w). TAG precursors, namely monoacylglycerols (MAG), diacylglycerols (DAG) and fatty acids (FA), accounted for 22% of total neutral lipids and WE for about 7%. Nevertheless, according to the applied response surface model, further improvement of neutral lipids content is still possible if even lower nitrogen concentrations are used. The fatty acids detected in TAG extracts ranged from myristic acid (C14:0) to linoleic acid (C18:2), being the most abundant palmitic acid (C16:0), stearic acid (C18:0) and oleic acid (C18:1). This study shows the feasibility of combining treatment of hydrocarbon contaminated wastewater, herein demonstrated for lubricant-based wastewater, with the production of bacterial neutral lipids using open mixed bacterial communities. This approach can decrease the costs associated to both processes and contribute to a more sustainable waste management and production of lipid-based biofuels.

Mixed culture polyhydroxyalkanoate (PHA) synthesis from nutrient rich wet oxidation liquors

Organic waste residues can be hydrothermally treated to produce organic acid rich liquors. These hydrothermal liquors are a potential feedstock for polyhydroxyalkanoate (PHA) production. We investigated the effect of dissolved oxygen concentration and substrate feeding regimes on PHA accumulation and yield using two hydrothermal liquors derived from a mixture of primary and secondary municipal wastewater treatment sludge and food waste. The enriched culture accumulated a maximum of 41% PHA of cell dry weight within 7 h; which is among the highest reported for N and P rich hydrothermal liquors. Recovered PHA was 77% polyhydroxybutyrate and 23% polyhydroxyvalerate by mass. The families Rhodocyclaceae (84%) and Saprospiraceae (20.5%) were the dominant Proteobacteria (73%) in the enriched culture. The third most abundant bacterial genus, Bdellovibrio, includes species of known predators of PHA producers which may lead to suboptimal PHA accumulation. The PHA yield was directly proportional to DO concentration for ammonia stripped liquor (ASL) and inversely proportional to DO concentration for low strength liquor (LSL). The highest yield of 0.50 Cmol PHA/Cmol substrate was obtained for ASL at 25% DO saturation. A progressively increasing substrate feeding regime resulted in increased PHA yields. These findings demonstrate that substrate feeding regime and oxygen concentration can be used to control the PHA yield and accumulation rate thereby enhancing PHA production viability from nutrient rich biomass streams.

Metabolic engineering of Escherichia coli for the synthesis of polyhydroxyalkanoates using acetate as a main carbon source

BACKGROUND

High production cost of bioplastics polyhydroxyalkanoates (PHA) is a major obstacle to replace traditional petro-based plastics. To address the challenges, strategies towards upstream metabolic engineering and downstream fermentation optimizations have been continuously pursued. Given that the feedstocks especially carbon sources account up to a large portion of the production cost, it is of great importance to explore low cost substrates to manufacture PHA economically.

RESULTS

Escherichia coli was metabolically engineered to synthesize poly-3-hydroxybutyrate (P3HB), poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P3HB4HB), and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) using acetate as a main carbon source. Overexpression of phosphotransacetylase/acetate kinase pathway was shown to be an effective strategy for improving acetate assimilation and biopolymer production. The recombinant strain overexpressing phosphotransacetylase/acetate kinase and P3HB synthesis operon produced 1.27 g/L P3HB when grown on minimal medium supplemented with 10 g/L yeast extract and 5 g/L acetate in shake flask cultures. Further introduction succinate semialdehyde dehydrogenase, 4-hydroxybutyrate dehydrogenase, and CoA transferase lead to the accumulation of P3HB4HB, reaching a titer of 1.71 g/L with a 4-hydroxybutyrate monomer content of 5.79 mol%. When 1 g/L of α-ketoglutarate or citrate was added to the medium, P3HB4HB titer increased to 1.99 and 2.15 g/L, respectively. To achieve PHBV synthesis, acetate and propionate were simultaneously supplied and propionyl-CoA transferase was overexpressed to provide 3-hydroxyvalerate precursor. The resulting strain produced 0.33 g/L PHBV with a 3-hydroxyvalerate monomer content of 6.58 mol%. Further overexpression of propionate permease improved PHBV titer and 3-hydroxyvalerate monomer content to 1.09 g/L and 10.37 mol%, respectively.

CONCLUSIONS

The application of acetate as carbon source for microbial fermentation could reduce the consumption of food and agro-based renewable bioresources for biorefineries. Our proposed metabolic engineering strategies illustrate the feasibility for producing polyhydroxyalkanoates using acetate as a main carbon source. Overall, as an abundant and renewable resource, acetate would be developed into a cost-effective feedstock to achieve low cost production of chemicals, materials, and biofuels.

Analysis of Medium-Chain-Length Polyhydroxyalkanoate-Producing Bacteria in Activated Sludge Samples Enriched by Aerobic Periodic Feeding

Analysis of mixed microbial populations responsible for the production of medium-chain-length polyhydroxyalkanoates (MCL-PHAs) under periodic substrate feeding in a sequencing batch reactor (SBR) was conducted. Regardless of activated sludge samples and the different MCL alkanoic acids used as the sole external carbon substrate, denaturing gradient gel electrophoresis analysis indicated that Pseudomonas aeruginosa was the dominant bacterium enriched during the SBR process. Several P. aeruginosa strains were isolated from the enriched activated sludge samples. The isolates were subdivided into two groups, one that produced only MCL-PHAs and another that produced both MCL- and short-chain-length PHAs. The SBR periodic feeding experiments with five representative MCL-PHA-producing Pseudomonas species revealed that P. aeruginosa has an advantage over other species that enables it to become dominant in the bacterial community.

Engineering Escherichia coli for efficient coproduction of polyhydroxyalkanoates and 5-aminolevulinic acid

Single-cell biorefineries are an interesting strategy for using different components of feedstock to produce multiple high-value biochemicals. In this study, a strategy was applied to refine glucose and fatty acid to produce 5-aminolevulinic acid (ALA) and polyhydroxyalkanoates (PHAs). To express the ALA and PHAs dual-production system efficiently and stably, multiple copies of the poly-β-3-hydroxybutyrate (PHB) synthesis operon were integrated into the chromosome of Escherichia coli DH5αΔpoxB. The above strain harboring the ALA C5 synthesis pathway genes hemA and hemL resulted in coproduction of 38.2% PHB (cell dry weight, CDW) and 3.2 g/L extracellular ALA. To explore coproduction of ALA and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), the PHBV synthetic pathway was also integrated into engineered E. coli and coexpressed with hemA and hemL; cells produced 38.9% PHBV (CDW) with 10.3 mol% 3HV fractions and 3.0 g/L ALA. The coproduction of ALA with PHB and PHBV can improve the utilization of carbon sources and maximize the value derived from the feedstock.

Polyhydroxyalkanoates (PHA) production from fermented crude glycerol: Study on the conversion of 1,3-propanediol to PHA in mixed microbial consortia

Crude glycerol, a by-product from the biodiesel industry, can be converted by mixed microbial consortia into 1,3-propanediol (1,3-PDO) and volatile fatty acids. In this study, further conversion of these main products into polyhydroxyalkanoates (PHA) was investigated with the focus on 1,3-PDO. Two different approaches for the enrichment of PHA accumulating microbial consortia using an aerobic dynamic feeding strategy were applied. With the first approach, where nitrogen was present during the whole cycle, no net production of PHA from 1,3-PDO was observed in the fermented effluent, not even in a nitrogen-limited PHA accumulation assay. Nevertheless, experiments in synthetic substrates revealed that the conversion of 1,3-PDO to PHA was possible under nitrogen limiting conditions. Thus, a different enrichment strategy was formulated where nitrogen was limited during the feast phase to stimulate the storage response. Nitrogen was still supplied during the famine phase. With the latter strategy, a net production of PHA from 1,3-PDO was observed at a yield of 0.24 C_mol PHA/C_mol 1,3-PDO. The overall yield from the fermented effluent was 0.42 C_mol PHA/C_mol substrate. Overall, the PHA yield from 1,3-PDO seemed to be limited, similarly to when using glycerol as a substrate, by a decarboxylation step and accumulation of other storage polymers such as glycogen, and possibly, lipid inclusions.

Impact of phosphate limitation on PHA production in a feast-famine process

Double-limitation systems have shown to induce polyhydroxyalkanoates (PHA) production in chemostat studies limited in e.g. carbon and phosphate. In this work the impact of double substrate limitation on the enrichment of a PHA producing community was studied in a sequencing batch process. Enrichments at different C/P concentration ratios in the influent were established and the effect on the PHA production capacity and the enrichment community structure was investigated. Experimental results demonstrated that when a double substrate limitation is imposed at a C/P ratio in the influent in a range of 150 (C-mol/mol), the P-content of the biomass and the specific substrate uptake rates decreased. Nonetheless, the PHA storage capacity remained high (with a maximum of 84 wt%). At a C/P ratio of 300, competition in the microbial community is based on phosphate uptake, and the PHA production capacity is lost. Biomass specific substrate uptake rates are a linear function of the cellular P-content, offering advantages for scaling-up the PHA production process due to lower oxygen requirements.

Controlling cell volume for efficient PHB production by Halomonas

Bacterial morphology is decided by cytoskeleton protein MreB and cell division protein FtsZ encoded by essential genes mreB and ftsZ, respectively. Inactivating mreB and ftsZ lead to increasing cell sizes and cell lengths, respectively, yet seriously reduce cell growth ability. Here we develop a temperature-responsible plasmid expression system for compensated expression of relevant gene(s) in mreB or ftsZ disrupted recombinants H. campaniensis LS21, allowing mreB or ftsZ disrupted recombinants to grow normally at 30°C in a bioreactor for 12h so that a certain cell density can be reached, followed by 36h cell size expansions or cell shape elongations at elevated 37°C at which the mreB and ftsZ encoded plasmid pTKmf failed to replicate in the recombinants and thus lost themselves. Finally, 80% PHB yield increase was achieved via controllable morphology manipulated H. campaniensis LS21. It is concluded that controllable expanding cell volumes (widths or lengths) provides more spaces for accumulating more inclusion body polyhydroxybutyrate (PHB) and the resulting cell gravity precipitation benefits the final separation of cells and product during downstream.

Controlling microbial PHB synthesis via CRISPRi

Microbial polyhydroxyalkanoates (PHA) are a family of biopolyesters with properties similar to petroleum plastics such as polyethylene (PE) or polypropylene (PP). Polyhydroxybutyrate (PHB) is the most common PHA known so far. Clustered regularly interspaced short palindromic repeats interference (CRISPRi), a technology recently developed to control gene expression levels in eukaryotic and prokaryotic genomes, was employed to regulate PHB synthase activity influencing PHB synthesis. Recombinant Escherichia coli harboring an operon of three PHB synthesis genes phaCAB cloned from Ralstonia eutropha, was transformed with various single guided RNA (sgRNA with its guide sequence of 20-23 bases) able to bind to various locations of the PHB synthase PhaC, respectively. Depending on the binding location and the number of sgRNA on phaC, CRISPRi was able to control the phaC transcription and thus PhaC activity. It was found that PHB content, molecular weight, and polydispersity were approximately in direct and reverse proportion to the PhaC activity, respectively. The higher the PhaC activity, the more the intracellular PHB accumulation, yet the less the PHB molecular weights and the wider the polydispersity. This study allowed the PHB contents to be controlled in the ranges of 1.47-75.21% cell dry weights, molecular weights from 2 to 6 millions Dalton and polydispersity of 1.2 to 1.43 in 48 h shake flask studies. This result will be very important for future development of ultrahigh molecular weight PHA useful to meet high strength application requirements.

Production of polyhydroxyalkanoates (PHA) using sludge from different wastewater treatment processes and the potential for medical and pharmaceutical applications

In this study, seven strains of bacteria with polyhydroxyalkanoates (PHA)-producing ability (i.e. Bacillus cereus, Pseudomonas putida, Bacillus pumilus, Pseudomona huttiensis, Yersinia frederiksenii, Aeromonas ichthiosmia, and Sphingopyxis terrae) were isolated from various waste treatment plants in Hong Kong. Simultaneous wastewater treatment and PHA accumulation were successfully achieved in the bioreactors using isolated bacteria from different sludges. At the organic loading less than 13,000 ppm, more than 95% of chemical oxygen demand (COD) was removed by the isolated strains before the decrease of PHA accumulation. In addition, more than 95% of nitrogen removal was achieved by all isolated strains. In the bioreactors inoculated with single strains, the highest yields of poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxyvalerate) (PHV) were obtained in A. ichthiosmia (84 mg PHB/g) and B. cereus (69 mg/g), respectively. For the mixed culture, the highest yields of PHB and PHV were increased by 55% and 45% in the system inoculated with B. pumilus and A. ichthiosmia. The biologically synthesized PHA also showed the potential applications in drug delivery and tissue engineering. PHA-nanoparticles loaded with pyrene were successfully prepared by recombinant Escherichia coli. The results of in vitro drug release and biocompatibility tests revealed that nanoparticles could be used as safer dray carriers with high loading capacity and efficiency. After 20 days, the cells successfully grew on 90% of the PHA-aortic valve.

Polyhydroxyalkanoates (PHA) production from synthetic waste using Pseudomonas pseudoflava: PHA synthase enzyme activity analysis from P. pseudoflava and P. palleronii

Synthetic wastewater (SW) at various carbon concentrations (5-60g/l) were evaluated for polyhydroxyalkanoates (PHA) production using the bacteria Pseudomonas pseudoflava. Bacteria showed highest PHA production with 20g/l (57±5%), and highest carbon removal at 5g/l (74±6%) concentrations respectively. Structure, molecular weight, and thermal properties of the produced PHA were evaluated using various analytical techniques. Bacteria produced homo-polymer [poly-3-hydroxybutyrate (P3HB)] when only acetate was used as carbon source; and it produced co-polymer [poly-(3-hydroxybutyrate-co-3-hydroxyvalerate) P(3HB-co-3HV)] by addition of co-substrate propionate. PHA synthase, the enzyme which produce PHA was extracted from two bacterial strains i.e., P. pseudoflava and P. palleronii and its molecular weight was analysed using SDS-PAGE. Protein concentration, and PHA synthase enzyme activity of P. pseudoflava and P. palleronii was carried out using spectrophotometer. Results denoted that P. pseudoflava can be used for degradation of organic carbon persistent in wastewaters and their subsequent conversion into PHA.

The link of feast-phase dissolved oxygen (DO) with substrate competition and microbial selection in PHA production

Polyhydroxyalkanoates (PHAs) are biobased and biodegradable polyesters with the potential to replace conventional plastics. Aeration requires large amounts of energy in PHA production by mixed microbial cultures (MMCs), particularly during the feast phase due to substrate uptake. The objective of this study was to investigate the impact of DO concentrations on microbial selection, substrate competition and PHA production performance by MMCs. This represents the first study investigating DO impact on PHA production while feeding the multiple volatile fatty acids (VFAs) typically encountered in real fermented feedstocks, as well as the substrate preferences at different DO levels. Efficient microbial cultures were enriched under both high (3.47 ± 1.12 mg/L) and low (0.86 ± 0.50 mg/L) DO conditions in the feast phase containing mostly the same populations but with different relative abundance. The most abundant microorganisms in the two MMCs were Plasticicumulans, Zoogloea, Paracoccus, and Flavobacterium. Butyrate and valerate were found to be the preferred substrates as compared to acetate and propionate regardless of DO concentrations. In the accumulation step, the PHA storage capacity and yield were less affected by the change of DO levels when applying the culture selected under low DO in the feast phase (PHA storage capacity >60% and yield > 0.9 Cmol PHA/Cmol VFA). A high DO level is required for maximal PHA accumulation rates with the four VFAs (acetate, propionate, butyrate and valerate) present, due to the lower specific uptake rates of acetate and propionate under low DO conditions. However, butyrate and valerate specific uptake rates were less impacted by DO levels and hence low DO for PHA accumulation may be effective when feed is composed of these substrates only.

Evaluation of short-chain-length polyhydroxyalkanoate accumulation in Bacillus aryabhattai

This study was focused on the polyhydroxybutyrate (PHB) accumulation property of Bacillus aryabhattai isolated from environment. Twenty-four polyhydroxyalkanoate (PHA) producers were screened out from sixty-two environmental bacterial isolates based on Sudan Black B colony staining. Based on their PHA accumulation property, six promising isolates were further screened out. The most productive isolate PHB10 was identified as B. aryabhattai PHB10. The polymer production maxima were 3.264 g/L, 2.181 g/L, 1.47 g/L, 1.742 g/L and 1.786 g/L in glucose, fructose, maltose, starch and glycerol respectively. The bacterial culture reached its stationary and declining phases at 18 h and 21 h respectively and indicated growth-associated PHB production. Nuclear Magnetic Resonance (NMR) spectra confirmed the material as PHB. The material has thermal stability between 30 and 140 °C, melting point at 170 °C and maximum thermal degradation at 287 °C. The molecular weight and poly dispersion index of the polymer were found as 199.7 kDa and 2.67 respectively. The bacterium B. aryabhattai accumulating PHB up to 75% of cell dry mass utilizing various carbon sources is a potential candidate for large scale production of bacterial polyhydroxybutyrate.

Microbial Degradation of Polyhydroxyalkanoates with Different Chemical Compositions and Their Biodegradability

The study addresses degradation of polyhydroxyalkanoates (PHA) with different chemical compositions-the polymer of 3-hydroxybutyric acid [P(3HB)] and copolymers of P(3HB) with 3-hydroxyvalerate [P(3HB/3HV)], 4-hydroxybutyrate [P(3HB/4HB)], and 3-hydroxyhexanoate [P(3HB/3HHx)] (10-12 mol%)-in the agro-transformed field soil of the temperate zone. Based on their degradation rates at 21 and 28 °C, polymers can be ranked as follows: P(3HB/4HB) > P(3HB/3HHx) > P(3HB/3HV) > P(3HB). The microbial community on the surface of the polymers differs from the microbial community of the soil with PHA specimens in the composition and percentages of species. Thirty-five isolates of bacteria of 16 genera were identified as PHA degraders by the clear zone technique, and each of the PHA had both specific and common degraders. P(3HB) was degraded by bacteria of the genera Mitsuaria, Chitinophaga, and Acidovorax, which were not among the degraders of the three other PHA types. Roseateles depolymerans, Streptomyces gardneri, and Cupriavidus sp. were specific degraders of P(3HB/4HB). Roseomonas massiliae and Delftia acidovorans degraded P(3HB/3HV), and Pseudoxanthomonas sp., Pseudomonas fluorescens, Ensifer adhaerens, and Bacillus pumilus were specific P(3HB/3HHx) degraders. All four PHA types were degraded by Streptomyces.

Co-metabolism of substrates by Bacillus thuringiensis regulates polyhydroxyalkanoate co-polymer composition

Polyhydroxyalkanoate (PHA) production by Bacillus thuringiensis EGU45 was studied by co-metabolism of crude glycerol (CG) (1%, v/v), glucose (0.05-0.5%, w/v) and propionic acid (0.05-0.5%, v/v) under batch (shake flask) culture conditions. Glycerol+PA combination resulted in 15-100mg/L PHA co-polymers with a HV content of 33-81mol%. The addition of NH₄Cl (0.5%, w/v) to CG+PA enhanced PHA production by 1.55-fold, with a HV content of 58-70mol%. The time period of incubation of PA to the feed: CG+glucose was optimized to be 3h after initiation of fermentation. The PHA contents were found to be stable at 1900-2050mg/L up scaling from 0.4 to 2.0L feed material. Biochemical characterization through GC-MS of PHA co-polymer revealed the presence of 3-hydroxydecanoate (3-HDD), 3-hydroxyoctadecanoate (3HOD), 3-hydroxyhexadecanoate (3HHD).

Biotransformation of volatile fatty acids to polyhydroxyalkanoates by employing mixed microbial consortia: The effect of pH and carbon source

Mixed microbial cultures that undergo successful enrichment, following eco-biotechnological approaches, to form a community dominant in polyhydroxyalkanoates (PHA) forming bacteria, represent an attractive economic alternative towards the production of those biopolymers. In the present study, an enriched mixed culture was investigated for the production of PHA at different initial pH values under non-controlled conditions in order to minimize process control and operational costs. Short-chain fatty acids were provided as PHA precursors and they were tested as sole carbon sources and as mixtures under nitrogen deficiency. By the obtained kinetic and stoichiometric parameters it was shown that at an initial pH value of 6.90 PHA production was favored. Butyrate was characterized as the preferred carbon source, whereas simultaneous feeding led to increased rates and yields when butyrate and acetate were present.

Polyhydroxyalkanoate synthesis by mixed microbial consortia cultured on fermented dairy manure: Effect of aeration on process rates/yields and the associated microbial ecology

Polyhydroxyalkanoates (PHAs) are biodegradable polymers that can substitute for petroleum-based plastics in a variety of applications. One avenue to commercial PHA production involves coupling waste-based synthesis with the use of mixed microbial consortia (MMC). In this regard, production requires maximizing the enrichment of a MMC capable of feast-famine PHA synthesis, with the metabolic response induced through imposition of aerobic-dynamic feeding (ADF) conditions. However, the concept of PHA production in complex matrices remains unrefined; process operational improvements are needed, along with an enhanced understanding of the MMC. Research presented herein investigated the effect of aeration on feast-famine PHA synthesis, with four independent aeration state systems studied; MMC were fed volatile fatty acid (VFA)-rich fermented dairy manure. Regardless of the aeration state, all MMC exhibited a feast-famine response based on observed carbon cycling. Moreover, there was no statistical difference in PHA synthesis rates, with q_PHA ranging from 0.10 to 0.19 CmmolPHA gVSS^-1 min^-1; VFA uptake rates exhibited similar statistical indifferences. PHA production assessments on the enriched MMC resulted in maximum intracellular concentrations ranging from 22.5 to 90.7% (mgPHA mgVSS^-1); at maximum concentration, the mean hydroxyvalerate mol content was 73 ± 0.6%. While a typical feast-famine dissolved oxygen (DO) pattern was observed at maximum aeration, less resolution was observed at decreasing aeration rates, suggesting that DO may not be an optimal process monitoring parameter. At lower aeration states, nitrogen cycling patterns, supported by molecular investigations targeting AOBs and NOBs, indicate that NO₂ and NO₃ sustained feast-famine PHA synthesis. Next-generation sequencing analysis of the respective MMC revealed numerous and diverse genera exhibiting the potential to achieve PHA synthesis, suggesting functional redundancy embedded in the diverse MMC. Ultimately, results demonstrate that aeration can be controlled in waste-based ADF systems to sustain PHA production potential, while enriching for a diverse MMC that exhibits potential functional redundancy. Reduced aeration could also enhance cost competitiveness of waste-based PHA production, with potential further benefits associated with nitrogen treatment.

Beyond feast and famine: Selecting a PHA accumulating photosynthetic mixed culture in a permanent feast regime

Currently, the feast and famine (FF) regime is the most widely applied strategy to select for polyhydroxyalkanoate (PHA) accumulating organisms in PHA production systems with mixed microbial cultures. As an alternative to the FF regime, this work studied the possibility of utilizing a permanent feast regime as a new operational strategy to select for PHA accumulating photosynthetic mixed cultures (PMCs). The PMC was selected in an illuminated environment and acetate was constantly present in the mixed liquor to guarantee a feast regime. During steady-state operation, the culture presented low PHA accumulation levels, likely due to low light availability, which resulted in most of the acetate being used for biomass growth (Y_x/s of 0.64 ± 0.18 Cmol X/Cmol Acet). To confirm the light limitation on the PMC, SBR tests were conducted with higher light availability, at similar levels as would be expectable from natural sunlight. In this case, the Y_x/s reduced to 0.11 ± 0.01 Cmol X/Cmol Acet and the culture presented a PHB production yield on acetate of 0.67 ± 0.01 Cmol PHB/Cmol Acet, leading to a maximum PHB content of 60%. Unlike other studied PMCs, the PMC was capable of simultaneous growth and PHB accumulation continuously throughout the cycle. Thus far, 60% PHA content is the maximum value ever reported for a PMC, a result that prospects the utilization of feast regimes as an alternative strategy for the selection of PHA accumulating PMCs. Furthermore, the PMC also presented high phosphate removal rates, delivering an effluent that complies with phosphate discharge limits. The advantages of selecting PMCs under a permanent feast regime are that no aeration inputs are required; it allows higher PHA contents and phosphate removal rates in comparison to FF-operated PMC systems; and it represents a novel means of integrating wastewater treatment with resource recovery in the form of PHA.

Polyhydroxyalkanoates (PHAs) production from fermented cheese whey by using a mixed microbial culture

Two fermented cheese wheys (FCW), FCW1 composed of lactic, acetic and butyric acids in the proportion of 58/16/26 (% CODOrganic Acid (OA)) and FCW2 composed of acetic, propionic, butyric, lactic and valeric acids in the proportion of 58/19/13/6/4 (% CODOA) were used to produce polyhydroxyalkanoates (PHAs) by using a pre-selected mixed microbial culture (MMC). PHA accumulation gave for fermented FCW1 a PHA yield (Ytot) of 0.24±0.02mgCODPHAmgCODSolubleSubstrate(SS)(-1) and a total PHA production, referred to the substrate used, of 60gPHAkgcheesewheyTotalSolids(TS)(-1). For fermented FCW2 results were: PHA yield (Ytot) of 0.42±0.03mgCODPHAmgCODSS(-1) and PHA from a substrate of 70gPHAkgcheesewheyTS(-1). Qualitatively, PHAs from FCW1 was made up exclusively of 3-hydroxybutyrate (HB), while those obtained from FCW2 were composed of 40% of 3-hydroxyvalerate (HV) and 60% of HB.

Survival of the fastest: Selective removal of the side population for enhanced PHA production in a mixed substrate enrichment

The success of enriching PHA-producers in a feast/famine regime strongly depends on the substrate utilized. A distinction can be made between substrates that select for PHA-producers (e.g. volatile fatty acids) and substrates that select for growing organisms (e.g. methanol). In this study the feasibility of using such a mixed substrate was evaluated. A sedimentation step was introduced in the cycle after acetate depletion and the supernatant containing methanol was discharged. This process configuration resulted in an increased maximum PHA storage capacity of the biomass from 48wt% to 70wt%. A model based on the experimental results indicated that the length of the pre-settling period and the supernatant volume that is discharged play a significant role for the elimination of the side population. However, the kinetic properties of the two different populations determine the success of the proposed strategy.

Synthesis of High-Molecular-Weight Polyhydroxyalkanoates by Marine Photosynthetic Purple Bacteria

Polyhydroxyalkanoate (PHA) is a biopolyester/bioplastic that is produced by a variety of microorganisms to store carbon and increase reducing redox potential. Photosynthetic bacteria convert carbon dioxide into organic compounds using light energy and are known to accumulate PHA. We analyzed PHAs synthesized by 3 purple sulfur bacteria and 9 purple non-sulfur bacteria strains. These 12 purple bacteria were cultured in nitrogen-limited medium containing acetate and/or sodium bicarbonate as carbon sources. PHA production in the purple sulfur bacteria was induced by nitrogen-limited conditions. Purple non-sulfur bacteria accumulated PHA even under normal growth conditions, and PHA production in 3 strains was enhanced by nitrogen-limited conditions. Gel permeation chromatography analysis revealed that 5 photosynthetic purple bacteria synthesized high-molecular-weight PHAs, which are useful for industrial applications. Quantitative reverse transcription polymerase chain reaction analysis revealed that mRNA levels of phaC and PhaZ genes were low under nitrogen-limited conditions, resulting in production of high-molecular-weight PHAs. We conclude that all 12 tested strains are able to synthesize PHA to some degree, and we identify 5 photosynthetic purple bacteria that accumulate high-molecular-weight PHA molecules. Furthermore, the photosynthetic purple bacteria synthesized PHA when they were cultured in seawater supplemented with acetate. The photosynthetic purple bacteria strains characterized in this study should be useful as host microorganisms for large-scale PHA production utilizing abundant marine resources and carbon dioxide.