Rhodococcus aetherivorans IAR1, a new bacterial strain synthesizing poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from toluene

Microbial production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate), from lab to the shelf: A review

Polyhydroxyalkanoates (PHAs) are natural biopolyesters produced by microorganisms that represent one of the most promising candidates for the replacement of conventional plastics due to their complete biodegradability and advantageous material properties which can be modulated by varying their monomer composition. Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] has received particular research attention because it can be synthesized based on the same microbial platform developed for poly(3-hydroxybutyrate) [P(3HB)] without much modification, with as high productivity as P(3HB). It also offers more useful mechanical and thermal properties than P(3HB), which broaden its application as a biocompatible and biodegradable polyester. However, a significant commercial disadvantage of P(3HB-co-3HV) is its rather high production cost, thus many studies have investigated the economical synthesis of P(3HB-co-3HV) from structurally related and unrelated carbon sources in both wild-type and recombinant microbial strains. A large number of metabolic engineering strategies have also been proposed to tune the monomer composition of P(3HB-co-3HV) and thus its material properties. In this review, recent metabolic engineering strategies designed for enhanced production of P(3HB-co-3HV) are discussed, along with their current status, limitations, and future perspectives.

Copolymers and Blends Based on 3-Hydroxybutyrate and 3-Hydroxyvalerate Units

This review presents a comprehensive update of the biopolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), emphasizing its production, properties, and applications. The overall biosynthesis pathway of PHBV is explored in detail, highlighting recent advances in production techniques. The inherent physicochemical properties of PHBV, along with its degradation behavior, are discussed in detail. This review also explores various blends and composites of PHBV, demonstrating their potential for a range of applications. Finally, the versatility of PHBV-based materials in multiple sectors is examined, emphasizing their increasing importance in the field of biodegradable polymers.

Screening of xylene degrading bacteria and optimization of their degradation characteristics in heavily polluted areas

Aiming at the problems of high xylene concentration and difficult removal in heavily polluted areas, high-efficient degrading bacteria of volatile organic compounds (VOCs) xylene in heavily polluted areas were selected and screened from sewage sludge, and their degradation characteristics were studied. The response surface methodology (RSM) optimized the optimal degradation conditions. The results showed that the screened degrading strain was identified as Klebsiella by the 16SrDNA technology and named H-16. During the start-up phase of the reactor, the removal rate of xylene by strain H-16 fluctuated, and it was stable above 71.3% for 150 min. At 40°C, the degradation rate is the highest, reaching 63.25%. With an increasing inoculum amount of strain H-16, the degradation rate of xylene gradually increased, and the degradation rate could reach 86.1% when the inoculation amount was 25%. A neutral environment was more conducive to the degradation and removal of xylene. Through the analysis of the model and RSM, the optimal conditions for the degradation of xylene by H-16 were obtained: 38.89°C, pH 6.94 and 18.07%. GC-MS results showed that the possible degradation pathway of xylene began with demethylation, formation of pentene diacid by benzene ring cleavage, and finally oxidation to generate CO2 and H2O.

Screening potential polyhydroxyalkanoate-producing bacteria from wastewater sludge

We applied fluorescence staining of Nile red, polymerase chain reaction (PCR), and carbon substrate utilization and pressure tolerance analysis to execute three-stage screening for potential polyhydroxyalkanoate (PHA) producers in the sludge samples of 21 large-scale wastewater treatment plants of city and industrial parks in Taiwan area. Total 35,429 colonies were grown on 196 plates, the screened 30 strains were subjected to 16S rRNA analysis, and 18 identified genera belonged to Proteobacteria (67%), Firmicutes (17%), and Actinomycetota (16%). The PHA accumulation results revealed that nine genera (50% of 18 screened) produced PHAs by limiting the nitrogen source and excess single carbon sources of glucose in an aerobic status. The PHA accumulation percentage was 1.44-58.77% at dry cell weight, and the theoretical yield from glucose was 0.52-58.76%. Our results indicate that our triple-screening method is promising for identifying a high biodiversity of PHA-accumulating bacteria from activated sludge for future industrial applications.

From Organic Wastes and Hydrocarbons Pollutants to Polyhydroxyalkanoates: Bioconversion by Terrestrial and Marine Bacteria

The use of fossil-based plastics has become unsustainable because of the polluting production processes, difficulties for waste management sectors, and high environmental impact. Polyhydroxyalkanoates (PHA) are bio-based biodegradable polymers derived from renewable resources and synthesized by bacteria as intracellular energy and carbon storage materials under nutrients or oxygen limitation and through the optimization of cultivation conditions with both pure and mixed culture systems. The PHA properties are affected by the same principles of oil-derived polyolefins, with a broad range of compositions, due to the incorporation of different monomers into the polymer matrix. As a consequence, the properties of such materials are represented by a broad range depending on tunable PHA composition. Producing waste-derived PHA is technically feasible with mixed microbial cultures (MMC), since no sterilization is required; this technology may represent a solution for waste treatment and valorization, and it has recently been developed at the pilot scale level with different process configurations where aerobic microorganisms are usually subjected to a dynamic feeding regime for their selection and to a high organic load for the intracellular accumulation of PHA. In this review, we report on studies on terrestrial and marine bacteria PHA-producers. The available knowledge on PHA production from the use of different kinds of organic wastes, and otherwise, petroleum-polluted natural matrices coupling bioremediation treatment has been explored. The advancements in these areas have been significant; they generally concern the terrestrial environment, where pilot and industrial processes are already established. Recently, marine bacteria have also offered interesting perspectives due to their advantageous effects on production practices, which they can relieve several constraints. Studies on the use of hydrocarbons as carbon sources offer evidence for the feasibility of the bioconversion of fossil-derived plastics into bioplastics.

Rational engineering of natural polyhydroxyalkanoates producing microorganisms for improved synthesis and recovery

Microbial production of biopolymers derived from renewable substrates and waste streams reduces our heavy reliance on petrochemical plastics. One of the most important biodegradable polymers is the family of polyhydroxyalkanoates (PHAs), naturally occurring intracellular polyoxoesters produced for decades by bacterial fermentation of sugars and fatty acids at the industrial scale. Despite the advances, PHA production still suffers from heavy costs associated with carbon substrates and downstream processing to recover the intracellular product, thus restricting market positioning. In recent years, model-aided metabolic engineering and novel synthetic biology approaches have spurred our understanding of carbon flux partitioning through competing pathways and cellular resource allocation during PHA synthesis, enabling the rational design of superior biopolymer producers and programmable cellular lytic systems. This review describes these attempts to rationally engineering the cellular operation of several microbes to elevate PHA production on specific substrates and waste products. We also delve into genome reduction, morphology, and redox cofactor engineering to boost PHA biosynthesis. Besides, we critically evaluate engineered bacterial strains in various fermentation modes in terms of PHA productivity and the period required for product recovery.

Enhanced polyhydroxybutyrate (PHB) production by newly isolated rare actinomycetes Rhodococcus sp. strain BSRT1-1 using response surface methodology

Poly-β-hydroxybutyrate (PHB) is a biodegradable polymer, synthesized as carbon and energy reserve by bacteria and archaea. To the best of our knowledge, this is the first report on PHB production by a rare actinomycete species, Rhodococcus pyridinivorans BSRT1-1. Response surface methodology (RSM) employing central composite design, was applied to enhance PHB production in a flask scale. A maximum yield of 3.6 ± 0.5 g/L in biomass and 43.1 ± 0.5 wt% of dry cell weight (DCW) of PHB were obtained when using RSM optimized medium, which was improved the production of biomass and PHB content by 2.5 and 2.3-fold, respectively. The optimized medium was applied to upscale PHB production in a 10 L stirred-tank bioreactor, maximum biomass of 5.2 ± 0.5 g/L, and PHB content of 46.8 ± 2 wt% DCW were achieved. Furthermore, the FTIR and ¹H NMR results confirmed the polymer as PHB. DSC and TGA analysis results revealed the melting, glass transition, and thermal decomposition temperature of 171.8, 4.03, and 288 °C, respectively. In conclusion, RSM can be a promising technique to improve PHB production by a newly isolated strain of R. pyridinivorans BSRT1-1 and the properties of produced PHB possessed similar properties compared to commercial PHB.

The impact of environmental parameters on the conversion of toluene to CO2 and extracellular polymeric substances in a differential soil biofilter

The fraction of pollutant converted to CO₂ versus biomass in biofiltration influences the process efficacy and the lifetime of the bed due to pressure drop increases. This work determined the relative quantitative importance and potential interactions between three critical environmental parameters: toluene concentration (Tol), matric potential (ψ) and temperature (T) on % CO₂, elimination capacity (EC) and the production rate of non-CO₂ products. These parameters are the most variable in typical biofilter operation. The data was fit to a non-linear model of the form y=a(Tol)^bT^cψ^d. A rigorous carbon balance (100.5 ± 7.0%) tracked the fate of degraded toluene as CO₂ and non-CO₂ carbon endpoints. The % CO₂ mineralization varied from (34-91%) with environmental parameters: temperature (20-40 °C), matric potential, (-10 to -100 cm_H2O) and residual toluene, (20-180 ppm). The highest conversion to CO₂ was at the wettest conditions (-10 cm_H2O) and lowest residual toluene concentration (18 ppm). Matric potential had twice the impact of toluene concentration on % CO₂, while temperature had less impact. The elimination capacity varied from 11 to 50 g_C⋅m^-3h^-1 and was highest at 40 °C, the wettest conditions with limited impact by toluene concentrations. Temperature increased the EC and non-CO₂ production rates strongly while matric potential and toluene concentration had less influence (4x - 10x less). This study illustrated the quantitative significance and simultaneous interaction between critical environmental parameters on carbon endpoints and biofilter performance. This kind of multivariable parameter study provides valuable insights which can address performance and clogging issues in biofilters.

Advanced Rhodococcus Biocatalysts for Environmental Biotechnologies

The review is devoted to biocatalysts based on actinobacteria of the genus Rhodococcus, which are promising for environmental biotechnologies. In the review, biotechnological advantages of Rhodococcus bacteria are evaluated, approaches used to develop robust and efficient biocatalysts are discussed, and their relevant applications are given. We focus on Rhodococcus cell immobilization in detail (methods of immobilization, criteria for strains and carriers, and optimization of process parameters) as the most efficient approach for stabilizing biocatalysts. It is shown that advanced Rhodococcus biocatalysts with improved working characteristics, enhanced stress tolerance, high catalytic activities, human and environment friendly, and commercially viable are developed, which are suitable for wastewater treatment, bioremediation, and biofuel production.

Biotic and Abiotic Synthesis of Renewable Aliphatic Polyesters from Short Building Blocks Obtained from Biotechnology

Biobased polymers have seen their attractiveness increase in recent decades thanks to the significant development of biorefineries to allow access to a wide variety of biobased building blocks. Polyesters are one of the best examples of the development of biobased polymers because most of them now have their monomers produced from renewable resources and are biodegradable. Currently, these polyesters are mainly produced by using traditional chemical catalysts and harsh conditions, but recently greener pathways with nontoxic enzymes as biocatalysts and mild conditions have shown great potential. Bacterial polyesters, such as poly(hydroxyalkanoate)s (PHA), are the best example of the biotic production of high molar mass polymers. PHAs display a wide variety of macromolecular architectures, which allow a large range of applications. The present contribution aims to provide an overview of recent progress in studies on biobased polyesters, especially those made from short building blocks, synthesized through step-growth polymerization. In addition, some important technical aspects of their syntheses through biotic or abiotic pathways have been detailed.

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) co-produced with L-isoleucine in Corynebacterium glutamicum WM001

Background

Co-production of polyhydroxyalkanoate (PHA) and amino acids makes bacteria effective microbial cell factories by secreting amino acids outside while accumulating PHA granules inside. Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is one of the PHAs with biocompatibility and fine mechanical properties, but its production is limited by the low level of intracellular propionyl-CoA.

Results

l-Isoleucine producing Corynebacterium glutamicum strain WM001 were analyzed by genome and transcriptome sequencing. The results showed that the most over-expressed genes in WM001 are relevant not only to l-isoleucine production but also to propionyl-CoA accumulation. Compared to the wild-type C. glutamicum ATCC13869, the transcriptional levels of the genes prpC2, prpD2, and prpB2, which are key genes relevant to propionyl-CoA accumulation, increased 2^6.7, 2^5.8, and 2^8.4-folds in WM001, respectively; and the intracellular level of propionyl-CoA increased 16.9-fold in WM001. When the gene cluster phaCAB for PHA biosynthesis was introduced into WM001, the recombinant strain WM001/pDXW-8-phaCAB produced 15.0 g/L PHBV with high percentage of 3-hydroxyvalerate as well as 29.8 g/L l-isoleucine after fed-batch fermentation. The maximum 3-hydroxyvalerate fraction in PHBV produced by WM001/pDXW-8-phaCAB using glucose as the sole carbon source could reach 72.5%, which is the highest reported so far.

Conclusions

Genome and transcriptome analysis showed that C. glutamicum WM001 has potential to accumulate l-isoleucine and propionyl-CoA pool. This was experimentally confirmed by introducing the phaCAB gene cluster into WM001. The recombinant strain WM001/pDXW-8-phaCAB produced high levels of PHBV with high 3-hydroxyvalerate fraction as well as l-isoleucine. Because of its high level of intracellular propionyl-CoA pool, WM001 might be used for producing other propionyl-CoA derivatives.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0942-7) contains supplementary material, which is available to authorized users.

Aerobic Growth of Rhodococcus aetherivorans BCP1 Using Selected Naphthenic Acids as the Sole Carbon and Energy Sources

Naphthenic acids (NAs) are an important group of toxic organic compounds naturally occurring in hydrocarbon deposits. This work shows that Rhodococcus aetherivorans BCP1 cells not only utilize a mixture of eight different NAs (8XNAs) for growth but they are also capable of marked degradation of two model NAs, cyclohexanecarboxylic acid (CHCA) and cyclopentanecarboxylic acid (CPCA) when supplied at concentrations from 50 to 500 mgL-1. The growth curves of BCP1 on 8XNAs, CHCA, and CPCA showed an initial lag phase not present in growth on glucose, which presumably was related to the toxic effects of NAs on the cell membrane permeability. BCP1 cell adaptation responses that allowed survival on NAs included changes in cell morphology, production of intracellular bodies and changes in fatty acid composition. Transmission electron microscopy (TEM) analysis of BCP1 cells grown on CHCA or CPCA showed a slight reduction in the cell size, the production of EPS-like material and intracellular electron-transparent and electron-dense inclusion bodies. The electron-transparent inclusions increased in the amount and size in NA-grown BCP1 cells under nitrogen limiting conditions and contained storage lipids as suggested by cell staining with the lipophilic Nile Blue A dye. Lipidomic analyses revealed significant changes with increases of methyl-branched (MBFA) and polyunsaturated fatty acids (PUFA) examining the fatty acid composition of NAs-growing BCP1 cells. PUFA biosynthesis is not usual in bacteria and, together with MBFA, can influence structural and functional processes with resulting effects on cell vitality. Finally, through the use of RT (Reverse Transcription)-qPCR, a gene cluster (chcpca) was found to be transcriptionally induced during the growth on CHCA and CPCA. Based on the expression and bioinformatics results, the predicted products of the chcpca gene cluster are proposed to be involved in aerobic NA degradation in R. aetherivorans BCP1. This study provides first insights into the genetic and metabolic mechanisms allowing a Rhodococcus strain to aerobically degrade NAs.

Engineering a bzd cassette for the anaerobic bioconversion of aromatic compounds

Microorganisms able to degrade aromatic contaminants constitute potential valuable biocatalysts to deal with a significant reusable carbon fraction suitable for eco‐efficient valorization processes. Metabolic engineering of anaerobic pathways for degradation and recycling of aromatic compounds is an almost unexplored field. In this work, we present the construction of a functional bzd cassette encoding the benzoyl‐CoA central pathway for the anaerobic degradation of benzoate. The bzd cassette has been used to expand the ability of some denitrifying bacteria to use benzoate as sole carbon source under anaerobic conditions, and it paves the way for future pathway engineering of efficient anaerobic biodegraders of aromatic compounds whose degradation generates benzoyl‐CoA as central intermediate. Moreover, a recombinant Azoarcus sp. CIB strain harbouring the bzd cassette was shown to behave as a valuable biocatalyst for anaerobic toluene valorization towards the synthesis of poly‐3‐hydroxybutyrate (PHB), a biodegradable and biocompatible polyester of increasing biotechnological interest as a sustainable alternative to classical oil‐derived polymers.

Recent Advances and Challenges towards Sustainable Polyhydroxyalkanoate (PHA) Production

Sustainable biofuels, biomaterials, and fine chemicals production is a critical matter that research teams around the globe are focusing on nowadays. Polyhydroxyalkanoates represent one of the biomaterials of the future due to their physicochemical properties, biodegradability, and biocompatibility. Designing efficient and economic bioprocesses, combined with the respective social and environmental benefits, has brought together scientists from different backgrounds highlighting the multidisciplinary character of such a venture. In the current review, challenges and opportunities regarding polyhydroxyalkanoate production are presented and discussed, covering key steps of their overall production process by applying pure and mixed culture biotechnology, from raw bioprocess development to downstream processing.

1,4-Dioxane degradation potential of members of the genera Pseudonocardia and Rhodococcus

In recent years, several strains capable of degrading 1,4-dioxane have been isolated from the genera Pseudonocardia and Rhodococcus. This study was conducted to evaluate the 1,4-dioxane degradation potential of phylogenetically diverse strains in these genera. The abilities to degrade 1,4-dioxane as a sole carbon and energy source and co-metabolically with tetrahydrofuran (THF) were evaluated for 13 Pseudonocardia and 12 Rhodococcus species. Pseudonocardia dioxanivorans JCM 13855^T, which is a 1,4-dioxane degrading bacterium also known as P. dioxanivorans CB1190, and Rhodococcus aetherivorans JCM 14343^T could degrade 1,4-dioxane as the sole carbon and energy source. In addition to these two strains, ten Pseudonocardia strains could degrade THF, but no Rhodococcus strains could degrade THF. Of the ten Pseudonocardia strains, Pseudonocardia acacia JCM 16707^T and Pseudonocardia asaccharolytica JCM 10410^T degraded 1,4-dioxane co-metabolically with THF. These results indicated that 1,4-dioxane degradation potential, including degradation for growth and by co-metabolism with THF, is possessed by selected strains of Pseudonocardia and Rhodococcus, although THF degradation potential appeared to be widely distributed in Pseudonocardia. Analysis of soluble di-iron monooxygenase (SDIMO) α-subunit genes in THF and/or 1,4-dioxane degrading strains revealed that not only THF and 1,4-dioxane monooxygenases but also propane monooxygenase-like SDIMOs can be involved in 1,4-dioxane degradation.

Optimization of macroelement concentrations, pH and osmolarity for triacylglycerol accumulation in Rhodococcus opacus strain PD630

The refinement of biodiesel or renewable diesel from bacterial lipids has a great potential to make a contribution for energy production in the future. This study provides new data concerning suitable nutrient concentrations for cultivation of the Gram-positive Rhodococcus opacus PD630, which is able to accumulate large amounts of lipids during nitrogen limitation. Enhanced concentrations of magnesium have been shown to increase the final optical density and the lipid content of the cells. Elevated phosphate concentrations slowed down the onset of the accumulation phase, without a clear effect on the final optical density and the cell's lipid content. A robust growth of R. opacus was possible in the presence of ammonium concentrations of up to 1.4 g l(-1) and sucrose concentrations of up to 240 g l(-1), with an optimum regarding growth and lipid storage observed in the range of 0.2 to 0.4 g l(-1) ammonium and 20 to 40 g l(-1) sucrose, respectively. Moreover, R. opacus showed tolerance to high salt concentrations.

Biosynthesis and characterization of polyhydroxyalkanoate containing high 3-hydroxyhexanoate monomer fraction from crude palm kernel oil by recombinant Cupriavidus necator

The potential of plant oils as sole carbon sources for production of P(3HB-co-3HHx) copolymer containing a high 3HHx monomer fraction using the recombinant Cupriavidus necator strain Re2160/pCB113 has been investigated. Various types and concentrations of plant oils were evaluated for efficient conversion of P(3HB-co-3HHx) copolymer. Crude palm kernel oil (CPKO) at a concentration of 2.5 g/L was found to be most suitable for production of copolymer with a 3HHx content of approximately 70 mol%. The time profile of these cells was also examined in order to study the trend of 3HHx monomer incorporation, PHA production and PHA synthase activity. (1)H NMR and (13)C NMR analyses confirmed the presence of P(3HB-co-3HHx) copolymer containing a high 3HHx monomer fraction, in which monomers were not randomly distributed. The results of various characterization analyses revealed that the copolymers containing a high 3HHx monomer fraction demonstrated soft and flexible mechanical properties.

Production of triacylglycerol and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by the toluene-degrading bacterium Rhodococcus aetherivorans IAR1

Poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) produced by various bacteria has been intensively investigated as a promising biodegradable plastic, but required a supply of an expensive precursor as a secondary carbon source for its production. In a previous study, we identified a new bacterial strain, Rhodococcus aetherivorans IAR1, which synthesizes PHBV from toluene without the supply of a precursor. Toluene is the volatile organic compound most abundantly emitted to the environment. In the present paper, we show that R. aetherivorans IAR1 produces triacylglycerols (TAGs) simultaneously with PHBV. Both PHBV and TAGs were synthesized before the nitrogen source is completely exhausted. The cellular content of PHBV reached 10% of cell dry weight (CDW) and its synthesis ceased even during intermittent supply of toluene. However, accumulation of TAGs continued during cultivation and their cellular content reached 24% of CDW at the end of cultivation. Cerulenin inhibited TAG production and increased PHBV cellular content up to 30% of CDW. The mole fraction of 3-hydroxyvalerate (3HV) in PHBV produced from toluene increased from 60% to 80% during its accumulation. Fatty acid compositions of TAGs produced from acetate and toluene were different. At the end of cultivation, the mole fraction of C17:0, one of odd-carbon number fatty acids, was 5% on toluene or 10% on acetate while the mole fraction of 3HV in PHBV from toluene was as high as that in PHBV from acetate, suggesting that a C5 intermediate of toluene degradation might directly become a precursor of 3HV whereas propionyl-CoA is required for the incorporation of C17:0 into TAGs.