Overcoming substrate inhibition during biological treatment of monoaromatics: recent advances in bioprocess design

Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica

Substrate inhibition of enzymes can be a major obstacle to the production of valuable chemicals in engineered microorganisms. Here, we show substrate inhibition of lycopene cyclase as the main limitation in carotenoid biosynthesis in Yarrowia lipolytica. To overcome this bottleneck, we exploit two independent approaches. Structure-guided protein engineering yields a variant, Y27R, characterized by complete loss of substrate inhibition without reduction of enzymatic activity. Alternatively, establishing a geranylgeranyl pyrophosphate synthase-mediated flux flow restrictor also prevents the onset of substrate inhibition by diverting metabolic flux away from the inhibitory metabolite while maintaining sufficient flux towards product formation. Both approaches result in high levels of near-exclusive β-carotene production. Ultimately, we construct strains capable of producing 39.5 g/L β-carotene at a productivity of 0.165 g/L/h in bioreactor fermentations (a 1441-fold improvement over the initial strain). Our findings provide effective approaches for removing substrate inhibition in engineering pathways for efficient synthesis of natural products.

Substrate inhibition has not been widely studied in the context of synthetic biology and metabolic engineering. Here, the authors report removal of lycopene substrate inhibition by two different strategies and enable high carotenoid productivity in Yarrowia lipolytica.

Self-regenerating tubing bioreactor for removal of toxic substrates: Operational strategies in response to severe dynamic loading conditions

A tubing TPPB (Two-Phase Partitioning Bioreactor) was operated with the objective of verifying the effective treatment of a phenolic synthetic wastewater with simultaneous polymeric tubing bioregeneration by introducing tubing effluent recycle and modifications to the Hydraulic Retention Time (HRT). 2,4-dichlorophenol (DCP) was employed as the target substrate and the bioreactor was operated for a 3 month period under severe loading conditions (from 77 to 384 mg/L d) with HRT in the tubing in the range of 2-4 h. Tubing effluent recycle (recycle flow rate/influent flow rate ratio = 0.3) was applied when a loss of performance was detected arising from the increased load. For HRT values of 3 and 4 h, almost complete DCP removal was achieved after a few days (1-5) of operation while for the 2 h HRT (i.e. in the most severe loading condition) the DCP removal was ≥97%. A beneficial effect on the process performance arising from recycle application was evident for all the operating conditions investigated, and was confirmed by statistical analysis. Essentially complete polymer bioregeneration was achieved when the bioreactor was operated at the lowest HRT (i.e. 2 h), combined with the application of tubing effluent recycle. The results of this study highlighted several advantages of the tubing TPPB configuration in a comparative analysis of different regeneration options, including the possibility of operating continuously with simultaneous bioregeneration and without the need for additional units or operational steps and extra-energy consumption.

Anaerobic phenol biodegradation: kinetic study and microbial community shifts under high-concentration dynamic loading

The anaerobic biodegradation of phenol has been realised in a sequencing batch reactor (SBR) under anaerobic conditions with phenol as sole carbon and energy source and with glucose as co-substrate. A step-change increase of phenol loading (from 100 up to 2000 mg/L of phenol concentration in the feed solution) has been applied during the acclimation phase in order to progressively induce the development of a specialised microbial consortium. This approach, combined with the dynamic sequence of operations characterising SBRs and with the high biomass retention time, led to satisfactory phenol and COD removal efficiencies with values > 70% for the highest phenol input (2000 mg/L) fed as the single carbon and energy source. Analysis of removal efficiencies and biodegradation rates suggested that the use of glucose as co-substrate did not induce a significant improvement in process performance. Kinetic tests have been performed at different initial phenol (400-1000 mg/L) and glucose (1880-0 mg/L) concentrations to kinetically characterise the developed biomass: estimated kinetic constants are suitable for application and no inhibitory effect due to high concentrations of phenol has been observed in all investigated conditions. The microbial community has been characterised at different operating conditions through molecular tools: results confirm the successful adaptation-operation approach of the microbial consortium showing a gradual increase in richness and diversity and the occurrence and selection of a high proportion of phenol-degrading genera at the end of the experimentation. Key Points • Anaerobic phenol removal in the range of 70-99% in a sequencing batch reactor. • Negligible effect of co-substrate on removal efficiencies and biodegradation rates. • No biomass inhibition due to phenol concentration in the range of 400-1000 mg/L. • Increasing phenol loads promoted the culture enrichment of phenol-degrading genera.

Attenuated substrate inhibition of a haloketone reductase via structure-guided loop engineering

Substrate inhibition of enzymes is one of the main obstacles encountered frequently in industrial biocatalysis. Haloketone reductase SsCR was seriously inhibited by substrate 2,2',4'-trichloroacetophenone. In this study, two essential loops were found that have a relationship with substrate binding by conducting X-ray crystal structure analysis. Three key residues were selected from the tips of the loops and substituted with amino acids with lower hydrophobicity to weaken the hydrophobic interactions that bridge the two loops, resulting in a remarkable reduction of substrate inhibition. Among these variants, L211H showed a significant attenuation of substrate inhibition, with a K_i of 16 mM, which was 16 times that of the native enzyme. The kinetic parameter k_cat/K_m of L211H was 3.1 × 10³ s^-1 mM^-1, showing the comparable catalytic efficiency to that of the wild-type enzyme (WT). At the substrate loading of 100 mM, the space time yield of variant L211H in asymmetric reduction of the haloketone was 3-fold higher than that of the WT.

The biological treatment of synthetic fracking fluid in an extractive membrane bioreactor: Selective transport and biodegradation of hydrophobic and hydrophilic contaminants

The biodegradation of selected organic constituents present in hydraulic fracturing wastewater were examined in an extractive membrane bioreactor (EMB) operating with Hytrel™ 3548 tubing. Synthetic hydraulic fracturing wastewater was generated via an extensive literature review and contained high concentrations (1000 mg L^-1) of contaminant compounds of varied hydrophobicity, viz. methyl ethyl ketone, benzene, phenol and acetic acid, as well as 30-120 g L^-1 of Cl^- at low pH. This hostile wastewater was circulated through the polymeric tubing, selectively transporting the organic compounds through the membrane for biological degradation by an enriched bacterial consortium. 16S rDNA analysis revealed the presence of five dominant microbial strains within the consortium, including: Pseudomonas sp., Comamonas sp., Achromobacter sp., Lysinibacillus sp., and Oxalobacter sp. EMBs in batch operation achieved 99% removal of methyl ethyl ketone, benzene, and phenol after 72 h and effectively removed acetic acid up to its ionization point. Continuous EMB operation provided 99% removal of benzene and phenol, 96% removal of methyl ethyl ketone, and 53% of acetic acid. The treatment of synthetic hydraulic fracturing fluid demonstrated the effectiveness of carefully selected amphiphilic polymers in EMBs for treating the hydrophilic and hydrophobic organic profile found in hydraulic fracturing wastewaters.

Polymer extraction and ex situ biodegradation of xenobiotic contaminated soil: Modelling of the process concept

An integrated model of a two-step process for the ex situ bioremediation of xenobiotic contaminated soil has been formulated. The process is characterized by an initial extraction step of the organic contaminants from the polluted soil by contact with inexpensive and commercially-available polymer beads, followed by release and biodegradation of the xenobiotics, with parallel polymer bioregeneration, in a Two-Phase Partitioning Bioreactor (TPPB). The regenerated polymer is cyclically reused in the extraction step, so reflecting the robust and otherwise-inert properties of such polymers. The model was calibrated and validated for a soil contaminated with 4-nitrophenol (4NP) and treated with the DuPont polymer Hytrel 8206. In the model calibration, the partition coefficient polymer-soil, P_ps, and the mass transfer coefficient, K, were evaluated, as 105.3 and 0.24 h^-1 respectively. A diffusion coefficient within the polymer of 6.3 10^-8 cm² s^-1 was determined from the fitting of sorption/desorption data. The model was then tested for two alternative process configurations consisting of either one or two soil extraction units, followed by the biodegradation/bioregeneration step. The latter configuration resulted in more effective polymer utilization and is suitable if each extraction step requires a shorter time than the regeneration step. The model predicted that an extraction time of 12 h was sufficient to reach removal efficiencies ≥90% while the biodegradation/bioregeneration step required 24 h to reach efficiencies ≥93%, with a good agreement with experimental data (R² > 0.98 for both cases). The simulation of the process operated with two extraction units showed a better performance with a final concentration ∼0.2 g_4NP kg_ds^-1 vs. 1.69 g_4NP kg_ds^-1 obtained with single extraction unit, for a soil contaminated with 10 g_4NP kg_ds^-1. Corresponding extraction efficiencies were 96 and 83%, respectively.

Biotrickling filter modeling for styrene abatement. Part 2: Simulating a two-phase partitioning bioreactor

A dynamic model describing styrene abatement was developed for a two-phase partitioning bioreactor operated as a biotrickling filter (TPPB-BTF). The model was built as a coupled set of two different systems of partial differential equations depending on whether an irrigation or a non-irrigation period was simulated. The maximum growth rate was previously calibrated from a conventional BTF treating styrene (Part 1). The model was extended to simulate the TPPB-BTF based on the hypothesis that the main change associated with the non-aqueous phase is the modification of the pollutant properties in the liquid phase. The three phases considered were gas, a water-silicone liquid mixture, and biofilm. The selected calibration parameters were related to the physical properties of styrene: Henry's law constant, diffusivity, and the gas-liquid mass transfer coefficient. A sensitivity analysis revealed that Henry's law constant was the most sensitive parameter. The model was successfully calibrated with a goodness of fit of 0.94. It satisfactorily simulated the performance of the TPPB-BTF at styrene loads ranging from 13 to 77 g C m^-3 h^-1 and empty bed residence times of 30-15 s with the mass transfer enhanced by a factor of 1.6. The model was validated with data obtained in a TPPB-BTF removing styrene continuously. The experimental outlet emissions associated to oscillating inlet concentrations were satisfactorily predicted by using the calibrated parameters. Model simulations demonstrated the potential improvement of the mass-transfer performance of a conventional BTF degrading styrene by adding silicone oil.

Emerging contaminant degradation and removal in algal wastewater treatment ponds: Identifying the research gaps

Whereas the fate of emerging contaminants (ECs) during 'conventional' and 'advanced' wastewater treatment (WWT) has been intensively studied, little research has been conducted on the algal WWT ponds commonly used in provincial areas. The long retention times and large surface areas exposed to light potentially allow more opportunities for EC removal to occur, but experimental evidence is lacking to enable definite predictions about EC fate across different algal WWT systems. This study reviews the mechanisms of EC hydrolysis, sorption, biodegradation, and photodegradation, applying available knowledge to the case of algal WWT. From this basis the review identifies three main areas that need more research due to the unique environmental and ecological conditions occurring in algal WWT ponds: i) the effect of diurnally fluctuating pH and dissolved oxygen upon removal mechanisms; ii) the influence of algae and algal biomass on biodegradation and sorption under relevant conditions; and iii) the significance of EC photodegradation in the presence of dissolved and suspended materials. Because of the high concentration of dissolved organics typically found in algal WWT ponds, most EC photodegradation likely occurs via indirect mechanisms rather than direct photolysis in these systems.

Enhanced degradation of phenol by Sphingomonas sp. GY2B with resistance towards suboptimal environment through adsorption on kaolinite

The effects of clay minerals on microbial degradation of phenol under unfavorable environmental conditions were investigated. Degradation of phenol by Sphingomonas sp. GY2B adsorbed on kaolinite, montmorillonite, and vermiculite were evaluated in comparison with free bacteria under optimal conditions. Kaolinite was found to be the most effective in accelerating degradation rate (reducing the degradation time) as well as improving degradation efficiency (increasing the percentage of phenol degraded), with GY2B/kaolinite complex achieving a degradation efficiency of 96% within 6 h. GY2B adsorbed on kaolinite was more competent than free GY2B in degradation under conditions with high phenol concentrations and at alkaline pH. Kaolinite reduced the time required for degradation by 8-12 h and improved the degradation efficiency by as much as 82% at high phenol concentrations. Meanwhile, the GY2B/kaolinite complex reduced the degradation time by 24 h and improved the degradation efficiency by 46% at pH 12. The improvement was partially due to the buffering effects of kaolinite. It was also shown that Cr(VI) and kaolinite synergistically enhanced the degradation by GY2B, with Cr(VI) and kaolinite both increasing the degradation rate and kaolinite being primarily responsible for enhanced degradation efficiency. These results showed one of the common clay minerals, kaolinite, is able to significantly improve the microbial degradation performance, and protect microorganisms against unfavorable environment. Kaolinite can collaborate with Cr(VI) to further improve the microbial degradation performance. It is implied that clay minerals have great potential to be applied in enhancing the biodegradation of phenol.

Osmotic membrane bioreactor for phenol biodegradation under continuous operation

Continuous phenol biodegradation was accomplished in a two-phase partitioning osmotic membrane bioreactor (TPPOMBR) system, using extractant impregnated membranes (EIM) as the partitioning phase. The EIMs alleviated substrate inhibition during prolonged operation at influent phenol concentrations of 600-2000mg/L, and also at spiked concentrations of 2500mg/L phenol restricted to 2 days. Filtration of the effluent through forward osmosis maintained high biomass concentration in the bioreactor and improved effluent quality. Steady state was reached in 5-6 days at removal rates varying between 2000 and 5500mg/L-day under various conditions. Due to biofouling and salt accumulation, the permeate flux varied from 1.2-7.2 LMH during 54 days of operation, while maintaining an average hydraulic retention time of 7.4h. A washing cycle, comprising 1h osmotic backwashing using 0.5M NaCl and 2h washing with water, facilitated biofilm removal from the membranes. Characterization of the extracellular polymeric substances (EPS) through FTIR showed peaks between 1700 and 1500cm(-1), 1450-1450cm(-1) and 1200-1000cm(-1), indicating the presence of proteins, phenols and polysaccharides, respectively. The carbohydrate to protein ratio in the EPS was estimated to be 0.3. These results indicate that TPPOMBR can be promising in continuous treatment of phenolic wastewater.

Regeneration strategies of polymers employed in ex-situ remediation of contaminated soil: Bioregeneration versus solvent extraction

In this study we evaluated the feasibility of two regeneration strategies of contaminated polymers employed for ex-situ soil remediation in a two-step process. Soil decontamination is achieved by sorption of the pollutants on the polymer beads, which are regenerated in a subsequent step. Tested soil was contaminated with a mixture of 4-chlorophenol and pentachlorophenol, and a commercial polymer, Hytrel, has been employed for extraction. Removal efficiencies of the polymer-soil extraction are in the range of 51-97% for a contact time ≤ 24 h. Two polymer regeneration strategies, solvent extraction and biological regeneration (realized in a two-phase partitioning bioreactor), were tested and compared. Performance was assessed in terms of removal rates and efficiencies and an economic analysis based on the operating costs has been performed. Results demonstrated the feasibility of both regeneration strategies, but the bioregeneration was advantageous in that provided the biodegradation of the contaminants desorbed from the polymer. Practically complete removal for 4-chlorophenol and up to 85% biodegradation efficiency for pentachlorophenol were achieved. Instead, in the solvent extraction, a relevant production (184-831 L kg(pol)(-1)) of a highly polluted stream to be treated or disposed of is observed. The cost analysis of the two strategies showed that the bioregeneration is much more convenient with operating costs of ∼12 €/kg(pol) i.e. more than one order of magnitude lower in comparison to ∼233 €/kg(pol) of the solvent extraction.

Sequential chemical-biological processes for the treatment of industrial wastewaters: review of recent progresses and critical assessment

When direct wastewater biological treatment is unfeasible, a cost- and resource-efficient alternative to direct chemical treatment consists of combining biological treatment with a chemical pre-treatment aiming to convert the hazardous pollutants into more biodegradable compounds. Whereas the principles and advantages of sequential treatment have been demonstrated for a broad range of pollutants and process configurations, recent progresses (2011-present) in the field provide the basis for refining assessment of feasibility, costs, and environmental impacts. This paper thus reviews recent real wastewater demonstrations at pilot and full scale as well as new process configurations. It also discusses new insights on the potential impacts of microbial community dynamics on process feasibility, design and operation. Finally, it sheds light on a critical issue that has not yet been properly addressed in the field: integration requires complex and tailored optimization and, of paramount importance to full-scale application, is sensitive to uncertainty and variability in the inputs used for process design and operation. Future research is therefore critically needed to improve process control and better assess the real potential of sequential chemical-biological processes for industrial wastewater treatment.

The use of used automobile tyres in a partitioning bioreactor for the biodegradation of xenobiotic mixtures

Waste tyres were utilized as the sorption phase in a two-phase partitioning bioreactor (TPPB) for the biodegradation of a binary mixture of 2,4-dichlorophenol (DCP) and 4-nitrophenol (4NP). These compounds are extensively used in the chemical industry and are found in many industrial effluents. Although both compounds are toxic and are on the EPA list of priority pollutants, a higher inhibitory effect on microorganisms is exerted by DCP, and our experimental tests were focused on strategies to reduce its negative impact on microbial activity. Sorption/desorption tests for the DCP-4NP mixture were first performed to verify the related uptake/release rates by the tyres, which showed that the tyres had a higher capacity for DCP uptake and practically no affinity for 4NP. An acclimatized mixed culture was then utilized in a sequencing batch reactor (SBR) operated in conventional and two-phase mode. For the binary DCP-4NP mixture a significant reduction in DCP toxicity, and a concomitant enhancement in substrate removal efficiency (up to 83%for DCP and approximate 100% for 4NP) were clearly seen for the TPPB operated with 10% and 15% v/v tyres, for influent concentrations up to 180 mg/L, with practically negligible biodegradation in the conventional single phase reactor. The long-term utilization of tyres was confirmed at an influent loading of 180 mg/L with a test performed over 20 work cycles showing an improvement of the removal performance for both compounds.

Feasibility of operating a solid-liquid bioreactor with used automobile tires as the sequestering phase for the biodegradation of inhibitory compounds

Finding new uses for waste or discarded material is an important environmental goal; being able to use a waste material to treat another waste is an even more attractive objective, and this was the purpose of the present work. We previously showed that used automobile tires have an affinity for a toxic contaminant, dichlorophenol (DCP), absorbing and releasing it based on concentration driving forces. Here we have exploited this phenomenon by using used tires as the sequestering phase in a Two-Phase Partitioning Bioreactor (TPPB) to treat otherwise-toxic levels of DCP, far out-performing single phase operation in a sequencing batch bioreactor. A comprehensive examination of substrate loading, reactor exchange ratio, and tire fraction used, demonstrated that the tire-TPPB system could handle a 40% higher influent substrate loading and an increase of the exchange ratio value from 0.5 (prohibitive for single phase operation) to 0.7. Such improvement was obtained with a tire fraction ≤9%, comparable to that for commercial polymers previously employed in TPPBs. This study has opened the door to the identification of other waste plastics suitable for use in TPPBs for the treatment of recalcitrant organic contaminants.

Simultaneous biodegradation of volatile and toxic contaminant mixtures by solid-liquid two-phase partitioning bioreactors

Microbial inhibition and stripping of volatile compounds are two common problems encountered in the biotreatment of contaminated wastewaters. Both can be addressed by the addition of a hydrophobic auxiliary phase that can absorb and subsequently re-release the substrates, lowering their initial aqueous concentrations. Such systems have been described as Two Phase Partitioning Bioreactors (TPPBs). In the current work the performances of a solid-liquid TPPB, a liquid-liquid TPPB and a single phase reactor for the simultaneous degradation of butyl acetate (the volatile component) and phenol (the toxic component) have been compared. The auxiliary phase used in the solid-liquid TPPB was a 50:50 polymer mixture of styrene-butadiene rubber and Hytrel 8206, with high affinities for butyl acetate and phenol, respectively. The liquid-liquid TPPB employed silicone oil which has fixed physical properties, and had no capacity to absorb the toxic contaminant (phenol). Butyl acetate degradation was enhanced in both TPPBs relative to the single phase, arising from its sequestration into the auxiliary phase, thereby reducing volatilization losses. The solid-liquid TPPB additionally showed a substantial increase in the phenol degradation rate, relative to the silicone oil system, demonstrating the superiority and versatility of polymer based systems.

Biodegradation of endocrine disruptors in solid-liquid two-phase partitioning systems by enrichment cultures

Naturally occurring and synthetic estrogens and other molecules from industrial sources strongly contribute to the endocrine disruption of urban wastewater. Because of the presence of these molecules in low but effective concentrations in wastewaters, these endocrine disruptors (EDs) are only partially removed after most wastewater treatments, reflecting the presence of these molecules in rivers in urban areas. The development of a two-phase partitioning bioreactor (TPPB) might be an effective strategy for the removal of EDs from wastewater plant effluents. Here, we describe the establishment of three ED-degrading microbial enrichment cultures adapted to a solid-liquid two-phase partitioning system using Hytrel as the immiscible water phase and loaded with estrone, estradiol, estriol, ethynylestradiol, nonylphenol, and bisphenol A. All molecules except ethynylestradiol were degraded in the enrichment cultures. The bacterial composition of the three enrichment cultures was determined using 16S rRNA gene sequencing and showed sequences affiliated with bacteria associated with the degradation of these compounds, such as Sphingomonadales. One Rhodococcus isolate capable of degrading estrone, estradiol, and estriol was isolated from one enrichment culture. These results highlight the great potential for the development of TPPB for the degradation of highly diluted EDs in water effluents.

Pulse respirometry in two-phase partitioning bioreactors: case study of terephthalic acid biodegradation

Two-phase partitioning bioreactors (TPPBs) are based on the addition of an organic phase, often called vector, to a bioreactor in order to increase mass transfer of oxygen or gaseous substrates from the gaseous phase to the aqueous phase. In TPPBs, like in any other reactor design, the characterization of the bioprocess is often required for design, control, and operation purposes. Pulse respirometry is a method that allows for microbial processes characterization through the determination of several stoichiometric and kinetic parameters with relatively little experimental effort. Despite its interest and its previous application in countless applications, pulse respirometry has never been applied in TPPBs. In this work, pulse respirometry was assessed in a model TPPB degrading terephthalic acid and using Elvax™ as solid vector to enhance oxygen transfer. The results indicated that the addition of 10 to 20% Elvax increased oxygen transfer by up to 97%, compared to control with no vector. Pulse respirometry was successfully applied and allowed for the determination of the growth yield, the substrate affinity constant, and the maximum growth rate, within other. It is concluded that pulse respirometry is a useful method, not only for the characterization of processes in TPPBs but also for the selection of a vector within several brands commercially available.

Substrate mass transport in two-phase partitioning bioreactors employing liquid and solid non-aqueous phases

The mass transfer of phenol and butyl acetate to/from water was studied in two-phase partitioning bioreactors using immiscible organic solvents and solid polymer beads as the partitioning phases in a 5-L stirred tank bioreactor. Virtually instantaneous mass transfer was observed with phenol in water/2-undecanone, and with butyl acetate in water/silicone oil systems. The mass transfer of butyl acetate to silicone oil was rapid irrespective of the viscosity of the partitioning phase. When Hytrel® polymer beads were employed as the partitioning phase, substrate transport to the polymer was found not to be externally mass transfer limited, but rather internally by substrate diffusion into the polymer. In contrast to gaseous, poorly soluble substrates studied in other works, mass transfer of soluble substrates such as phenol and butyl acetate to the polymer was unaffected by impeller speed but rather by polymer mass fraction.