Modeling of growth kinetics for Pseudomonas putida during toluene degradation

Mathematical modeling for operative improvement of the decoloration of Acid Red 27 by a novel microbial consortium of Trametes versicolor and Pseudomonas putida: A multivariate sensitivity analysis

In this work, it is presented a first approach of a mathematical and kinetic analysis for improving the decoloration and further degradation process of an azo dye named acid red 27 (AR27), by means of a novel microbial consortium formed by the fungus Trametes versicolor and the bacterium Pseudomonas putida. A multivariate analysis was carried out by simulating scenarios with different operating conditions and developing a specific mathematical model based on kinetic equations describing all stages of the biological process, from microbial growth and substrate consuming to decoloration and degradation of intermediate compounds. Additionally, a sensitivity analysis was performed by using a factorial design and the Response Surface Method (RSM), for determining individual and interactive effects of variables like, initial glucose concentration, initial dye concentration and the moment in time for bacterial inoculation, on response variables assessed in terms of the minimum time for: full decoloration of AR27 (R1 = 2.375 days); maximum production of aromatic metabolites (R2 = 1.575 days); and full depletion of aromatic metabolites (R3 = 12.9 days). Using RSM the following conditions improved the biological process, being: an initial glucose concentration of 20 g l-1, an initial AR27 concentration of 0.2 g l-1 and an inoculation moment in time of P. putida at day 1. The mathematical model is a feasible tool for describing AR27 decoloration and its further degradation by the microbial consortium of T. versicolor and P. putida, this model will also work as a mathematical basis for designing novel bio-reaction systems than can operate with the same principle of the described consortium.

Effects of temperature, pH, and salinity on the growth kinetics of Pseudomonas sp. NB-1, a newly isolated cold-tolerant, alkali-resistant, and high-efficiency nitrobenzene-degrading bacterium

ABSTRACTStrain NB-1, which can efficiently degrade nitrobenzene, was identified as Pseudomonas frederiksbergensis. NB-1 was resistant to cold and alkali with the widest temperature (4-35 °C) and pH (5-11) adaptive range, compared with other reported nitrobenzene-degrading microorganisms. Based on the Haldane-Andrews model, the real maximum specific growth rate μ_m', specific affinity a_A, and inhibition coefficient K_i were used in response surface methodology (RSM) simultaneously for the first time to guide NB-1 to treat nitrobenzene wastewater. According to the RSM model, the environmental factors (temperature, pH, salinity) corresponding to the optimal values of μ_m', a_A, and K_i were determined. By comparing the specific growth rates corresponding to the optimal values of μ_m', a_A, and K_i, respectively, the optimum growth conditions of NB-1 were determined under different nitrobenzene concentrations. The study of μ_m', a_A, and K_i by RSM provided a new approach for a more accurate optimization of biological wastewater treatment conditions.

Gas-phase degradation of VOCs using supported bacteria biofilms

Herein we report the use of Pseudomonas putida F1 biofilms grown on carbonized cellulosic fibers to achieve biodegradation of airborne volatile organic compounds (VOCs) in the absence of any bulk aqueous-phase media. It is believed that direct exposure of gaseous VOC substrates to biomass may eliminate aqueous-phase mass transfer resistance and facilitate VOC capture and degradation. When tested with toluene vapor as a model VOC, the supported biofilm could grow optimally at 300 p.p.m. toluene and 80% relative humidity, with a specific growth rate of 0.425 day^-1 . During long-term VOC biodegradation tests in a tubular packed bed reactor, biofilms achieved a toluene degradation rate of 2.5 mg g_DCW ^-1  h^-1 during the initial growth phase. Interestingly, the P. putida F1 film kept biodegrading activity even at the stationary nongrowth phase. The supported biofilms with a biomass loading of 20% (wt) could degrade toluene at a rate of 1.9 mg g_DCW ^-1  h^-1 during the stationary phase, releasing CO₂ at a rate of 6.4 mg g_DCW ^-1  h^-1 at the same time (indicating 100% conversion of substrate carbon to CO₂ ). All of these observations promised a new type of "dry" biofilm reactors for efficient degradation of toxic VOCs without involving a large amount of water.

Production and purification of bioflocculants from newly isolated bacterial species: a comparative decolourization study of cationic and anionic textile dyes

Bioflocculant-producing bacteria were isolated from various water reservoirs and sediments of the water treatment plant. Four promising strains were identified by standard biochemical methods and 16s rRNA gene sequencing. Bioflocculants were produced in a batch bioreactor of 3 L under optimized conditions. Fourier transformed infrared spectroscopy and scanning electron microscopy (SEM) were used to confirm the chemical and morphological nature of bioflocculants. Anionic and cationic textile dyes congo red (CR) and rhodamine-B (RB) decolourization efficiency by ethanol precipitated bioflocculants were accessed under different values of pH, temperature, dose of flocculant and presence of monovalent, divalent and trivalent cations. Bioflocculants of all the four isolates were found to be highly efficient in decolourization of dye from an aqueous medium with the removal rate up to 99.56%. The removal rate of CR and RB from aqueous medium was largely influenced by the physiochemical condition of the solution viz. pH, temperature, concentration of ions and dose of flocculants. The microbial bioflocculants are biodegradable and highly stable as well as possess abroad range of pH, temperature and ions tolerance range. So, they may be economical and can be greener substitutes for the present harsh chemical-based wastewater effluent treatment methods.

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

BACKGROUND

Pseudomonas putida is a promising candidate for the industrial production of biofuels and biochemicals because of its high tolerance to toxic compounds and its ability to grow on a wide variety of substrates. Engineering this organism for improved performances and predicting metabolic responses upon genetic perturbations requires reliable descriptions of its metabolism in the form of stoichiometric and kinetic models.

RESULTS

In this work, we developed kinetic models of P. putida to predict the metabolic phenotypes and design metabolic engineering interventions for the production of biochemicals. The developed kinetic models contain 775 reactions and 245 metabolites. Furthermore, we introduce here a novel set of constraints within thermodynamics-based flux analysis that allow for considering concentrations of metabolites that exist in several compartments as separate entities. We started by a gap-filling and thermodynamic curation of iJN1411, the genome-scale model of P. putida KT2440. We then systematically reduced the curated iJN1411 model, and we created three core stoichiometric models of different complexity that describe the central carbon metabolism of P. putida. Using the medium complexity core model as a scaffold, we generated populations of large-scale kinetic models for two studies. In the first study, the developed kinetic models successfully captured the experimentally observed metabolic responses to several single-gene knockouts of a wild-type strain of P. putida KT2440 growing on glucose. In the second study, we used the developed models to propose metabolic engineering interventions for improved robustness of this organism to the stress condition of increased ATP demand.

CONCLUSIONS

The study demonstrates the potential and predictive capabilities of the kinetic models that allow for rational design and optimization of recombinant P. putida strains for improved production of biofuels and biochemicals. The curated genome-scale model of P. putida together with the developed large-scale stoichiometric and kinetic models represents a significant resource for researchers in industry and academia.

Mechanisms of distinct activated carbon and biochar amendment effects on petroleum vapour biofiltration in soil

We studied the effects of two percent by weight activated carbon versus biochar amendments in 93 cm long sand columns on the biofiltration of petroleum vapours released by a non-aqueous phase liquid (NAPL) source. Activated carbon greatly enhanced, whereas biochar slightly reduced, the biofiltration of volatile petroleum hydrocarbons (VPHs) over 430 days. Sorbent amendment benefitted the VPH biofiltration by retarding breakthrough during the biodegradation lag phase. Subsequently, sorbent amendment briefly reduced the mineralization of petroleum hydrocarbons by limiting their bioavailability. During the last and longest study period, when conditions became less supportive of microbial growth, because of inorganic nutrient scarcity, the sorbents again improved the pollution attenuation by preventing the degrading microorganisms from being overloaded with VPHs. A 16S rRNA gene based analysis showed sorbent amendment effects on soil microbial communities. Nocardioidaceae benefitted the most from petroleum hydrocarbons in activated carbon amended soil, whereas Pseudomonadacea predominated in unamended soil. Whilst the degrading microorganisms were overloaded with VPHs in the unamended soil, the reduced mobility and bioavailability of VPHs in the activated carbon amended soil led to the emergence of communities with higher specific substrate affinity, which removed bioavailable VPHs effectively at low concentrations. A numerical pollutant fate model reproduced these experimental observations by considering sorption effects on the pollutant migration and bioavailability for growth of VPH degrading biomass, which is limited by a maximum soil biomass carrying capacity. Activated carbon was a much stronger sorbent for VPHs than biochar, which explained the diverging effects of the two sorbents in this study.

Inhibition of selected bacterial growth by three hydrocarbons: mathematical evaluation of toxicity using a toxicodynamic equation

The individual toxicity of different hydrocarbons (naphthalene, cyclododecane and aniline) on the growth of selected bacteria (Pseudomonas sp., Phaeobacter sp. and Leuconostoc mesenteroides) was studied by means of a toxicodynamic model combination of two sigmoid equations (logistic and Weibull). All the toxicological effects on growth parameters and kinetic properties were characterized and the global toxicity of such chemicals was evaluated. It was observed that two kinetic parameters (maximum growth and maximum growth rate) were in almost all cases influenced by the hydrocarbons studied. Aniline was less toxic than cyclododecane and naphthalene. The presented approach is a reasonable starting point for understanding and modeling complete and real assessment of chemical toxic effects on bacterial growths. The values of EC50,τ could be used for a most efficient comparison of the individual toxicity of chemicals.

Impact of nitrate dose on toluene degradation under denitrifying condition

In this study, we investigated the impact of nitrate dose on toluene degradation by Pseudomonas putida to elucidate the upper limit of nitrate concentration and whether an optimum ratio of nitrate to toluene concentration exists. Batch microcosm studies were conducted in order to monitor toluene degradation for various ratios (2-20) of nitrate to toluene with nitrate concentrations ranging from 0 to 700 mg L(-1) for a given toluene concentration of 50 and 25 mg L(-1) during 4-day (short term) and 14-day (long term) incubation time, respectively. The short-term study revealed that nitrate concentration of 500 mg L(-1) was toxic to bacteria and the optimum concentration was 300 mg L(-1) yielding the highest toluene degradation rate (0.083 mg L(-1) h(-1)). In the batch study of long term, toluene degradation was limited to 6 days after which the nitrate at 50 mg L(-1) was depleted, indicating that nitrate was a necessary electron acceptor. For both batch studies, an optimum ratio of 6 was found yielding the highest toluene degradation rate. This indicates that an appropriate nitrate dose is essential for efficient degradation of toluene when bioremediation of groundwater contaminated with toluene is under consideration.

Growth behaviors of bacteria in biofouling cake layer in a dead-end microfiltration system

The growth behaviors of three bacterial species, i.e. Escherichia coli, Pseudomonas putida and Aquabaculum hongkongensis, in biofouling cake layer (attached form) were investigated using an unstirred dead-end continuous microfiltration system, and were compared with those in suspended form. Results showed that all the three bacteria had larger average growth rates in suspended form than in attached form under high substrates levels. Under oligotrophic conditions, the average growth rates in the attached form were faster than those in the suspended form, especially for A. hongkongensis. The growth behaviors analysis presented the same results due to all the tested bacteria had higher maximum growth rate and saturation constant in suspended form than attached form, indicating the dominant growth mode would be shifted from attached form to suspended form with substrate concentration increase. Finally, total filtration resistance determined in the experiments increased significantly with the bacterial growth in filtration system.