Modeling growth kinetics and carbazole degradation kinetics of a Pseudomonas aeruginosa strain isolated from refinery sludge and uptake considerations during growth on carbazole

A novel pbd gene cluster responsible for pyrrole and pyridine ring cleavage in Rhodococcus ruber A5

Pyridine and pyrrole, which are regarded as recalcitrant chemicals, are released into the environment as a result of industrial manufacturing processes, posing serious hazards to both the environment and human health. However, the pyrrole degradation mechanism and the pyridine-degrading gene in Rhodococcus are unknown. Herein, a highly efficient pyridine and pyrrole degradation strain Rhodococcus ruber A5 was isolated. Strain A5 completely degraded 1000 mg/L pyridine in a mineral salt medium within 24 h. The pyridine degradation of strain A5 was optimized using the BoxBehnken design. The optimum degradation conditions were found to be pH 7.15, temperature 28.06 ℃, and inoculation amount 1290.94 mg/L. The pbd gene clusters involved in pyridine degradation were discovered via proteomic analysis. The initial ring cleavage of pyridine and pyrrole in strain A5 was carried out by the two-component flavin-dependent monooxygenase PbdA/PbdE. The degradation pathways of pyridine and pyrrole were proposed by the identification of metabolites and comparisons of homologous genes. Additionally, homologous pbd gene clusters were found to exist in different bacterial genomes. Our study revealed the ring cleavage mechanisms of pyrrole and pyridine, and strain A5 was identified as a promising resource for pyridine bioremediation.

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.

Kinetics of Benzo(a)pyrene biodegradation and bacterial growth in sandy soil by Sphingobacterium spiritovorum

Biodegradation is the economically viable solution to restore land contaminated by hazardous pollutants such as benzo(a)pyrene (BaP). The present study focuses on the biodegradation of benzo(a)pyrene by Sphingobacterium spiritovorum in contaminated soil. The biodegradation kinetics and bacterial growth were evaluated while the biokinetic model that described the benzo(a)pyrene biodegradation was established. The Monod, Haldane, Powell and Edward models were used to model the bacterial growth in benzo(a)pyrene contaminated soil. Excel template was developed with Fourth order Runga-Kutta numerical algorithm to find the biokinetic parameters of the complex non-linear regression model. An Excel Solver function was used to obtain reasonable best-fit values of kinetic parameters. The Haldane and Edward models are well fit to describe the growth trend and model the kinetics of benzo(a)pyrene biodegradation. Enzyme substrate inhibition is the critical factor that affects the benzo(a)pyrene degradation by S. spiritovorum, which the model defines physically. The results demonstrated that removing benzo(a)pyrene showed positive interaction between substrate inhibition, the concentration of benzo(a)pyrene and sorption of the contaminants on soil particles.

Characterization and biodegradability assessment of water-soluble fraction of oily sludge using stir bar sorptive extraction and GCxGC-TOF MS

Percolation of water through oily sludge during storage and handling of the sludge can cause soil and groundwater contamination. In this study, oily sludge from a refinery was equilibrated with water to obtain the water-soluble fraction (WSF) of oily sludge. The WSF had dissolved organic carbon (DOC) of 166 mg/L. Human cell line-based toxicity assay revealed IC₅₀ of 41 mg/L indicating its toxic nature. The predominant compounds in WSF of oily sludge included isomers of methyl, dimethyl and trimethyl quinolines and naphthalenes along with phenol derivatives and other polynuclear aromatic hydrocarbons (PAHs). Biodegradation of WSF of oily sludge was studied using a consortium of Rhodococcus ruber, Bacillus sp. and Bacillus cereus isolated from the refinery sludge. The consortium of the three strains resulted in 70% degradation over 15 days with a first-order degradation rate of 0.161 day^-1. Further analysis of the WSF was performed using the stir-bar sorptive extraction (SBSE) followed by GCxGC-TOF MS employing a PDMS Twister. The GCxGC analysis showed that Bacillus cereus was capable of degrading the quinoline, phenol and naphthalene derivatives in WSF of oily sludge at a faster rate compared to pyridine and benzoquinoline derivatives. Quinoline, phenol, biphenyl, naphthalene, pyridine and benzoquinolines derivatives in the WSF of oily sludge were reduced by 87%, 92%, 88%, 77%, 40% and 62%, respectively with respect to the controls. The WSF of oily sludge contained, n-alkanes, ranging from n-C12 to n-C18 which were removed within 2 days of biodegradation.

Elucidation of substrate interaction effects in multicomponent systems containing 3-ring homocyclic and heterocyclic polynuclear aromatic hydrocarbons

Bacterial growth and degradation experiments were conducted on carbazole (CBZ), fluorene (FLU) and dibenzothiophene (DBT) individually and in various mixture combinations using an efficient polynuclear aromatic hydrocarbon (PAH) degrading bacterial strain, Pseudomonas aeruginosa RS1. In single component systems, bacterial growth on CBZ (specific growth rate, μ = 0.99 day^-1) was much higher compared to that on FLU (μ = 0.38 day^-1) and DBT (μ = 0.33 day^-1) and bacterial growth was inhibited in the presence of FLU and DBT in binary (μ = 0.64 day^-1) and ternary (μ = 0.75 day^-1) mixtures. Multisubstrate additive modelling indicated growth inhibition in all the systems. The degradation of the compounds was significantly inhibited in binary mixtures. While the degradation of the compounds in binary mixtures varied from 35 ± 4% to 73 ± 3%, their degradation varied from 61 ± 5% to 91 ± 4%, when applied as sole substrates and from 77 ± 3% to 96 ± 3%, when applied in a ternary mixture. Degradation experiments were also conducted in ternary mixtures using a 2³ full factorial design and the results were examined using analysis of variance (ANOVA) and Tukey's honest significant difference (HSD) tests. At a low concentration of the heterocyclics, CBZ and DBT (5 mg L^-1 each), the degradation of the PAH, FLU, was significantly enhanced (from 81 ± 1% to 93 ± 0.3%) when its concentration was increased from 5 to 30 mg L^-1. The full factorial design can provide valuable insights into substrate interaction effects in mixtures.

Characterization of lipopeptide biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis: The role of biosurfactant in carbazole solubilisation

AIM

Characterization of biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis and proteomic analysis of intracellular proteins of bacterium while growing on glucose and carbazole medium.

METHODS AND RESULTS

The bacterium R. cervicalis was isolated from a soil sample contaminated with crude petroleum oil. PCR amplification ascertained the existence of some hydrocarbon-degrading catabolic genes (alkB and PAH-RHDα, C12O, and C23O) in the bacterial genome. GC-MS and RP-HPLC analyses demonstrated 62% and 60% carbazole degradation, respectively, by R. cervicalis 144 h post-incubation at 37℃ and pH 6.5. Due to the paucity of protein databases, expressions of only 29 and 14 intracellular proteins were explicitly recognized and quantitated by mass spectrometry analysis when R. cervicalis was grown in carbazole and glucose medium, respectively. FTIR, NMR and HR-MS/MS analyses demonstrated the lipopeptide nature of the purified biosurfactant produced by R. cervicalis. The biosurfactant is also presumed to assist in the solubilization of carbazole.

CONCLUSION

The isolated R. cervicalis strain is a potential candidate for the bioremediation of carbazole in petroleum-oil-contaminated sites.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of the promising R. cervicalis strain proficient in carbazole biodegradation.

Growth kinetics of Pseudomonas aeruginosa RS1 on fluorene and dibenzothiophene, concomitant degradation kinetics and uptake mechanism

The current study illustrates the growth kinetics of an efficient PAH and heterocyclic PAH degrading bacterial strain, Pseudomonas aeruginosa RS1 on fluorene (FLU) and dibenzothiophene (DBT) over the concentration 25-500 mg L-1 and their concomitant degradation kinetics. The specific growth rate (µ) was found to lie within the range of 0.32-0.57 day-1 for FLU and 0.24-0.45 day-1 for DBT. The specific substrate utilization rate (q) of FLU and DBT over the log growth phase was between 0.01 and 0.14 mg FLU mg VSS-1 day-1 for FLU and between 0.01 and 0.18 mg DBT mg VSS-1 day-1 for DBT, respectively. The µ and q values varied within a narrow range for both FLU and DBT and they did not follow any specific trend. Dissolution together with direct interfacial uptake was the possible uptake mechanism for both FLU and DBT. The q values over the log growth phase depicts the specific substrate transformation rates. Kirby-Bauer disc diffusion studies performed using an E. coli strain indicated accumulation of some toxic intermediates of FLU and DBT during their degradation. Decrease in TOC and toxicity towards the end of the degradation experiments indicates further utilization of the intermediates.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02742-7.