Enrichment culture, isolation, screening, and selection of IBU degrading bacteria
The main objectives behind this study was for the characterization bacteria with the potential to degrade IBU. The experiments was conducted with the collection of samples and enriched with IBU in shake flask study. During initial degradation no visible changes was appeared in conical flasks containing IBU. The 5 colonies of IBU degrading bacteria were seen on BHM agar plates supplemented with IBU. The tolerance of the individual strain at the amount of IBU. Out of 5 microbial colonies, 3 colonies were isolated from wastewater industry samples of Yamunanagar site, while two strains were observed from paper and pulp industry waste Yamunanagar India, samples. Out of these 5 strains only 2 strains has shown the tolerance of 8 mg/L of IBU.
Identification and molecular characterization of IBU degrading strains
The isolated strains recovered from enrichment culture were the true degrading strains and they were further characterized via morphological, microscopic examining based on Gram’s staining test, biochemical tests, and molecular aracterization based on 16S rRNA sequencing. The degrading isolates was coded as PYI2 and YPI2. The isolate PYI2 found was Gram-positive and YPI2 Gram-negative. Both the strains had rod-shaped structure but a cocci structure observed to isolate PYI2. On biochemical characterization with malonate test conducted with KB013 kit. The negative reaction seen in PYI2, and YPI2 for the malonate and Voges-Proskauer test while all other results were positive, except for arginine which has shown variable reaction for both of these strains (Table 1).
The DNA extracted from PYI2, and YPI2 bacterial isolates by alkaline lysis method and gel electrophoresis was performed. After running the DNA through electrophoresis, there was a single band detected. Later the amplification of genomic DNA was done with universal (27F and 1492R) primers and standard protocols was followed for the PCR. Afterwards, the PCR products were again run on agarose gel electrophoresis, which resulted in a single band of almost 1500 bp. The PCR product was purified and sent to Eurofins Genomics India Pvt. Ltd. for sequencing. The Sangar’s DNA sequencing method used to perform sequencing of the strain, and from this sequence t the chimera was detected by DECIPHER online tool (DECIPHER v11.9: http://www.deciphergenomics.org). There was no chimera was detected in this sequencs. Later, the 16S rRNA sequences were submitted to NCBI and the GenBank accession number was assigned by NCBI (Table 2). The tree was built by the sum of branch length: 18.25543457 for PYI2, and 0.01185045 for YPI2. The phylogenetic tree between the 10-nucleotide sequences of all strains was created out by using the NJ algorithm (Fig 1). Our results were in consistent with other similar studies . The strain like Nocardia sp. NRRL 5646, Variovorax Ibu-1, Sphingomonas Ibu-2, Patulibacter sp. I11, and Bacillus thuringiensis B1 (2015b) were identified in previous IBU degradation studies (Chen and Rosazza 1994; Li and Rosazza 1997; Murdoch and Hay 2005b, 2013; Almeida et al. 2013; Marchlewicz et al. 2017b; Salgado et al. 2020).
Optimization studies and statistical analysis of the degradation of IBU
To analyze the best physical condition for the degradation of IBU mediated by the strains PYI2, and YPI2. The conditions was optimized with parameters of A: pH (3-10), B: Temperature (10-60°C), C: Agitation speed (50-280 rpm), and D: Concentration on IBU (0.25-30 mg/L). The BBD model generated the matrix of 29 experiments (Table 3) using a randomized subtype under the response surface study . The central composite design with a quadratic design model with no blocks was used to generate this matrix. The experiments were performed in the laboratory according to the designed matrix. The IBU degradation percentage was entered into the matrix and further processed with BBD-quadratic model.
ANOVA analysis has been performed with BBD-quadratic model for the degradation of IBU by PYI2 and YPI2 strains. The model was significant with the value to the sum of squares of 15868.17 and 5573.39 , degree of freedom (df) of 14 for each, mean square of 1133.44 and 398.10 , F-value of 14.16, and 2.55 respectively, and p-values of < 0.0001 and 0.0451, respectively reported for thease strains (Supplementary Table S1 and S2). Subsequently ANOVA analysis , has been performed based on final equation for actual factor . Further, the report was generated based on the graph between the predicted value wrt actual values having a residual difference (Fig 2). The contour plots and 3D plots has been generated between two parameters viz. time vs % degradation of IBU( represented as AB vs % degradation) . Similarly, the contour plots, and 3D-plots were used for the analysis of all other parameters. Finally, the optimal values for the parameters. viz. pH, temperature, agitation speed, and amount of IBU were reorted for PYI2 at 6.9, 42°C, 240 rpm, 1.4 mg/L and YPI2 at 5.8, 32°C, 100 rpm, and 0.8 mg/L ,respectively, optimized by the software. The modeling and optimization study for the degradation of pharmaceutical acetaminophen, their kinetic analysis and modeling had indicated that, physical conditions viz. pH,temperature, rpm, had considerable effect on biodegradation (Chopra and Kumar 2020b).
In the previous studies, IBU-degrading microbe Novospingobium and Pseudomonas has been isolated from IBU-rich sediments and they can degrade 400 and 300 µM of IBU in 3 and 8 days, respectively (Rutere et al. 2020). Sphingobium yanoikuyae can remove IBU/ 80 days (Balciunas et al., 2020). There is little information available about Ibuprofen metabolization by microorganisms. Though, some microbial strains have the capability to produce hydroxyl-ibuprofen and carboxylated-ibuprofen during degradation (Hanlon et al. 1994; Zwiener et al. 2002; Quintana et al. 2005; Marco-Urrea et al. 2010b; Salgado et al. 2020). The metabolic pathway of IBU have been determined in Sphingomonas Ibu-2 (Murdoch and Hay 2013, 2015).
Kinetic study of IBU degrading strains
The IBU degradation data, growth of bacteria, and biomass data has been subjected to Haldane’s growth model in Origin 2017 software. This model suggested that the specific growth rate (μ)for the strains PYI2 and YPI2 was 14.2, and 4.8 mg/L, respectively. Further, the μmax and half-saturation constant were determined (Table 4).
Identification of metabolites and pathways for IBU degradation
The intermediate produced during biodegradation of IBU has been identified by analysis of GC/MS chromatogram. The peaks obtained in the chromatogram of the standard compound from the degraded samples was analyzed. The peaks in the chromatogram were resulting from the IBU mineralization observed during cell lysis. The comparison of chromatogram peaks has been done with the standard chromatogram peaks (without IBU and with bacteria) and the standard peak of IBU. The standard IBU retention time was at 15.738 with 99.69 area cover. The possible intermediate compounds were those metabolites that were not detected in the standard chromatogram. Moreover, the silicon-bearing molecule present in IBU was simplifying the identification, such compounds were not present in media This protocol suggested that 4 metabolites for IBUmainly hydroxyl-ibuprofen, 2- (4-hydroxyphenyl-) propionic acid, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol were identified with the retention time of 14.987, 15.654, 11.765, and 10.827, respectively. Afterwards, the mass-spectroscopy (MS) chart was used to detect the compound structure and molecular weight. Thishas suggested that the compound hydroxyl-ibuprofen, 2- (4-hydroxyphenyl-) propionic acid, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol have a molecular weight of 222, 166, 110, and 124 g/mol, respectively (Table 5). Joss et al., (2006) has been observed, that biodegradation models used for first order kinetic equations for the drug compound. The Monod-based kinetic equation and models used in many other drug biodegradation of PPCPs observed (Chopra and Kumar, 2020b, 2020c).
Finally, the prediction of degradation pathway has been done, based on GC-MS data and the literature available intended for degradation of IBU. Further, the compounds were confirmed by comparing it with the database of PubChem (https://pubch em.ncbi.nlm.nih.gov/). Compounds like hydroxyl-ibuprofen, 2- (4-hydroxyphenyl-) propionic acid, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol, were suggested based on the analysis of GC–MS chromatogram . In this wa,y metabolic pathway was predicted. PathPred deployed for the confirmation of the metabolic pathway. The instigation of IBU metabolism of occurred by the catabolic pathway and transforming IBU into hydroxyl-ibuprofen, 2- (4-hydroxyphenyl-) propionic acid, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol, asdentified during GC–MS analysis and PathPred (Fig. 3).
The fungal Nocardiacan degrade it into carboxylic acid, further into alcohol, and acetylate(Chen and Rosazza 1994). IBU is further transformed into isobutyl catechol, due to cleavage of estradiol ring Patulibacter sp. strain I11 has showed the involvement of enzymes in hydrolysis by ibuprofen (Almeida et al. 2013). Patulibacter medicamentivorans under aerobic conditions degraded IBU into two main intermediates, viz.2-phenylpropanoid acid and isobutyl benzene(Salgado et al. 2020). IBUs has been cleaved by enzyme estradiol dioxygenase to form 5-formyl-2-hydroxy-7-methylocta-2,4-dienoic acid by Bacillus thuringiensis B1 (2015b) (Marchlewicz et al. 2017a). The most important intermediate metabolite formed during IBU cleavage was hydroxylated with the isopropyl chain of ibuprofen 1 and 2-hydroxy-ibuprofen and the final metabolite generated was 1,2-dihydroxy-ibuprofen hydroxylation and carboxylated derivatives was common in microbial metabolism (Zwiener et al. 2002; Rodil et al. 2012). The decline started with 1,4-hydroquinone and another with 2-hydroxyquinol. 1,4-Hydroquinone were e product of acyl-CoA synthase/thiolase activity and can be further converted to 2-hydroxy-1,4-quinol by hydroquinone monooxygenase enzyme. Furthermore, hydroxyquinol-1,2-dioxygenase activity was seen after incorporation with ibuprofen, due to the presence of glucose andthe enzyme was completely inactive. Enzyme hydroxyquinol 1,2-dioxygenase binds to 2-hydroxy-1,4-quinol and is involved in ortho-cleavage of this compound to 3-hydroxylase, and cis-muconic acid. During the biodegradation of IBU by Nocardia sp.NRRL 5646, two major metabolites, nitrophenol, and ibprophenol acetatewere generated. Withthe passage of time, these metabolites has been further metabolized by bacteria (Chen and Rosazza 1994). Murdoch and Hay (2005, 2013) characterized the best-known IBU degradation pathway in Sphingomonas Ibu-2 strain of bacteria, and this can use IBU as the sole source of carbon and energy. They also identified five gene clusters (Ipf ABDEF) involved in IBU mineralization. The ipf A and ipf B genes were encoded for two dioxygenase subunits. The ipf D gene was encoded as an enzyme that removes/ads acylacyl-CoA synthetase groups. The Ipf F was encoded by the coenzyme-A ligase gene. And finally, the function of the ipf E gene has not been explained. The degradation began with the degradation by Ibu-2 strain by coenzyme A. This enzyme has been involved in the removal of propionic acid chain, and further, reaction with oxygen resulted in the formation of isobutyl catechol. This compound has been susceptible to oxygen degradation(Murdoch and Hay 2013).