Biodegradation of endocrine disruptor dibutyl phthalate (DBP) by a newly isolated Methylobacillus sp. V29b and the DBP degradation pathway

Improving key gene expression and di-n-butyl phthalate (DBP) degrading ability in a novel Pseudochrobactrum sp. XF203 by ribosome engineering

Di-n-butyl phthalate (DBP) is one of the important phthalates detected commonly in soils and crops, posing serious threat to human health. Pseudochrobactrum sp. XF203 (XF203), a new strain related with DBP biodegradation, was first identified from a natural habitat lacking human disturbance. Genomic analysis coupled with gene expression comparison assay revealed this strain harbors the key aromatic ring-cleaving gene catE203 (encoding catechol 2,3-dioxygenase/C23O) involved DBP biodegradation. Following intermediates identification and enzymatic analysis also indicated a C23O dependent DBP lysis pathway in XF203. The gene directed ribosome engineering was operated and to generate a desirable mutant strain XF203R with highest catE203 gene expression level and strong DBP degrading ability. The X203R removed DBP in soil jointly by reassembling bacterial community. These results demonstrate a great value of XF203R for the practical DBP bioremediation application, highlighting the important role of the key gene-directed ribosome engineering in mining multi-pollutants degrading bacteria from natural habitats where various functional genes are well conserved.

Construction of Metal-Organic Framework-Based Heterogeneous Pepsin and Its Degradation Performance and Mechanism for Phthalic Acid Esters

Biological enzyme-driven degradation of environmental pollutants has attracted widespread attention because it is ecofriendly and highly efficient. Immobilized enzyme technology has emerged as a promising technique in enzymology that addresses the limitations associated with free enzymes. Traditional solid-loaded enzyme substrates are often affected by blockages and restricted substrate accessibility. In this study, we synthesized an efficient heterogeneous pepsin catalyst, named PEP@M-MIL100(Fe), by covalently combining carboxylated ferrite structural expanded metal-organic frameworks with pepsin. This catalyst demonstrated excellent environmental adaptability and remarkable catalytic degradation capabilities. Notably, it rapidly degraded the persistent microplastic pollutant diisononyl phthalate (DINP) within just 150 min, with a removal efficiency of up to 95.88%. Impressively, even after 10 consecutive uses, the catalyst maintained its high performance. We proposed an innovative steady-state heterogeneous enzyme-catalyzed degradation mechanism, i.e., diffusion (D)-absorption (A)-binding (B)-reaction (R)-degradation (D)-link mechanism, which emphasizes the influence of substrate diffusion rates in this process. This work presents the first successful application of pepsin to DINP degradation and offers a sustainable and effective approach for addressing contemporary pollution challenges.

Exploring the potential of a new marine bacterium associated with plastisphere to metabolize dibutyl phthalate and bis(2-ethylhexyl) phthalate by enrichment cultures combined with multi-omics analysis

Phthalic acid esters (PAEs) plasticizers are virulent endocrine disruptors that are mixed into plastics while fabricating and can filter out once they release into the surrounding environments. Plastic surfaces serve as new habitats for microorganisms, referred to as 'plastisphere'. Previous metagenomic investigations of the 'plastisphere' indicated that marine plastic surfaces may harbor microbes that degrade PAEs plasticizers. To our knowledge, the potential of microorganisms in the marine 'plastisphere' to metabolize PAEs is poorly understood. In this study, by screening the natural microbial community on plastic debris that had been deployed in situ for up to 20 months, a novel marine bacterium, Microbacterium esteraromaticum DEHP-1, was successfully isolated, which could degrade and mineralize 10-200 mg/L dibutyl phthalate (DBP) and bis(2-ethylhexyl) phthalate (DEHP). According to the results of gas chromatography-mass spectrometry (GC-MS) and whole genome mining of strain DEHP-1, we found that strain DEHP-1 may metabolize DBP by successive removal of the ester side chain by esterase 2518 to produce mono-butyl phthalate (MBP) and phthalic acid (PA), whereas the degradation of DEHP may take place by the direct action of monooxygenase 0132 on the fatty acid side chain of the DEHP molecule to produce di-n-hexyl phthalate (DnHP) and DBP, and then the subsequent hydrolysis of DBP by de-esterification to PA and finally into the tricarboxylic acid (TCA) cycle. Non-targeted metabolomics results showed that intracellular degradation of PAEs did not happen. However, exposure to PAEs was found to significantly affect pathways such as arginine and proline, riboflavin, glutathione and lysine degradation. Therefore, the intracellular metabolic behavior of strain DEHP-1 exposed to PAEs was proposed for the first time. This study sheds light on the metabolic capacity and strategies of bacteria in the marine 'plastisphere' to effectively degrade PAEs and highlights the importance of marine microbes in mitigating plastic poisonousness.

Exposure to cadmium induced gut antibiotic resistance genes (ARGs) and microbiota alternations of Babylonia areolata

Cadmium (Cd) is widely distributed in aquatic environments and has multiple adverse effects on aquatic organisms such as the ivory shell (Babylonia areolata). However, its effects on antibiotic resistance genes (ARGs) and gut microbiota of B. areolata remain unclear. In this study, we explored the effects of different concentrations (0, 0.03, 0.18 and 1.08 mg/L) of Cd on intestinal microbial communities and ARGs in B. areolata through 16S rRNA gene sequencing and high-throughput quantitative PCR. The results showed that the structure and diversity of ARGs and microbiota in B. areolata gut were altered upon Cd exposure. Tetracycline, Vancomycin and Macrolide-Lincosamide-Streptogramin B (MLSB) resistance genes were identified as the major ARGs in B. areolata gut. The absolute abundance and alpha diversity of ARGs in B. areolata gut increased with the rise of cadmium concentration. The microbial communities at genus level were enriched in the low and medium Cd concentration groups, while decreased in the high Cd concentration group compared to the control groups. In addition, the influence of microbiota on the ARG profile was more significant than that of Cd concentration and MGEs in B. areolata gut. Null model analysis demonstrated that stochastic processes dominated ARG assembly in the Cd-exposed groups and were enhanced with the increasing Cd concentrations. Four opportunistic bacterial pathogens (Bacteroides, Legionella, Acinetobacter and Escherichia) detected in B. areolata gut maybe the potential hosts of ARGs. Our findings provide references for the hazards assessment of environmental Cd exposure of gut microbiome in aquatic animals.

Exploring Potent Fungal Isolates from Sanitary Landfill Soil for In Vitro Degradation of Dibutyl Phthalate

Di-n-butyl phthalate (DBP) is one of the most extensively used plasticizers for providing elasticity to plastics. Being potentially harmful to humans, investigating eco-benign options for its rapid degradation is imperative. Microbe-mediated DBP mineralization is well-recorded, but studies on the pollutant's fungal catabolism remain scarce. Thus, the present investigation was undertaken to exploit the fungal strains from toxic sanitary landfill soil for the degradation of DBP. The most efficient isolate, SDBP4, identified on a molecular basis as Aspergillus flavus, was able to mineralize 99.34% dibutyl phthalate (100 mg L^-1) within 15 days of incubation. It was found that the high production of esterases by the fungal strain was responsible for the degradation. The strain also exhibited the highest biomass (1615.33 mg L^-1) and total soluble protein (261.73 µg mL^-1) production amongst other isolates. The DBP degradation pathway scheme was elucidated with the help of GC-MS-based characterizations that revealed the formation of intermediate metabolites such as benzyl-butyl phthalate (BBP), dimethyl-phthalate (DMP), di-iso-butyl-phthalate (DIBP) and phthalic acid (PA). This is the first report of DBP mineralization assisted with A. flavus, using it as a sole carbon source. SDBP4 will be further formulated to develop an eco-benign product for the bioremediation of DBP-contaminated toxic sanitary landfill soils.

Biodegradation of diethyl phthalate and phthalic acid by a new indigenous Pseudomonas putida

Diethyl phthalate (DEP) is one of the extensively used plasticizers which has been considered a priority hazardous pollutant due to its carcinogenic, endocrine disrupter, and multi-toxic effects on humans. The identification of DEP in different parts of the ecosphere has increased the global community's attention to the elimination of this pollutant in a bio-eco-friendly way. In this research, a novel aerobic bacterial strain nominates as ShA (GenBank accession number: MN298858) capable of consuming DEP as carbon and energy sources, was isolated from the upper phase (0-10 cm) of Anzali international wetland sediments by enrichment culture method. Morphological characteristics and 16S rRNA gene sequence analysis demonstrated that strain ShA belonged to Pseudomonas putida. The substrate utilization test demonstrated that strain ShA was able to grow in mineral salt medium containing dimethyl phthalate (DMP) and phthalic acid (PA) isomers including terephthalic and isophthalic acid. Degradation assay showed strain ShA completely degraded 200 mg/L DEP within 22 h (pH 7.0, 30 °C). Surprisingly, PA as the main intermediate of DEP biodegradation was identified by GC-FID. Moreover, the rapid degradation of 2000 mg/L PA to CO₂ and H₂O was viewed in 22 h by strain ShA. The possible route of DEP degradation was DEP directly to PA and then PA consumption for growth. This study obtained results that provide a great contribution to applying strain ShA in the biodegradation of low molecular weight of PAEs and PA isomers in natural ecosystems. This is the first report of a P. putida strain able to degrade DEP and PA.

Impacts of dibutyl phthalate on biological municipal wastewater treatment in a pilot-scale A2/O-MBR system

Dibutyl phthalate (DBP) is a typical contaminant in pharmaceutical wastewater with strong bio-depressive properties which potentially affects the operation of municipal wastewater treatment systems. Based on a year-round monitoring of the quality of influent and effluent of a full-scale pharmaceutical wastewater treatment plant in Northeast China, the DBP was found to be the representative pollutant and its concentration in the effluent ranged 4.28 ± 0.93 mg/L. In this study, the negative effects of DBP on a pilot-scale A²/O-MBR system was investigated. When the influent DBP concentration reached 8.0 mg/L, the removals of chemical oxygen demand (COD) and total nitrogen (TN) were significantly inhabited (P < 0.01), with the effluent concentration of 54.7 ± 2.6 mg/L and 22.8 ± 3.7 mg/L, respectively. The analysis of pollutant removal characteristics of each process unit showed that DBP had the most significant effects on the removals of COD and TN in the anoxic tank. The α- and β-diversity in the system decreased significantly when the influent DBP concentration reached 8.0 mg/L. The impacts of DBP on known nitrifying bacteria, such as Nitrospira, and phosphorus accumulating organisms (PAOs), such as Cadidatus Accumulibacter, were not remarkable. Whereas, DBP negatively affected the proliferation of key denitrifying bacteria, represented by Simplicispira, Dechloromonas and Acinetobacter. This study systematically revealed the impacts of DBP on the pollutants removal performance and the bacterial community structure of the biological municipal wastewater treatment process, which would provide insights for understanding the potential impacts of residues in treated pharmaceutical wastewater on biological municipal wastewater treatment.

Does bacterial community succession within the polyethylene mulching film plastisphere drive biodegradation?

Agricultural fields are severely contaminated with polyethylene mulching film (PMF) and this plastic in the natural environment can be colonized by biofilm-forming microorganisms that differ from those in the surrounding environment. In this study, we investigated the succession of the soil microbial communities in the PMF plastisphere using an artificial micro-ecosystem as well as exploring the degradation of PMF by plastisphere communities. The results indicated a significant and gradual decrease in the alpha diversity of the bacterial communities in the plastisphere and surrounding liquid. The community compositions in the plastisphere and surrounding liquid differed significantly from that in agricultural soil. Phyla and genera with the capacity to degrade polyethylene and hydrocarbon were enriched in the plastisphere, and some of these microorganisms were core members of the plastisphere community. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis detected increases in metabolism pathways for PMF plastisphere Xenobiotics Biodegradation and Metabolism, thereby suggesting the possibility of polyethylene degradation in the plastisphere. Observations by scanning electron microscopy (SEM) and confocal laser scanning microscopy demonstrated the formation of biofilms on the incubated PMF. SEM, atomic force microscopy, Fourier transform infrared spectroscopy and water contact angle detected significant changes in the surface microstructure, chemical composition and hydrophobicity change of the films, thereby suggesting that the plastisphere community degraded PMF during incubation. In conclusion, this study provides insights into the changes in agricultural soil microorganisms in the PMF plastisphere and the degradation of PMF.

Metal resistant gut microbiota facilitates snails feeding on metal hyperaccumulator plant Sedum alfredii in the phytoremediation field

The interactions between hyperaccumulators and their associated herbivores have been mostly investigated in their natural habitats and largely ignored in the phytoremediation practice. Herein, we investigated the herbivory status of Zn/Cd-hyperaccumulating plant Sedum alfredii from both their natural habitats and their applied remediation field, and inspected the adaptive strategies of the herbivores from the perspective of their facilitative gut microbiota. Field investigations showed that snail species Bradybaena ravida was the dominant herbivore feeding on S. alfredii and they can be only found in sites with lower levels of heavy metals compared with the plant natural habitat. Gut microbial community was analyzed using two sequencing methods (16S rRNA and czcA-Zn/Cd resistant gene) to comparatively understand the effect of gut microbes in facilitating snail feeding on the hyperaccumulators. The results revealed significant differences in the diversity and richness between the gut microbiota of the two snail populations, which was more pronounced by the czcA sequencing method. Despite of the compositional differences, their functions seemed to converge into three categories as metal-tolerant and contaminant degraders, gut symbionts, and pathogens. Further function potentials predicted by Tax4Fun based on 16 S sequencing data were in accordance with this categorization as the most abundant metabolic pathways were two-component system and ABC transporter, which was closely related to metal stress adaptation. The prevalence of positive interactions (~80%) indicated by the co-occurrence network analysis based on czcA sequencing data in both groups of gut microbiota further suggested the facilitative effect of these metal-tolerant gut microbes in coping with the high metal diet, which ultimately assist the snails to successfully feed on S. alfredii plants and thrive. This work for the first time provides evidence that the herbivore adaptation to hyperaccumulators were also associated with their gut microbial adaptation to metals.

Mass balance and kinetics of biodegradation of endocrine disrupting phthalates by Cellulosimicrobium funkei in a continuous stirred tank reactor system

This study investigated the potential ofCellulosimicrobium funkeifor degrading dimethyl phthalate (DMP) and diethyl phthalate (DEP). Effect of different initial concentrations of phthalates on their biodegradation and growth ofC. funkeiwas examined using shake flasks and a continuous stirred tank reactor (CSTR). Complete degradation of both DMP and DEP was achieved in CSTR, even up to 3000 and 2000 mg/L initial concentrations, respectively. Simultaneous degradation of the phthalates in mixture, i.e. more than 80% and 55% biodegradation efficiency were achieved at 1000 and 2000 mg/L initial concentrations of DMP and DEP, respectively, using the CSTR. Mass balance analysis of the degradation results suggested proficient degradation of DMP and DEP with biomass yield values of 0.64 and 0.712, respectively. The high values of inhibition constant Kiestimated using the Tessier and Edward substrate inhibition models indicated very good tolerance ofC. funkeitoward biodegradation of DMP and DEP.

Degradation of dibutyl phthalate by Paenarthrobacter sp. Shss isolated from Saravan landfill, Hyrcanian Forests, Iran

Phthalic acid esters are predominantly used as plasticizers and are industrially produced on the million ton scale per year. They exhibit endocrine-disrupting, carcinogenic, teratogenic, and mutagenic effects on wildlife and humans. For this reason, biodegradation, the major process of phthalic acid ester elimination from the environment, is of global importance. Here, we studied bacterial phthalic acid ester degradation at Saravan landfill in Hyrcanian Forests, Iran, an active disposal site with 800 tons of solid waste input per day. A di-n-butyl phthalate degrading enrichment culture was established from which Paenarthrobacter sp. strain Shss was isolated. This strain efficiently degraded 1 g L^-1 di-n-butyl phthalate within 15 h with a doubling time of 5 h. In addition, dimethyl phthalate, diethyl phthalate, mono butyl phthalate, and phthalic acid where degraded to CO₂, whereas diethyl hexyl phthalate did not serve as a substrate. During the biodegradation of di-n-butyl phthalate, mono-n-butyl phthalate was identified in culture supernatants by ultra-performance liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry. In vitro assays identified two cellular esterase activities that converted di-n-butyl phthalate to mono-n-butyl phthalate, and the latter to phthalic acid, respectively. Our findings identified Paenarthrobacter sp. Shss amongst the most efficient phthalic acid esters degrading bacteria known, that possibly plays an important role in di-n-butyl phthalate elimination at a highly phthalic acid esters contaminated landfill.

Combining Culture-Dependent and Independent Approaches for the Optimization of Epoxiconazole and Fludioxonil-Degrading Bacterial Consortia

Epoxiconazole (EPO) and fludioxonil (FLU) are two widely used fluorinated pesticides known to be highly persistent and with high ecotoxicological potential, turning them into pollutants of concern. This work aimed to optimize two degrading bacterial consortia, previously obtained from an agricultural soil through enrichment with EPO and FLU, by characterizing the contribution of their corresponding bacterial isolates to the biodegradation of these pesticides using both culture-dependent and independent methodologies. Results showed that a co-culture of the strains Hydrogenophaga eletricum 5AE and Methylobacillus sp. 8AE was the most efficient in biodegrading EPO, being able to defluorinate ca. 80% of this pesticide in 28 days. This catabolic performance is likely the result of a commensalistic cooperation, in which H. eletricum may be the defluorinating strain and Methylobacillus sp. may assume an accessory, yet pivotal, catabolic role. Furthermore, 16S rRNA metabarcoding analysis revealed that these strains represent a minority in their original consortium, showing that the biodegradation of EPO can be driven by less abundant phylotypes in the community. On the other hand, none of the tested combinations of bacterial strains showed potential to biodegrade FLU, indicating that the key degrading strains were not successfully isolated from the original enrichment culture. Overall, this work shows, for the first time, the direct involvement of two bacterial species, namely H. eletricum and Methylobacillus sp., in the biodegradation of EPO, while also offering insight on how they might cooperate to accomplish this process. Moreover, the importance of adequate culture-dependent approaches in the engineering of microbial consortia for bioremediation purposes is also emphasized.

Enhanced esterase activity during the degradation of dibutyl phthalate by Fusarium species in liquid fermentation

Dibutyl phthalate (DBP) is one of the most abundantly produced and used plasticizers and is incorporated into plastic to make it more flexible and malleable. DBP has been found to be an environmental contaminant and reported as an endocrine disruptor. Therefore, it is crucial to develop ecofriendly alternatives to eliminate phthalate pollution. In the present research, the growth of F. culmorum and F. oxysporum in the presence of DBP was studied in liquid fermentation. The esterase activity, specific growth rate, and growth and enzymatic yield parameters were determined in DBP-supplemented media (1,500 or 2,000 mg/L) and in control medium (lacking DBP). These results show that in general, for both Fusarium species, the highest esterase activities, specific growth rates, and yield parameters were observed in media supplemented with DBP. It was observed that 1,500 and 2,000 mg of DBP/L did not inhibit F. culmorum or F. oxysporum growth and that DBP induced esterase production in both fungi. These organisms have much to offer in the mitigation of environmental pollution caused by the endocrine disruptor DBP. This study reports, for the first time, esterase production during the degradation of high concentrations (i.e., 1,500 and 2,000 mg/L) of DBP by F. culmorum F. oxysporum.

The effect of plastic additives on Shewanella oneidensis growth and function

Plastic waste has the potential for significant consequences on various ecosystems; yet, there are gaps in our understanding of the interaction of bacteria with polymer additives. We studied the impact of representative additive molecules to the viability and cell function of Shewanella oneidensis MR-1. Specifically, we explored the toxicity of three bisphenols (bisphenol A (BPA), bisphenol S (BPS), and tetrabromo bisphenol A (TBBPA)) and two diesters (dibutyl sebacate (DBS) and diisobutyl phthalate (DIBP)) in order to evaluate the generalizability of toxicity based on similar molecular structures. TBBPA caused significant, dose-dependent decreases in viability for acute (4 h) exposures in aerobic and anaerobic conditions. While the other 4 additives showed no significant toxicity upon 4 h exposures, chronic (2 day) anaerobic exposures revealed a significant impact to growth. BPA and BPS cause a significant decrease in growth rates for all exposure doses (8-131 μM) while DBS and DIBP had decreases in growth for the lowest exposure concentrations, though recovered to growth rates similar to the control at the highest concentrations. This highlights that S. oneidensis may have the ability to use the diesters as a carbon source if present in high enough concentrations. Riboflavin secretion was monitored as a marker of cellular health. Most additives stimulated riboflavin secretion as a survival response. Yet, there was no generalizable trend observed for these molecules, indicating the importance of considering the nuances of molecular structure to toxicity responses and the need for further work to understand the consequences of plastic waste in our environment.

Biodegradation of diisononyl phthalate by a consortium of saline soil bacteria: optimisation and kinetic characterisation

Diisononyl phthalate (DINP) is one of plasticisers most employed in the production of plastic materials and belongs to the most important environmental contaminants. In this work, a consortium of saline soil bacterial (SSB) capable of degrading DINP is presented. The genera of SSB-consortium were Serratia sp., Methylobacillus sp., Achromobacter sp., Pseudomonas sp., Stenotrophomonas sp., Methyloversatilis sp., Delftia sp. and Brevundimonas sp. Response surface methodology (RSM) study was employed to optimise and evaluate the culture conditions to improve the biodegradation of DINP. The optimal conditions were a pH 7.0, 31 °C and an initial DINP concentration of 500 mg L^-1, resulting in almost complete biodegradation (99%) in 168 h. DINP degradation followed a first-order kinetic model, and the half-life was 12.76 h. During the biodegradation of DINP, 4-derived compounds were identified: monoisononyl phthalate, methyl nonyl phthalate, iso-nonanol and dimethyl phthalate. The metabolite profiling indicated that DINP was degraded through simultaneous pathways of de-esterification and β-oxidation. Results suggest that the SSB-consortium could be useful for efficient biodegradation of the DINP-contaminated environments. KEY POINTS: • DINP degradation is mediated by de-esterification and β-oxidation processes. • Temperature and the concentration of the substrate are key factors for DINP biodegradation • The SSB-consortium has the ability to biodegrade 99% of DINP (500 mg L^-1).

Anaerobic biodegradation of fluoxetine using a high-performance bacterial community

Fluoxetine (FLX), an antidepressant extensively used worldwide is considered an emerging pollutant. The present work intends to investigate for the first time the capacity of a bacterial community containing sulphate-reducing bacteria (SRB) enriched from an anaerobic sludge to biodegrade and use FLX as sole carbon source, since current literature suggests that this drug is poorly biodegraded being mainly removed by adsorption to sediments, where it persists. FLX was biodegraded under sulphate reducing conditions until reaching its lowest and reliably detectable concentration, when 20 mg/L of the drug was used as sole carbon source, while 66 ± 9% of 50 mg/L FLX was removed, after 31 days. The initial bacterial population was mainly constituted by Desulfomicrobium and Desulfovibrio whereas during the experiments using FLX as unique carbon source a clear shift occurred with the increase of vadinBC27 wastewater-sludge group, Macellibacteroidetes, Dethiosulfovibrio, Bacteroides, Tolumonas, Sulfuricurvum, f_Enterobacteriaceae_OTU_18 that are assumed for the first time as FLX degrading bacteria. Although the main mechanism of FLX removal described in literature is by adsorption, in the results herein presented anaerobic biodegradation appears to play the main role in the removal of the FLX, thus demonstrating the potentialities that the anaerobic processes can play in wastewater treatment aiming the removal of new emerging compounds.

The key active degrader, metabolic pathway and microbial ecology of triclosan biodegradation in an anoxic/oxic system

A lab-scale anoxic/oxic (A/O) system was used to reveal the key active triclosan-degrading bacteria (TCS-DB) in this study. The results showed that TCS was mainly removed by metabolism of heterotrophic bacteria (accounting for about 62%), and the potential metabolic pathway was the break of ether bond in TCS formed 2,4-dichlorophenol, and further dechlorination formed phenol or other metabolic end products. DNA-based stable isotope probing (DNA-SIP) assay further revealed that Methylobacillus accounting for 20.75% in ¹³C sample was the key active TCS-DB. Furthermore, methylotrophy and methanol oxidation were found to be the potential metabolic routes of TCS degradation by functional annotation of prokaryotic taxa analysis. Interestingly, TCS accelerated the propagation of antibiotic resistance genes (fabI) and intI1 which positively correlated with several functional microorganisms (p < 0.05). This study contributes to comprehend the potential mechanism, metabolic pathway and microbial ecology of TCS biodegradation in A/O system.

Bioremediation of di-(2-ethylhexyl) phthalate contaminated red soil by Gordonia terrae RL-JC02: Characterization, metabolic pathway and kinetics

Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer and a representative endocrine disrupting chemical. The toxicological effects of DEHP on environmental and human health have been widely investigated. In this study, the DEHP-degrading bacterial strain RL-JC02 was isolated from red soil with long-term usage of plastic mulch, and it was identified as Gordonia terrae by 16S rRNA gene analysis coupled with physiological and biochemical characterization. The biodegrading capacity of different phthalic acid esters and related intermediates was investigated as well as the performance of strain RL-JC02 under different environmental conditions, such as temperature, pH, salinity and DEHP concentration. Specifically, strain RL-JC02 showed good tolerance to low pH, with 86.6% of DEHP degraded under the initial pH of 5.0 within 72 h. The metabolic pathway of DEHP was examined by metabolic intermediate identification via a high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS) analysis in which DEHP was hydrolyzed into phthalic acid (PA) and 2-ethylhexanol (2-EH) via mono (2-ethylhexyl) phthalate (MEHP). PA and 2-EH were further utilized through the protocatechuic acid metabolic pathway and β-oxidation via protocatechuic acid and 2-ethylhexanoic acid, respectively. The application potential of strain RL-JC02 was confirmed through the bioremediation of artificial DEHP-contaminated red soil showing 91.8% DEHP degradation by strain RL-JC02 within 30 d. The kinetics analysis of DEHP degradation by strain RL-JC02 in soil demonstrated that the process followed the modified Gompertz model. Meanwhile, the cell concentration monitoring of strain RL-JC02 in soil with absolute quantification polymerase chain reaction (qPCR) suggested that strain RL-JC02 survived well during bioremediation. This study provides sufficient evidence of a robust degrader for the bioremediation of PAE-contaminated red soil.

Complete metabolic study by dibutyl phthalate degrading Pseudomonas sp. DNB-S1

The primary purpose of this study was to systematically explore the complete metabolic pathway and tolerance mechanism of strain DNB-S1 to dibutyl phthalate (DBP), and the effect of DBP on energy metabolism of DNB-S1. Here, DNB-S1, a strain of Pseudomonas sp. that was highly effective in degrading DBP, was identified, and differentially expressed metabolites and metabolic networks of DBP were studied. The results showed that the differentially expressed metabolites were mainly aromatic compounds and lipid compounds, with only a few toxic intermediate metabolites. It speculated that phthalic acid, salicylic acid, 3-hydroxybenzoate acid, 3-Carboxy-cis, cis-muconate, fumarypyravate were intermediate metabolites of DBP. Their up-regulation indicated that there were two metabolic pathways in the degradation of DBP (protocatechuate pathway and gentisate pathway), which had been verified by peak changes at 290 nm, 320 nm, 330 nm, and 375 nm in the enzymatic method. Also, aspartate, GSH, and other metabolites were up-regulation, indicating that DNB-S1 had a high tolerance to DBP and maintained cell homeostasis, which was also one of the essential reasons to ensure the efficient degradation of DBP. Altogether, this study firstly proposed two pathways to degrade DBP and comprehensively explored the effect of DBP on the metabolic function of DNB-S1, which enriched the study of microbial metabolism of organic pollutants, and which provided a basis for the application of metabolomics.

Plasticizer Degradation by Marine Bacterial Isolates: A Proteogenomic and Metabolomic Characterization

Many commercial plasticizers are toxic endocrine-disrupting chemicals that are added to plastics during manufacturing and may leach out once they reach the environment. Traditional phthalic acid ester plasticizers (PAEs), such as dibutyl phthalate (DBP) and bis(2-ethyl hexyl) phthalate (DEHP), are now increasingly being replaced with more environmentally friendly alternatives, such as acetyl tributyl citrate (ATBC). While the metabolic pathways for PAE degradation have been established in the terrestrial environment, to our knowledge, the mechanisms for ATBC biodegradation have not been identified previously and plasticizer degradation in the marine environment remains underexplored. From marine plastic debris, we enriched and isolated microbes able to grow using a range of plasticizers and, for the first time, identified the pathways used by two phylogenetically distinct bacteria to degrade three different plasticizers (i.e., DBP, DEHP, and ATBC) via a comprehensive proteogenomic and metabolomic approach. This integrated multi-OMIC study also revealed the different mechanisms used for ester side-chain removal from the different plasticizers (esterases and enzymes involved in the β-oxidation pathway) as well as the molecular response to deal with toxic intermediates, that is, phthalate, and the lower biodegrading potential detected for ATBC than for PAE plasticizers. This study highlights the metabolic potential that exists in the biofilms that colonize plastics-the Plastisphere-to effectively biodegrade plastic additives and flags the inherent importance of microbes in reducing plastic toxicity in the environment.

Metabolic process of di-n-butyl phthalate (DBP) by Enterobacter sp. DNB-S2, isolated from Mollisol region in China

The accumulation of phthalate acid esters (PAEs) in the environment has aroused a global concern. Microbial degradation is the most promising method for removing PAEs from polluted environment. Di-n-butyl phthalate (DBP) is one of the most widely used PAEs. In this study, a highly efficient DBP-degrading strain, Enterobacter sp. DNB-S2 was isolated from Mollisol in northeast China, and the degradation rate of 500 mg L^-1 DBP reached 44.10% at 5 °C and 91.08% at 50 °C within 7 days. A new intermediate, n-butyl benzoate BP, was detected, implying a new degradation pathway. The complete genome of the strain DNB-S2 was successfully sequenced to comprehensively understand of the entire DBP catabolic process. Key genes were proposed to be involved in DBP degradation, such as esterases, 3,4-dihydroxybenzoate decarboxylase and catechol 2,3-dioxygenase genes. Intermediate-utilization tests and real-time quantitative polymerase chain reaction (RT-qPCR) validated the proposed DBP catabolic pathway. The aboriginal bacterium DNB-S2 is a promising germplasm for restoring PAE-contaminated Mollisol regions at low temperature. This study provides novel insight into the catabolic mechanisms and abundant gene resources of PAE biodegradation.

Bioremediation of dibutyl phthalate in a simulated agricultural ecosystem by Gordonia sp. strain QH-11 and the microbial ecological effects in soil

Bioremediation of organic pollutants has been identified as an economically efficient and environmentally friendly method. Here, a pot experiment was conducted to evaluate the bioremediation efficiency of dibutyl phthalate (DBP) by Gordonia phthalatica sp. nov. QH-11 in agricultural soils, along with the effect of this exogenous organism on the native microbial community and ecosystem functions during the bioremediation process. The results showed that inoculation with strain QH-11 accelerated DBP degradation in the soil and decreased DBP accumulation in plants, thereby reducing the health risks associated with vegetables grown in those soils. High-throughput sequencing demonstrated that both DBP contamination and the bioremediation process significantly altered prokaryotic community composition, structure, and network interactions; however, these effects were greatly reduced after 30 d. Dibutyl phthalate affected the prokaryotic community by influencing soil properties rather than directly impacting on microorganisms. In addition, ecosystem functions, like the nitrogen cycle, were significantly altered. Contamination with DBP promoted nitrogen fixation and the denitrification processes while inhibiting nitrification. Bioremediation may mitigate some of the changes to nitrogen cycling, helping to maintain the balance of prokaryotic community function. According to this study, bioremediation through highly efficient degradation bacteria may be a safe and promising method for reducing PAEs contamination in soil-vegetable systems.

Biodegradation of di‑n‑butyl phthalate by psychrotolerant Sphingobium yanoikuyae strain P4 and protein structural analysis of carboxylesterase involved in the pathway

A priority pollutant Phthalate Esters (PAEs) are widely used as plasticizers and are responsible mainly for carcinogenicity and endocrine disruption in human. For the bioremediation of PAEs, a psychrotolerant Sphingobium yanoikuyae strain P4, capable of utilizing many phthalates di‑methyl phthalate (DMP), di‑ethyl phthalate (DEP), di‑n‑butyl phthalate (DBP), di‑isobutyl phthalate (DIBP), butyl benzyl phthalate (BBP), and few Polycyclic Aromatic Hydrocarbons as the sole source of carbon and energy was isolated from Palampur, Kangra, Himachal Pradesh, India. 100% utilization of DBP (1 g L^-1) by the strain was observed within 24 h of incubation at 28 °C. Interestingly the strain also degraded DBP completely at 20 °C and 15 °C within 36 h and 60 h, respectively. Esterase involved in DBP degradation was found to be inducible in nature and intracellular. Comparative sequence analysis of carboxylesterase enzyme sequences revealed conserved motifs: G-X-S-X-G and -HGG- which were the characteristic peptide motifs reported in different esterases. Structural analysis showed that the enzyme belongs to serine hydrolase superfamily, which has an α/β hydrolase fold. Interaction and binding of DBP to a catalytic Ser¹⁸⁴ residue in the esterase enzyme were also analysed. In conclusion, carboxylesterase possess the required active site which may be involved in the catabolism of DBP.

Kinetics and pathway of biodegradation of dibutyl phthalate by Pleurotus ostreatus

Dibutyl phthalate (DBP) is a plasticizer, whose presence in the environment as a pollutant has attained a great deal of attention due to its reported association with endocrine system disturbances on animals. Growth parameters, glucose uptake, percentage of removal efficiency (%E) of DBP, biodegradation constant of DBP (k) and half-life of DBP biodegradation (t_1/2) were evaluated for Pleurotus ostreatus grown on media containing glucose and different concentrations of DBP (0, 500 and 1000 mg l^-1). P. ostreatus degraded 99.6 % and 94 % of 500 and 1000 mg of DBP l^-1 after 312 h and 504 h, respectively. The k was 0.0155 h^-1 and 0.0043 h^-1 for 500 and 1000 mg of DBP l^-1, respectively. t_1/2 was 44.7 h and 161 h for 500 and 1000 mg of DBP l^-1, respectively. Intermediate compounds of biodegraded DBP were identified by GC-MS and a DBP biodegradation pathway was proposed using quantum chemical calculation. DBP might be metabolized to benzene and acetyl acetate, the first would be oxidated to muconic acid and the latter would enter into the Krebs cycle. P. ostreatus has the ability to degrade DBP and utilizes it as source of carbon and energy.

Characterization and Genome Analysis of a Phthalate Esters-Degrading Strain Sphingobium yanoikuyae SHJ

A bacterium capable of utilizing dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-butyl phthalate (DBP), and diisobuthyl phthalate (DIBP) as the sole carbon and energy source was isolated from shallow aquifer sediments. The strain was identified as Sphingobium yanoikuyae SHJ based on morphological characteristics, 16S rDNA gene phylogeny, and whole genome average nucleotide identity (ANI). The degradation half-life of DBP with substrate concentration of 8.5 and 50.0 mg/L by strain SHJ was 99.7 and 101.4 hours, respectively. The optimum degradation rate of DBP by SHJ was observed at 30°C and weak alkaline (pH 7.5). Genome sequence of the strain SHJ showed a circular chromosome and additional two circular plasmids with whole genome size of 5,669,383 bp and GC content of 64.23%. Functional annotation of SHJ revealed a total of 5,402 genes, with 5,183 protein-encoding genes, 143 pseudogenes, and 76 noncoding RNA genes. Based on genome annotation, 44 genes were identified to be involved in PAEs hydrolysis potentially. Besides, a region with size of about 6.9 kb comprised of seven ORFs, which is located on the smaller plasmid pSES189, was presumed to be responsible for the biodegradation of phthalate. These results provide insights into the genetic basis of DBP biodegradation in this strain.

Mineralization of high concentrations of the endocrine disruptor dibutyl phthalate by Fusarium culmorum

Dibutyl phthalate (DBP) is a widely used plasticizer, whose presence in the environment as a pollutant raises concern because of its endocrine-disrupting toxicity. Growth kinetics, glucose uptake, biodegradation constant of DBP (k), half-life of DBP biodegradation (t_1/2) and percentage of removal efficiency (%E) were evaluated for Fusarium culmorum grown on media containing glucose and different concentrations of DBP (500 and 1000 mg/l). Intermediate compounds of biodegraded DBP were identified by GC-MS and a novel DBP biodegradation pathway was proposed on the basis of the intermolecular flow of electrons of the intermediates identified using quantum chemical modeling. F. culmorum degraded 99% of both 1000 and 500 mg of DBP/l after an incubation period of 168 and 228 h, respectively. %E was 99.5 and 99.3 for 1000 and 500 mg of DBP/l, respectively. The k was 0.0164 and 0.0231 h^-1 for 500 and 1000 mg of DBP/l, respectively. DBP was fully metabolized to fumaric and malic acids, which are compounds that enter into the Krebs cycle. F. culmorum has a promising ability for bioremediation of environments polluted with DBP because it efficiently degrades DBP and uses high concentrations of this compound as carbon and energy source.

Characterization and application of a newly isolated pyrene-degrading bacterium, Pseudomonas monteilii

Pseudomonas monteilii PL5 (PL5) was newly isolated from soil sample and was identified by 16S rDNA sequence analysis. The strain PL5 had a high potential to degrade pyrene (PYR) in both liquid solution and soil and was able to degrade 51.8% of PYR at 25 °C and pH 7.0 condition within 10 days. At 25 °C, the ability of strain PL5 to degrade PYR at different pH values followed the following order pH 6.0 > pH 7.0 > pH 8.0 > pH 9.0. Degradation of total PYR was 56.5 and 51.8% after 10 days at pH 6.0 and 7.0 with PYR half-lives of 8.8 and 9.2 days, respectively. The ability of strain PL5 degraded PYR under different temperatures was 35 > 25 > 15 °C at pH 6.0. Among the tested soils contaminated by PYR, the best degradation of PYR by strain PL5 occurred in paddy soil where the degradation was 57.5% after 10 days, and the half-life of PYR was reduced 19-fold in the presence of strain PL5. This study suggested that P. monteilii PL5 could be used for the bioremediation of the contaminated soil and water through the degradation of PYR.

Biodegradation of pyrene and benzo[a]pyrene in the liquid matrix and soil by a newly identified Raoultella planticola strain

In the current study, the PL7 strain was isolated from soil and identified as Raoultella planticola based on its physiological characteristics and 16S rDNA sequence. By the 10th day, the PL7 strain degraded 52.0% of the pyrene (PYR) content and 50.8% of the benzo[a]pyrene (BaP) content in 20 mg L^-1 PYR and 10 mg L^-1 BaP in the liquid matrix. The half-life of PYR and BaP by PL7 degradation was 8.59 and 9.46 days, respectively. At pH 8.0, the degradation rates of PYR and BaP by PL7 were significantly higher at 30 °C than at 20 and 40 °C. The degradation ability of PL7 differed in red soil, paddy soil and fluvo-aquic soil; red soil produced the fastest degradation rates. The half-life of PYR and BaP by PL7 degradation in red soil was 21.7 and 11.9 days, respectively; however, without PL7 the half-life of PYR in red soil was 91.2 days. This study demonstrated the significant potential of the PL7 strain for bioremediation applications in the liquid matrix and soil contaminated by PAHs.